Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold224
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: 1473716
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 92095 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:881920 original size:115 final size:116
Alignment explanation
Indices: 881717--881946 Score: 385
Period size: 115 Copynumber: 2.0 Consensus size: 116
881707 CTAACCCTTA
*
881717 ACATTCACATAATGTTAGATTTAGAAAAATGTTTTTTACTAGTACTAACAATTAATAATTTTATA
1 ACATTCACATAATGTTAGATTTAGAAAAATGTTTTTGACTAGTACTAACAATTAATAATTTTATA
*
881782 TAATTTGATAATTTTACTAACCATTAATACAATTTATCGGATAATAATTTT
66 TAATTTGATAATTTTACTAACCATTAATACAATTTATCAGATAATAATTTT
*
881833 ACATTCACATAATGTTAGATTTGGAAAAATG-TTTTGACT-GATACTAACAATTAATAATTTTAT
1 ACATTCACATAATGTTAGATTTAGAAAAATGTTTTTGACTAG-TACTAACAATTAATAATTTTAT
*
881896 ATAATTTGA-AATTTTTACTAACCATTAATACAATTTATCAGTTAATAATTT
65 ATAATTTGATAA-TTTTACTAACCATTAATACAATTTATCAGATAATAATTT
881947 CACAAACTTA
Statistics
Matches: 108, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
114 3 0.03
115 75 0.69
116 30 0.28
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (116 bp):
ACATTCACATAATGTTAGATTTAGAAAAATGTTTTTGACTAGTACTAACAATTAATAATTTTATA
TAATTTGATAATTTTACTAACCATTAATACAATTTATCAGATAATAATTTT
Found at i:884046 original size:24 final size:25
Alignment explanation
Indices: 884019--884071 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
884009 GAGTATGCTT
884019 TGAATCGTGGATTTTCTTCTTC-TC
1 TGAATCGTGGATTTTCTTCTTCATC
884043 TGAATCGTGGATTTTCTTCTTCATC
1 TGAATCGTGGATTTTCTTCTTCATC
884068 TGAA
1 TGAA
884072 CTCCTTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (25 bp):
TGAATCGTGGATTTTCTTCTTCATC
Found at i:888208 original size:28 final size:28
Alignment explanation
Indices: 888176--888233 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
888166 CCTGTGAACT
888176 CATCCTCCTGAGATGACTAACCAAGCAA
1 CATCCTCCTGAGATGACTAACCAAGCAA
*
888204 CATCCTCCTGAGATGACTATCCAAGCAA
1 CATCCTCCTGAGATGACTAACCAAGCAA
888232 CA
1 CA
888234 GATAGTCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (28 bp):
CATCCTCCTGAGATGACTAACCAAGCAA
Found at i:895397 original size:40 final size:40
Alignment explanation
Indices: 895314--895397 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
895304 TAATCCTCTC
* **
895314 AATTTCCTTCCAAATTTCTCTCAAACCCATATTTAATTTT
1 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATAAT
* * *
895354 AATTTCCTTTCAAAATTCTCTCAAATCCATTTTTTAA-AAT
1 AATTTCCTTCCAAAATTCTCTCAAACCCA-TATTTAATAAT
895394 AATT
1 AATT
895398 ATAAATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (40 bp):
AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATAAT
Found at i:895419 original size:30 final size:31
Alignment explanation
Indices: 895383--895446 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
895373 CTCAAATCCA
895383 TTTTTTAAAATAATTATAAA-TTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
895413 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
895444 TTT
1 TTT
895447 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:895558 original size:14 final size:15
Alignment explanation
Indices: 895539--895568 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
895529 TTTGTAATTA
895539 TTATTTAAG-ATTTT
1 TTATTTAAGTATTTT
895553 TTATTTAAGTATTTT
1 TTATTTAAGTATTTT
895568 T
1 T
895569 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTATTTAAGTATTTT
Found at i:896543 original size:7 final size:7
Alignment explanation
Indices: 896531--896555 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
896521 AGTCGATTGA
896531 TATTTAG
1 TATTTAG
896538 TATTTAG
1 TATTTAG
896545 TATTTAG
1 TATTTAG
896552 TATT
1 TATT
896556 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:897228 original size:18 final size:18
Alignment explanation
Indices: 897207--897241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
897197 AGGTATGTTT
* *
897207 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
897225 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
897242 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:897530 original size:24 final size:24
Alignment explanation
Indices: 897501--897555 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
897491 TGCCAAACCA
897501 GAAGAACCACAACCACCACCGGAG
1 GAAGAACCACAACCACCACCGGAG
* *
897525 GAAGAATCACAATCACCACCGGAG
1 GAAGAACCACAACCACCACCGGAG
897549 GAAGAAC
1 GAAGAAC
897556 AACCGCCGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.31, G:0.22, T:0.04
Consensus pattern (24 bp):
GAAGAACCACAACCACCACCGGAG
Found at i:897825 original size:29 final size:29
Alignment explanation
Indices: 897785--898011 Score: 300
Period size: 29 Copynumber: 7.7 Consensus size: 29
897775 AAAACACTAA
897785 CCTAA-CCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
897813 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
* *
897842 CCTAACCCTAACCTAAATTATTTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
897871 CCTAACCCTAACCTAACCTAACCTAAATAAAAAC
1 CCTAACCCTAACCTAA-CT----TAATTAAAAAC
897905 CCTAACCCTAACCTAACTTAACCTT--AAAC
1 CCTAACCCTAACCTAACTTAA--TTAAAAAC
*
897934 CCTAGCCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
897963 CCTAATCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
897992 CCTAA-CCTAACCTAAATTAA
1 CCTAACCCTAACCTAACTTAA
898012 NNNNNNNNNN
Statistics
Matches: 179, Mismatches: 10, Indels: 20
0.86 0.05 0.10
Matches are distributed among these distances:
27 2 0.01
28 19 0.11
29 129 0.72
30 1 0.01
31 1 0.01
33 2 0.01
34 25 0.14
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (29 bp):
CCTAACCCTAACCTAACTTAATTAAAAAC
Found at i:897910 original size:92 final size:90
Alignment explanation
Indices: 897762--898011 Score: 341
Period size: 92 Copynumber: 2.8 Consensus size: 90
897752 AAATAAAAAC
* * *
897762 CCTAATTTAATTGAAAACACTAACCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACCT
1 CCTAAATTAATTAAAAACCCTAACCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACCT
897827 AAATTAA-TTAAAAACCCTAACCCTAA
66 AAATTAACTT--AAACCCTAACCCTAA
* * *
897853 CCTAAATTATTTAAAAACCCTAACCCTAACCTAACCTAACCTAAATAAAAACCCTAACCCTAACC
1 CCTAAATTAATTAAAAACCCTAA-CCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACC
* *
897918 TAACTTAACCTTAAACCCTAGCCCTAA
65 TAAATTAA-CTTAAACCCTAACCCTAA
*
897945 CCTAACTTAATTAAAAACCCTAA--T--CCTAACCTAACTTAATTAAAAACCCTAA-CCTAACCT
1 CCTAAATTAATTAAAAACCCTAACCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACCT
898005 AAATTAA
66 AAATTAA
898012 NNNNNNNNNN
Statistics
Matches: 143, Mismatches: 13, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
86 14 0.10
87 26 0.18
89 1 0.01
91 19 0.13
92 81 0.57
94 2 0.01
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.25
Consensus pattern (90 bp):
CCTAAATTAATTAAAAACCCTAACCTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACCT
AAATTAACTTAAACCCTAACCCTAA
Found at i:897953 original size:23 final size:23
Alignment explanation
Indices: 897908--897954 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
897898 TAAAAACCCT
*
897908 AACCCTAACCTAACTTAACCTTA
1 AACCCTAACCTAACCTAACCTTA
*
897931 AACCCTAGCCCTAACCTAA-CTTA
1 AACCCTA-ACCTAACCTAACCTTA
897954 A
1 A
897955 TTAAAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.23
Consensus pattern (23 bp):
AACCCTAACCTAACCTAACCTTA
Found at i:898423 original size:29 final size:28
Alignment explanation
Indices: 898353--898629 Score: 383
Period size: 28 Copynumber: 9.8 Consensus size: 28
898343 NNNNNNNNNN
898353 AACCCTAATCTAACCTAAATTAATTAAA
1 AACCCTAATCTAACCTAAATTAATTAAA
* *
898381 ATCCCTAATCTAACCTAAATTAACTAAA
1 AACCCTAATCTAACCTAAATTAATTAAA
* * *
898409 AACCCTAAACCTAACATAAATTAACTAAA
1 AACCCT-AATCTAACCTAAATTAATTAAA
*
898438 AACCCTAATCGAACCTAAATTAATTAAA
1 AACCCTAATCTAACCTAAATTAATTAAA
898466 AACCCTAATCTAACCTAAATTAATTAAA
1 AACCCTAATCTAACCTAAATTAATTAAA
*
898494 AACCCTAAACCTAACCTAAATTAATTAAA
1 AACCCT-AATCTAACCTAAATTAATTAAA
* * **
898523 AACCCTAAACCTAACCTAAATTTACAAAA
1 AACCCT-AATCTAACCTAAATTAATTAAA
* *
898552 AACCCTAAACCTAGCCTAAATTAATTAAA
1 AACCCT-AATCTAACCTAAATTAATTAAA
*
898581 AACCCTAATCTAACCTAAATTAACTAAA
1 AACCCTAATCTAACCTAAATTAATTAAA
*
898609 AACCCTAAACTAACCTAAATT
1 AACCCTAATCTAACCTAAATT
898630 TTTTGGCTTA
Statistics
Matches: 225, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
28 121 0.54
29 104 0.46
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.25
Consensus pattern (28 bp):
AACCCTAATCTAACCTAAATTAATTAAA
Found at i:898444 original size:57 final size:56
Alignment explanation
Indices: 898353--898629 Score: 392
Period size: 57 Copynumber: 4.9 Consensus size: 56
898343 NNNNNNNNNN
* * * *
898353 AACCCTAATCTAACCTAAATTAATTAAAATCCCTAATCTAACCTAAATTAACTAAA
1 AACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAA
* * * *
898409 AACCCTAAACCTAACATAAATTAACTAAAAACCCTAATCGAACCTAAATTAATTAAA
1 AACCCT-AATCTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAA
*
898466 AACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAA
1 AACCCTAATCTAACCTAAATTAACTAAAAACCCT-AACCTAACCTAAATTAATTAAA
* * * *
898523 AACCCTAAACCTAACCTAAATTTACAAAAAACCCTAAACCTAGCCTAAATTAATTAAA
1 AACCCT-AATCTAACCTAAATTAACTAAAAACCCT-AACCTAACCTAAATTAATTAAA
*
898581 AACCCTAATCTAACCTAAATTAACTAAAAACCCTAAACTAACCTAAATT
1 AACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATT
898630 TTTTGGCTTA
Statistics
Matches: 197, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
56 44 0.22
57 101 0.51
58 52 0.26
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.25
Consensus pattern (56 bp):
AACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAA
Found at i:898662 original size:26 final size:26
Alignment explanation
Indices: 898628--898682 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
898618 CTAACCTAAA
898628 TTTTTTGGCTTAATAATTTTACATAT
1 TTTTTTGGCTTAATAATTTTACATAT
898654 TTTTTTGGCTTAATAATTTTACATAT
1 TTTTTTGGCTTAATAATTTTACATAT
898680 TTT
1 TTT
898683 GAACACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (26 bp):
TTTTTTGGCTTAATAATTTTACATAT
Found at i:898793 original size:10 final size:10
Alignment explanation
Indices: 898778--898802 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
898768 ATTTAGCTTA
898778 ATAATTTTAC
1 ATAATTTTAC
898788 ATAATTTTAC
1 ATAATTTTAC
898798 ATAAT
1 ATAAT
898803 GTTAGATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:901955 original size:127 final size:127
Alignment explanation
Indices: 901728--901967 Score: 462
Period size: 127 Copynumber: 1.9 Consensus size: 127
901718 NNNNNNNNNN
901728 AAAAAAAATTTATTTCTTACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAC
1 AAAAAAAATTTATTTCTTACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAC
901793 AATTTCTTCTCAAATAGCATCCTCGTAGAAACGATTTTATACTATTTGCTCAGAAACATCAG
66 AATTTCTTCTCAAATAGCATCCTCGTAGAAACGATTTTATACTATTTGCTCAGAAACATCAG
901855 AAAAAAAATTTATTTCTTACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAC
1 AAAAAAAATTTATTTCTTACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAC
* *
901920 AATTTCTTCTCAAATAGCATCCTGGTAGAAGCGATTTTATACTATTTG
66 AATTTCTTCTCAAATAGCATCCTCGTAGAAACGATTTTATACTATTTG
901968 ACCAGAGACG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 111 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (127 bp):
AAAAAAAATTTATTTCTTACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAC
AATTTCTTCTCAAATAGCATCCTCGTAGAAACGATTTTATACTATTTGCTCAGAAACATCAG
Found at i:904006 original size:17 final size:17
Alignment explanation
Indices: 903963--904038 Score: 63
Period size: 17 Copynumber: 4.7 Consensus size: 17
903953 CGAATATAAT
*
903963 AAATATTTTTAATTTTT
1 AAATATTTTTAATTTTA
* *
903980 TAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
903997 AAATA-CTTT--TTTT-
1 AAATATTTTTAATTTTA
904010 AAAT-TTTTTAAATTTTA
1 AAATATTTTT-AATTTTA
*
904027 AAATTTTTTTAA
1 AAATATTTTTAA
904039 AATACTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
13 7 0.15
14 4 0.09
16 7 0.15
17 23 0.50
18 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:904051 original size:26 final size:26
Alignment explanation
Indices: 904022--904076 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
904012 ATTTTTTAAA
904022 TTTTAAAATTTTTTTAAAATACTTTT
1 TTTTAAAATTTTTTTAAAATACTTTT
**
904048 TTTTTTAATTTTTTTAAAATACTTTT
1 TTTTAAAATTTTTTTAAAATACTTTT
904074 TTT
1 TTT
904077 AATTTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTAAAATTTTTTTAAAATACTTTT
Found at i:904083 original size:9 final size:9
Alignment explanation
Indices: 903968--904064 Score: 56
Period size: 9 Copynumber: 10.8 Consensus size: 9
903958 ATAATAAATA
903968 TTTTTAA-T
1 TTTTTAATT
903976 TTTTTAATT
1 TTTTTAATT
903985 TTTTTAATT
1 TTTTTAATT
** *
903994 TTAAAATACTT
1 TT--TTTAATT
*
904005 TTTTTAAAT
1 TTTTTAATT
*
904014 TTTTTAAAT
1 TTTTTAATT
**
904023 TTTAAAATT
1 TTTTTAATT
*
904032 TTTTTAAAAT
1 TTTTT-AATT
**
904042 ACTTT--TT
1 TTTTTAATT
904049 TTTTTAATT
1 TTTTTAATT
904058 TTTTTAA
1 TTTTTAA
904065 AATACTTTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
7 4 0.06
8 7 0.11
9 42 0.65
10 6 0.09
11 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTAATT
Found at i:904088 original size:26 final size:25
Alignment explanation
Indices: 904033--904090 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
904023 TTTAAAATTT
*
904033 TTTTAAAATACTTTTTTTTTTAATTT
1 TTTTAAAATACTTTTTTTTTT-ATTG
904059 TTTTAAAATACTTTTTTTAATTT-TTG
1 TTTTAAAATACTTTTTTT--TTTATTG
904085 TTTTAA
1 TTTTAA
904091 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 26 0.90
28 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTAAAATACTTTTTTTTTTATTG
Found at i:918410 original size:20 final size:19
Alignment explanation
Indices: 918369--918420 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
918359 AATTTTGATT
*
918369 TTTTTTATTTTTAAAATCA
1 TTTTTTAATTTTAAAATCA
918388 TTTTTTAATTTTAAAGAGT-A
1 TTTTTTAATTTTAAA-A-TCA
918408 TTTTTATAATTTT
1 TTTTT-TAATTTT
918421 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 7 0.24
21 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTTAATTTTAAAATCA
Found at i:919651 original size:20 final size:19
Alignment explanation
Indices: 919611--919649 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
919601 TTTTATTACG
919611 ATAATTTAAAAAATAAAAA
1 ATAATTTAAAAAATAAAAA
*
919630 ATAATTTTAAAAATAAAAA
1 ATAATTTAAAAAATAAAAA
919649 A
1 A
919650 ATCTCAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATTTAAAAAATAAAAA
Found at i:921422 original size:19 final size:17
Alignment explanation
Indices: 921398--921432 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
921388 ATTGTTTGGA
921398 TATTGTATAATTATTGTTT
1 TATTGT-TAATT-TTGTTT
921417 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
921433 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:921438 original size:18 final size:19
Alignment explanation
Indices: 921398--921438 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
921388 ATTGTTTGGA
*
921398 TATTGTATAATTATTGTTT
1 TATTGTATAATTATTGTTC
921417 TATTGT-TAATT-TTGTTAC
1 TATTGTATAATTATTGTT-C
921435 TATT
1 TATT
921439 TTAGAGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTATTGTTC
Found at i:928582 original size:14 final size:15
Alignment explanation
Indices: 928561--928611 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
928551 TAATAAATAT
928561 ATTTTTTTAATTTTA
1 ATTTTTTTAATTTTA
**
928576 ATTTTTTTAA-AATA
1 ATTTTTTTAATTTTA
* *
928590 ATTTTTTTATTTTTT
1 ATTTTTTTAATTTTA
928605 ATTTTTT
1 ATTTTTT
928612 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTTTAATTTTA
Found at i:928590 original size:34 final size:34
Alignment explanation
Indices: 928552--928626 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
928542 GCCCGAATAT
928552 AATAAATATATT-TTTTTAATTTTAATT-TTTTTAA
1 AATAAATATATTATTTTTAATTTT--TTATTTTTAA
* * * *
928586 AATAATTTTTTTATTTTTTATTTTTTATTTTTAA
1 AATAAATATATTATTTTTAATTTTTTATTTTTAA
928620 AATAAAT
1 AATAAAT
928627 TTTTGGTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
33 2 0.06
34 22 0.65
35 10 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (34 bp):
AATAAATATATTATTTTTAATTTTTTATTTTTAA
Found at i:928612 original size:28 final size:30
Alignment explanation
Indices: 928555--928611 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
928545 CGAATATAAT
928555 AAATATATTTTTTTAATTTTAATTTTTTTA
1 AAATATATTTTTTTAATTTTAATTTTTTTA
* *
928585 AAATA-ATTTTTTTATTTTTTATTTTTT
1 AAATATATTTTTTTAATTTTAATTTTTT
928612 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (30 bp):
AAATATATTTTTTTAATTTTAATTTTTTTA
Found at i:928617 original size:35 final size:35
Alignment explanation
Indices: 928563--928630 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
928553 ATAAATATAT
*
928563 TTTTTTAATTTTAATTTTTTTAAAATAATTTTTTTA
1 TTTTTTAATTTTAA-TTTTTTAAAATAAATTTTTTA
* *
928599 TTTTTTATTTTTTA-TTTTTAAAATAAATTTTT
1 TTTTTTAATTTTAATTTTTTAAAATAAATTTTT
928631 GGTGTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 17 0.59
36 12 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (35 bp):
TTTTTTAATTTTAATTTTTTAAAATAAATTTTTTA
Found at i:928618 original size:6 final size:7
Alignment explanation
Indices: 928592--928617 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
928582 TTAAAATAAT
928592 TTTTTTA
1 TTTTTTA
928599 TTTTTTA
1 TTTTTTA
928606 TTTTTTA
1 TTTTTTA
928613 TTTTT
1 TTTTT
928618 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:930421 original size:23 final size:23
Alignment explanation
Indices: 930388--930440 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
930378 NNNNNNNNNN
*
930388 TTATATATTTATAAATTTTTATT
1 TTATATATTTATAAATTTATATT
*
930411 TTATATTTTTATAAATTTATATT
1 TTATATATTTATAAATTTATATT
930434 TTATATA
1 TTATATA
930441 ATTTTCAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATATATTTATAAATTTATATT
Found at i:930431 original size:16 final size:17
Alignment explanation
Indices: 930410--930441 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
930400 AAATTTTTAT
930410 TTTATATTTT-TATAAA
1 TTTATATTTTATATAAA
930426 TTTATATTTTATATAA
1 TTTATATTTTATATAA
930442 TTTTCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATTTTATATAAA
Found at i:933134 original size:45 final size:45
Alignment explanation
Indices: 933070--933199 Score: 197
Period size: 45 Copynumber: 2.9 Consensus size: 45
933060 NNNNNNNNNN
*
933070 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACTGAC
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
* **
933115 TCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGGT
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
** *
933160 TCAACACTTTGTGTGTTGAATACTGTTACTGTTACTGTTA
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTA
933200 TTGATTACTG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (45 bp):
TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
Found at i:934217 original size:30 final size:31
Alignment explanation
Indices: 934176--934235 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
934166 ATGTCAAAAT
* *
934176 TAAAGTATAGAGATTAAAATCCAAATTTAAG
1 TAAAGTATAGAGATCAAAATCAAAATTTAAG
*
934207 TAAA-TATAGAGATCAAAATTAAAATTTAA
1 TAAAGTATAGAGATCAAAATCAAAATTTAA
934236 CAATTCTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (31 bp):
TAAAGTATAGAGATCAAAATCAAAATTTAAG
Found at i:934609 original size:49 final size:47
Alignment explanation
Indices: 934540--934642 Score: 165
Period size: 49 Copynumber: 2.2 Consensus size: 47
934530 CCCCCTCCCA
934540 TCCCTCT--CCCTCTTCCCCACCATCCCTCCCCCTACTCTGATTCTCT
1 TCCCTCTCCCCCTCTTCCCCACCATCCCTCCCCCTACTCTGATTCT-T
*
934586 CTCCCTCTCCCCCTCTTCCCCACCATCCCTCCTCCTACTCTGATTCTT
1 -TCCCTCTCCCCCTCTTCCCCACCATCCCTCCCCCTACTCTGATTCTT
934634 TCCCTCTCC
1 TCCCTCTCC
934643 TCCACCGTCC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
47 16 0.30
48 1 0.02
49 36 0.68
ACGTcount: A:0.08, C:0.57, G:0.02, T:0.33
Consensus pattern (47 bp):
TCCCTCTCCCCCTCTTCCCCACCATCCCTCCCCCTACTCTGATTCTT
Found at i:949915 original size:42 final size:42
Alignment explanation
Indices: 949806--950076 Score: 411
Period size: 42 Copynumber: 6.4 Consensus size: 42
949796 GTTTGTGAAA
* * *
949806 TAAGCGCCGCTATAGAATATTA-CTTTTAGCGGCG-TTTCCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTT--TTCC
*
949849 AAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGCTTTTTCC
1 TAAGCGCCGCT-AAAGAACATGATCTTTAGCGGCGCTTTTTCC
949892 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
949934 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
949976 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
* *
950018 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTACG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-CTTTTT-CC
*
950062 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
950077 TTAGTGACGT
Statistics
Matches: 215, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
42 149 0.69
43 29 0.13
44 33 0.15
45 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCC
Found at i:952252 original size:17 final size:17
Alignment explanation
Indices: 952230--952296 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
952220 AATCTTAGAG
952230 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
952247 TTCTAATTGTGTAATCTTAGAG
1 TTCTAATTGTAT-A-C--AG-C
952269 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
952286 TTTTAATTGTA
1 TTCTAATTGTA
952297 GCCAGTGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 21 0.52
18 3 0.08
19 1 0.03
20 1 0.03
21 3 0.08
22 11 0.28
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:952271 original size:39 final size:39
Alignment explanation
Indices: 952217--952295 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
952207 GATATGATTA
952217 TGTAATCTTAGAGTTCTAATTGTATACAGCTTCTAATTG
1 TGTAATCTTAGAGTTCTAATTGTATACAGCTTCTAATTG
*
952256 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
1 TGTAATCTTAGAGTTCTAATTGTATACAGCTTCTAATTG
952295 T
1 T
952296 AGCCAGTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (39 bp):
TGTAATCTTAGAGTTCTAATTGTATACAGCTTCTAATTG
Found at i:957351 original size:39 final size:39
Alignment explanation
Indices: 957297--957375 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
957287 GATATGATAA
957297 TGTAATCTTAAAGTTCTAATTGTATACAACTTCTAATTG
1 TGTAATCTTAAAGTTCTAATTGTATACAACTTCTAATTG
* * *
957336 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
1 TGTAATCTTAAAGTTCTAATTGTATACAACTTCTAATTG
957375 T
1 T
957376 AGCCATTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (39 bp):
TGTAATCTTAAAGTTCTAATTGTATACAACTTCTAATTG
Found at i:958669 original size:14 final size:16
Alignment explanation
Indices: 958652--958689 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
958642 CTTATAACTT
958652 AATAAATA-ATT-AAA
1 AATAAATATATTCAAA
958666 AATAAA-ATATTCAAA
1 AATAAATATATTCAAA
958681 AATAAATAT
1 AATAAATAT
958690 TTGAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 9 0.43
15 9 0.43
16 2 0.10
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATATATTCAAA
Found at i:971213 original size:99 final size:99
Alignment explanation
Indices: 971042--971242 Score: 402
Period size: 99 Copynumber: 2.0 Consensus size: 99
971032 ACTTCCTGAG
971042 GTAGTTAATCTTTAGTTTCTACAACGTCAGATGGCAATGATTATTAACAATTTATTATAATATAA
1 GTAGTTAATCTTTAGTTTCTACAACGTCAGATGGCAATGATTATTAACAATTTATTATAATATAA
971107 ACAAAGCGAGCCTGTGTATTAATAATATGAAACA
66 ACAAAGCGAGCCTGTGTATTAATAATATGAAACA
971141 GTAGTTAATCTTTAGTTTCTACAACGTCAGATGGCAATGATTATTAACAATTTATTATAATATAA
1 GTAGTTAATCTTTAGTTTCTACAACGTCAGATGGCAATGATTATTAACAATTTATTATAATATAA
971206 ACAAAGCGAGCCTGTGTATTAATAATATGAAACA
66 ACAAAGCGAGCCTGTGTATTAATAATATGAAACA
971240 GTA
1 GTA
971243 TTATCTAATA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 102 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (99 bp):
GTAGTTAATCTTTAGTTTCTACAACGTCAGATGGCAATGATTATTAACAATTTATTATAATATAA
ACAAAGCGAGCCTGTGTATTAATAATATGAAACA
Found at i:997181 original size:92 final size:92
Alignment explanation
Indices: 997023--997205 Score: 339
Period size: 92 Copynumber: 2.0 Consensus size: 92
997013 CTCTTTCATA
*
997023 GCTGTGCTAGTCATCTCCATCTCATCCATCATGAGCAACAGAATAAAAGCATCATATAGATACAT
1 GCTGTGCTAGTCATCTCCATCTCATCCATCATGAACAACAGAATAAAAGCATCATATAGATACAT
997088 AGATGCAGCTAAATTCACCTAATAATG
66 AGATGCAGCTAAATTCACCTAATAATG
*
997115 GCTGTGCTAGTCATCTCCATCTCATCCATCATGAACAACAGAATAAAAGCATCATATAGATGCAT
1 GCTGTGCTAGTCATCTCCATCTCATCCATCATGAACAACAGAATAAAAGCATCATATAGATACAT
*
997180 AGATGCAGCTAAATTCATCTAATAAT
66 AGATGCAGCTAAATTCACCTAATAAT
997206 ATAAACAACT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (92 bp):
GCTGTGCTAGTCATCTCCATCTCATCCATCATGAACAACAGAATAAAAGCATCATATAGATACAT
AGATGCAGCTAAATTCACCTAATAATG
Found at i:1001792 original size:23 final size:23
Alignment explanation
Indices: 1001741--1001793 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1001731 TTTCGATAAA
* *
1001741 ATTATATAAAAATGTTTTAATTC
1 ATTATATAAAAATGATTAAATTC
* *
1001764 ACTTATATAAATATGATTAAATTT
1 A-TTATATAAAAATGATTAAATTC
1001788 ATTATA
1 ATTATA
1001794 ATAATTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTATATAAAAATGATTAAATTC
Found at i:1002489 original size:22 final size:22
Alignment explanation
Indices: 1002453--1002495 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1002443 TTGCTTGTTA
* *
1002453 CCATTTTGATGTTATTTTGCTG
1 CCATTTTGATATTATATTGCTG
*
1002475 CCATTTTGCTATTATATTGCT
1 CCATTTTGATATTATATTGCT
1002496 ACTAGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.53
Consensus pattern (22 bp):
CCATTTTGATATTATATTGCTG
Found at i:1008029 original size:13 final size:13
Alignment explanation
Indices: 1008011--1008057 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1008001 TCTTCATTGC
*
1008011 TTTTGAAATGTGT
1 TTTTGAAAAGTGT
1008024 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
* * *
1008037 TGTGGAAAAGTGC
1 TTTTGAAAAGTGT
1008050 TTTTGAAA
1 TTTTGAAA
1008058 GGTTTGGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:1021030 original size:43 final size:42
Alignment explanation
Indices: 1020938--1021064 Score: 117
Period size: 36 Copynumber: 3.1 Consensus size: 42
1020928 CTTACGTATG
* *
1020938 ATCACTTATCATTTGTC-CCTGATCAGATAAGTGTAGCTAAGC-T
1 ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGC--A-CTT
* *
1020981 ACCACTTATCACTTTGTCACTTGATCAGATAAGAATAGCACTT
1 ATCACTTATCA-TTTGTCACTTGATCAGATAAGTATAGCACTT
*
1021024 ATCAC---T--TTT-TCACTTGATCAGATAAGTATAACACTT
1 ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTT
1021060 ATCAC
1 ATCAC
1021065 GTTTCAGTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
36 30 0.41
37 3 0.04
40 1 0.01
42 1 0.01
43 16 0.22
44 6 0.08
45 17 0.23
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (42 bp):
ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTT
Found at i:1021077 original size:35 final size:35
Alignment explanation
Indices: 1020983--1021085 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 35
1020973 GCTAAGCTAC
* *
1020983 CACTTATCACTTTGTCACTTGATCAGATAAGAATAG
1 CACTTATCACTTT-TCACTTGATCAGATAAGTATAA
1021019 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCAC-TTTTCACTTGATCAGATAAGTATAA
* *
1021055 CACTTATCACGTTTCAGTTGATCAGATAAGT
1 CACTTATCACTTTTCACTTGATCAGATAAGT
1021086 GTAGCTAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 19 0.31
36 40 0.65
37 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (35 bp):
CACTTATCACTTTTCACTTGATCAGATAAGTATAA
Found at i:1021360 original size:30 final size:30
Alignment explanation
Indices: 1021326--1021537 Score: 424
Period size: 30 Copynumber: 7.1 Consensus size: 30
1021316 TAGACTACTA
1021326 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021356 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021386 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021416 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021446 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021476 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021506 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1021536 CA
1 CA
1021538 AACCTTAATT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 182 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.20
Consensus pattern (30 bp):
CATAGCCTTTCATACTCAAAACCGCAACAC
Found at i:1022567 original size:37 final size:38
Alignment explanation
Indices: 1022481--1022574 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 38
1022471 ACACACCAAT
*
1022481 TTGGCACCCAGTGCCTCATCGGATAATACGAAGTAATAAA
1 TTGGCACCCAATGCCTCATCGGATAATACGAAG--ATAAA
* * *
1022521 TTGACACCCAATGTCTCATCGGTTAA-ACCGAAG-TAAA
1 TTGGCACCCAATGCCTCATCGGATAATA-CGAAGATAAA
1022558 TTGGCACCCAATGCCTC
1 TTGGCACCCAATGCCTC
1022575 CACGAATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
37 19 0.40
39 1 0.02
40 27 0.57
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (38 bp):
TTGGCACCCAATGCCTCATCGGATAATACGAAGATAAA
Found at i:1023624 original size:12 final size:12
Alignment explanation
Indices: 1023607--1023667 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1023597 CATTAACTTT
1023607 TCTTTCTTTTTC
1 TCTTTCTTTTTC
1023619 TCTTTCTTTTTC
1 TCTTTCTTTTTC
* *
1023631 CCTTATGTTTCGTTTC
1 TCTT-T-CTT--TTTC
*
1023647 ACTTTCTTTTTC
1 TCTTTCTTTTTC
*
1023659 TTTTTCTTT
1 TCTTTCTTT
1023668 CATTTATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 26 0.67
13 1 0.03
14 4 0.10
15 1 0.03
16 7 0.18
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.70
Consensus pattern (12 bp):
TCTTTCTTTTTC
Found at i:1029060 original size:13 final size:13
Alignment explanation
Indices: 1029041--1029103 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
1029031 TAAACCAAAA
1029041 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
1029054 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
1029067 TTTT-ACACAGCAC
1 TTTTCA-AAAGCAC
*
1029080 TTTTC-AAAGTAC
1 TTTTCAAAAGCAC
1029092 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1029104 TTGCCAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
12 11 0.27
13 30 0.73
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1030537 original size:8 final size:7
Alignment explanation
Indices: 1030512--1030563 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
1030502 TTACTCTTGC
1030512 AAAAAT-
1 AAAAATA
1030518 AAAAAT-
1 AAAAATA
1030524 AAAAATAA
1 AAAAAT-A
1030532 AAAAATA
1 AAAAATA
1030539 AAAAATA
1 AAAAATA
1030546 AAAAATA
1 AAAAATA
1030553 AAAAATA
1 AAAAATA
1030560 AAAA
1 AAAA
1030564 GCTTCAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.27
7 26 0.59
8 6 0.14
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:1055298 original size:21 final size:21
Alignment explanation
Indices: 1055265--1055305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1055255 TAAAAAACAT
*
1055265 ATAAAATTATTAAATAATAAA
1 ATAAAATTATTAAAAAATAAA
1055286 ATAAATATT-TTAAAAAATAA
1 ATAAA-ATTATTAAAAAATAA
1055306 TATGGGCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAATTATTAAAAAATAAA
Found at i:1057151 original size:31 final size:31
Alignment explanation
Indices: 1057084--1057154 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1057074 TTGGTCACTT
* * *
1057084 AACTATTTAAAAGTTTCCATTTAAGTCATTG
1 AACTATTAAAAAGTTTCCATTTAAGCCATAG
**
1057115 AACTATTAAAAAGTTTTTATTTAAGCCACTAG
1 AACTATTAAAAAGTTTCCATTTAAGCCA-TAG
1057147 -ACTATTAA
1 AACTATTAA
1057155 TTCTTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (31 bp):
AACTATTAAAAAGTTTCCATTTAAGCCATAG
Found at i:1057722 original size:30 final size:31
Alignment explanation
Indices: 1057663--1057722 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1057653 ACAAAATGGT
1057663 CATTGAACTATTAAAAAATTTTCATTTAAGC
1 CATTGAACTATTAAAAAATTTTCATTTAAGC
* *
1057694 CATTGAACTATTTAAAAGTTTT-ATTTAAG
1 CATTGAACTATTAAAAAATTTTCATTTAAG
1057723 TTACTAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (31 bp):
CATTGAACTATTAAAAAATTTTCATTTAAGC
Found at i:1071836 original size:27 final size:27
Alignment explanation
Indices: 1071806--1071872 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1071796 CCTATCAGGT
1071806 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
1071833 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
1071860 AGGCGCCAATGAA
1 AGGCGCCAATGAA
1071873 TATTGTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.33, T:0.13
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:1071895 original size:19 final size:19
Alignment explanation
Indices: 1071871--1071956 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
1071861 GGCGCCAATG
1071871 AATATTGTAATTTTGTATT
1 AATATTGTAATTTTGTATT
*
1071890 AATATTGTAATTAT-T-TT
1 AATATTGTAATTTTGTATT
* *
1071907 -ATAAT-TAAATTTGTATT
1 AATATTGTAATTTTGTATT
* *
1071924 TATATTGTAATTTTTTGTATG
1 AATATTGTAA--TTTTGTATT
1071945 AATATTGTAATT
1 AATATTGTAATT
1071957 ATTTTATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.09
16 5 0.09
17 4 0.08
18 5 0.09
19 18 0.34
21 16 0.30
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
AATATTGTAATTTTGTATT
Found at i:1071942 original size:21 final size:22
Alignment explanation
Indices: 1071916--1071961 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1071906 TATAATTAAA
**
1071916 TTTGTATTTATATTGTAATT-T
1 TTTGTATGAATATTGTAATTAT
1071937 TTTGTATGAATATTGTAATTAT
1 TTTGTATGAATATTGTAATTAT
1071959 TTT
1 TTT
1071962 ATAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (22 bp):
TTTGTATGAATATTGTAATTAT
Found at i:1071954 original size:55 final size:52
Alignment explanation
Indices: 1071872--1071974 Score: 170
Period size: 55 Copynumber: 1.9 Consensus size: 52
1071862 GCGCCAATGA
*
1071872 ATATTGTAATTTTGTATTAATATTGTAATTATTTTATAATTAAATTTGTATTT
1 ATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATT-AATTTGTATTT
1071925 ATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAATTTGT
1 ATATTGTAA--TTTTGTATGAATATTGTAATTATTTTATAATTAATTTGT
1071975 TAGTAAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
53 9 0.19
54 7 0.15
55 31 0.66
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (52 bp):
ATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTATTT
Found at i:1072033 original size:11 final size:11
Alignment explanation
Indices: 1071998--1072033 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1071988 TTATGTTATA
1071998 AATTTATTAGT
1 AATTTATTAGT
*
1072009 AACTTATTAGT
1 AATTTATTAGT
*
1072020 AATTTATTACT
1 AATTTATTAGT
1072031 AAT
1 AAT
1072034 AAATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (11 bp):
AATTTATTAGT
Found at i:1072281 original size:27 final size:28
Alignment explanation
Indices: 1072243--1072319 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
1072233 CAAGCCCCGC
*
1072243 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
1072270 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
1072297 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
1072320 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:1080725 original size:41 final size:41
Alignment explanation
Indices: 1080663--1080770 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
1080653 CATTGAATGT
* *
1080663 AAGGGGTTGCTAAGTGTAGATTCCCCGAACCACTTATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAACCACTGATCAAA
* * *
1080704 AAGGGGATGCTAAGTGGAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAACCACTGATCAAA
1080745 AAGGGGTTGCTAAGTGCAGATTCCCC
1 AAGGGGTTGCTAAGTGCAGATTCCCC
1080771 AAGGGGTTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAACCACTGATCAAA
Found at i:1080781 original size:26 final size:26
Alignment explanation
Indices: 1080745--1080794 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
1080735 ACTGATCAAA
1080745 AAGGGGTTGCTAAGTGCA-GATTCCCC
1 AAGGGGTTGCTAAGTG-ATGATTCCCC
1080771 AAGGGGTTGCTAAGTGATGATTCC
1 AAGGGGTTGCTAAGTGATGATTCC
1080795 ACCGTATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (26 bp):
AAGGGGTTGCTAAGTGATGATTCCCC
Found at i:1086833 original size:43 final size:41
Alignment explanation
Indices: 1086700--1086889 Score: 161
Period size: 41 Copynumber: 4.6 Consensus size: 41
1086690 ATTGAATGTT
* * * * *
1086700 AGGGGTTGCCAAGTGCAGATTCCCTGAATCACTGA-TCAAAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATTC-TAA
*
1086741 AGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATTCTAA
* *
1086782 AGGTGGTTGCTAAGTGCTGATTCCACC-ATATCCTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGA-ATCATTGATTCT-AA
* * * * * *
1086826 AGGGGTTGCTATGTGCTGATTACCCGTATCACTGAATAT-A
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATTCTAA
* *
1086866 AGTTGGTTGCTAAATGCTGATTCC
1 AG-GGGTTGCTAAGTGCTGATTCC
1086890 ACTGAGTAAC
Statistics
Matches: 122, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
40 3 0.02
41 52 0.43
42 33 0.27
43 29 0.24
44 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATTCTAA
Found at i:1099237 original size:17 final size:17
Alignment explanation
Indices: 1099204--1099240 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1099194 AAAAAGTATT
**
1099204 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
1099221 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
1099238 TTA
1 TTA
1099241 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:1101480 original size:69 final size:69
Alignment explanation
Indices: 1101361--1101500 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
1101351 TAATGGCAAC
* **
1101361 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACTAGGGAATCCTTCATAGTACTTC
1 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACTAGAGAATCAGTCATAGTACTTC
1101426 TACT
66 TACT
* * * *
1101430 TTCAACTGCGTCCATGGTTGGTGAATCCTCATCCAACACTACTTGAGAATCAGTCATAGTACTTG
1 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACTAGAGAATCAGTCATAGTACTTC
1101495 TACT
66 TACT
1101499 TT
1 TT
1101501 TATCCAGAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (69 bp):
TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACTAGAGAATCAGTCATAGTACTTC
TACT
Found at i:1102548 original size:35 final size:35
Alignment explanation
Indices: 1102502--1102574 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
1102492 TCTTTAAGTT
1102502 GAATTATTCATTTATAGAGGAAAAACATATGCTTA
1 GAATTATTCATTTATAGAGGAAAAACATATGCTTA
1102537 GAATTATTCATTTATAGAGGAAAAACATATGCTTA
1 GAATTATTCATTTATAGAGGAAAAACATATGCTTA
1102572 GAA
1 GAA
1102575 GTCTCAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (35 bp):
GAATTATTCATTTATAGAGGAAAAACATATGCTTA
Found at i:1107916 original size:14 final size:15
Alignment explanation
Indices: 1107893--1107925 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1107883 CTCTTTGATT
*
1107893 AAAAATCAAATT-AC
1 AAAAACCAAATTAAC
1107907 AAAAACCAAATTAAC
1 AAAAACCAAATTAAC
1107922 AAAA
1 AAAA
1107926 GCGGTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAACCAAATTAAC
Found at i:1111232 original size:2 final size:2
Alignment explanation
Indices: 1111225--1111261 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1111215 CCACTCTCCA
1111225 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1111262 ATTTTTCGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1114669 original size:14 final size:14
Alignment explanation
Indices: 1114629--1114669 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1114619 AAACACATAC
1114629 ATCTTCATGTTTAT
1 ATCTTCATGTTTAT
* *
1114643 AACTT--TTTTTAT
1 ATCTTCATGTTTAT
1114655 ATCTTCATGTTTAT
1 ATCTTCATGTTTAT
1114669 A
1 A
1114670 ATATAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
12 10 0.48
14 11 0.52
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (14 bp):
ATCTTCATGTTTAT
Found at i:1121559 original size:346 final size:346
Alignment explanation
Indices: 1120921--1121697 Score: 1441
Period size: 346 Copynumber: 2.2 Consensus size: 346
1120911 CAATAGTCTC
* * * * *
1120921 ATTCACAAATTTTATCTCCATGGTTTAATCTTTTACCTACATAAAAAATAAAAAAATTTATATTA
1 ATTC-CAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAAAATTTATATTA
1120986 AAATAATAAAAATAGCATGTTAATAAAAAAATAACAAAAACATAACATAAACGATACATAATAAA
65 AAATAATAAAAATAGCATGTTAATAAAAAAATAACAAAAACATAACATAAACGATACATAATAAA
1121051 TACGAATATTTTGATTTAAAATATAATATATATAATAACATGCCAACTTAACTATTGTCAAAAAT
130 TACGAATATTTTGATTTAAAATATAATATATATAATAACATGCCAACTTAACTATTGTCAAAAAT
1121116 TATAAGTTTTTTTTGCATAGAACTTCAAAAGAAATTTTATTTTTAATATTTATAAAAATTTAAAA
195 TATAAGTTTTTTTTGCATAGAACTTCAAAAGAAATTTTATTTTTAATATTTATAAAAATTTAAAA
1121181 TAAAATTTAAAAACATAAATTCTTATTCTCAATTA-TAAAATCTTAAAAAATTAGAACATGTAAA
260 TAAAATTTAAAAACATAAATTCTTATTCTCAATTATTAAAATCTT-AAAAATTAGAACATGTAAA
1121245 CTAATTCCTAATTTATCTCATAA
324 CTAATTCCTAATTTATCTCATAA
1121268 ATTCCAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAAAATTTATATTAA
1 ATTCCAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAAAATTTATATTAA
1121333 AATAATAAAAATAGCATGTTAATAAAAAAATAACAAAAACATAACATAAACGATACATAATAAAT
66 AATAATAAAAATAGCATGTTAATAAAAAAATAACAAAAACATAACATAAACGATACATAATAAAT
1121398 ACGAATATTTTGATTTAAAATATAATATATATAATAACATGCCAACTTAACTATTGTCAAAAATT
131 ACGAATATTTTGATTTAAAATATAATATATATAATAACATGCCAACTTAACTATTGTCAAAAATT
1121463 ATAAGTTTTTTTTGCATAGAACTTCAAAAGAAATTTTATTTTTAATATTTATAAAAATTTAAAAT
196 ATAAGTTTTTTTTGCATAGAACTTCAAAAGAAATTTTATTTTTAATATTTATAAAAATTTAAAAT
1121528 AAAATTTAAAAACATAAATTCTTATTCTCAATTATTAAAATCTTAAAAATTAGAACATGTAAACT
261 AAAATTTAAAAACATAAATTCTTATTCTCAATTATTAAAATCTTAAAAATTAGAACATGTAAACT
1121593 AATTCCTAATTTATCTCATAA
326 AATTCCTAATTTATCTCATAA
*
1121614 ATTCCAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAATAA-TAATATTA
1 ATTCCAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAA-AATTTATATTA
* *
1121678 AAATAATCAAAATAACATGT
65 AAATAATAAAAATAGCATGT
1121698 CAAATAAATT
Statistics
Matches: 420, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
346 405 0.96
347 15 0.04
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (346 bp):
ATTCCAAATTTCATATCAATGGTCTCATCTTTTACCTACATAAAAAATAAAAAAATTTATATTAA
AATAATAAAAATAGCATGTTAATAAAAAAATAACAAAAACATAACATAAACGATACATAATAAAT
ACGAATATTTTGATTTAAAATATAATATATATAATAACATGCCAACTTAACTATTGTCAAAAATT
ATAAGTTTTTTTTGCATAGAACTTCAAAAGAAATTTTATTTTTAATATTTATAAAAATTTAAAAT
AAAATTTAAAAACATAAATTCTTATTCTCAATTATTAAAATCTTAAAAATTAGAACATGTAAACT
AATTCCTAATTTATCTCATAA
Found at i:1121884 original size:40 final size:40
Alignment explanation
Indices: 1121839--1121919 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1121829 TATGAATGAA
*
1121839 TGAAAATATAAAATAAATACAAACATACCTTCATAGCTCT
1 TGAAAATATAAAATAAATACAAACATACATTCATAGCTCT
1121879 TGAAAATATAAAATAAATACAAACATACATTCATAGCTCT
1 TGAAAATATAAAATAAATACAAACATACATTCATAGCTCT
1121919 T
1 T
1121920 TTTAATCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.28
Consensus pattern (40 bp):
TGAAAATATAAAATAAATACAAACATACATTCATAGCTCT
Found at i:1122026 original size:27 final size:27
Alignment explanation
Indices: 1121988--1122062 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
1121978 CAAGGTGTGG
*
1121988 CGCCTATCAGATAGGTACCACCAGTGC
1 CGCCTATCAGATAGGCACCACCAGTGC
*** **
1122015 CGCCTATCAGATAGGGGTCACTGGTGC
1 CGCCTATCAGATAGGCACCACCAGTGC
*
1122042 TGCCTATCAGATAGGCACCAC
1 CGCCTATCAGATAGGCACCAC
1122063 ACCCCTATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACCACCAGTGC
Found at i:1133594 original size:29 final size:33
Alignment explanation
Indices: 1133548--1133682 Score: 102
Period size: 34 Copynumber: 4.1 Consensus size: 33
1133538 TTTTATTTAT
**
1133548 TTAAGGTTTA-AGAATTTTAA-AAAT-A-TAAA
1 TTAAGGTTTAGAGTTTTTTAAGAAATAATTAAA
*
1133577 TTAAGGTTTAGAGTTTTTTTAAAATAATAATTAAA
1 TTAAGGTTTAGAG-TTTTTTAAGA-AATAATTAAA
* * * *
1133612 TT-AGGTTTTAGGGGTTTTAAATAAATAAATTAAA
1 TTAAGG-TTTAGAGTTTTTTAAGAAAT-AATTAAA
*
1133646 TTAGGGTTTAGAG-TTTTTAAGAAAATTAATTAAA
1 TTAAGGTTTAGAGTTTTTTAAG-AAA-TAATTAAA
1133680 TTA
1 TTA
1133683 GGATTTATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
29 10 0.12
30 2 0.02
31 6 0.07
32 1 0.01
33 12 0.14
34 39 0.46
35 15 0.18
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (33 bp):
TTAAGGTTTAGAGTTTTTTAAGAAATAATTAAA
Found at i:1133643 original size:34 final size:32
Alignment explanation
Indices: 1133593--1133689 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 32
1133583 TTTAGAGTTT
* *
1133593 TTTTAAAATAATAATTAAATTAGGTTTTAGGGG
1 TTTTAAAA-AATAATTAAATTAGGATTTAGAGG
* *
1133626 TTTTAAATAAATAAATTAAATTAGGGTTTAGAGT
1 TTTTAAA-AAAT-AATTAAATTAGGATTTAGAGG
1133660 TTTTAAGAAAATTAATTAAATTAGGATTTA
1 TTTTAA-AAAA-TAATTAAATTAGGATTTA
1133690 TTTTTTTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
33 10 0.18
34 44 0.79
35 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.42
Consensus pattern (32 bp):
TTTTAAAAAATAATTAAATTAGGATTTAGAGG
Found at i:1133979 original size:124 final size:124
Alignment explanation
Indices: 1133758--1134149 Score: 520
Period size: 125 Copynumber: 3.1 Consensus size: 124
1133748 AGGATTCAAT
* * * *
1133758 TTTTTTTACAGTAGCTT-CAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAA
1 TTTTTCTACAGTAG-TTCCTGAAAAA-TAATTTTGAGAAGACGATTCTGAAAA-ATAGTGTCAAA
* * * *
1133822 AACGCTTCAAGCAGGATGTACTATCAGCAAAATTACTGAAAAAA-CTACCATGTGGACACTC
63 AACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
* * *
1133883 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTAAGAACACGATTCTGGAAAAATAGTTTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCT-GAAAAATAGTGTCAAAAA
* *
1133948 CGCTTCAAGCAGGATGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGTGGACACTT
65 CGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
* * *
1134008 TTTTTCCACAGTAGTTCCTGAAAAATAATTTTGAGAAGACAATTTTGAAAAATTAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCTGAAAAA-TAGTGTCAAAAA
* * * * *
1134073 TGCTTCAAGCAGGATACAC-AGTCAGCAAAATTACTAAAAAAAGCTCCCACATGGACGCTA
65 CGCTTCAAGCAGGATGCACTA-TCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
1134133 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
1134150 ATGTTTGGCC
Statistics
Matches: 236, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
124 78 0.33
125 158 0.67
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGATTCTGAAAAATAGTGTCAAAAAC
GCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTA
Found at i:1139855 original size:6 final size:6
Alignment explanation
Indices: 1139844--1139870 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1139834 TTATTTATAG
1139844 ATTTAA ATTTAA ATTTAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATT
1139871 AATATATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:1139884 original size:18 final size:18
Alignment explanation
Indices: 1139839--1139885 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1139829 AGATGTTATT
*
1139839 TATAGATTTAAATTTAAA
1 TATAAATTTAAATTTAAA
*
1139857 TTTAAATTTAAA-TTAATA
1 TATAAATTTAAATTTAA-A
*
1139875 TATAACTTTAA
1 TATAAATTTAA
1139886 CACTAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TATAAATTTAAATTTAAA
Found at i:1141619 original size:16 final size:17
Alignment explanation
Indices: 1141593--1141631 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1141583 TCAAATCGAG
*
1141593 TTTTCTTTGGATTTGGA
1 TTTTCTTTGGACTTGGA
1141610 TTTT-TTTGGACTTGGA
1 TTTTCTTTGGACTTGGA
1141626 TTTTCT
1 TTTTCT
1141632 CATTGAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.62
Consensus pattern (17 bp):
TTTTCTTTGGACTTGGA
Found at i:1147191 original size:14 final size:14
Alignment explanation
Indices: 1147172--1147211 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1147162 TTGATTGCCA
1147172 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
1147186 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
1147200 GGAAAATGTTTT
1 GTAAAATGTTTT
1147212 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:1147220 original size:20 final size:20
Alignment explanation
Indices: 1147195--1147235 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1147185 CGTAAAATGA
*
1147195 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1147215 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1147235 T
1 T
1147236 GAAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1147224 original size:34 final size:35
Alignment explanation
Indices: 1147180--1147246 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1147170 CAGTAAAATG
*
1147180 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
1147214 TTTTCTGTAAAATGATTTACTTGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1147247 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1149944 original size:2 final size:2
Alignment explanation
Indices: 1149937--1149965 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1149927 TGGGCTAATT
1149937 TA 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 TA T
1149966 GCTGGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1150486 original size:14 final size:14
Alignment explanation
Indices: 1150467--1150497 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1150457 ATAAAAAATA
1150467 ATATTAAAATACTT
1 ATATTAAAATACTT
*
1150481 ATATTAAAATGCTT
1 ATATTAAAATACTT
1150495 ATA
1 ATA
1150498 AGAGGAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATTAAAATACTT
Found at i:1153823 original size:16 final size:16
Alignment explanation
Indices: 1153779--1153828 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
1153769 TAACACAATT
1153779 ATATTTAATGTTAAG-
1 ATATTTAATGTTAAGA
*
1153794 A-ATTT-AT-ATAAGA
1 ATATTTAATGTTAAGA
1153807 ATATTTAATGTTAAGA
1 ATATTTAATGTTAAGA
1153823 AT-TTTA
1 ATATTTA
1153829 TTAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.14
13 3 0.10
14 8 0.28
15 7 0.24
16 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATTTAATGTTAAGA
Found at i:1153982 original size:18 final size:17
Alignment explanation
Indices: 1153954--1153988 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1153944 ATTATTAAGA
*
1153954 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1153971 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1153989 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1154242 original size:16 final size:16
Alignment explanation
Indices: 1154221--1154254 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1154211 TTGAATTGCT
1154221 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
* *
1154237 ATTACGCGTCTATTCC
1 ATTACGCCTCTAATCC
1154253 AT
1 AT
1154255 CACAGCGAAC
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:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:1166049 original size:23 final size:24
Alignment explanation
Indices: 1166023--1166069 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1166013 TTAATATTAA
1166023 GAATATATTTACA-AATTTTTATT
1 GAATATATTTACATAATTTTTATT
* *
1166046 GAATATTTTTATATAATTTTTATT
1 GAATATATTTACATAATTTTTATT
1166070 ACTATCCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
GAATATATTTACATAATTTTTATT
Found at i:1172158 original size:13 final size:13
Alignment explanation
Indices: 1172140--1172165 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1172130 ATATCTAAGG
1172140 AAAAAAGAAGAGA
1 AAAAAAGAAGAGA
1172153 AAAAAAGAAGAGA
1 AAAAAAGAAGAGA
1172166 TATCCATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAGA
Found at i:1178050 original size:38 final size:37
Alignment explanation
Indices: 1177979--1178050 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
1177969 TAAATAATAA
* *
1177979 ATAATTTAATCATATTTTAACATAATTATTATTAAAT
1 ATAATTTAATAAAATTTTAACATAATTATTATTAAAT
*
1178016 ATAATTTAATAAAATTCTTAATATAATTATTATTA
1 ATAATTTAATAAAATT-TTAACATAATTATTATTA
1178051 TTTGAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
ATAATTTAATAAAATTTTAACATAATTATTATTAAAT
Found at i:1191055 original size:35 final size:36
Alignment explanation
Indices: 1191016--1191085 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1191006 TCCTTTAAAT
* *
1191016 ATAATTGTTGGTA-ACTTAAAAAGTAATCTTAAAAA
1 ATAATGGTTAGTATACTTAAAAAGTAATCTTAAAAA
1191051 ATAATGGTTAGTATACTTAAAAAGTAATCTTAAAA
1 ATAATGGTTAGTATACTTAAAAAGTAATCTTAAAA
1191086 TTGTGAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (36 bp):
ATAATGGTTAGTATACTTAAAAAGTAATCTTAAAAA
Found at i:1200854 original size:25 final size:25
Alignment explanation
Indices: 1200826--1200875 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1200816 AATACGTTAG
1200826 GGCACAATTTATCAAAATATTAAAC
1 GGCACAATTTATCAAAATATTAAAC
1200851 GGCACAATTTATCAAAATATTAAAC
1 GGCACAATTTATCAAAATATTAAAC
1200876 ATTGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (25 bp):
GGCACAATTTATCAAAATATTAAAC
Found at i:1202693 original size:50 final size:49
Alignment explanation
Indices: 1202631--1202854 Score: 199
Period size: 50 Copynumber: 4.6 Consensus size: 49
1202621 GCCAGGGGGA
* * * * * *
1202631 TAAGATCTGCTGTTGTAGCATCAATCTTTATAATTGCAAT-GTCAGGGAAG
1 TAAGATCCGCTGTTGTAGCTTCAATCTTT-CAACTGCAATACT-AGGAAAG
*
1202681 TAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAATACTAGGAAAG
1 TAAGATCCGCTGTTGTAGCTTCAATCT-TTCAACTGCAATACTAGGAAAG
* **
1202731 TAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG---T-CGGGGAAA-
1 TAAGATCCGCTGTTGTAGCTTCAATC-TTTCAACTGCAATACTAGGAAAG
* * * * ** *
1202776 CAAAATCCACTGTTGTAGCTTCAATTTGTTCCGCTGCAACACTAGGAAAG
1 TAAGATCCGCTGTTGTAGCTTCAATCT-TTCAACTGCAATACTAGGAAAG
*
1202826 TAAGATCCACTGTTGTAGCTTCAATCTTT
1 TAAGATCCGCTGTTGTAGCTTCAATCTTT
1202855 TTAANNNNNN
Statistics
Matches: 141, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
44 1 0.01
45 27 0.19
46 6 0.04
47 1 0.01
49 8 0.06
50 94 0.67
51 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (49 bp):
TAAGATCCGCTGTTGTAGCTTCAATCTTTCAACTGCAATACTAGGAAAG
Found at i:1202820 original size:95 final size:97
Alignment explanation
Indices: 1202605--1202858 Score: 307
Period size: 95 Copynumber: 2.6 Consensus size: 97
1202595 ATGGTTTTAT
* * ** * * *
1202605 TCTGTTCCACTGCAACGCCAGG-GGGATAAGATCTGCTGTTGTAGCATCAATCTTTATAATTGCA
1 TCTGTTCCACTGCAACACTAGGAAAG-TAAGATCCGCTGTTGTAGCTTCAATCTTTTTAA-T-C-
** * *
1202669 ATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAA
62 ATGTCAGGGAAACAAAATCCACTGTTGTAGCTTCAA
*
1202705 TCTGTTCCACTGCAATACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAA-C-TGT
1 TCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATCATGT
*
1202768 CGGGGAAACAAAATCCACTGTTGTAGCTTCAA
66 CAGGGAAACAAAATCCACTGTTGTAGCTTCAA
* * *
1202800 TTTGTTCCGCTGCAACACTAGGAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTTAA
1 TCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAA
1202859 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
95 85 0.62
97 1 0.01
100 49 0.36
101 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (97 bp):
TCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATCATGT
CAGGGAAACAAAATCCACTGTTGTAGCTTCAA
Found at i:1203070 original size:50 final size:47
Alignment explanation
Indices: 1202995--1203128 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 47
1202985 NNNNNNNNNN
*
1202995 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAATACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGC-A-AC-AGGAAAGC
* ** * *
1203045 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGC--CGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACAGGAAAGC
1203090 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAAC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAAC
1203129 CTGGAAGTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
45 38 0.52
46 1 0.01
47 1 0.01
50 33 0.45
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (47 bp):
AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACAGGAAAGC
Found at i:1203376 original size:100 final size:100
Alignment explanation
Indices: 1203103--1203774 Score: 911
Period size: 100 Copynumber: 6.8 Consensus size: 100
1203093 ATCCGCTGTT
* * *
1203103 GTAGCTTCAATCTGTTCCACTGCA--ACCT-GGAAGTAAGATTCACCGTTATGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
* * ** *
1203165 TGAATTACAATGTCGGGAAAGTGAGATTTACTGTC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
*
1203200 GTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
* * * *
1203264 TGAATTGTAATGTCAGGGAAGTGAGATTCGCTGCC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
* * * * *
1203299 GTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTCACTGTAGTGACTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
** *
1203364 TGAATTGCAATGTCAAGGAAGTGAGATTCGCTGTC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
*
1203399 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
*
1203464 TGAATTACAATGTCGGGGAAGTGAGATTCGCCGTC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
* * * *
1203499 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAATAGGATTCGCTGTTGTGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
* * *
1203564 TGAATTGTAATGTCGGGGAAGTGAGATTCACCATC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
* * * **
1203599 GTATCTTCAATCTGTTCCGCTGTATCGCTTGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
* * **
1203664 TAAATTGTAATGTCGGGGAAGCAAGATTCGCCGTC
66 TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
* * * *
1203699 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAATAAGATTCGCCGTTGTAGCTTTAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATC-TT
*
1203764 TTAAATTGCAA
65 TTGAATTGCAA
1203775 ACTATGGTTT
Statistics
Matches: 514, Mismatches: 57, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
97 23 0.04
99 91 0.18
100 388 0.75
101 12 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
TGAATTGCAATGTCGGGGAAGTGAGATTCGCCGTC
Found at i:1203533 original size:200 final size:199
Alignment explanation
Indices: 1203003--1203774 Score: 920
Period size: 200 Copynumber: 3.9 Consensus size: 199
1202993 NNAAGATCCG
* * * * * *
1203003 CTGTTGTAGCTTCAATCTGTTCCACTGCAAT--ACTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
1 CTGTCGTAGCTTCAATCTGTTCCACTGC-ATCGCCT-GGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
1203066 AATC-TTT---TTA-ACTGCCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGC
64 AATCTTTTGAATTATAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGC
* * * *
1203126 A--ACCT-GGAAGTAAGATTCACCGTTA-TGGCTTCAATCTTTTGAATTACAATGTCGGGAAAGT
129 ATCGCCTGGGAAATAAGATTCACTG-TAGTGGCTTCAATCTTTTGAATTGCAATGTCGGG-AAGT
*
1203187 GAGATTTA
192 GAGATTCA
*
1203195 CTGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAGTAAGATTCGCCGTTGTGGCTTCAA
1 CTGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
* * ** * * *
1203259 TCTTTTGAATTGTAATGTCAGGGAAGTGAGATTCGCTGCCGTAGCTTCAATCTATTCCACTGCAT
66 TCTTTTGAATTATAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAT
* * *
1203324 CGCCTGGGAAGTAAGATTCACTGTAGTGACTTCAATCTTTTGAATTGCAATGTCAAGGAAGTGAG
131 CGCCTGGGAAATAAGATTCACTGTAGTGGCTTCAATCTTTTGAATTGCAATGTC-GGGAAGTGAG
*
1203389 ATTCG
195 ATTCA
*
1203394 CTGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAA
1 CTGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
* ** *
1203459 TCTTTTGAATTACAATGTCGGGGAAGTGAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCAT
66 TCTTTTGAATTATAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAT
* * * *
1203524 CGCCTGGGAAATAGGATTCGCTGTTGTGGCTTCAATCTTTTGAATTGTAATGTCGGGGAAGTGAG
131 CGCCTGGGAAATAAGATTCACTGTAGTGGCTTCAATCTTTTGAATTGCAATGTC-GGGAAGTGAG
1203589 ATTCA
195 ATTCA
** * * * * *
1203594 CCATCGTATCTTCAATCTGTTCCGCTGTATCGCTTGGGAAGTAAGATTCGTCGTTGTGGCTTCAA
1 CTGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
* * *
1203659 TCTTTTAAATTGTAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCAT
66 TCTTTTGAATTATAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAT
* * * * * *
1203724 CGCCTGGGAAATAAGATTCGCCGTTGTAGCTTTAATCTTTTTAAATTGCAA
131 CGCCTGGGAAATAAGATTCACTGTAGTGGCTTCAATC-TTTTGAATTGCAA
1203775 ACTATGGTTT
Statistics
Matches: 505, Mismatches: 61, Indels: 19
0.86 0.10 0.03
Matches are distributed among these distances:
191 29 0.06
192 29 0.06
193 2 0.00
195 2 0.00
196 42 0.08
198 5 0.01
199 86 0.17
200 299 0.59
201 11 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (199 bp):
CTGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAA
TCTTTTGAATTATAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAT
CGCCTGGGAAATAAGATTCACTGTAGTGGCTTCAATCTTTTGAATTGCAATGTCGGGAAGTGAGA
TTCA
Found at i:1203733 original size:50 final size:50
Alignment explanation
Indices: 1203008--1203761 Score: 394
Period size: 50 Copynumber: 15.3 Consensus size: 50
1202998 ATCCGCTGTT
* * * * *
1203008 GTAGCTTCAATCTGTTCCACTGCAAT--ACTAGGAAAGTAAGATCCGCTGTT
1 GTAGCTTCAATCTGTTCCACTGC-ATCGCCT-GGGAAGTAAGATTCGCCGTC
* ** * * * *
1203058 GTAGCTTCAATCTTTTTAACTGC--CG---GGGAAGCAAGATCCGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * *
1203103 GTAGCTTCAATCTGTTCCACTGCA--ACCT-GGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * * ** * * * * ** *
1203150 ATGGCTTCAATCTTTTGAATTACAAT-GTC-GGGAAAGTGAGATTTACTGTC
1 GTAGCTTCAATCTGTTCCACTGC-ATCGCCTGGG-AAGTAAGATTCGCCGTC
* *
1203200 GTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAGTAAGATTCGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * ** * * * * * * *
1203249 GTGGCTTCAATCTTTTGAATTGTAAT-GTCAGGGAAGTGAGATTCGCTGCC
1 GTAGCTTCAATCTGTTCCACTG-CATCGCCTGGGAAGTAAGATTCGCCGTC
* * * *
1203299 GTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTCACTGTA
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* ** * * ** * *
1203349 GT-GACTTCAATCTTTTGAATTGCAAT-GTCAAGGAAGTGAGATTCGCTGTC
1 GTAG-CTTCAATCTGTTCCACTGC-ATCGCCTGGGAAGTAAGATTCGCCGTC
* *
1203399 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * ** * * * * *
1203449 GTGGCTTCAATCTTTTGAATTACAAT-GTCGGGGAAGTGAGATTCGCCGTC
1 GTAGCTTCAATCTGTTCCACTGC-ATCGCCTGGGAAGTAAGATTCGCCGTC
* * * * *
1203499 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAATAGGATTCGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * ** * * * * * * *
1203549 GTGGCTTCAATCTTTTGAATTGTAAT-GTCGGGGAAGTGAGATTCACCATC
1 GTAGCTTCAATCTGTTCCACTG-CATCGCCTGGGAAGTAAGATTCGCCGTC
* * * * * *
1203599 GTATCTTCAATCTGTTCCGCTGTATCGCTTGGGAAGTAAGATTCGTCGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
* * ** * * * * *
1203649 GTGGCTTCAATCTTTTAAATTGTAAT-GTCGGGGAAGCAAGATTCGCCGTC
1 GTAGCTTCAATCTGTTCCACTG-CATCGCCTGGGAAGTAAGATTCGCCGTC
* * *
1203699 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAATAAGATTCGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
*
1203749 GTAGCTTTAATCT
1 GTAGCTTCAATCT
1203762 TTTTAAATTG
Statistics
Matches: 509, Mismatches: 170, Indels: 50
0.70 0.23 0.07
Matches are distributed among these distances:
45 38 0.07
47 31 0.06
48 1 0.00
49 46 0.09
50 384 0.75
51 9 0.02
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
GTAGCTTCAATCTGTTCCACTGCATCGCCTGGGAAGTAAGATTCGCCGTC
Found at i:1204877 original size:22 final size:22
Alignment explanation
Indices: 1204852--1204897 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1204842 CCTTGGCTTC
1204852 TTCATTTTT-ACTTTTTCATTTT
1 TTCATTTTTCA-TTTTTCATTTT
1204874 TTCATTTTTCATTTTTCATTTT
1 TTCATTTTTCATTTTTCATTTT
1204896 TT
1 TT
1204898 TGACTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCATTTTTCATTTTTCATTTT
Found at i:1204897 original size:8 final size:7
Alignment explanation
Indices: 1204852--1204896 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
1204842 CCTTGGCTTC
1204852 TTCATTT
1 TTCATTT
1204859 TT-ACTTT
1 TTCA-TTT
1204866 TTCATTTT
1 TTCA-TTT
1204874 TTCATTT
1 TTCATTT
1204881 TTCATTT
1 TTCATTT
1204888 TTCATTT
1 TTCATTT
1204895 TT
1 TT
1204897 TTGACTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 1 0.03
7 26 0.74
8 8 0.23
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCATTT
Found at i:1205730 original size:17 final size:16
Alignment explanation
Indices: 1205696--1205732 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1205686 TGACCTCTCC
*
1205696 TTTTTCTTTTTTTTTA
1 TTTTTCTTTTTTTCTA
1205712 TTTTTCTTTTTTTCCTA
1 TTTTTCTTTTTTT-CTA
1205729 TTTT
1 TTTT
1205733 GACTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTA
Found at i:1205762 original size:7 final size:8
Alignment explanation
Indices: 1205742--1205781 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
1205732 TGACTTTAAT
1205742 TTTTTTGA
1 TTTTTTGA
1205750 TTTTTTTGA
1 -TTTTTTGA
1205759 TTTTTTGA
1 TTTTTTGA
1205767 TTTTTTGAA
1 TTTTTTG-A
1205776 TTTTTT
1 TTTTTT
1205782 TTGAGTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 15 0.50
9 15 0.50
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (8 bp):
TTTTTTGA
Found at i:1205764 original size:17 final size:17
Alignment explanation
Indices: 1205742--1205781 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1205732 TGACTTTAAT
1205742 TTTTTTGATTTTTTTG-A
1 TTTTTTGA-TTTTTTGAA
1205759 TTTTTTGATTTTTTGAA
1 TTTTTTGATTTTTTGAA
1205776 TTTTTT
1 TTTTTT
1205782 TTGAGTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTTGATTTTTTGAA
Found at i:1208712 original size:14 final size:15
Alignment explanation
Indices: 1208683--1208724 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1208673 CAATGTAAAT
1208683 AAAATGAAACATATAA
1 AAAAT-AAACATATAA
*
1208699 ACAATAAACA-ATAA
1 AAAATAAACATATAA
*
1208713 AAAATAATCATA
1 AAAATAAACATA
1208725 CGGGCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAACATATAA
Found at i:1211677 original size:90 final size:90
Alignment explanation
Indices: 1211506--1211695 Score: 210
Period size: 90 Copynumber: 2.1 Consensus size: 90
1211496 AAATAATAAT
* *
1211506 AAAAAAAATAATTAAGCCTCTCCTTTTTTTTTTGCACTCAATTGATCAATTGAGCTTTCAAAATG
1 AAAAAAAACAATTAAGCCCCTCC-TTTTTTTTTGCACTCAATTGATCAATTGAGCTTTCAAAATG
* *
1211571 TATCAAAAAGGCCCTCAAACTTCTTC
65 CATCAAAAAGACCCTCAAACTTCTTC
* * *
1211597 AAAAAAAAGCAATTAAGCCCCTGCC-TTTTTTTT-CACTTAATTGGAT-ACTTGATCTTTCAAAA
1 AAAAAAAA-CAATTAAGCCCCT-CCTTTTTTTTTGCACTCAATT-GATCAATTGAGCTTTCAAAA
* * * *
1211659 TGCATCAAAAATATCCTCAAA--ACTTA
63 TGCATCAAAAAGACCCTCAAACTTCTTC
1211685 AAAAAAAACAA
1 AAAAAAAACAA
1211696 ACAATTAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
87 3 0.04
88 11 0.13
90 39 0.46
91 19 0.22
92 11 0.13
93 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (90 bp):
AAAAAAAACAATTAAGCCCCTCCTTTTTTTTTGCACTCAATTGATCAATTGAGCTTTCAAAATGC
ATCAAAAAGACCCTCAAACTTCTTC
Found at i:1211743 original size:9 final size:9
Alignment explanation
Indices: 1211731--1211873 Score: 51
Period size: 10 Copynumber: 15.6 Consensus size: 9
1211721 AAATTAGAAA
1211731 AAAAATTAT
1 AAAAATTAT
*
1211740 AAAAAATGAT
1 -AAAAATTAT
** *
1211750 AAATTTTAG
1 AAAAATTAT
1211759 AAAAATTATT
1 AAAAATTA-T
**
1211769 AAATTTTAAT
1 AAAAATT-AT
1211779 AAAAATT-T
1 AAAAATTAT
1211787 AAAAATT-T
1 AAAAATTAT
* *
1211795 TAAATTTATT
1 AAAAATTA-T
1211805 AAAAATTAT
1 AAAAATTAT
*** *
1211814 AATTTTTAAA
1 AAAAATT-AT
*
1211824 AGAAAATCAT
1 A-AAAATTAT
1211834 AAAAA-TA-
1 AAAAATTAT
*
1211841 AAAAATTGT
1 AAAAATTAT
*
1211850 AAAATTTTAT
1 AAAA-ATTAT
*
1211860 AAAAATCAT
1 AAAAATTAT
1211869 AAAAA
1 AAAAA
1211874 ATTAACGGCC
Statistics
Matches: 93, Mismatches: 31, Indels: 19
0.65 0.22 0.13
Matches are distributed among these distances:
7 5 0.05
8 16 0.17
9 32 0.34
10 37 0.40
11 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1211764 original size:18 final size:19
Alignment explanation
Indices: 1211741--1211776 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1211731 AAAAATTATA
1211741 AAAAATGA-TAAATTTTAG
1 AAAAATGATTAAATTTTAG
*
1211759 AAAAATTATTAAATTTTA
1 AAAAATGATTAAATTTTA
1211777 ATAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
AAAAATGATTAAATTTTAG
Found at i:1211801 original size:46 final size:47
Alignment explanation
Indices: 1211731--1211838 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 47
1211721 AAATTAGAAA
1211731 AAAAATTATAAAAAATGATAAATTT-TAGAAAAATTATTAAATTTTAAT
1 AAAAATTATAAAAAATGATAAATTTAT-GAAAAATTA-TAAATTTTAAT
** * * *
1211779 AAAAATT-T-AAAAATTTTAAATTTATTAAAAATTATAATTTTTAAA
1 AAAAATTATAAAAAATGATAAATTTATGAAAAATTATAAATTTTAAT
*
1211824 AGAAAATCATAAAAA
1 A-AAAATTATAAAAA
1211839 TAAAAAATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
45 10 0.20
46 26 0.52
47 3 0.06
48 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (47 bp):
AAAAATTATAAAAAATGATAAATTTATGAAAAATTATAAATTTTAAT
Found at i:1211806 original size:18 final size:16
Alignment explanation
Indices: 1211784--1211824 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
1211774 TTAATAAAAA
*
1211784 TTTAAAAATTTTAAATT
1 TTTAAAAATTAT-AATT
1211801 TATTAAAAATTATAATT
1 T-TTAAAAATTATAATT
1211818 TTTAAAA
1 TTTAAAA
1211825 GAAAATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 6 0.27
18 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAATTATAATT
Found at i:1211809 original size:26 final size:28
Alignment explanation
Indices: 1211759--1211811 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1211749 TAAATTTTAG
1211759 AAAAATTATTAAATTTTAATAAAAATTT
1 AAAAATTATTAAATTTTAATAAAAATTT
*
1211787 AAAAATT-TTAAA-TTTATTAAAAATT
1 AAAAATTATTAAATTTTAATAAAAATT
1211812 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 5 0.21
28 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAAATTATTAAATTTTAATAAAAATTT
Found at i:1211820 original size:25 final size:27
Alignment explanation
Indices: 1211760--1211823 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
1211750 AAATTTTAGA
*
1211760 AAAATTATTAAATTTTAATAAAAATTT
1 AAAATTTTTAAATTTTAATAAAAATTT
* *
1211787 AAAAATTTTAAA-TTTATTAAAAA-TT
1 AAAATTTTTAAATTTTAATAAAAATTT
*
1211812 ATAATTTTTAAA
1 AAAATTTTTAAA
1211824 AGAAAATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 12 0.38
26 10 0.31
27 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATTTTTAAATTTTAATAAAAATTT
Found at i:1216082 original size:37 final size:37
Alignment explanation
Indices: 1216041--1216111 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1216031 TTTTGTAGAA
**
1216041 AATCGTTATTGTTCATCTTTGTCTTTTCTTTACAGAG
1 AATCGTTATTGTTCATCTTCATCTTTTCTTTACAGAG
*
1216078 AATCGTTATTGTTCATCTTCATTTTTTCTTTACA
1 AATCGTTATTGTTCATCTTCATCTTTTCTTTACA
1216112 AAATGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (37 bp):
AATCGTTATTGTTCATCTTCATCTTTTCTTTACAGAG
Found at i:1244309 original size:22 final size:19
Alignment explanation
Indices: 1244283--1244322 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
1244273 TTTTCAGAAG
1244283 TAATTAAATAATACAATATTAT
1 TAATT-AAT-ATA-AATATTAT
1244305 TAATTAATATAAATATTA
1 TAATTAATATAAATATTA
1244323 ATTGCATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 3 0.17
22 5 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTAATATAAATATTAT
Found at i:1244809 original size:136 final size:137
Alignment explanation
Indices: 1244645--1244919 Score: 534
Period size: 136 Copynumber: 2.0 Consensus size: 137
1244635 TATTATTTTC
1244645 ACTTTATTTTACATTTATATATTTCAAAATTTTCTAACTTTATTTTTTAAAATTGGTTTTTTTTG
1 ACTTTATTTTA-ATTTATATATTTCAAAATTTTCTAACTTTATTTTTTAAAATTGGTTTTTTTTG
1244710 GAAATTTAAAATATCTATATGTTATATATGATATATATTTTTTTATTTTTATTAATATAATGCAT
65 GAAATTTAAAATATCTATATGTTATATATGATATATATTTTTTTATTTTTATTAATATAATGCAT
1244775 AATATTAA
130 AATATTAA
1244783 ACTTTATTTT-ATTTATATATTTCAAAATTTTCTAACTTTATTTTTTAAAATTGGTTTTTTTTGG
1 ACTTTATTTTAATTTATATATTTCAAAATTTTCTAACTTTATTTTTTAAAATTGGTTTTTTTTGG
1244847 AAATTTAAAATATCTATATGTTATATATGATATATATTTTTTTATTTTTATTAATATAATGCATA
66 AAATTTAAAATATCTATATGTTATATATGATATATATTTTTTTATTTTTATTAATATAATGCATA
1244912 ATATTAA
131 ATATTAA
1244919 A
1 A
1244920 AAATAAAAGA
Statistics
Matches: 137, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
136 127 0.93
138 10 0.07
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (137 bp):
ACTTTATTTTAATTTATATATTTCAAAATTTTCTAACTTTATTTTTTAAAATTGGTTTTTTTTGG
AAATTTAAAATATCTATATGTTATATATGATATATATTTTTTTATTTTTATTAATATAATGCATA
ATATTAA
Found at i:1248623 original size:16 final size:17
Alignment explanation
Indices: 1248604--1248651 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1248594 AGTATATATA
1248604 TATTTATT-TATTTTTG
1 TATTTATTATATTTTTG
1248620 TATTT-TTAGTATTTTTG
1 TATTTATTA-TATTTTTG
*
1248637 -ATGTATTATATTTTT
1 TATTTATTATATTTTT
1248652 TAAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.07
16 15 0.54
17 11 0.39
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (17 bp):
TATTTATTATATTTTTG
Found at i:1254320 original size:24 final size:25
Alignment explanation
Indices: 1254283--1254396 Score: 88
Period size: 25 Copynumber: 4.6 Consensus size: 25
1254273 ATTCATATAT
*
1254283 GCTCCTCCAAGCTGTA-AACGGAAA
1 GCTCATCCAAGCTGTATAACGGAAA
* * * *
1254307 TCTCTTCCAAGCTGAATAACGGGAA
1 GCTCATCCAAGCTGTATAACGGAAA
* * *
1254332 GCTCATCCGAGCTGTATAATGGGAA
1 GCTCATCCAAGCTGTATAACGGAAA
* * *
1254357 GCTCATGCGAGCTGTAAAAC-GAGAA
1 GCTCATCCAAGCTGTATAACGGA-AA
* *
1254382 GCTCATACGAGCTGT
1 GCTCATCCAAGCTGT
1254397 GGTGTGTCCG
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
24 14 0.19
25 60 0.81
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.21
Consensus pattern (25 bp):
GCTCATCCAAGCTGTATAACGGAAA
Found at i:1254396 original size:25 final size:25
Alignment explanation
Indices: 1254316--1254396 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
1254306 ATCTCTTCCA
*
1254316 AGCTG-AATAACGGGAAGCTCATCCG
1 AGCTGTAA-AACGGGAAGCTCATACG
* * *
1254341 AGCTGTATAATGGGAAGCTCATGCG
1 AGCTGTAAAACGGGAAGCTCATACG
*
1254366 AGCTGTAAAACGAGAAGCTCATACG
1 AGCTGTAAAACGGGAAGCTCATACG
1254391 AGCTGT
1 AGCTGT
1254397 GGTGTGTCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
AGCTGTAAAACGGGAAGCTCATACG
Found at i:1256899 original size:3 final size:3
Alignment explanation
Indices: 1256799--1256879 Score: 101
Period size: 3 Copynumber: 27.3 Consensus size: 3
1256789 TATTGTTAAC
* * * * * *
1256799 ATT ATT ATT -TT AAT GTT ATC ATT ATC ATC ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1256846 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1256880 CCGTCTTTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1257776 original size:109 final size:109
Alignment explanation
Indices: 1257610--1258248 Score: 967
Period size: 109 Copynumber: 5.9 Consensus size: 109
1257600 AAATTTTTCT
* * * * * * *
1257610 AAATGAGGCAATATTTAGCATTTGGAAATTTGAGGAAACGTGCCCTAAGGTGTTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
** * **
1257675 TTTCTCGTTCAACCAAATATCTAAATATCCTTCTAAAAATTCCA
66 TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
1257719 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* * **
1257784 TTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAATTCCA
66 TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
*
1257828 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
1257893 TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
* *
1257937 AAATAAGG-AATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
1258001 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
* * *
1258045 AAATAAGACAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
1258110 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
* * * *
1258154 AAATAAGACAAT-TTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGCTGCTGAGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* * *
1258218 TTTCTCGTTTAACCAAATTGCCAAATATCCT
66 TTTCTCGTTCAACCAAATGGCTAAATATCCT
1258249 CTTGAATTTT
Statistics
Matches: 501, Mismatches: 28, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
108 180 0.36
109 321 0.64
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
TTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
Found at i:1258051 original size:217 final size:216
Alignment explanation
Indices: 1257610--1258248 Score: 981
Period size: 217 Copynumber: 2.9 Consensus size: 216
1257600 AAATTTTTCT
* * * * * *
1257610 AAATGAGGCAATATTTAGCATTTGGAAATTTGAGGAAACGTGCCCTAAGGTGTTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* * * **
1257675 TTTCTCGTTCAACCAAATATCTAAATATCCTTCTAAAAATTCCAAAATAAGGCAATATTTTGCGT
66 TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTAAAATAAGG-AAT-TTTTGCGT
1257740 TTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
129 TTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
1257805 TAAATATCCTTCTAAAAATTCCA
194 TAAATATCCTTCTAAAAATTCCA
* *
1257828 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
1257893 TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTAAAATAAGGAATGTTTTGCATT
66 TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTAAAATAAGGAAT-TTTTGCGTT
*
1257958 TGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCT
130 TGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCT
* * **
1258023 TAATATCCTTTTAAAAATTTTA
195 AAATATCCTTCTAAAAATTCCA
* *
1258045 AAATAAGACAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
1258110 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGACAATTTTTGCGTT
66 TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTAAAATAAG-GAATTTTTGCGTT
* * * * * *
1258175 TGGAAATTTGAGAAAACATGCCCTAAGCTGCTGAGTGTCGATTTTTCTCGTTTAACCAAATTGCC
130 TGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCT
1258240 AAATATCCT
195 AAATATCCT
1258249 CTTGAATTTT
Statistics
Matches: 386, Mismatches: 34, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
217 279 0.72
218 107 0.28
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (216 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
TTTCTCGTTCAACCAAATGTCTTAATATCCTTTTAAAAATTTTAAAATAAGGAATTTTTGCGTTT
GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTA
AATATCCTTCTAAAAATTCCA
Done.