Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 100 of 210
Found at i:29264549 original size:5 final size:5
Alignment explanation
Indices: 29264539--29264564 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29264529 TCATATTAAT
29264539 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
29264565 ACCTCTCCAC
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:29264599 original size:5 final size:5
Alignment explanation
Indices: 29264589--29264619 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29264579 TCCCTCTCTC
29264589 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT C
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT C
29264620 ACCCCGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCCT
Found at i:29264910 original size:11 final size:11
Alignment explanation
Indices: 29264888--29264931 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
29264878 AACTAATCCT
29264888 CTCTCAAATTTC
1 CTCTC-AATTTC
29264900 CTCTCAATTTC
1 CTCTCAATTTC
*
29264911 CTCTAAATTTC
1 CTCTCAATTTC
29264922 CTCTCAATTT
1 CTCTCAATTT
29264932 TGGTGTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.83
12 5 0.17
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29264920 original size:22 final size:23
Alignment explanation
Indices: 29264888--29264931 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
29264878 AACTAATCCT
29264888 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
29264911 CTCT-AAATTTCCTCTCAATTT
1 CTCTCAAATTTCCTCTCAATTT
29264932 TGGTGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:29265084 original size:27 final size:28
Alignment explanation
Indices: 29265030--29265094 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 28
29265020 TTATAAAAAA
29265030 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
29265058 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
29265085 ACCAAAATAT
1 ACCAAAATAT
29265095 ACCAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:29265178 original size:27 final size:27
Alignment explanation
Indices: 29265148--29265224 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
29265138 GGCCAATCAC
*
29265148 ATTGGCGGCACCAAAGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
*
29265175 ATTGGCGACACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
* *
29265202 TTTCGCGGCACCAATGGTGCCAA
1 ATTGGCGGCACCAATGGTGCCAA
29265225 AGGACTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.21
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATGTG
Found at i:29265599 original size:19 final size:19
Alignment explanation
Indices: 29265535--29265601 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
29265525 ATTAAAATAG
29265535 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
29265554 TTATAATGTAATAA-ACTAT
1 TT-TAATTTAATAACTCTAT
* *
29265573 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
29265592 TTTAATTTAA
1 TTTAATTTAA
29265602 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 9 0.24
19 19 0.50
20 10 0.26
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:29265781 original size:82 final size:82
Alignment explanation
Indices: 29265682--29265846 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
29265672 AAAAGGAAAA
29265682 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTATTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTATTAATAGACTTATAA
29265747 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
* * *
29265764 AAATAATGGAAATATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTATTAATAGACTTATAA
29265829 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
29265846 A
1 A
29265847 TTTTAATTAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (82 bp):
AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTATTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:29265954 original size:18 final size:19
Alignment explanation
Indices: 29265915--29266010 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
29265905 ATTTTATATT
29265915 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29265934 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29265952 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29265971 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29265989 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
29266008 TTA
1 TTA
29266011 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:29265956 original size:37 final size:37
Alignment explanation
Indices: 29265915--29266010 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
29265905 ATTTTATATT
*
29265915 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
29265952 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
29265989 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
29266011 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:29266733 original size:28 final size:27
Alignment explanation
Indices: 29266686--29266750 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
29266676 TTTTTTTGGT
* **
29266686 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAAAAAAAAAAGTTATA
29266713 ATATTTTGGTAAACAAAAAAAAGTTATA
1 ATATTTTGGTAAA-AAAAAAAAGTTATA
29266741 ATATTTTGGT
1 ATATTTTGGT
29266751 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 13 0.38
28 21 0.62
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAAAAAAAAAAGTTATA
Found at i:29268386 original size:9 final size:9
Alignment explanation
Indices: 29268336--29268385 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
29268326 TTTGGTTAAA
29268336 AATTAACCG
1 AATTAACCG
*
29268345 AATTAACTG
1 AATTAACCG
*
29268354 AATTAACCA
1 AATTAACCG
29268363 AATTAACCG
1 AATTAACCG
*
29268372 AATTACCCG
1 AATTAACCG
29268381 AATTA
1 AATTA
29268386 CTCGAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:29268391 original size:9 final size:9
Alignment explanation
Indices: 29268336--29268393 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
29268326 TTTGGTTAAA
*
29268336 AATTAACCG
1 AATTACCCG
* *
29268345 AATTAACTG
1 AATTACCCG
* *
29268354 AATTAACCA
1 AATTACCCG
*
29268363 AATTAACCG
1 AATTACCCG
29268372 AATTACCCG
1 AATTACCCG
*
29268381 AATTACTCG
1 AATTACCCG
29268390 AATT
1 AATT
29268394 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTACCCG
Found at i:29268391 original size:18 final size:19
Alignment explanation
Indices: 29268336--29268393 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
29268326 TTTGGTTAAA
29268336 AATTAACCGAATTAACT-G
1 AATTAACCGAATTAACTCG
*
29268354 AATTAACCAAATTAAC-CG
1 AATTAACCGAATTAACTCG
*
29268372 AATTACCCGAATT-ACTCG
1 AATTAACCGAATTAACTCG
29268390 AATT
1 AATT
29268394 GAATCACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.06
18 33 0.94
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTAACCGAATTAACTCG
Found at i:29268433 original size:37 final size:37
Alignment explanation
Indices: 29268392--29268466 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
29268382 ATTACTCGAA
* *
29268392 TTGAATCACTACATAATTAAAAATATTATATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
29268429 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
29268466 T
1 T
29268467 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:29268638 original size:38 final size:39
Alignment explanation
Indices: 29268594--29268671 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
29268584 ACTTAAGAGT
*
29268594 TAGACTTTAGTTTTATTTTTATTGGGTT-AGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGAGTAATTGGG
*
29268632 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGAGTAATTGGG
29268671 T
1 T
29268672 TGGGATGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 27 0.73
39 10 0.27
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGAGTAATTGGG
Found at i:29268683 original size:17 final size:17
Alignment explanation
Indices: 29268661--29268702 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
29268651 TATTGGGTTG
29268661 GGTAATTGGGTTGGGAT
1 GGTAATTGGGTTGGGAT
*
29268678 GGTAATTGGGTTGGGTT
1 GGTAATTGGGTTGGGAT
29268695 GGATAATT
1 GG-TAATT
29268703 TTATTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (17 bp):
GGTAATTGGGTTGGGAT
Found at i:29277762 original size:18 final size:18
Alignment explanation
Indices: 29277739--29277773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29277729 GCCAAGTGTA
* *
29277739 TATCCTAGCCTTTATATG
1 TATCCTAACCCTTATATG
29277757 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
29277774 ATTTTCTTTT
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:0.26, G:0.06, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:29278272 original size:9 final size:9
Alignment explanation
Indices: 29278253--29278292 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
29278243 TTTGGTTAAA
*
29278253 AATTAACCG
1 AATTACCCG
*
29278262 AATTACTCG
1 AATTACCCG
29278271 AATTACCCG
1 AATTACCCG
29278280 AATTACCCG
1 AATTACCCG
29278289 AATT
1 AATT
29278293 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTACCCG
Found at i:29278322 original size:17 final size:17
Alignment explanation
Indices: 29278300--29278362 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
29278290 ATTGAATCAC
29278300 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
29278317 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
29278337 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
29278354 TACATAATT
1 TACATAATT
29278363 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:29278337 original size:37 final size:37
Alignment explanation
Indices: 29278291--29278365 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29278281 ATTACCCGAA
*
29278291 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
29278328 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
29278365 T
1 T
29278366 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:29278544 original size:23 final size:23
Alignment explanation
Indices: 29278518--29278562 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29278508 TTATTAGGTT
29278518 GGTAATTGGGTAGACTTTAGTTG
1 GGTAATTGGGTAGACTTTAGTTG
29278541 GGTAATTGGGTAGACTTTAGTT
1 GGTAATTGGGTAGACTTTAGTT
29278563 TTAGTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.40
Consensus pattern (23 bp):
GGTAATTGGGTAGACTTTAGTTG
Found at i:29278589 original size:13 final size:13
Alignment explanation
Indices: 29278585--29278614 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29278575 GGTTGGGTAA
29278585 TTGGGTAATTGGG
1 TTGGGTAATTGGG
*
29278598 TTGGGTAATTTGG
1 TTGGGTAATTGGG
29278611 TTGG
1 TTGG
29278615 ATTGGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (13 bp):
TTGGGTAATTGGG
Found at i:29282427 original size:128 final size:126
Alignment explanation
Indices: 29282080--29282441 Score: 471
Period size: 126 Copynumber: 2.9 Consensus size: 126
29282070 AAGGGTAAGT
*
29282080 AAGAACTATTGTAGAAAAAGAGCGTCCACGTAGGAACTTTTTTCAGTAATTTTGCTAATG-GTGC
1 AAGAACTATTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAA-GAGTGC
* * *
29282144 ATCCTGCTTGAAGCGTTTTT-TATATTATTTTTTCGAAACCATCTTCTCATAATTATTTTTCC
65 ATCCTGCTTGAAGCGTTTTTGT-CATTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTCC
* * *
29282206 AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
1 AAGAACTATTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAAGAGTGCA
* **
29282271 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAAAACTGTCTTCTCAAAATTAATTTTTCC
66 TCCTGCTTGAAGCGTTTTTGTCATTATTTTTTCAAAACCATCTTCTCAAAATT-ATTTTTCC
* * * * * * *
29282333 -AGAAACTATTATAGAAAAAGAGCATTCACAT-GAGAGCTTTTTTTCAATACTTTTGCTAAGAAT
1 AAG-AACTATTGTAGAAAAAGAGCGTCCACGTAG-GAGC-TTTTTTCAGTAATTTTGCTAAGAGT
* *
29282396 GCATCCTGCTTGAAGCATTTTTGTCACTATTTTTTCAAAACCATCT
63 GCATCCTGCTTGAAGCGTTTTTGTCATTATTTTTTCAAAACCATCT
29282442 CATTATTATT
Statistics
Matches: 205, Mismatches: 25, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
126 109 0.53
127 35 0.17
128 61 0.30
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (126 bp):
AAGAACTATTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAAGAGTGCA
TCCTGCTTGAAGCGTTTTTGTCATTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTCC
Found at i:29282606 original size:34 final size:34
Alignment explanation
Indices: 29282568--29282647 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
29282558 ATTATTTTTA
29282568 AAAAACCCTAAACCCTAATTTAATTAA-TTTTCTT
1 AAAAACCCTAAACCCTAATTTAATTAATTTTTC-T
*
29282602 AAAAACCTTAAA-CCTAATTTAATTAATTTTTCT
1 AAAAACCCTAAACCCTAATTTAATTAATTTTTCT
*
29282635 -AAAATCCTAAACC
1 AAAAACCCTAAACC
29282648 TTGATTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 9 0.22
33 16 0.39
34 16 0.39
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (34 bp):
AAAAACCCTAAACCCTAATTTAATTAATTTTTCT
Found at i:29282680 original size:28 final size:27
Alignment explanation
Indices: 29282629--29282702 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
29282619 TTTAATTAAT
29282629 TTTTCTAAAATC-CTAAACCTTGATTTA
1 TTTT-TAAAATCTCTAAACCTTGATTTA
29282656 TTGTTTAAAATCTCTAAATCC-TGATTTA
1 TT-TTTAAAATCTCTAAA-CCTTGATTTA
29282684 TTTTTAAAATCTCTAAACC
1 TTTTTAAAATCTCTAAACC
29282703 CTAAACAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.05
27 24 0.55
28 16 0.36
29 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.45
Consensus pattern (27 bp):
TTTTTAAAATCTCTAAACCTTGATTTA
Found at i:29289345 original size:2 final size:2
Alignment explanation
Indices: 29289338--29289372 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29289328 CCTAAATTAA
29289338 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29289373 ATGCATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29290600 original size:2 final size:2
Alignment explanation
Indices: 29290595--29290625 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29290585 AATATATATA
29290595 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29290626 AAATTCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29291359 original size:48 final size:48
Alignment explanation
Indices: 29291304--29291406 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 48
29291294 AGCGCCAGCC
29291304 TCAGTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGT
1 TCAGTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGT
29291352 TCAGTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGT
1 TCAGTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGT
*
29291400 TGAGTTT
1 TCAGTTT
29291407 CGAAATAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (48 bp):
TCAGTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGT
Found at i:29291933 original size:21 final size:21
Alignment explanation
Indices: 29291908--29291952 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29291898 TAAAATATGA
29291908 AAATTTATAAATTAATTTAAT
1 AAATTTATAAATTAATTTAAT
29291929 AAATTTATAAATTAATTTAAT
1 AAATTTATAAATTAATTTAAT
29291950 AAA
1 AAA
29291953 ATATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTATAAATTAATTTAAT
Found at i:29293547 original size:319 final size:319
Alignment explanation
Indices: 29292968--29293606 Score: 1188
Period size: 319 Copynumber: 2.0 Consensus size: 319
29292958 AATGCATGCT
* * *
29292968 TTTATGTGTGTTCCATCTGTGGCACTAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
1 TTTATGTGTGCTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
29293033 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
66 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
*
29293098 TGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
131 TGTATCATGTCGAATATAGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
29293163 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
196 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
29293228 TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
261 TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
* *
29293287 TTTATGTGTGCTCCATCTATGGCTCCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAT
1 TTTATGTGTGCTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
29293352 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
66 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
* *
29293417 TGTATCATGTCGAATATAGTTCGGTATTTCCTCGAATTGACCTTTAGTGGGTTTAATCGTGTCTA
131 TGTATCATGTCGAATATAGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
*
29293482 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCGACTAACAGTTTCCCCAGATCGT
196 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
*
29293547 TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATGTACAATGATAA
261 TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
29293606 T
1 T
29293607 GCTAACTTCT
Statistics
Matches: 310, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
319 310 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (319 bp):
TTTATGTGTGCTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
TGTATCATGTCGAATATAGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
Found at i:29298890 original size:33 final size:33
Alignment explanation
Indices: 29298848--29298914 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29298838 GGACACTTTA
29298848 TAAAACATTTTTTATAAAGTTTATATATTATTT
1 TAAAACATTTTTTATAAAGTTTATATATTATTT
29298881 TAAAACATTTTTTATAAAGTTTATATATTATTT
1 TAAAACATTTTTTATAAAGTTTATATATTATTT
29298914 T
1 T
29298915 TAAGTTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (33 bp):
TAAAACATTTTTTATAAAGTTTATATATTATTT
Found at i:29301124 original size:17 final size:17
Alignment explanation
Indices: 29301102--29301155 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
29301092 CAAATATGGA
*
29301102 ATGTAATCTTCGAAGAT
1 ATGTAATCTTAGAAGAT
* *
29301119 ATGTAATCTTGGATGAT
1 ATGTAATCTTAGAAGAT
29301136 ATGTAATCTTAGAAGAT
1 ATGTAATCTTAGAAGAT
29301153 ATG
1 ATG
29301156 ATTCTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (17 bp):
ATGTAATCTTAGAAGAT
Found at i:29301168 original size:24 final size:23
Alignment explanation
Indices: 29301140--29301186 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
29301130 GATGATATGT
29301140 AATCTTAGAAGATATGATTCTGTA
1 AATCTTAG-AGATATGATTCTGTA
* *
29301164 AATCTTAGAGATTTGATTTTGTA
1 AATCTTAGAGATATGATTCTGTA
29301187 GATTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (23 bp):
AATCTTAGAGATATGATTCTGTA
Found at i:29305334 original size:30 final size:30
Alignment explanation
Indices: 29305254--29305477 Score: 121
Period size: 30 Copynumber: 7.5 Consensus size: 30
29305244 GATGGTTGAC
* * *
29305254 CCATCCCTTTTCATAATTCAATAACTGAAG
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
** * * * *
29305284 TTATCCCTTTTTATAGTTTGACAGCCGAAG
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
* * * ** *
29305314 CTATCCCTTTTCATAATTTGATGGTAGTCA-
1 CCATCCCTTTTCATAATTCGATAGCCG-AAG
*** * * *
29305344 CCATCCCTTTTCATTGCTCGATGGTCGTCA-
1 CCATCCCTTTTCATAATTCGATAGCCG-AAG
* *
29305374 CCATCCCTTTTCATAATTTGATAGCTGAAG
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
* * * *
29305404 CTATCCCTTTTCATAAATCGACAGCCGAAT
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
* * * *
29305434 CCATCCCTTTTCATATTTCGATGGTCGTCA-
1 CCATCCCTTTTCATAATTCGATAGCCG-AAG
29305464 CCATCCCTTTTCAT
1 CCATCCCTTTTCAT
29305478 TGTTGATGGT
Statistics
Matches: 147, Mismatches: 44, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.01
30 144 0.98
31 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTCGATAGCCGAAG
Found at i:29305350 original size:60 final size:58
Alignment explanation
Indices: 29305286--29305477 Score: 172
Period size: 60 Copynumber: 3.2 Consensus size: 58
29305276 AACTGAAGTT
* * * *
29305286 ATCCCTTTTTATAGTTTGACAGCCGAAGCTATCCCTTTTCATAATTTGATGGTAGTCACC
1 ATCCCTTTTCATAGATCGACAGCCGAA-CCATCCCTTTTCATAATTTGATGGT-GTCACC
* * ** * * * * *
29305346 ATCCCTTTTCATTGCTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCTG-AAGCT
1 ATCCCTTTTCATAGATCGACAGCCG-AACCATCCCTTTTCATAATTTGAT-GGTGTCA-CC
*
29305406 ATCCCTTTTCATAAATCGACAGCCGAATCCATCCCTTTTCAT-ATTTCGATGGTCGTCACC
1 ATCCCTTTTCATAGATCGACAGCCGAA-CCATCCCTTTTCATAATTT-GATGGT-GTCACC
29305466 ATCCCTTTTCAT
1 ATCCCTTTTCAT
29305478 TGTTGATGGT
Statistics
Matches: 103, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
59 8 0.08
60 91 0.88
61 4 0.04
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.38
Consensus pattern (58 bp):
ATCCCTTTTCATAGATCGACAGCCGAACCATCCCTTTTCATAATTTGATGGTGTCACC
Found at i:29305383 original size:90 final size:90
Alignment explanation
Indices: 29305286--29305477 Score: 244
Period size: 90 Copynumber: 2.1 Consensus size: 90
29305276 AACTGAAGTT
* * * * ** * *
29305286 ATCCCTTTTTATAGTTTGACAGCCGAAGCTATCCCTTTTCATAATTTGATGGTAGTCA-CCATCC
1 ATCCCTTTTCATAATTTGACAGCCGAAGCTATCCCTTTTCATAAATCGACAGCAG-AATCCATCC
29305350 CTTTTCAT-TGCTCGATGGTCGTCACC
65 CTTTTCATAT-CTCGATGGTCGTCACC
* * *
29305376 ATCCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAATCCATCCC
1 ATCCCTTTTCATAATTTGACAGCCGAAGCTATCCCTTTTCATAAATCGACAGCAGAATCCATCCC
*
29305441 TTTTCATATTTCGATGGTCGTCACC
66 TTTTCATATCTCGATGGTCGTCACC
29305466 ATCCCTTTTCAT
1 ATCCCTTTTCAT
29305478 TGTTGATGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
89 1 0.01
90 86 0.98
91 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.38
Consensus pattern (90 bp):
ATCCCTTTTCATAATTTGACAGCCGAAGCTATCCCTTTTCATAAATCGACAGCAGAATCCATCCC
TTTTCATATCTCGATGGTCGTCACC
Found at i:29305497 original size:29 final size:30
Alignment explanation
Indices: 29305316--29305507 Score: 141
Period size: 30 Copynumber: 6.4 Consensus size: 30
29305306 AGCCGAAGCT
* *
29305316 ATCCCTTTTCATAATTT-GATGGTAGTCACC
1 ATCCCTTTTCAT-ATTTCGATGGTCGTCAAC
* *
29305346 ATCCCTTTTCAT-TGCTCGATGGTCGTCACC
1 ATCCCTTTTCATAT-TTCGATGGTCGTCAAC
* *
29305376 ATCCCTTTTCATAATTT-GATAG-C-TGAAGC
1 ATCCCTTTTCAT-ATTTCGATGGTCGTCAA-C
** ** *
29305405 TATCCCTTTTCATAAATCGACAGCCG--AATCC
1 -ATCCCTTTTCATATTTCGATGGTCGTCAA--C
*
29305436 ATCCCTTTTCATATTTCGATGGTCGTCACC
1 ATCCCTTTTCATATTTCGATGGTCGTCAAC
29305466 ATCCCTTTTCAT-TGTT-GATGGTCGTCAAC
1 ATCCCTTTTCATAT-TTCGATGGTCGTCAAC
29305495 ATCCCTTTTCATA
1 ATCCCTTTTCATA
29305508 ATCGATAACT
Statistics
Matches: 131, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.02
29 30 0.23
30 93 0.71
31 3 0.02
32 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATATTTCGATGGTCGTCAAC
Found at i:29312543 original size:18 final size:18
Alignment explanation
Indices: 29312520--29312565 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29312510 TCAGTGAAAA
* *
29312520 TGGGCTCACACGCCTATG
1 TGGGCTCACACACCCATG
*
29312538 TGGGCTCAAACACCCATG
1 TGGGCTCACACACCCATG
*
29312556 TGGGCCCACA
1 TGGGCTCACA
29312566 TGCCCGTGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.17
Consensus pattern (18 bp):
TGGGCTCACACACCCATG
Found at i:29336822 original size:81 final size:81
Alignment explanation
Indices: 29336715--29336916 Score: 296
Period size: 81 Copynumber: 2.5 Consensus size: 81
29336705 TTTAAGATTT
*
29336715 TGCCACAAAGGCAATTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACACCACAAAGG
1 TGCCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCAATTCTTTCAGAGTACACCACAAAGG
*
29336780 CAGTTCTTTCAGAGTA
66 CAGTACTTTCAGAGTA
* * * * * *
29336796 TGCCACCAATGCAATTCTTTTAGAGTATGCCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGG
1 TGCCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCAATTCTTTCAGAGTACACCACAAAGG
* *
29336861 TAGTACTTTTAGAGTA
66 CAGTACTTTCAGAGTA
**
29336877 CACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
1 TGCCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29336917 GCTCTTAGTT
Statistics
Matches: 104, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 104 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (81 bp):
TGCCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCAATTCTTTCAGAGTACACCACAAAGG
CAGTACTTTCAGAGTA
Found at i:29336922 original size:27 final size:27
Alignment explanation
Indices: 29336717--29336916 Score: 265
Period size: 27 Copynumber: 7.4 Consensus size: 27
29336707 TAAGATTTTG
29336717 CCACAAAGGCAATTCTTTCAGAGTACA
1 CCACAAAGGCAATTCTTTCAGAGTACA
29336744 CCACAAAGGCAATTCTTTCAGAGTACA
1 CCACAAAGGCAATTCTTTCAGAGTACA
* **
29336771 CCACAAAGGCAGTTCTTTCAGAGTATG
1 CCACAAAGGCAATTCTTTCAGAGTACA
* * * **
29336798 CCACCAATGCAATTCTTTTAGAGTATG
1 CCACAAAGGCAATTCTTTCAGAGTACA
* *
29336825 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAATTCTTTCAGAGTACA
* * * *
29336852 CCACAAAGGTAGTACTTTTAGAGTACA
1 CCACAAAGGCAATTCTTTCAGAGTACA
*
29336879 CCACAAAGGCAATTCTTTCAGAGTACG
1 CCACAAAGGCAATTCTTTCAGAGTACA
29336906 CCACAAAGGCA
1 CCACAAAGGCA
29336917 GCTCTTAGTT
Statistics
Matches: 152, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (27 bp):
CCACAAAGGCAATTCTTTCAGAGTACA
Found at i:29340490 original size:12 final size:12
Alignment explanation
Indices: 29340473--29340497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29340463 AAAAATACAT
29340473 AAAATTCTATAA
1 AAAATTCTATAA
29340485 AAAATTCTATAA
1 AAAATTCTATAA
29340497 A
1 A
29340498 TATTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTCTATAA
Found at i:29340516 original size:17 final size:17
Alignment explanation
Indices: 29340494--29340543 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
29340484 AAAAATTCTA
29340494 TAAATATTTTATGTTAT
1 TAAATATTTTATGTTAT
29340511 TAAATATTTT-T-TATAT
1 TAAATATTTTATGT-TAT
29340527 TAAATATTTTAATGTTA
1 TAAATATTTT-ATGTTA
29340544 AATATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 10 0.34
18 3 0.10
19 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TAAATATTTTATGTTAT
Found at i:29340529 original size:16 final size:16
Alignment explanation
Indices: 29340494--29340551 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 16
29340484 AAAAATTCTA
29340494 TAAATATTTTATGT-TAT
1 TAAATATTTT-T-TATAT
29340511 TAAATATTTTTTATAT
1 TAAATATTTTTTATAT
* *
29340527 TAAATA-TTTTAATGT
1 TAAATATTTTTTATAT
29340542 TAAATATTTT
1 TAAATATTTT
29340552 AATGTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.38
16 13 0.35
17 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAAATATTTTTTATAT
Found at i:29340544 original size:15 final size:15
Alignment explanation
Indices: 29340510--29340561 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
29340500 TTTTATGTTA
* *
29340510 TTAAATATTTTTTATA
1 TTAAATA-TTTTAATG
29340526 TTAAATATTTTAATG
1 TTAAATATTTTAATG
29340541 TTAAATATTTTAATG
1 TTAAATATTTTAATG
29340556 TTAAAT
1 TTAAAT
29340562 TAATTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 27 0.79
16 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TTAAATATTTTAATG
Found at i:29353420 original size:31 final size:31
Alignment explanation
Indices: 29353384--29353444 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
29353374 AAATTAATCT
*
29353384 AGTGACTTAAATAAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTCGAATAGTTC
*
29353415 AGTGACTTAAATGAAAACTTTCGAATAGTT
1 AGTGACTTAAATAAAAACTTTCGAATAGTT
29353445 TAATGATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTCGAATAGTTC
Found at i:29355547 original size:40 final size:40
Alignment explanation
Indices: 29355486--29355563 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
29355476 TGATTGAAAT
* * * *
29355486 TACCGAAGTATAAATAGGGGCACGTATGTGCAATCAGGGG
1 TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGGGG
*
29355526 TACCAAAGTACAAATAAGGGCACGTACGTGCATTCAGG
1 TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGG
29355564 TATAGTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (40 bp):
TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGGGG
Found at i:29355997 original size:27 final size:27
Alignment explanation
Indices: 29355931--29355987 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
29355921 TCGAATTCAA
29355931 CATACACCCATAACAACTCATAAAATT
1 CATACACCCATAACAACTCATAAAATT
29355958 CATACACCCATAACAACTCATAAAATT
1 CATACACCCATAACAACTCATAAAATT
29355985 CAT
1 CAT
29355988 TCTTTCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (27 bp):
CATACACCCATAACAACTCATAAAATT
Found at i:29360019 original size:50 final size:51
Alignment explanation
Indices: 29359896--29360136 Score: 204
Period size: 50 Copynumber: 4.7 Consensus size: 51
29359886 ATAATAACAA
* * * * * *
29359896 GCCAAAGCCATGTCCTAGACATGGTCTTACTTGGGA-TGTTTC-T-TCTACT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATATCAAGT
* * * * *
29359945 GCCAATGCCATATCCTAGATATGGTCTTACACGGGAGTTCTCATATC-AGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCAAGT
* ** * * *
29359995 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTC-GGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCAAGT
* * *
29360045 GCCAACGCCATGTCCCAGACATGGTTTTACATGGGACATCTCATAACCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TCAA-G-T
*
29360101 GCCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
29360137 TCTCTTTACC
Statistics
Matches: 155, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
49 34 0.22
50 82 0.53
51 2 0.01
53 2 0.01
55 1 0.01
56 34 0.22
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (51 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCAAGT
Found at i:29360087 original size:100 final size:105
Alignment explanation
Indices: 29359896--29360130 Score: 241
Period size: 99 Copynumber: 2.3 Consensus size: 105
29359886 ATAATAACAA
* * ** ** * * *
29359896 GCCAAAGCCATGTCCTAGACATGGTCTTACTTGGGATGTTTCTTCTAC--TGCCAATGCCATATC
1 GCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGGTGCCAACGCCATATC
* * **
29359959 CTAGATATGGTCTTACACGGGAGTTCTCAT-A-TC-A-G-T
65 CCAGACATGGTCTTACACGGGACATCTCATAACTCAATGAT
* *
29359995 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 GCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATATCC
* *
29360060 CAGACATGGTTTTACATGGGACATCTCATAACCTCAATGAT
66 CAGACATGGTCTTACACGGGACATCTCATAA-CTCAATGAT
*
29360101 GCCAATTCCATGTCCCAGACATGGTCTTAC
1 GCCAATGCCATGTCCCAGACATGGTCTTAC
29360131 ATGGGATCTC
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
98 1 0.01
99 37 0.34
100 37 0.34
101 1 0.01
103 2 0.02
104 1 0.01
105 1 0.01
106 29 0.27
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (105 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATATCC
CAGACATGGTCTTACACGGGACATCTCATAACTCAATGAT
Found at i:29362207 original size:13 final size:13
Alignment explanation
Indices: 29362189--29362217 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29362179 TACAATATTC
29362189 ATTTTTATTTTAA
1 ATTTTTATTTTAA
29362202 ATTTTTATTTTAA
1 ATTTTTATTTTAA
29362215 ATT
1 ATT
29362218 ATACTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTATTTTAA
Found at i:29363786 original size:3 final size:3
Alignment explanation
Indices: 29363778--29363825 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
29363768 TACAATTTGG
29363778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29363826 GATGATAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29364944 original size:20 final size:20
Alignment explanation
Indices: 29364916--29364953 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29364906 GGCCAACTGT
29364916 GTACAGAGGTCG-ACGTGGCG
1 GTACAGAGG-CGAACGTGGCG
*
29364936 GTACGGAGGCGAACGTGG
1 GTACAGAGGCGAACGTGG
29364954 GAAAGGTGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.21, C:0.18, G:0.47, T:0.13
Consensus pattern (20 bp):
GTACAGAGGCGAACGTGGCG
Found at i:29366084 original size:31 final size:28
Alignment explanation
Indices: 29366040--29366102 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
29366030 AGCGTAAAGG
*
29366040 CTAAATTTTAATTTTAT-CAAATTTAGTCT
1 CTAAATTTTAATTTT-TGAAAATTTAGT-T
29366069 CTAAACTTTTCAATTTTTGAAAATTTAGTT
1 CTAAA-TTTT-AATTTTTGAAAATTTAGTT
29366099 CTAA
1 CTAA
29366103 TCAAATGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 10 0.33
31 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (28 bp):
CTAAATTTTAATTTTTGAAAATTTAGTT
Found at i:29370213 original size:20 final size:20
Alignment explanation
Indices: 29370188--29370226 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29370178 TAATAGTATT
29370188 TTATTAATTTAATATTAAAG
1 TTATTAATTTAATATTAAAG
*
29370208 TTATTATTTTAATATTAAA
1 TTATTAATTTAATATTAAA
29370227 TTTAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTATTAATTTAATATTAAAG
Found at i:29370303 original size:12 final size:12
Alignment explanation
Indices: 29370271--29370304 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29370261 TATTATTTTA
29370271 ATAATATTTAAT
1 ATAATATTTAAT
29370283 ATTAA-ATTTAAT
1 A-TAATATTTAAT
29370295 ATAATATTTA
1 ATAATATTTA
29370305 TCTTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:29371729 original size:90 final size:90
Alignment explanation
Indices: 29371515--29371731 Score: 256
Period size: 90 Copynumber: 2.4 Consensus size: 90
29371505 CAATAGAACC
* * * * ** * * *
29371515 ACCACCCAAAGCATGGGATATGAATTCATTAAGAATATTTAGTGGCTCATCCTATAAATTTAGTA
1 ACCACCCAAACCCTGGGTTATGAAATCATTAAGAGCATCTAGTAGTTCATCCTATAAATTTAGTA
* * *
29371580 GGTTTATCAAGTCCGTCTTAATATG
66 GATTCATCAAGTCCGTCTTAACATG
29371605 ACCACCCAAACCCTGGGTTATGAAATCATTAAGAGCATCTAGTAGTTCATCCTATAAATTTAGT-
1 ACCACCCAAACCCTGGGTTATGAAATCATTAAGAGCATCTAGTAGTTCATCCTATAAATTTAGTA
* *
29371669 GAATTCATTAAGTTCGTCTTAACATG
66 G-ATTCATCAAGTCCGTCTTAACATG
* * * *
29371695 ACCACCCTAACTCTGGGTTATGAACTTATTAAGAGCA
1 ACCACCCAAACCCTGGGTTATGAAATCATTAAGAGCA
29371732 AGGAGCTCAT
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 1 0.01
90 107 0.99
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (90 bp):
ACCACCCAAACCCTGGGTTATGAAATCATTAAGAGCATCTAGTAGTTCATCCTATAAATTTAGTA
GATTCATCAAGTCCGTCTTAACATG
Found at i:29379497 original size:24 final size:24
Alignment explanation
Indices: 29379466--29379584 Score: 166
Period size: 24 Copynumber: 5.0 Consensus size: 24
29379456 GGCATTCCCG
* * *
29379466 AATACGCCACAAAGGCACTTGCAG
1 AATACGCCATAAAGGCACTTACAA
* *
29379490 AATACGCCACAAAGGCACATACAA
1 AATACGCCATAAAGGCACTTACAA
*
29379514 AATACGCCATAAATGCACTTACAA
1 AATACGCCATAAAGGCACTTACAA
*
29379538 AATACACCATAAAGGCACTTACAA
1 AATACGCCATAAAGGCACTTACAA
*
29379562 AATACGCCATAATGGCACTTACA
1 AATACGCCATAAAGGCACTTACA
29379585 TAATCACGTG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 85 1.00
ACGTcount: A:0.45, C:0.27, G:0.13, T:0.16
Consensus pattern (24 bp):
AATACGCCATAAAGGCACTTACAA
Found at i:29379925 original size:66 final size:66
Alignment explanation
Indices: 29379819--29379950 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
29379809 CCCCACCAAA
29379819 GGCATCACAAAGAATGTTATACATAGAAGTTACTTACACAAATTTGGTCACATACTCGTCCGATG
1 GGCATCACAAAGAATGTTATACATAGAAGTTACTTACACAAATTTGGTCACATACTCGTCCGATG
29379884 C
66 C
29379885 GGCATCACAAAGAATGTTATACATAGAAGTTACTTACACAAATTTGGTCACATACTCGTCCGATG
1 GGCATCACAAAGAATGTTATACATAGAAGTTACTTACACAAATTTGGTCACATACTCGTCCGATG
29379950 C
66 C
29379951 TTACTCTCTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (66 bp):
GGCATCACAAAGAATGTTATACATAGAAGTTACTTACACAAATTTGGTCACATACTCGTCCGATG
C
Found at i:29393690 original size:260 final size:261
Alignment explanation
Indices: 29393229--29393754 Score: 919
Period size: 260 Copynumber: 2.0 Consensus size: 261
29393219 GTTCATACGA
* * *
29393229 ACTTACCTGGCTAAATTGCAAAAATTTCAAAGTCCAAGGGCATTTTTACCATTCTCCCCGATTTT
1 ACTTACCTGGCTAAATTGCAAAAATGTCAAAGTACAAGAGCATTTTTACCATTCTCCCCGATTTT
*
29393294 CCATCCGATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
66 CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
*
29393359 TTTTATGCAATTTATTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
131 TTTTATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
29393424 ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCC-AAAATTGAGCCTAGCCGAA
196 ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGCCGAA
29393488 T
261 T
* * *
29393489 ACTTACCTGGCTAAATTGTAGAAATGTCAAAGTACAAGAGCATTTTTACCATTCTCCTCGATTTT
1 ACTTACCTGGCTAAATTGCAAAAATGTCAAAGTACAAGAGCATTTTTACCATTCTCCCCGATTTT
*
29393554 CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACATTAAAAAATGTA
66 CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
* *
29393619 TTTTATGCAATTTAGTCATTTTTTACATTTTTACAAAATTACCCCTAAAGTTTTACTTTTGTTCA
131 TTTTATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
* **
29393684 ATTTAGTCCCTGAGCCTAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTATTCGAA
196 ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGCCGAA
29393749 T
261 T
29393750 ACTTA
1 ACTTA
29393755 TTGCATCCAA
Statistics
Matches: 251, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
260 228 0.91
261 23 0.09
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (261 bp):
ACTTACCTGGCTAAATTGCAAAAATGTCAAAGTACAAGAGCATTTTTACCATTCTCCCCGATTTT
CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
TTTTATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGCCGAA
T
Found at i:29395664 original size:21 final size:21
Alignment explanation
Indices: 29395640--29395682 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29395630 TGGAATTTTT
*
29395640 AAGTTAAACAAATTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
* *
29395661 AAGTTAAATAGAGTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
29395682 A
1 A
29395683 CTGTAACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (21 bp):
AAGTTAAACAAAGTTTTGAAA
Found at i:29397813 original size:31 final size:31
Alignment explanation
Indices: 29397777--29397848 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
29397767 AGTTATAATG
*
29397777 TCTAAATTATCCC-TATTGATTTTTGC-TACTA
1 TCTAAAATA-CCCTTATTGATTTTT-CATACTA
29397808 TCTAAAATACCCTTATTGATTTTTCATACTA
1 TCTAAAATACCCTTATTGATTTTTCATACTA
29397839 TCTAAAATAC
1 TCTAAAATAC
29397849 TCCTATTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.44
Consensus pattern (31 bp):
TCTAAAATACCCTTATTGATTTTTCATACTA
Found at i:29398926 original size:21 final size:20
Alignment explanation
Indices: 29398873--29398928 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
29398863 TATTAATTTA
*
29398873 TTTTTATATAATTTATAACT
1 TTTTTATTTAATTTATAACT
** * *
29398893 TTAATAATAAATTTAGTAACT
1 TTTTTATTTAATTTA-TAACT
29398914 TTTTTATTTAATTTA
1 TTTTTATTTAATTTA
29398929 ATAAACTAAT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTATTTAATTTATAACT
Found at i:29402761 original size:43 final size:43
Alignment explanation
Indices: 29402662--29402770 Score: 105
Period size: 43 Copynumber: 2.5 Consensus size: 43
29402652 GCAGCTTGTC
* * *
29402662 TGCACCGTTTAGTGGTTAATCCACACCATATTAGTAGCTTGTT
1 TGCAACGTTTAGTGGTTAATCCACACCATACTAGTAGCTTATT
** * * *
29402705 TGC-ACTGAATAGTGGTTTATCCACATCGTACTAGTAG-TTCATT
1 TGCAAC-GTTTAGTGGTTAATCCACACCATACTAGTAGCTT-ATT
*
29402748 TGCAACGTTTAGTGGTTCATCCA
1 TGCAACGTTTAGTGGTTAATCCA
29402771 TACTGTACTG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
42 3 0.06
43 47 0.90
44 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (43 bp):
TGCAACGTTTAGTGGTTAATCCACACCATACTAGTAGCTTATT
Found at i:29405505 original size:21 final size:22
Alignment explanation
Indices: 29405461--29405505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
29405451 TATAAATAAT
* *
29405461 TAAATCTATTCATATTTCTTTA
1 TAAATATATTCATATTTATTTA
*
29405483 TAAATATATT-ATTTTTATTTA
1 TAAATATATTCATATTTATTTA
29405504 TA
1 TA
29405506 CAATGCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (22 bp):
TAAATATATTCATATTTATTTA
Found at i:29419093 original size:62 final size:62
Alignment explanation
Indices: 29418979--29419165 Score: 196
Period size: 62 Copynumber: 3.0 Consensus size: 62
29418969 CATGACTCAT
* * * * * * *
29418979 ACGGCTTGGGTACACGCCCATGTCCCTAACCGTGTTGTTTTATATCACAAACAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGCCGTGTGGTCTTGTACCACAAACAGTGAGTTAC
* * * *
29419041 ACGGCTTGGGTACATGCCCGTGTCCCTAGCCGTGTGGTCTTGTACCATAAACAGTAAGGTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGCCGTGTGGTCTTGTACCACAAACAGTGAGTTAC
* * * ** * *
29419103 ACGGCCTGAGCACAAGCTTGTGTCCCAAGCCGTGTGGTCTTG-ACCCACAAATAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGCCGTGTGGTCTTGTA-CCACAAACAGTGAGTTAC
29419165 A
1 A
29419166 GGGCCTGGAC
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
61 1 0.01
62 102 0.99
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.26
Consensus pattern (62 bp):
ACGGCTTGGGTACAAGCCCGTGTCCCTAGCCGTGTGGTCTTGTACCACAAACAGTGAGTTAC
Found at i:29419171 original size:62 final size:62
Alignment explanation
Indices: 29419024--29419185 Score: 175
Period size: 62 Copynumber: 2.6 Consensus size: 62
29419014 TGTTTTATAT
* * * * *
29419024 CACAAACAGTGAGTTACACGGCTTGGGTACATGCCCGTGTCCCTAGCCGTGTGGTCTTGTAC
1 CACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTCTTGTAC
* * * **
29419086 CATAAACAGTAAGGTACACGGCCTGAGCACAAGCTTGTGTCCCAAGCCGTGTGGTCTTG-ACC
1 CACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTCTTGTA-C
* * *
29419148 CACAAATAGTGAGTTACAGGGCCTG-GACACACGCCCGT
1 CACAAACAGTGAGTTACACGGCCTGAG-CACAAGCCCGT
29419186 ATCCATGGCT
Statistics
Matches: 80, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
61 2 0.03
62 78 0.98
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.22
Consensus pattern (62 bp):
CACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTCTTGTAC
Found at i:29420593 original size:16 final size:16
Alignment explanation
Indices: 29420574--29420609 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29420564 ATTTGTTTTT
*
29420574 GTTCTGTATTCAGCTA
1 GTTCTGCATTCAGCTA
*
29420590 GTTCTGCATTTAGCTA
1 GTTCTGCATTCAGCTA
29420606 GTTC
1 GTTC
29420610 ATATTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
GTTCTGCATTCAGCTA
Found at i:29421180 original size:21 final size:22
Alignment explanation
Indices: 29421154--29421195 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29421144 CTAATAAATT
29421154 AAAATAAATCT-AATAATTTTA
1 AAAATAAATCTAAATAATTTTA
* *
29421175 AAAATATATTTAAATAATTTT
1 AAAATAAATCTAAATAATTTT
29421196 TATTCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATAAATCTAAATAATTTTA
Found at i:29421353 original size:20 final size:20
Alignment explanation
Indices: 29421312--29421349 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
29421302 TTGAAGTTAC
*
29421312 AAATTATATAAAATAACTAT
1 AAATTATATAAAATAAATAT
*
29421332 AAATTATA-ACAATAAATA
1 AAATTATATAAAATAAATA
29421350 ATAATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTATATAAAATAAATAT
Found at i:29422395 original size:35 final size:34
Alignment explanation
Indices: 29422356--29422424 Score: 79
Period size: 35 Copynumber: 2.0 Consensus size: 34
29422346 AAATAGATTA
29422356 TAATTCACTTAATGGATAT-A-TTTTAATCTATATTT
1 TAATT-ACTT-ATGGATATGAGTTTTAATCTA-ATTT
* *
29422391 TAATTACTTTTGGATATGAGTTTTTATCTAATTT
1 TAATTACTTATGGATATGAGTTTTAATCTAATTT
29422425 GGCATGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
33 7 0.23
34 9 0.30
35 14 0.47
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (34 bp):
TAATTACTTATGGATATGAGTTTTAATCTAATTT
Found at i:29424819 original size:50 final size:50
Alignment explanation
Indices: 29424715--29424812 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
29424705 ACATTAAGGG
* * * *
29424715 AATGAGA--TCCCATGTAAAACCTTGTCTGGGACATGGCGTTGGCTCCGA
1 AATGAGATGTCCCATGTAAAACCATGTCTGGGACATGGCATGGGCACCGA
* *
29424763 AATGAGATGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 AATGAGATGTCCCATGTAAAACCATGTCTGGGACATGGCATGGGCACCGA
29424813 TGTGAGAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 7 0.17
50 35 0.83
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AATGAGATGTCCCATGTAAAACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:29424833 original size:50 final size:50
Alignment explanation
Indices: 29424715--29424833 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
29424705 ACATTAAGGG
* * * * *
29424715 AATGAG-A-TCCCATGTAAAACCTTGTCTGGGACATGGCGTTGGCTCCGA
1 AATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
** *
29424763 AATGAGATGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 AATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
** *
29424813 TGTGAGAACTCCCATATAAGA
1 AATGAGAACTCCCATGTAAGA
29424834 TTATATCTAG
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 6 0.11
50 50 0.89
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
AATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:29430969 original size:23 final size:23
Alignment explanation
Indices: 29430940--29431015 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
29430930 AGTGTTATTG
*
29430940 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
29430963 TTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
29430986 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
29431009 ATCAGTG
1 ATCAGTG
29431016 TGGCACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:29434956 original size:43 final size:41
Alignment explanation
Indices: 29434898--29435052 Score: 197
Period size: 43 Copynumber: 3.7 Consensus size: 41
29434888 TAAATTCAGT
*
29434898 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAGTCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCA-ATTCAAA
* *
29434940 GATACGGTGGAATCAGCACTTAACAACCACCTTT-ATATTCAATA
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTCA-ATTCAA-A
29434984 -ATACGGGGAATCAGCACATAGCAACCCCTTTCTAATTCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTC-AATTCAAA
*
29435025 AATACGGTGGAATCAGCACATAGCAACC
1 GATACGG-GGAATCAGCACATAGCAACC
29435053 ACCTCTAGAG
Statistics
Matches: 100, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
41 6 0.06
42 37 0.37
43 51 0.51
44 6 0.06
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (41 bp):
GATACGGGGAATCAGCACATAGCAACCCCTTTCAATTCAAA
Found at i:29435009 original size:42 final size:42
Alignment explanation
Indices: 29434868--29435094 Score: 219
Period size: 42 Copynumber: 5.4 Consensus size: 42
29434858 CTTGATGGAT
* * * * *
29434868 TCAGCACTTAGCAACCACC-ATAAATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAA
* *
29434909 TCAGCACATAGCAACC-CCTTTCACAGTCAA-AGATACGGTGGAA
1 TCAGCACATAGCAACCACCTTT-ATATTCAATA-ATACGG-GGAA
* *
29434952 TCAGCACTTAACAACCACCTTTATATTCAATAATACGGGGAA
1 TCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAA
* *
29434994 TCAGCACATAGCAACC-CCTTTCTAATTCAAAAATACGGTGGAA
1 TCAGCACATAGCAACCACCTTTAT-ATTCAATAATACGG-GGAA
* * * * *
29435037 TCAGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAA
1 TCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAA
* *
29435079 TCAACACTTAGCAACC
1 TCAGCACATAGCAACC
29435095 CCTCTGGGAA
Statistics
Matches: 154, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.01
41 22 0.14
42 60 0.39
43 60 0.39
44 10 0.06
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.21
Consensus pattern (42 bp):
TCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAA
Found at i:29435010 original size:85 final size:85
Alignment explanation
Indices: 29434863--29435097 Score: 312
Period size: 85 Copynumber: 2.8 Consensus size: 85
29434853 CATTACTTGA
* *
29434863 TGGATTCAGCACTTAGCAACCACC-ATAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCC
1 TGGAATCAGCACTTAGCAACCACCTATAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCC
*
29434927 TTTC-ACAGTCAAAGATACGG
66 TTTCTA-AGTCAAAAATACGG
* * * *
29434947 TGGAATCAGCACTTAACAACCACCTTTATATTCAATAATACGGGGAATCAGCACATAGCAACCCC
1 TGGAATCAGCACTTAGCAACCACCTATAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCC
*
29435012 TTTCTAATTCAAAAATACGG
66 TTTCTAAGTCAAAAATACGG
* * * * * * *
29435032 TGGAATCAGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAATCAACACTTAGCAACCCC
1 TGGAATCAGCACTTAGCAACCACCTATAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCC
29435097 T
66 T
29435098 CTGGGAATCT
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 22 0.17
85 109 0.83
86 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (85 bp):
TGGAATCAGCACTTAGCAACCACCTATAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCC
TTTCTAAGTCAAAAATACGG
Found at i:29442176 original size:42 final size:43
Alignment explanation
Indices: 29442128--29442286 Score: 184
Period size: 43 Copynumber: 3.7 Consensus size: 43
29442118 TAAATTCAGT
*
29442128 GATACGG-GGAATCAGCACATAGCAACTCCTTTCACAATCAAA
1 GATACGGTGGAATCAGCACATAGCAACACCTTTCACAATCAAA
* * *
29442170 GATACGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAATA
1 GATACGGTGGAATCAGCACATAGCAA-CACCTTTCACAATCAA-A
* *
29442214 -ATACGG-GGAATCAGCACATAACAACCCCTTTC-CAATTCAAA
1 GATACGGTGGAATCAGCACATAGCAACACCTTTCACAA-TCAAA
*
29442255 AATACGGTGGAATCAGCACATAGCAACCACCT
1 GATACGGTGGAATCAGCACATAGCAA-CACCT
29442287 CTAGAGTCAG
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 8 0.08
42 33 0.34
43 46 0.47
44 11 0.11
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (43 bp):
GATACGGTGGAATCAGCACATAGCAACACCTTTCACAATCAAA
Found at i:29442244 original size:85 final size:85
Alignment explanation
Indices: 29442101--29442327 Score: 314
Period size: 85 Copynumber: 2.7 Consensus size: 85
29442091 GATGGATTTT
* *
29442101 GCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACTCCTTTCACAA
1 GCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTC-CAA
*
29442165 -TCAAAGATACGGTGGAATCA
65 TTCAAAAATACGGTGGAATCA
* * *
29442185 GCACTTAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACATAACAACCCCTTTCCAAT
1 GCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCCAAT
29442250 TCAAAAATACGGTGGAATCA
66 TCAAAAATACGGTGGAATCA
* * * * * * *
29442270 GCACATAGCAACCACCTCTAGAGTCAGTAATTCAGGGAATCAGCACTTAGCAACCCCT
1 GCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCT
29442328 CGGGGAATTT
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 19 0.15
85 107 0.85
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (85 bp):
GCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCCAAT
TCAAAAATACGGTGGAATCA
Found at i:29442321 original size:42 final size:40
Alignment explanation
Indices: 29442101--29442328 Score: 181
Period size: 42 Copynumber: 5.4 Consensus size: 40
29442091 GATGGATTTT
* * *
29442101 GCACTTAGCAACCACCT-TAAATTCAGTGATACGGGGAATCA
1 GCACATAGCAACC-CCTCT-AATTCAATAATACGGGGAATCA
* * *
29442142 GCACATAGCAACTCCTTTCACAATCAA-AGATACGGTGGAATCA
1 GCACATAGCAACCCCTCT-A-ATTCAATA-ATACGG-GGAATCA
* *
29442185 GCACTTAGCAACCACCTTTATATTCAATAATACGGGGAATCA
1 GCACATAGCAACC-CCTCTA-ATTCAATAATACGGGGAATCA
* * *
29442227 GCACATAACAACCCCTTTCCAATTCAAAAATACGGTGGAATCA
1 GCACATAGCAACCCC--TCTAATTCAATAATACGG-GGAATCA
* * * *
29442270 GCACATAGCAACCACCTCTAGAGTCAGTAATTCAGGGAATCA
1 GCACATAGCAACC-CCTCTA-ATTCAATAATACGGGGAATCA
*
29442312 GCACTTAGCAACCCCTC
1 GCACATAGCAACCCCTC
29442329 GGGGAATTTG
Statistics
Matches: 153, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
40 3 0.02
41 19 0.12
42 63 0.41
43 60 0.39
44 8 0.05
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (40 bp):
GCACATAGCAACCCCTCTAATTCAATAATACGGGGAATCA
Found at i:29444173 original size:34 final size:34
Alignment explanation
Indices: 29444135--29444226 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 34
29444125 TAAAGTCATG
29444135 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
* *
29444169 CATTA---AA--TT-AAGTCTTGTT-AGTTT--A-
1 CATTATGTAACTTTCATGT-TAGTTAAGTTTGCAT
29444194 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
29444227 TTCAAGCCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 23
0.61 0.06 0.33
Matches are distributed among these distances:
24 4 0.09
26 1 0.02
27 2 0.05
28 8 0.19
29 12 0.28
30 8 0.19
31 2 0.05
32 1 0.02
34 5 0.12
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:29446649 original size:50 final size:49
Alignment explanation
Indices: 29446528--29446706 Score: 182
Period size: 50 Copynumber: 3.6 Consensus size: 49
29446518 GGGAATGAGA
* * * * *
29446528 TCCCTTGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG-TGAGAAG
** *
29446578 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGATGTGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA-GTGAGAAG
* * * * * *
29446628 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAG-GA-AACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACT-GAGTGAGAA-G
29446677 TCCCATGTAAGACCATGTCTGGGACATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
29446707 TTTCGCATGT
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
48 2 0.02
49 29 0.27
50 74 0.69
51 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGTGAGAAG
Found at i:29447080 original size:15 final size:14
Alignment explanation
Indices: 29447053--29447079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29447043 TTTACGCTTA
29447053 CTCCTTTTATTTTC
1 CTCCTTTTATTTTC
29447067 CTCCTTTTATTTT
1 CTCCTTTTATTTT
29447080 TTATAGTATC
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:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (14 bp):
CTCCTTTTATTTTC
Found at i:29449931 original size:7 final size:7
Alignment explanation
Indices: 29449919--29449944 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29449909 GAGGAAGTGA
29449919 TCTGTAT
1 TCTGTAT
29449926 TCTGTAT
1 TCTGTAT
29449933 TCTGTAT
1 TCTGTAT
29449940 TCTGT
1 TCTGT
29449945 TTGAGTATAT
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:0.15, G:0.15, T:0.58
Consensus pattern (7 bp):
TCTGTAT
Found at i:29464515 original size:201 final size:202
Alignment explanation
Indices: 29464158--29464632 Score: 817
Period size: 201 Copynumber: 2.4 Consensus size: 202
29464148 TTTTGCCATC
* *
29464158 TGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCCCTTTTCTGCTTCAGGAA
1 TGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTTCTGCTTCAGGAA
29464223 GAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCG
66 GAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCG
* *
29464288 AAGGCACTCTAGATGGCCTTCACAGATCAGAATGAATATACTCCAATGTTCCCTTCGTGTTATGG
131 AAGGCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAATGTTCCCTTCCTGTTATGG
29464353 C-TTTTT
196 CTTTTTT
*
29464359 TGTTATTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTTCTGCTTCAGGAA
1 TGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTTCTGCTTCAGGAA
*
29464424 GAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGGTCCACCTCTCG
66 GAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCG
* *
29464489 AAGGCACTCTAGATGGCCTCCACAGATTAGAATTAATATACTCCAATGTTCCCTTCCTGTTATGG
131 AAGGCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAATGTTCCCTTCCTGTTATGG
29464554 CTTTTTT
196 CTTTTTT
* * * * * *
29464561 TGTTTTTCAATAAGAGTATTCCAAGATTTAAATGTGGAAGACACATCACTTTTCTGCTTTAGGAA
1 TGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTTCTGCTTCAGGAA
29464626 GAACGCC
66 GAACGCC
29464633 GTCTTTTCTA
Statistics
Matches: 258, Mismatches: 15, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
201 188 0.73
202 70 0.27
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (202 bp):
TGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTTCTGCTTCAGGAA
GAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCG
AAGGCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAATGTTCCCTTCCTGTTATGG
CTTTTTT
Found at i:29466457 original size:26 final size:26
Alignment explanation
Indices: 29466428--29466508 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
29466418 AACACACCAA
29466428 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
29466454 TATCGCAGCAAAGCTACCACTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
29466480 TATCACAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
29466506 TAT
1 TAT
29466509 ACTTTCTCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:29466702 original size:27 final size:27
Alignment explanation
Indices: 29466672--29467219 Score: 452
Period size: 27 Copynumber: 20.4 Consensus size: 27
29466662 GGGTATAACA
* *
29466672 GTCATTTTACCCAATGAGGGTATTCCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29466699 GTCA-TTCACCCTATG-GGGTATCTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29466724 ATCATTTTACCCTAT-AGGGGTATTTTG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* *
29466751 GTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
29466778 GTCATTTTACCCTACGGGGGTATTCCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29466805 GTTATTTTACCCTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
** *
29466832 GTCATGCTACTCTAT-AGGGGTATTTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* *
29466859 ATCATTTTACCCTATCG-GGGTATTTTG
1 GTCATTTTACCCTAT-GAGGGTATTTCG
* * * * *
29466886 ATTATTTTACGCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *** *
29466913 GTCATTCTATATTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
*
29466940 GTCATTTTACCCTGT-AGGGGTATTTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* * *
29466967 GTAATTTTACGCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29466994 ATCATTCTACCCTATG-GAAGTATTTCG
1 GTCATTTTACCCTATGAG-GGTATTTCG
* * *
29467021 GTCATTTTACCGTATGGGGGTATTTCT
1 GTCATTTTACCCTATGAGGGTATTTCG
29467048 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
29467075 ATCTTTTTATCCTATG-GGCATATTTCG
1 GTCATTTTACCCTATGAGG-GTATTTCG
*
29467102 GTCATTCTACCCTATG-GGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29467128 GTTATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29467155 GTCATTCTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
29467182 GTCATTTTATCCTTTTAGGATATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
29467209 ATCATTTTACC
1 GTCATTTTACC
29467220 TATTTTGTGG
Statistics
Matches: 425, Mismatches: 82, Indels: 28
0.79 0.15 0.05
Matches are distributed among these distances:
25 11 0.03
26 44 0.10
27 368 0.87
28 2 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:29466787 original size:54 final size:53
Alignment explanation
Indices: 29466672--29467219 Score: 501
Period size: 54 Copynumber: 10.2 Consensus size: 53
29466662 GGGTATAACA
* * * *
29466672 GTCATTTTACCCAATGAGGGTATTCCGGTCA-TTCACCCTAT-GGGGTATCTCG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * *
29466724 ATCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * * *
29466778 GTCATTTTACCCTACGGGGGTATTCCAGTTATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTA-TGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
** * * * *
29466832 GTCATGCTACTCTATAGGGGTATTTCGATCATTTTACCCTATCGGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * * * *** *
29466886 ATTATTTTACGCTATGGGGGTATTTCAGTCATTCTATATTATAGGGGTATTTCA
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * *
29466940 GTCATTTTACCCTGTAGGGGTATTTCGGTAATTTTACGCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * * * *
29466994 ATCATTCTACCCTATGGAAGTATTTCGGTCATTTTACCGTATGGGGGTATTTCT
1 GTCATTTTACCCTATGG-GGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * *
29467048 GTCATTTTACCCTATGAGGGTATTTCGATCTTTTTATCCTAT-GGGCATATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATAGGG-GTATTTCG
* * * *
29467102 GTCATTCTACCCTATGGGGTATTTCGGTTATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
* * * * *
29467155 GTCATTCTATCCTATGGGGGTATTTCGGTCATTTTATCCTTTTA-GGATATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTA-CCCTATAGGGGTATTTCG
*
29467209 ATCATTTTACC
1 GTCATTTTACC
29467220 TATTTTGTGG
Statistics
Matches: 395, Mismatches: 90, Indels: 20
0.78 0.18 0.04
Matches are distributed among these distances:
52 25 0.06
53 56 0.14
54 309 0.78
55 5 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
Found at i:29467508 original size:20 final size:19
Alignment explanation
Indices: 29467467--29467508 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
29467457 AGCCCAATGA
**
29467467 GCCCACATGGCCCATTTTG
1 GCCCACATGGCCCATTACG
29467486 GCCCACCATGGCCCATTACG
1 GCCCA-CATGGCCCATTACG
29467506 GCC
1 GCC
29467509 AAAGCCCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (19 bp):
GCCCACATGGCCCATTACG
Found at i:29473296 original size:92 final size:91
Alignment explanation
Indices: 29473136--29473442 Score: 323
Period size: 92 Copynumber: 3.3 Consensus size: 91
29473126 CTGGCGTGTT
* * * * *
29473136 ATAGCTCTTATGAGCAATACGA-CATGTTATCAAGGGAGAATATTTAGCCTATAAGCTTTTCACC
1 ATAGCTCTTATGAGCAAT-CTAGCGTGTTATCAAGGGAGAATATTTAGCCTACAAGCTTTACACT
*
29473200 ATGTGCATCTGACATGTTATCGGTTGGA
65 ATGTGCATCT-ACATGTTATCAGTTGGA
* * **
29473228 ATAGCTCTTATTAGCAATCTAGCGTGTTAT-TAGGAGAGAATATTTAGCCTACGGGCTTTACACT
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATCAAGG-GAGAATATTTAGCCTACAAGCTTTACACT
* * *
29473292 ATGTGTATCTATCGTGTTATCATTTGGA
65 ATGTGCATCTA-CATGTTATCAGTTGGA
* * * * * * *
29473320 ATAGATGTTATGAGCAATTTGGCGTGTCATCAAGGGAGAATATTTAGCCTACAATCTTTGCACTA
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATCAAGGGAGAATATTTAGCCTACAAGCTTTACACTA
*
29473385 TGT-CAATCTAACATGTTATTAGTTGGA
66 TGTGC-ATCT-ACATGTTATCAGTTGGA
* * *
29473412 ATAACTCTTATGAGCAAACTAACGTGTTATC
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATC
29473443 GGATGGTTAC
Statistics
Matches: 173, Mismatches: 36, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
91 6 0.03
92 163 0.94
93 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (91 bp):
ATAGCTCTTATGAGCAATCTAGCGTGTTATCAAGGGAGAATATTTAGCCTACAAGCTTTACACTA
TGTGCATCTACATGTTATCAGTTGGA
Found at i:29476048 original size:25 final size:25
Alignment explanation
Indices: 29476020--29476073 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
29476010 TGTAGTGGCA
29476020 AGGTGGCGACACAAGTGTGGCAAGG
1 AGGTGGCGACACAAGTGTGGCAAGG
* * *
29476045 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCGACACAAGTGTGGCAAGG
29476070 AGGT
1 AGGT
29476074 TAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.46, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAAGTGTGGCAAGG
Found at i:29477496 original size:27 final size:27
Alignment explanation
Indices: 29477462--29477576 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 27
29477452 CGAAAAGGTT
29477462 GTAAAATTATCGAAATACCCCCGAAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* *
29477489 GTAAAATTATCGAAATACCCTCGATGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* * ** *
29477516 GTAAAATTACCAAAATACCTTCGATGG
1 GTAAAATTATCGAAATACCCCCGAAGG
* *
29477543 ATAAAATTATCGAAATACCCCCGTAGG
1 GTAAAATTATCGAAATACCCCCGAAGG
29477570 GTAAAAT
1 GTAAAAT
29477577 AACTGTTATA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCCCGAAGG
Found at i:29481671 original size:181 final size:182
Alignment explanation
Indices: 29481359--29481712 Score: 629
Period size: 181 Copynumber: 2.0 Consensus size: 182
29481349 TTTGCATAAA
* *
29481359 TTTTAAGGAATCCTTAGTTAAATAGTGAAATAGAAATATGCATATTTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTGAAATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
*
29481424 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATGGAATT
66 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
**
29481489 TTTCTTAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
131 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
*
29481541 TTTTAAGGAATCCTTAGTTAAACAGTGACATAGAAATATGCACA-TTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTGAAATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
* *
29481605 TAATATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCGTAGAATT
66 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
29481670 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
131 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
29481713 AAAGTTGCAG
Statistics
Matches: 164, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
181 123 0.75
182 41 0.25
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (182 bp):
TTTTAAGGAATCCTTAGTTAAACAGTGAAATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
Found at i:29487611 original size:6 final size:6
Alignment explanation
Indices: 29487600--29487637 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
29487590 GCCTAAAAGG
*
29487600 AATTTT AATTTT AATTTT AATTTT CAATTCT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT A
29487638 TGTTCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:29487633 original size:19 final size:18
Alignment explanation
Indices: 29487600--29487637 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
29487590 GCCTAAAAGG
*
29487600 AATTTTAATTTTAATTTT
1 AATTTTAATTCTAATTTT
29487618 AATTTTCAATTCTAATTTT
1 AATTTT-AATTCTAATTTT
29487637 A
1 A
29487638 TGTTCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTAATTCTAATTTT
Found at i:29495880 original size:51 final size:50
Alignment explanation
Indices: 29495819--29496002 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 50
29495809 TCGCTTCACA
* * *
29495819 TAGTATCCTGCACATAGTACTACACATGTGACAATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACAA-TACCATCCGGTACACG
* * * *
29495870 TAGTAGCCTGCACATAATATTACACACGTGATCGAA-ACTC-TCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-C-AATAC-CATCCGGTACACG
* * * *
29495921 TAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACAATACCA-TCCGGTACACG
*
29495971 TAGTAGCCTGCACATAGTACTCCACACGTGAC
1 TAGTAGCCTGCACATAGTACTACACACGTGAC
29496003 CATCACATTC
Statistics
Matches: 109, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 39 0.36
51 64 0.59
52 2 0.02
53 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACAATACCATCCGGTACACG
Found at i:29495999 original size:101 final size:101
Alignment explanation
Indices: 29495817--29496001 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
29495807 GTTCGCTTCA
* * *
29495817 CATAGTATCCTGCACATAGTACTACACATGTGACAATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGAC-ACTACCATCCGATACACGTAGTAGCCTGCA
*
29495882 CATAATATTACACACGTGATCGAAACTCTCCGGTACG
65 CATAATACTACACACGTGATCGAAACTCTCCGGTACG
* *
29495919 CATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCA-TCCGATACACGTAGTAGCCTGCA
* *
29495983 CATAGTACTCCACACGTGA
65 CATAATACTACACACGTGA
29496002 CCATCACATT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 32 0.43
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCATCCGATACACGTAGTAGCCTGCAC
ATAATACTACACACGTGATCGAAACTCTCCGGTACG
Found at i:29498855 original size:42 final size:42
Alignment explanation
Indices: 29498775--29498856 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
29498765 CGTTTTCTCT
* **
29498775 ATGCCATAGTCCAACTATGGTCTTAAACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
*
29498817 ATGCCATAGCCCAACTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTAAACA-TATGCACATAT
29498857 CACACCAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
Found at i:29501574 original size:51 final size:50
Alignment explanation
Indices: 29501513--29501699 Score: 200
Period size: 51 Copynumber: 3.7 Consensus size: 50
29501503 TCACTTCACA
*
29501513 TAGTATCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACG
** * * * * *
29501564 TAGTAGCCTGCACATAGTACTACAC-TCGTGATTGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACAT-GTGA-CCATACCATCCGATACACG
* * *
29501615 TAGTAGCCTGCACATAATACTACACATGCGACC-TATCATTCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACG
*
29501665 TAGTAGCCTGCACATAGTACT-CAACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTAC-ACATGTGACCAT
29501700 CACATTCACT
Statistics
Matches: 109, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 3 0.03
50 37 0.34
51 67 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACG
Found at i:29501695 original size:101 final size:101
Alignment explanation
Indices: 29501511--29501695 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
29501501 GTTCACTTCA
* * *
29501511 CATAGTATCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAATACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
*
29501576 CATAGTACTACACTCGTGATTGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATTGAAACTATCCGGTACG
*
29501613 CATAGTAGCCTGCACATAATACTACACATGCGACC-TATCATTCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAATACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
29501677 CATAGTACT-CAACACGTGA
65 CATAGTACTAC-ACACGTGA
29501696 CCATCACATT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 5 0.07
101 39 0.51
102 32 0.42
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAATACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATTGAAACTATCCGGTACG
Found at i:29501718 original size:101 final size:99
Alignment explanation
Indices: 29501502--29501729 Score: 230
Period size: 101 Copynumber: 2.3 Consensus size: 99
29501492 ATCAATGATG
* * * *
29501502 TTCACTTCACATAGTATCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAG
1 TTCACTTTACATAGTAGCCTGCACATAATACTACACATGCGACCA-TACCATCCGATACACGTAG
* * *
29501567 TAGCCTGCACATAGTACTACACTCGTGATTGAAAC
65 TAGCCTGCACATAGTACTACACACGTGAATCAAAC
** *
29501602 TATC-CGGTACGCATAGTAGCCTGCACATAATACTACACATGCGACC-TATCATTCCGATACACG
1 T-TCACTTTA--CATAGTAGCCTGCACATAATACTACACATGCGACCATACCA-TCCGATACACG
*
29501665 TAGTAGCCTGCACATAGTACT-CAACACGTGACCATCACA-
62 TAGTAGCCTGCACATAGTACTAC-ACACGTGA--ATCAAAC
* *
29501704 TTCACTTTTACATAGTGGCCTACACA
1 TTCAC-TTTACATAGTAGCCTGCACA
29501730 AAATCCGTGC
Statistics
Matches: 104, Mismatches: 15, Indels: 17
0.76 0.11 0.12
Matches are distributed among these distances:
100 8 0.08
101 57 0.55
102 34 0.33
103 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (99 bp):
TTCACTTTACATAGTAGCCTGCACATAATACTACACATGCGACCATACCATCCGATACACGTAGT
AGCCTGCACATAGTACTACACACGTGAATCAAAC
Found at i:29502986 original size:397 final size:397
Alignment explanation
Indices: 29502253--29503049 Score: 1450
Period size: 397 Copynumber: 2.0 Consensus size: 397
29502243 AAAAATGTAA
* *
29502253 AAATCATTAAAAACGGGGATAGAACGGAATTACAATTGAGCTTGGAAGCTTGAAAAACCTTATCC
1 AAATCATTAAAAACGGGGATAGAACGGAATTACAATCGAGCTTGGAAGCTTAAAAAACCTTATCC
* *
29502318 ATGGTTTATCCATGCAACTTTCGTCCTAGGGGTTGAATATGGACAAAAATTGGCTTTTAATTTTG
66 ATGGTTTATCAATGCAACTTTCGTACTAGGGGTTGAATATGGACAAAAATTGGCTTTTAATTTTG
* * *
29502383 TTTTTAATTCATTTTAATAACTAAATGACCAAAATACTCTTAATGGAAAACTTTGGAAACATGCC
131 TTTTTAAATCATTTTAATAACTAAATGACCAAAATACCCTTAATGAAAAACTTTGGAAACATGCC
29502448 CAACCATACCCATTTTTGTCCACCAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAAT
196 CAACCATACCCATTTTTGTCCACCAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAAT
*
29502513 TTAAAATTTCATAACAATTGGACACCTCTAAAATATGGAACTCAACTTTTATACTTTTTACAATT
261 TTAAAATTTCATAACAATTGGACACCTCTAAAATATAGAACTCAACTTTTATACTTTTTACAATT
* *
29502578 TAGTCCTTTTGACTAAATTGAGTGCCCAAACGTCAAAATTTTCGAACAAAATTTTCATTAAATCA
326 TAGTCCTTTTGACTAAATTGAGTGCCCAAACGTCAAAATTTTCAAACAAAATTTTCATGAAATCA
29502643 TCTTGTG
391 TCTTGTG
* *
29502650 AAATCATTAAAAACGGGGATAGAATGGAATTATAATCGAGCTTGGAAGCTTAAAAAACCTTATCC
1 AAATCATTAAAAACGGGGATAGAACGGAATTACAATCGAGCTTGGAAGCTTAAAAAACCTTATCC
*
29502715 ATGGTTTATTAATGCAACTTTCGTACTAGGGGTTGAATATGGACAAAAATTGGCTTTTAATTTTG
66 ATGGTTTATCAATGCAACTTTCGTACTAGGGGTTGAATATGGACAAAAATTGGCTTTTAATTTTG
*
29502780 TTTTTAAATCATTTTAATAACTAAATGACCAAAATGCCCTTAATGAAAAACTTTGGAAACATGCC
131 TTTTTAAATCATTTTAATAACTAAATGACCAAAATACCCTTAATGAAAAACTTTGGAAACATGCC
29502845 CAACCATACCCATTTTTGTCCACCAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAAT
196 CAACCATACCCATTTTTGTCCACCAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAAT
*
29502910 TTAAAATTTCATAACAATTGGACACCTCTAACATATAGAACTCAACTTTTATACTTTTTACAATT
261 TTAAAATTTCATAACAATTGGACACCTCTAAAATATAGAACTCAACTTTTATACTTTTTACAATT
*
29502975 TAGTCCTTTTGACTAAATTGAGTGCCCAAACGTCAAAATTTTCAAACGAAATTTTCATGAAATCA
326 TAGTCCTTTTGACTAAATTGAGTGCCCAAACGTCAAAATTTTCAAACAAAATTTTCATGAAATCA
29503040 TCTTGTG
391 TCTTGTG
29503047 AAA
1 AAA
29503050 CCGTAGACCA
Statistics
Matches: 384, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
397 384 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (397 bp):
AAATCATTAAAAACGGGGATAGAACGGAATTACAATCGAGCTTGGAAGCTTAAAAAACCTTATCC
ATGGTTTATCAATGCAACTTTCGTACTAGGGGTTGAATATGGACAAAAATTGGCTTTTAATTTTG
TTTTTAAATCATTTTAATAACTAAATGACCAAAATACCCTTAATGAAAAACTTTGGAAACATGCC
CAACCATACCCATTTTTGTCCACCAACTTAACCAATGGTCTAATTACCATATAAAGACCTCCAAT
TTAAAATTTCATAACAATTGGACACCTCTAAAATATAGAACTCAACTTTTATACTTTTTACAATT
TAGTCCTTTTGACTAAATTGAGTGCCCAAACGTCAAAATTTTCAAACAAAATTTTCATGAAATCA
TCTTGTG
Found at i:29504347 original size:19 final size:19
Alignment explanation
Indices: 29504323--29504360 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29504313 TTATCTCTCG
29504323 ACCTCACAGTCTAGATCGA
1 ACCTCACAGTCTAGATCGA
29504342 ACCTCACAGTCTAGATCGA
1 ACCTCACAGTCTAGATCGA
29504361 TTCGAGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (19 bp):
ACCTCACAGTCTAGATCGA
Found at i:29514830 original size:28 final size:28
Alignment explanation
Indices: 29514777--29514833 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
29514767 AGGCATTCCC
*
29514777 TTCATAGATCACCAAAAATGCTTCCTTT
1 TTCATAGATCACCAAAAATGCATCCTTT
* *
29514805 TTCATAGATCGCCATAAA-GACATCCTTT
1 TTCATAGATCACCAAAAATG-CATCCTTT
29514833 T
1 T
29514834 CTAGCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.35
Consensus pattern (28 bp):
TTCATAGATCACCAAAAATGCATCCTTT
Found at i:29518365 original size:101 final size:102
Alignment explanation
Indices: 29518255--29518439 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
29518245 AAAGTGATGG
* *
29518255 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGAACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGAACCAGATAGTGAT-GGTCACATGTGTAGT
29518318 ACAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
29518356 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGAACCAGATAGTGATGGTCACATGTGTAGTA
* *
29518421 CTATGTGCATGCTACTATG
66 CAATGTGCAGGCTACTATG
29518440 GGAACCGATA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 37 0.50
102 33 0.45
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGAACCAGATAGTGATGGTCACATGTGTAGTA
CAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:29518376 original size:51 final size:50
Alignment explanation
Indices: 29518308--29518439 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 50
29518298 TGATAGGTCG
*
29518308 CATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GATCA
* * * * *
29518359 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGATCA
*
29518410 CATGTGTAGTACTATGTGCATGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
29518440 GGAACCGATA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 68 0.97
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGATCA
Found at i:29518686 original size:16 final size:16
Alignment explanation
Indices: 29518665--29518696 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29518655 TGATTGAAAG
*
29518665 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
29518681 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
29518697 ACAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:29527178 original size:16 final size:16
Alignment explanation
Indices: 29527157--29527187 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29527147 GTTATTATGA
29527157 TTGATTAAAAAACAAC
1 TTGATTAAAAAACAAC
29527173 TTGATTAAAAAACAA
1 TTGATTAAAAAACAA
29527188 GTATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
TTGATTAAAAAACAAC
Found at i:29530371 original size:47 final size:47
Alignment explanation
Indices: 29530319--29530561 Score: 199
Period size: 47 Copynumber: 5.3 Consensus size: 47
29530309 CCATATAAGA
*
29530319 ATATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
** *
29530366 ATATTTGA-TATTAATTA-TTT-T-AAATTATATA-AATTTATATAAGA--
1 ATATTT-ATTATTAAGAATTTTATGAAATTATATATCA-TTAT-TAA-ATT
* *
29530410 AAATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
* ** *
29530457 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* *
29530501 AAATTGT-TTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATT-TATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
*
29530548 ATATTTAATATTAA
1 ATATTTATTATTAA
29530562 TTATTTTAAA
Statistics
Matches: 150, Mismatches: 24, Indels: 44
0.69 0.11 0.20
Matches are distributed among these distances:
43 5 0.03
44 47 0.31
45 17 0.11
46 17 0.11
47 59 0.39
48 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:29530416 original size:91 final size:91
Alignment explanation
Indices: 29530304--29530600 Score: 515
Period size: 91 Copynumber: 3.3 Consensus size: 91
29530294 ATGATTTTAG
* *
29530304 TAAATCCATATAAGAATATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
29530369 TTTGATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
29530395 TAAATTTATATAAGAAAATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
29530460 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
29530486 TAAATTCATATAAGAAAATTGT-TTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAAAATT-TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
29530550 ATTTAATATTAATTATTTTAAATTATA
65 ATTTAATATTAATTATTTTAAATTATA
*
29530577 CAAATTCATATAAGAAAATTTATT
1 TAAATTCATATAAGAAAATTTATT
29530601 AGTAATAATT
Statistics
Matches: 196, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
90 1 0.01
91 194 0.99
92 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:29530521 original size:101 final size:97
Alignment explanation
Indices: 29530324--29530678 Score: 441
Period size: 91 Copynumber: 3.7 Consensus size: 97
29530314 TAAGAATATT
*
29530324 TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTGATATTAATTATTTTAA
1 TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
*
29530389 ATTATATAAATTTATATAAG-AAA---ATT--
66 ATTATATAAATTCATATAAGAAAATTTATTAG
29530415 TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
1 TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
29530480 ATTATATAAATTCATATAAG-AAA---ATT-G
66 ATTATATAAATTCATATAAGAAAATTTATTAG
* *
29530507 T-TTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
1 TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
*
29530571 ATTATACAAATTCATATAAGAAAATTTATTAG
66 ATTATATAAATTCATATAAGAAAATTTATTAG
* * * * * * *
29530603 TAATAATTATTTTA-AATTTTATTAAATCATATAT-TTTAATTAAAATATATTTAATAATAATTG
1 ---T-ATT-TTTAAGAATTTTATGAAATTATATATCATT-ATTAAATTATATTTAATATTAATTA
*
29530666 TTTCAAATTATAT
60 TTTTAAATTATAT
29530679 TTTATAGTAT
Statistics
Matches: 235, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
91 169 0.72
92 4 0.02
95 3 0.01
96 1 0.00
99 1 0.00
100 2 0.01
101 53 0.23
102 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (97 bp):
TATTTTTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAA
ATTATATAAATTCATATAAGAAAATTTATTAG
Found at i:29530692 original size:59 final size:58
Alignment explanation
Indices: 29530628--29530936 Score: 215
Period size: 59 Copynumber: 5.2 Consensus size: 58
29530618 ATTTTATTAA
29530628 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTT-AAATTATATTTTATAGT
* * * * * * *
29530687 ATCATATATTATGAGTTTAGTAAAT-TCATATAAGAATTA-TGATT--ATTAAGAATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTGTTTAAATT-A-TATTTTA-TAG
*
29530747 A
58 T
*
29530748 ATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTT-AAATTATATTTTATAGT
* * * * * *
29530807 ATCATATATTATGATTTTAGTAAAT-TCATATAAGAAT-ATTGATT--ATTAAGAATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTGTTTAAATT-A-TATTTTA-TAG
*
29530867 A
58 T
* *
29530868 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGT-TTAAATTATATTTTATAGT
29530927 ATCATATATT
1 ATCATATATT
29530937 ATGCTTTGAG
Statistics
Matches: 187, Mismatches: 35, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
57 25 0.13
58 12 0.06
59 55 0.29
60 12 0.06
61 43 0.23
62 15 0.08
63 25 0.13
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTAAATTATATTTTATAGT
Found at i:29530741 original size:120 final size:120
Alignment explanation
Indices: 29530617--29531026 Score: 700
Period size: 120 Copynumber: 3.4 Consensus size: 120
29530607 AATTATTTTA
*
29530617 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
29530682 ATAGTATCATATATTATGAGTTTAGTAAATTCATATAAGAAT-TATGATTATTAAG
66 ATAGTATCATATATTATGACTTTAGTAAATTCATATAAGAATAT-TGATTATTAAG
29530737 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
29530802 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGACTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
29530857 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
*
29530921 TATAGTATCATATATTATG-CTTTGAGTAAATTCATACAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGACTTT-AGTAAATTCATATAAGAATATTGATTATTAAG
* * *
29530977 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
29531027 GTTAAAATAT
Statistics
Matches: 280, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 3 0.01
120 274 0.98
121 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGACTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:29530886 original size:18 final size:17
Alignment explanation
Indices: 29530858--29530892 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29530848 ATTATTAAGA
*
29530858 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29530875 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29530893 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:29530994 original size:59 final size:58
Alignment explanation
Indices: 29530691--29531001 Score: 159
Period size: 57 Copynumber: 5.2 Consensus size: 58
29530681 TATAGTATCA
29530691 TATATTATGAGTTT-AGTAAATTCATATAAGAAT-TATGATTATTAAGAATTTTATTAAAT
1 TATATTAT--GTTTAAGTAAATTCATATAAGAATAT-TGATTATTAAGAATTTTATTAAAT
* * * * * * *
29530750 CATA-TAT-TTTAATTAAAATAT-ATTTAATAATAATT-ATT-TCAAATTATATTTTA-TAGTAT
1 TATATTATGTTTAAGT-AAAT-TCATATAAGAAT-ATTGATTAT-TAA-GA-ATTTTATTA-AAT
*
29530809 CATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATG-TTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
* * * * * *
29530870 TATA-TAT-TTTAATTAAAATAT-ATTTAATAATAATT-ATGT-TAAATTATATTTTA-TAGTAT
1 TATATTATGTTTAAGT-AAAT-TCATATAAGAAT-ATTGAT-TATTAA-GA-ATTTTATTA-AAT
* *
29530929 CATATATTATGCTTTGAGTAAATTCATACAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATG-TTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
29530990 TATA-TAT-TTTAA
1 TATATTATGTTTAA
29531002 TTATAATATA
Statistics
Matches: 187, Mismatches: 31, Indels: 71
0.65 0.11 0.25
Matches are distributed among these distances:
55 3 0.02
56 12 0.06
57 34 0.18
58 22 0.12
59 28 0.15
61 23 0.12
62 21 0.11
63 33 0.18
64 11 0.06
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (58 bp):
TATATTATGTTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
Found at i:29531266 original size:16 final size:16
Alignment explanation
Indices: 29531245--29531277 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29531235 TTGATTTGCT
29531245 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
29531261 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
29531277 A
1 A
29531278 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29549481 original size:27 final size:27
Alignment explanation
Indices: 29549451--29549552 Score: 183
Period size: 27 Copynumber: 3.9 Consensus size: 27
29549441 TTGAAATCTC
29549451 GTCAAATCAATATTTTTTAAATATTAA
1 GTCAAATCAATATTTTTTAAATATTAA
29549478 GTC--AT-AATATTTTTTAAATATTAA
1 GTCAAATCAATATTTTTTAAATATTAA
29549502 GTCAAATCAATATTTTTTAAATATTAA
1 GTCAAATCAATATTTTTTAAATATTAA
29549529 GTCAAATCAATATTTTTTAAATAT
1 GTCAAATCAATATTTTTTAAATAT
29549553 CAAAATTTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
24 22 0.31
25 2 0.03
26 2 0.03
27 46 0.64
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (27 bp):
GTCAAATCAATATTTTTTAAATATTAA
Found at i:29549527 original size:51 final size:53
Alignment explanation
Indices: 29549451--29549552 Score: 181
Period size: 51 Copynumber: 1.9 Consensus size: 53
29549441 TTGAAATCTC
29549451 GTCAAATCAATATTTTTTAAATATTAAGTC-AT-AATATTTTTTAAATATTAA
1 GTCAAATCAATATTTTTTAAATATTAAGTCAATCAATATTTTTTAAATATTAA
29549502 GTCAAATCAATATTTTTTAAATATTAAGTCAAATCAATATTTTTTAAATAT
1 GTCAAATCAATATTTTTTAAATATTAAGTC-AATCAATATTTTTTAAATAT
29549553 CAAAATTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
51 30 0.62
53 2 0.04
54 16 0.33
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (53 bp):
GTCAAATCAATATTTTTTAAATATTAAGTCAATCAATATTTTTTAAATATTAA
Found at i:29551216 original size:28 final size:28
Alignment explanation
Indices: 29551162--29551293 Score: 135
Period size: 28 Copynumber: 4.8 Consensus size: 28
29551152 CTTTAAAGTG
* *
29551162 TACCACAAAGGCATTCC--CTTCATAGAT
1 TACCACAAAGGC-TTCCTTTTTCATAAAT
* *
29551189 TACCACAAATGCTTCCTTTTTCATAGAT
1 TACCACAAAGGCTTCCTTTTTCATAAAT
* * * *
29551217 TGCCATAAAGGCTTCCATATTCATAAAT
1 TACCACAAAGGCTTCCTTTTTCATAAAT
*
29551245 CT-CCACAAAGGCTTCCTTTTTCATAAAC
1 -TACCACAAAGGCTTCCTTTTTCATAAAT
*
29551273 CACCACAAAGGCTTCCTTTTT
1 TACCACAAAGGCTTCCTTTTT
29551294 AAGAGATCGC
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.05
27 11 0.12
28 72 0.82
29 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (28 bp):
TACCACAAAGGCTTCCTTTTTCATAAAT
Found at i:29557118 original size:3 final size:3
Alignment explanation
Indices: 29557112--29557154 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
29557102 TTAACAATAA
29557112 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
29557155 CTTTTCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.