Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold619
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1099986
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 119690 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:379398 original size:41 final size:40
Alignment explanation
Indices: 379297--380263 Score: 365
Period size: 41 Copynumber: 23.8 Consensus size: 40
379287 TGTAACTTAT
* * *
379297 ATGATTTCAATAGCGCTGAACAGTTCATTTAATATCCAATA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * *
379338 ATGAATTCAATATCATTGAACGTTTCATTCAGTATCTAATA
1 ATGATTTCAATAGCGTTGAACG-TTCATTCAGTATCCAATA
* * * *
379379 ATGATTTCAGTAGCGTTGAACGGTTAAATCAGTATCCAGTTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCA-ATA
* * ** * * **
379421 A-AATTACTTTAGCGTTGAATGGTTCATTCAGTATTCAGCA
1 ATGATTTCAATAGCGTTGAA-CGTTCATTCAGTATCCAATA
*
379461 ATGA--T---T--CGTTGAA--TGCAATATACATGTA--CAATA
1 ATGATTTCAATAGCGTTGAACGTTC-AT-T-CA-GTATCCAATA
* ** *
379494 GTGATTAT-TTTAGCTTTGAACGGGTTCATTCAGTATCCAATA
1 ATGATT-TCAATAGCGTTGAAC--GTTCATTCAGTATCCAATA
* * * * * *
379536 ATGAGTACAATAGCGTTAAACGGATCATTTAGTATCTTTGCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATC----CAATA
** * * *
379581 ATGATTGT-TTTAGTGTTGAACGGCTT-ATTCAATATACAATA
1 ATGATT-TCAATAGCGTTGAAC-G-TTCATTCAGTATCCAATA
* * * *
379622 ATGATTTCAA-AGTGTTGAAAGGTTC-TTAAAGTATCCAATT
1 ATGATTTCAATAGCGTTG-AACGTTCATT-CAGTATCCAATA
* * * *
379662 ATGAGTTAAATAGCGTTAAACGGTTCA-TC--T-T---GTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
** * * *
379696 ATGATTTTTATAGTG-TGAACAGTTCATTCAGAATCAAAATA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATC-CAATA
* * * * *
379737 ATGATTTCAAAAGCATTGGACGGTTTATTCAGTATCCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * *
379778 ATGATTAC-TTAGCGTTGAACGGTTCATTCAATATCCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * *
379818 GTTATTTCATTAGCGTTGAACGGTTCATTCAGTATCCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * * **
379859 ATGATTAC-TTCAGCGTTGAACGGTTCATTCAATATTCAGCA
1 ATGATTTCAAT-AGCGTTGAAC-GTTCATTCAGTATCCAATA
* * *
379900 ATGATTAC-TTCAGCGTTGAACAGTTCATTCAGTATCCAGTA
1 ATGATTTCAAT-AGCGTTGAAC-GTTCATTCAGTATCCAATA
* ** * * **
379941 ATGATTACTTTAGCGTTGAACGGTTCATTCAATATTCAGCA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * * *
379982 ATGATTAC-TTCAGCGTTGAACAGTTCATTTAGTACCCAGTA
1 ATGATTTCAAT-AGCGTTGAAC-GTTCATTCAGTATCCAATA
* ** *
380023 ATTATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* ** *
380064 ATTATTTCTTTAGCGTTGAACAGTTCATTCAGTATCCAGTA
1 ATGATTTCAATAGCGTTGAAC-GTTCATTCAGTATCCAATA
* * * * * *
380105 ATAATTAC-TTCAGCGTTGAACAGGTCATTTAGTATCCATTA
1 ATGATTTCAAT-AGCGTTGAAC-GTTCATTCAGTATCCAATA
* ** *
380146 ATTATTTCGTTAGCGTTGAACGATTCATTCAGTATCCAGTA
1 ATGATTTCAATAGCGTTGAACG-TTCATTCAGTATCCAATA
* ** *
380187 ATTATTTCTTTAGCGTTGAACGCTTCATTCAGTATCCAGTTA
1 ATGATTTCAATAGCGTTGAACG-TTCATTCAGTATCCA-ATA
* * *
380229 CTGAGTTCAATAGCGTTAAACGCTTCATTCTAGTA
1 ATGATTTCAATAGCGTTGAACG-TTCATTC-AGTA
380264 ATGATTTTTG
Statistics
Matches: 727, Mismatches: 144, Indels: 108
0.74 0.15 0.11
Matches are distributed among these distances:
31 2 0.00
32 2 0.00
33 16 0.02
34 23 0.03
35 3 0.00
36 2 0.00
37 2 0.00
38 2 0.00
39 4 0.01
40 77 0.11
41 487 0.67
42 71 0.10
43 6 0.01
44 2 0.00
45 27 0.04
46 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (40 bp):
ATGATTTCAATAGCGTTGAACGTTCATTCAGTATCCAATA
Found at i:379917 original size:82 final size:81
Alignment explanation
Indices: 379763--380226 Score: 619
Period size: 82 Copynumber: 5.7 Consensus size: 81
379753 TGGACGGTTT
*
379763 ATTCAGTATCCAGTAATGATTAC-TTAGCGTTGAACGGTTCATTCAATATCCAGTAGTTATTTCA
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGTAATTATTTC-
*
379827 TTAGCGTTGAACGGTTC
65 TTAGCGTTGAACAGTTC
* * * * *
379844 ATTCAGTATCCAGTAATGATTACTTCAGCGTTGAACGGTTCATTCAATATTCAGCAATGATTACT
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGTAATTATTTCT
379909 TCAGCGTTGAACAGTTC
66 T-AGCGTTGAACAGTTC
* * * *
379926 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATTCAGCAATGATTACT
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGTAATTATTTCT
379991 TCAGCGTTGAACAGTTC
66 T-AGCGTTGAACAGTTC
* * * * *
380008 ATTTAGTACCCAGTAATTATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATTATTTCT
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGTAATTATTTC-
380073 TTAGCGTTGAACAGTTC
65 TTAGCGTTGAACAGTTC
* * * * *
380090 ATTCAGTATCCAGTAATAATTACTTCAGCGTTGAACAGG-TCATTTAGTATCCATTAATTATTTC
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAAC-GGTTCATTCAATATCCAGTAATTATTTC
380154 GTTAGCGTTGAAC-GATTC
65 -TTAGCGTTGAACAG-TTC
* * * *
380172 ATTCAGTATCCAGTAATTATTTCTTTAGCGTTGAACGCTTCATTCAGTATCCAGT
1 ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGT
380227 TACTGAGTTC
Statistics
Matches: 346, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
81 27 0.08
82 315 0.91
83 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (81 bp):
ATTCAGTATCCAGTAATGATTACTTTAGCGTTGAACGGTTCATTCAATATCCAGTAATTATTTCT
TAGCGTTGAACAGTTC
Found at i:379930 original size:123 final size:122
Alignment explanation
Indices: 379756--380226 Score: 665
Period size: 123 Copynumber: 3.8 Consensus size: 122
379746 AAAGCATTGG
* * *
379756 ACGGTTTATTCAGTATCCAGTAATGATTACTTAGCGTTGAACGGTTCATTCAATATCCAGTAGTT
1 ACGGTTCATTCAGTATCCAGTAATGATTACTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATT
*
379821 ATTTCATTAGCGTTGAACGGTTCATTCAGTATCCAGTAATGATTACTTCAGCGTTGA
66 ATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATGATTACTTCAGCGTTGA
* * * *
379878 ACGGTTCATTCAATATTCAGCAATGATTACTTCAGCGTTGAACAGTTCATTCAGTATCCAGTAAT
1 ACGGTTCATTCAGTATCCAGTAATGATTACTT-AGCGTTGAACGGTTCATTCAGTATCCAGTAAT
* * * * *
379943 GATTACTTTAGCGTTGAACGGTTCATTCAATATTCAGCAATGATTACTTCAGCGTTGA
65 TATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATGATTACTTCAGCGTTGA
* * * * *
380001 ACAGTTCATTTAGTACCCAGTAATTATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAAT
1 ACGGTTCATTCAGTATCCAGTAATGATTAC-TTAGCGTTGAACGGTTCATTCAGTATCCAGTAAT
* *
380066 TATTTCTTTAGCGTTGAACAGTTCATTCAGTATCCAGTAATAATTACTTCAGCGTTGA
65 TATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATGATTACTTCAGCGTTGA
* * * * *
380124 ACAGG-TCATTTAGTATCCATTAATTATTTCGTTAGCGTTGAACGATTCATTCAGTATCCAGTAA
1 AC-GGTTCATTCAGTATCCAGTAATGATTAC-TTAGCGTTGAACGGTTCATTCAGTATCCAGTAA
*
380188 TTATTTCTTTAGCGTTGAACGCTTCATTCAGTATCCAGT
64 TTATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGT
380227 TACTGAGTTC
Statistics
Matches: 310, Mismatches: 36, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
122 28 0.09
123 279 0.90
124 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (122 bp):
ACGGTTCATTCAGTATCCAGTAATGATTACTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATT
ATTTCTTTAGCGTTGAACGGTTCATTCAGTATCCAGTAATGATTACTTCAGCGTTGA
Found at i:380349 original size:41 final size:41
Alignment explanation
Indices: 380304--380391 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
380294 TGACTTAAAC
*
380304 AGCGTTGAACAGTTCATTCAGTATCCAATTATGAGTTCAGT
1 AGCGTTGAACAGTTCATTCAGAATCCAATTATGAGTTCAGT
*
380345 AGCGTTGAACGGTTCATTCAGAATCCAATTATGAGTTCAGT
1 AGCGTTGAACAGTTCATTCAGAATCCAATTATGAGTTCAGT
380386 AGCGTT
1 AGCGTT
380392 CATTTAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
AGCGTTGAACAGTTCATTCAGAATCCAATTATGAGTTCAGT
Found at i:394536 original size:20 final size:20
Alignment explanation
Indices: 394511--394551 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
394501 CGAAACTTCT
394511 CGGCAGAGCTCGGATCATTC
1 CGGCAGAGCTCGGATCATTC
*
394531 CGGCAGAGCTCGGATCTTTC
1 CGGCAGAGCTCGGATCATTC
394551 C
1 C
394552 AGCTGTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (20 bp):
CGGCAGAGCTCGGATCATTC
Found at i:395323 original size:3 final size:3
Alignment explanation
Indices: 395315--395345 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
395305 TAAAATGTTA
395315 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
395346 TTACGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:397706 original size:36 final size:36
Alignment explanation
Indices: 397666--397741 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
397656 ACAGTCGAAG
397666 ATTGGATTAGAGGGGGAAAATAGATATTGTTTCTCC
1 ATTGGATTAGAGGGGGAAAATAGATATTGTTTCTCC
*
397702 ATTGGATTAGAGGGGGGAAATAGATATTGTTTCTCC
1 ATTGGATTAGAGGGGGAAAATAGATATTGTTTCTCC
397738 ATTG
1 ATTG
397742 CAACAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (36 bp):
ATTGGATTAGAGGGGGAAAATAGATATTGTTTCTCC
Found at i:398913 original size:173 final size:172
Alignment explanation
Indices: 398624--398969 Score: 683
Period size: 173 Copynumber: 2.0 Consensus size: 172
398614 GACATGGCCC
398624 TGACGTCACTACAAATTACACCCAATCGGGCGGAAGCTGTGGAGTTCACGGTTCCGTATCTGGAG
1 TGACGTCACTACAAATTACACCCAATCGGGCGGAAGCTGTGGAGTTCACGGTTCCGTATCTGGAG
398689 ACAGGGACGGCCATTATAGTGTCTCTAAGGAACGACACAATCTCGGCATACGCAATCTTAGGTGC
66 ACAGGGACGGCCATTATAGTGTCTCTAAGGAACGACACAATCTCGGCATACGCAATCTTAGGTGC
398754 TCCTTACTTTTATTTTGTTCGGAAATAGCATATATATATATA
131 TCCTTACTTTTATTTTGTTCGGAAATAGCATATATATATATA
398796 NTGACGTCACTACAAATTACACCCAATCGGGCGGAAGCTGTGGAGTTCACGGTTCCGTATCTGGA
1 -TGACGTCACTACAAATTACACCCAATCGGGCGGAAGCTGTGGAGTTCACGGTTCCGTATCTGGA
398861 GACAGGGACGGCCATTATAGTGTCTCTAAGGAACGACACAATCTCGGCATACGCAATCTTAGGTG
65 GACAGGGACGGCCATTATAGTGTCTCTAAGGAACGACACAATCTCGGCATACGCAATCTTAGGTG
398926 CTCCTTACTTTTATTTTGTTCGGAAATAGCATATATATATATA
130 CTCCTTACTTTTATTTTGTTCGGAAATAGCATATATATATATA
398969 T
1 T
398970 ATATATANNN
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 1 0.01
173 172 0.99
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (172 bp):
TGACGTCACTACAAATTACACCCAATCGGGCGGAAGCTGTGGAGTTCACGGTTCCGTATCTGGAG
ACAGGGACGGCCATTATAGTGTCTCTAAGGAACGACACAATCTCGGCATACGCAATCTTAGGTGC
TCCTTACTTTTATTTTGTTCGGAAATAGCATATATATATATA
Found at i:401403 original size:4 final size:4
Alignment explanation
Indices: 401387--401429 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
401377 GTGAACGTCA
* * * *
401387 AAAT AAAT CAAT AAAT AGAT AAAT AGAT TAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
401430 GATTATATCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:406940 original size:2 final size:2
Alignment explanation
Indices: 406933--406992 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
406923 AGACTGAAAA
406933 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
406975 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
406993 ATGTCGGCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:407649 original size:29 final size:29
Alignment explanation
Indices: 407607--407690 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
407597 TCAGAAGGCA
407607 GTTCATTTGTGTATATGAGTGTCTAGACT
1 GTTCATTTGTGTATATGAGTGTCTAGACT
* *
407636 GTTCATTTGTGTATATGAATGCCTAGACT
1 GTTCATTTGTGTATATGAGTGTCTAGACT
* *
407665 GTTCATTTGTCTACATGAGTGTCTAG
1 GTTCATTTGTGTATATGAGTGTCTAG
407691 GCAGTTCAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (29 bp):
GTTCATTTGTGTATATGAGTGTCTAGACT
Found at i:407697 original size:29 final size:29
Alignment explanation
Indices: 407605--407698 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
407595 TATCAGAAGG
407605 CAGTTCATTTGTGTATATGAGTGTCTAGA
1 CAGTTCATTTGTGTATATGAGTGTCTAGA
* * *
407634 CTGTTCATTTGTGTATATGAATGCCTAGA
1 CAGTTCATTTGTGTATATGAGTGTCTAGA
* * * *
407663 CTGTTCATTTGTCTACATGAGTGTCTAGG
1 CAGTTCATTTGTGTATATGAGTGTCTAGA
407692 CAGTTCA
1 CAGTTCA
407699 GATGTCTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (29 bp):
CAGTTCATTTGTGTATATGAGTGTCTAGA
Found at i:414061 original size:29 final size:30
Alignment explanation
Indices: 413983--414046 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
413973 TAATCATGAA
* * *
413983 TTTTATGTGTATGCGTGTATTTGTCTTGGT
1 TTTTATGTGTATGCATATATTTGTCTAGGT
414013 TTTTATGTGTATGCATATATTTGTCTAGGT
1 TTTTATGTGTATGCATATATTTGTCTAGGT
414043 TTTT
1 TTTT
414047 TGCTTACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.14, C:0.06, G:0.22, T:0.58
Consensus pattern (30 bp):
TTTTATGTGTATGCATATATTTGTCTAGGT
Found at i:420447 original size:2 final size:2
Alignment explanation
Indices: 420440--420507 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
420430 TTCCTAACTA
420440 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
420482 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
420508 CAATAAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:422038 original size:15 final size:15
Alignment explanation
Indices: 422020--422052 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
422010 CGTCATCGTA
422020 GATGACGACGACGAT
1 GATGACGACGACGAT
*
422035 GATGACGACGAGGAT
1 GATGACGACGACGAT
422050 GAT
1 GAT
422053 TTACGTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.15
Consensus pattern (15 bp):
GATGACGACGACGAT
Found at i:422292 original size:2 final size:2
Alignment explanation
Indices: 422285--422394 Score: 211
Period size: 2 Copynumber: 54.5 Consensus size: 2
422275 GATATGAATA
422285 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
422327 CT NCT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
422370 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
422395 AATTGATTAT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 105 0.98
3 2 0.02
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:427476 original size:32 final size:32
Alignment explanation
Indices: 427440--427502 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
427430 ATTTACATGT
* *
427440 ACATACAGATACTGGCATTTAGCGATGTATTA
1 ACATACAAATACTGGCATTTAGCAATGTATTA
*
427472 ACATACAAATATTGGCATTTAGCAATGTATT
1 ACATACAAATACTGGCATTTAGCAATGTATT
427503 TAATATGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (32 bp):
ACATACAAATACTGGCATTTAGCAATGTATTA
Found at i:432827 original size:2 final size:2
Alignment explanation
Indices: 432820--432853 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
432810 TCCGCGCATG
432820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432854 TTTACATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435241 original size:25 final size:24
Alignment explanation
Indices: 435192--435241 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
435182 AAAAGAGTGT
*
435192 GGGGGGGGGGGGTTGTTGGGGGGG
1 GGGGGGGGGGGGTTGTTAGGGGGG
*
435216 GGGGGGGGGGGGCTTGTTAGGTGGG
1 GGGGGGGGGGGG-TTGTTAGGGGGG
435241 G
1 G
435242 TGGTGGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.02, C:0.02, G:0.78, T:0.18
Consensus pattern (24 bp):
GGGGGGGGGGGGTTGTTAGGGGGG
Found at i:448960 original size:33 final size:32
Alignment explanation
Indices: 448923--449000 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
448913 TATAGTCAGC
448923 TTTCCGTAGGGGAAAAACTGCTATATAGCAATT
1 TTTCCG-AGGGGAAAAACTGCTATATAGCAATT
* * * *
448956 TTTCCGGGGGGAAGAACTGCTATTTAGCCATT
1 TTTCCGAGGGGAAAAACTGCTATATAGCAATT
*
448988 TGTCC--GGGGAAAA
1 TTTCCGAGGGGAAAA
449001 GATGATGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 7 0.18
32 26 0.67
33 6 0.15
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (32 bp):
TTTCCGAGGGGAAAAACTGCTATATAGCAATT
Found at i:448974 original size:32 final size:32
Alignment explanation
Indices: 448931--448996 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
448921 GCTTTCCGTA
*
448931 GGGGAAAAACTGCTATATAGCAATTTTTCCGG
1 GGGGAAAAACTGCTATATAGCAATTTGTCCGG
* * *
448963 GGGGAAGAACTGCTATTTAGCCATTTGTCCGG
1 GGGGAAAAACTGCTATATAGCAATTTGTCCGG
448995 GG
1 GG
448997 AAAAGATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (32 bp):
GGGGAAAAACTGCTATATAGCAATTTGTCCGG
Found at i:456915 original size:18 final size:18
Alignment explanation
Indices: 456860--456915 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
456850 CGCGCACACG
*
456860 GACGAATCACAGTTCACA
1 GACGGATCACAGTTCACA
* *
456878 GGA-AGATCACAGTTAACA
1 -GACGGATCACAGTTCACA
456896 GACGGATCACAGTTCACA
1 GACGGATCACAGTTCACA
456914 GA
1 GA
456916 AAGTAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (18 bp):
GACGGATCACAGTTCACA
Found at i:469680 original size:69 final size:68
Alignment explanation
Indices: 469559--469687 Score: 240
Period size: 69 Copynumber: 1.9 Consensus size: 68
469549 TCCAAACCCA
469559 AACTCTTTTTTGTGTGTGAAATACATATCTACATCGCACGTTGGATCACTCGTTGCTAAAGAGCA
1 AACTCTTTTTTGTGTGTGAAATACATATCTACATCGCACGTTGGATCACTCGTTGCTAAAGAGCA
469624 CTC
66 CTC
*
469627 AACTCTTCTTTTGTGTGTGAAATACATATCTACATCGCACGTTGGATCGCTCGTTGCTAAA
1 AACTCTT-TTTTGTGTGTGAAATACATATCTACATCGCACGTTGGATCACTCGTTGCTAAA
469688 AAGTACTCGG
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 7 0.12
69 52 0.88
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (68 bp):
AACTCTTTTTTGTGTGTGAAATACATATCTACATCGCACGTTGGATCACTCGTTGCTAAAGAGCA
CTC
Found at i:471113 original size:2 final size:2
Alignment explanation
Indices: 471106--471143 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
471096 AATAAGGCCG
471106 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
471144 AATCTTGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:472217 original size:2 final size:2
Alignment explanation
Indices: 472210--472264 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
472200 ACTCTAACCA
472210 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
472252 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
472265 GTTTTTTCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:472592 original size:1 final size:1
Alignment explanation
Indices: 472586--472619 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
472576 GTAAAAGTGT
472586 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
472620 CCGGTCACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:473270 original size:12 final size:12
Alignment explanation
Indices: 473255--473280 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
473245 TTTTTAATCA
473255 AAGTTATAATGT
1 AAGTTATAATGT
473267 AAGTTATAATGT
1 AAGTTATAATGT
473279 AA
1 AA
473281 AATAATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
AAGTTATAATGT
Found at i:480814 original size:1 final size:1
Alignment explanation
Indices: 480808--480833 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
480798 GACTCAGATT
480808 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
480834 CCCGGGCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:482516 original size:13 final size:12
Alignment explanation
Indices: 482498--482532 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
482488 CAACTAAACC
482498 CTGGGTTTACTTT
1 CTGGGTTTAC-TT
482511 CTGGGTTTAC-T
1 CTGGGTTTACTT
482522 CTGGGTTTACT
1 CTGGGTTTACT
482533 AGAGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (12 bp):
CTGGGTTTACTT
Found at i:482554 original size:11 final size:11
Alignment explanation
Indices: 482540--482581 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
482530 ACTAGAGTGG
* *
482540 ACCCTGAGTTA
1 ACCCAGAGTAA
482551 ACCCAGAGTAA
1 ACCCAGAGTAA
482562 ACCCCA-AGTAA
1 A-CCCAGAGTAA
482573 ACCCAGAGT
1 ACCCAGAGT
482582 GGACGCAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.14
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:482771 original size:22 final size:22
Alignment explanation
Indices: 482746--482803 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
482736 AAGCAATTCT
482746 CGAGTAAACCCAAAGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
482768 CGAGTAAACCCAAAGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
*
482790 CGAGTGAACCCAAA
1 CGAGTAAACCCAAA
482804 TTTTCAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.45, C:0.31, G:0.16, T:0.09
Consensus pattern (22 bp):
CGAGTAAACCCAAAGTAAACCC
Found at i:482838 original size:13 final size:11
Alignment explanation
Indices: 482748--482845 Score: 81
Period size: 11 Copynumber: 8.8 Consensus size: 11
482738 GCAATTCTCG
482748 AGTAAACCCAA
1 AGTAAACCCAA
**
482759 AGTAAACCCCG
1 AGTAAACCCAA
482770 AGTAAACCCAA
1 AGTAAACCCAA
**
482781 AGTAAACCCCG
1 AGTAAACCCAA
*
482792 AGTGAACCCAA
1 AGTAAACCCAA
*** **
482803 A-TTTTCAAAA
1 AGTAAACCCAA
482813 AGTAAACCCAA
1 AGTAAACCCAA
482824 AGTAAACCCAGAA
1 AGTAAACCC--AA
482837 AGTAAACCC
1 AGTAAACCC
482846 GGGGTTTAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
10 5 0.08
11 49 0.75
13 11 0.17
ACGTcount: A:0.48, C:0.28, G:0.12, T:0.12
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:492051 original size:4 final size:4
Alignment explanation
Indices: 492042--492089 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
492032 TACCCTTGTG
* * * * *
492042 TGTC TGTC TGTC CGTC CGTC CGTC CGTC CGTC TGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
492090 CGTCCGTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40
Consensus pattern (4 bp):
TGTC
Found at i:492068 original size:12 final size:12
Alignment explanation
Indices: 492047--492096 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
492037 TTGTGTGTCT
492047 GTCTGTCCGTCC
1 GTCTGTCCGTCC
*
492059 GTCCGTCCGTCC
1 GTCTGTCCGTCC
* *
492071 GTCTGTCTGTCT
1 GTCTGTCCGTCC
492083 GTCTGTCCGTCC
1 GTCTGTCCGTCC
492095 GT
1 GT
492097 AACAAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:492094 original size:4 final size:4
Alignment explanation
Indices: 492051--492096 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
492041 GTGTCTGTCT
* * * *
492051 GTCC GTCC GTCC GTCC GTCC GTCT GTCT GTCT GTCT GTCC GTCC GT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GT
492097 AACAAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.35
Consensus pattern (4 bp):
GTCC
Found at i:492396 original size:167 final size:167
Alignment explanation
Indices: 492120--493110 Score: 1486
Period size: 167 Copynumber: 6.0 Consensus size: 167
492110 GTCGCATTTA
* * * * *
492120 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAATACAGTGTCTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
492185 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
492250 TTAACCAAAATTTTCATACAAATTTTCGTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
492287 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* *
492352 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * * *
492416 TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * * *
492453 TCTCAGCAACTGTTTATCGCACATGCTTGAAATTTTTACACAGTATTTGTATAGGCGTTCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * * *
492518 CGTGGGATGTATTTTTGTACCAATCAGACTTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * * * *
492583 TT-TCCAAAATTTTCAAACAAATATCCGTCAATGAAT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
492619 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACTCACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * *
492684 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
492749 TTAACCAAAATTTTCAAACAAATTTTCCTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
492786 TCTCAGCAACTATTTATCGCAGATGCTTGAAA-TTTTACCACACTATTTGTTTAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTA-CACAGTATTTGTTTAGGCATGCCATA
* *
492850 TTGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
*
492915 TTTAACCAAAATTTTCAAACAAATTTGCGTCAAAGATT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
492953 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTTTCACAATATTTGTATAGGCATTCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * ** * *
493018 CGTGGGATATATTTCTATACCAATCGGGTGTCAACTTCCTGTTAAATAACGACTTTGATTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
493083 TT-GCCAAAATTTTCAAACAAATTTTCGT
131 TTAACCAAAATTTTCAAACAAATTTTCGT
493111 NGTATCTGAT
Statistics
Matches: 754, Mismatches: 66, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
166 328 0.44
167 422 0.56
168 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:494208 original size:4 final size:4
Alignment explanation
Indices: 494199--494228 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
494189 TGTTTTTAAT
494199 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
494229 AGTCAGTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:496209 original size:2 final size:2
Alignment explanation
Indices: 496202--496254 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
496192 TTAAGCTGAC
496202 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
496244 CA CA CA CA CA C
1 CA CA CA CA CA C
496255 TTACAGCAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:498527 original size:20 final size:20
Alignment explanation
Indices: 498502--498542 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
498492 ACCTCTTCTC
*
498502 TTATTTAGAT-ATCTTTGTTT
1 TTATTT-GATCATCGTTGTTT
498522 TTATTTGATCATCGTTGTTT
1 TTATTTGATCATCGTTGTTT
498542 T
1 T
498543 GAGTTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.63
Consensus pattern (20 bp):
TTATTTGATCATCGTTGTTT
Found at i:500585 original size:1 final size:1
Alignment explanation
Indices: 500579--500608 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
500569 GAAGATTTAT
*
500579 CCCCCCCTCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
500609 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:503763 original size:11 final size:11
Alignment explanation
Indices: 503747--503783 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
503737 ACATATGCCA
*
503747 TTCAGTCACAT
1 TTCAGTCACCT
*
503758 TTCAGTTACCT
1 TTCAGTCACCT
503769 TTCAGTCACCT
1 TTCAGTCACCT
503780 TTCA
1 TTCA
503784 ATTGACTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.08, T:0.41
Consensus pattern (11 bp):
TTCAGTCACCT
Found at i:522811 original size:12 final size:12
Alignment explanation
Indices: 522794--522832 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
522784 AATGGAGTGC
522794 ACACACACACAT
1 ACACACACACAT
522806 ACACACACACAT
1 ACACACACACAT
*
522818 ACATACACACAT
1 ACACACACACAT
522830 ACA
1 ACA
522833 TACGAACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.51, C:0.38, G:0.00, T:0.10
Consensus pattern (12 bp):
ACACACACACAT
Found at i:522814 original size:16 final size:16
Alignment explanation
Indices: 522793--522828 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
522783 AAATGGAGTG
522793 CACACACACACATACA
1 CACACACACACATACA
*
522809 CACACACATACATACA
1 CACACACACACATACA
522825 CACA
1 CACA
522829 TACATACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.42, G:0.00, T:0.08
Consensus pattern (16 bp):
CACACACACACATACA
Found at i:522833 original size:16 final size:16
Alignment explanation
Indices: 522802--522847 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
522792 GCACACACAC
*
522802 ACATACACACACACAT
1 ACATACACACATACAT
522818 ACATACACACATACAT
1 ACATACACACATACAT
522834 ACGA-ACACACATAC
1 AC-ATACACACATAC
522848 GCACGGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.50, C:0.35, G:0.02, T:0.13
Consensus pattern (16 bp):
ACATACACACATACAT
Found at i:522845 original size:12 final size:13
Alignment explanation
Indices: 522796--522848 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 13
522786 TGGAGTGCAC
522796 ACACACACATAC-
1 ACACACACATACG
*
522808 ACACACACATACAT
1 ACACACACATAC-G
522822 ACACACATACATACG
1 ACACAC--ACATACG
522837 A-ACACACATACG
1 ACACACACATACG
522849 CACGGTAGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 19 0.53
14 10 0.28
15 1 0.03
16 6 0.17
ACGTcount: A:0.49, C:0.36, G:0.04, T:0.11
Consensus pattern (13 bp):
ACACACACATACG
Found at i:528372 original size:131 final size:130
Alignment explanation
Indices: 528136--528385 Score: 335
Period size: 131 Copynumber: 1.9 Consensus size: 130
528126 CTATTGTAAC
* * *
528136 TTTAAACAAAATGTTAGAAAATAAATGAATATTCTACTTACTGCTAAACTATGCTAAACTATTCT
1 TTTAAACAAAATGTTAGAAAATAAATGAATATTCTACTCACTGCTAAACTAGGATAAACTATTCT
** * *
528201 CTTCGATTTGTATGACCAGGACCCAACGTCATCAAAATTGTCTTGCCACTCAACCAAATTCTAAA
66 CTTAAATATGTATGACCAGGACCCAACGACATCAAAATTGTCTTGCCACTCAACCAAATTCTAAA
* * * *
528266 TTTAAACAAACTGTTAGAAAATAAGTGAATATT-TCACTCACTAG-TATACTAGGATAAGTCTAC
1 TTTAAACAAAATGTTAGAAAATAAATGAATATTCT-ACTCACT-GCTAAACTAGGATAA-ACTA-
*
528329 TT-TCTTAAATATGTATGACCAGGCCCCAACGACATCAAAATTGTCTTGCCACTCAAC
62 TTCTCTTAAATATGTATGACCAGGACCCAACGACATCAAAATTGTCTTGCCACTCAAC
528386 ACAGTTCTCA
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
129 1 0.01
130 47 0.45
131 54 0.52
132 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (130 bp):
TTTAAACAAAATGTTAGAAAATAAATGAATATTCTACTCACTGCTAAACTAGGATAAACTATTCT
CTTAAATATGTATGACCAGGACCCAACGACATCAAAATTGTCTTGCCACTCAACCAAATTCTAAA
Found at i:529188 original size:1 final size:1
Alignment explanation
Indices: 529182--529217 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
529172 AGGGGCTCAA
* *
529182 CCCCCCCCCCCCCACCCCCCCCCCCCCCTCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
529218 ATGAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:529202 original size:15 final size:15
Alignment explanation
Indices: 529182--529217 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
529172 AGGGGCTCAA
529182 CCCCCCCCCCCCCAC
1 CCCCCCCCCCCCCAC
*
529197 CCCCCCCCCCCCCTC
1 CCCCCCCCCCCCCAC
529212 CCCCCC
1 CCCCCC
529218 ATGAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.03
Consensus pattern (15 bp):
CCCCCCCCCCCCCAC
Found at i:530378 original size:12 final size:12
Alignment explanation
Indices: 530355--530387 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
530345 ATCACATTTT
530355 GTCTGT-CGTCC
1 GTCTGTCCGTCC
530366 GTCTGTCCGTCC
1 GTCTGTCCGTCC
530378 GTCTGTCCGT
1 GTCTGTCCGT
530388 AAACTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.00, C:0.36, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:531004 original size:165 final size:166
Alignment explanation
Indices: 530557--531116 Score: 777
Period size: 166 Copynumber: 3.3 Consensus size: 166
530547 AGAAATTTTC
* *
530557 AAAAATCTTCTTCTCAAGAACCATAA--AGCCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTC-AGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
530620 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGAGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATAGGGG
530685 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
530723 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
530788 TAGAGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATCGGGGCT
66 TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGT
* *
530853 CGAACTTTTACATAGGAATATATAGAATAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
530889 -AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * * *
530953 AAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGAGTAGAGTGGGG-CACAATGTGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAA--T-----
*
531017 GGAGGGGGTCGAAGTTTTACATAGAAATACACGTATATAGAGTAAATCTTT
124 --AGGGGGTCGAAGTTTTACATAG---GA-A--TATATAGAGTAAATCTTT
531068 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG
531117 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 23, Indels: 22
0.89 0.06 0.06
Matches are distributed among these distances:
164 8 0.02
165 111 0.31
166 148 0.42
173 19 0.05
176 1 0.00
177 1 0.00
179 17 0.05
180 48 0.14
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:552788 original size:2 final size:2
Alignment explanation
Indices: 552783--552823 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
552773 NTATATATAT
552783 AG AG AG 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 AG AG AG A
552824 ATTTCAAAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:561371 original size:2 final size:2
Alignment explanation
Indices: 561366--561407 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
561356 CATTCACCAC
561366 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
561408 GCATTTTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:561671 original size:4 final size:4
Alignment explanation
Indices: 561664--561720 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
561654 AGCTAGCTGG
561664 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
561712 CTAT CTAT C
1 CTAT CTAT C
561721 ACTCATTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
CTAT
Found at i:587699 original size:166 final size:165
Alignment explanation
Indices: 587420--588191 Score: 1061
Period size: 166 Copynumber: 4.6 Consensus size: 165
587410 ACCATATGCT
* * *
587420 TCAGTTAGTGTAGATACAATA-TTGTGAAAATCATAACCCCCGGGGGTAGGGTGGGGCCACAATG
1 TCAGGTAGTGTAGATTCAA-AGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGGCCACAATG
*
587484 GGGGGTCGAGGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATG-AAC-
64 GGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAACT
* * * *
587547 CATCTGACCAGGAAAGCTGACACTTGTGAGGAAGCATCC
128 AATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCC
*
587586 TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGTGTAGGGTGGGGCCATAATGG
1 TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGG-GTAGGGTGGGGCCACAATGG
* *
587651 GGGATCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAA
65 GGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAA
* *
587716 TCAGCAAGGAAAGCTGACACTTGTGTGGAAGCATCC
130 TCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCC
* * *
587752 TCAGGTAGTGTAGATTTAAAGTTGTGAAAATCATGACCCCTTGGGGTAGGGTAGGGCCACAATGG
1 TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCC-CGGGGTAGGGTGGGGCCACAATGG
* * * *
587817 GGGGTCAAAGTATAACATAGGAATATATAGAGTACATCTTTAAAAATCTTTTTCTCAGAAACTAA
65 GGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAA
*
587882 TCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCC
130 TCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCC
** * ** **
587918 AGAGGTAGTGTAGATACAAAGTTGTGAAAATCATGACACCAAGGGGTA-GGTTAGGCCACAATGG
1 TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGAC-CCCCGGGGTAGGGTGGGGCCACAATGG
* * *
587982 GGGGTCGAAAATTTAACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATG-AACC
65 GGGGTCG-AAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAACT
* *
588046 ATATGA-CCAGGAAAGCTGAAACTTGTGTTGAAGCATCC
128 A-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCC
* * * * *
588084 TCAGTTAGTATAGATTTAAAGTTGTGAAAATCATTACCCCCGGGGGTAGGGTGGGGCCACAATGC
1 TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGGCCACAATGG
588149 GGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAA
65 GGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAA
588192 GGATGACGTT
Statistics
Matches: 539, Mismatches: 56, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
165 27 0.05
166 479 0.89
167 33 0.06
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (165 bp):
TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGTAGGGTGGGGCCACAATGGG
GGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAT
CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCC
Found at i:589592 original size:165 final size:164
Alignment explanation
Indices: 589076--589980 Score: 1294
Period size: 165 Copynumber: 5.5 Consensus size: 164
589066 AACAACATCC
* * * *
589076 TTAAAGATCTTTTTCTCAGAAACTAATCAGCCAGGGAAGCTGACACTTGTGTGAAAGCATCCTCA
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
* * * *
589141 GGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATTGGGG
66 GGTAGTGTAGATTCAAAGTTGTGAAAAT-ATGAGCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
* *
589206 TCGAAGTTTAATATAGGAATATATATAGTAAATCT
130 TCGAAGTTTAACATAGGAATATATAGAGTAAATCT
* * *
589241 TTAAAAATCTTCATCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTTG-AAGCATCTTC
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG-TGAAAGCATCCTC
*
589305 AGGTAGTGAAGATTCAAAGTTGTG-AAA-ATG-GCCCTCGGGGGTAGGGTGGGGCCACAATGGGG
65 AGGTAGTGTAGATTCAAAGTTGTGAAAATATGAGCCC-CGGGGGTAGGGTGGGGCCACAATGGGG
*
589367 TGTCAAAGTTTAACATAGGAATATATAGAGTAAATCT
129 -GTCGAAGTTTAACATAGGAATATATAGAGTAAATCT
*
589404 TTAAAAATCTTCTTCTCAGAAACTAACCAGCC-GGCAAAGCTGAAACTTGTGTGAAAGCATCCTC
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGTGAAAGCATCCTC
* *
589468 AGGTAGTGTAGATTCAAAATTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGG
65 AGGTAGTGTAGATTCAAAGTTGTGAAAAT-ATGAGCCCCGGGGGTAGGGTGGGGCCACAATGGGG
* *
589533 GTCGAAGTTTAATATAGGAATATATATAGTAAATCT
129 GTCGAAGTTTAACATAGGAATATATAGAGTAAATCT
* *
589569 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTTG-AAGCATCTTC
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG-TGAAAGCATCCTC
*
589633 AGGTAGTGAAGATTCAAAGTTGTG-AAA-ATG-GCCCTC-GGGGTAGGGTGGGGCCACAATGGGG
65 AGGTAGTGTAGATTCAAAGTTGTGAAAATATGAGCCC-CGGGGGTAGGGTGGGGCCACAATGGGG
*
589694 TGTCAAAGTTTAACATAGGAATATATAGAGTAAATCT
129 -GTCGAAGTTTAACATAGGAATATATAGAGTAAATCT
*
589731 TTAAAAATCTTCTTCTCAGAAACTAACCAGCC-GGCAAAGCTGAAACTTGTGTGAAAGCATCCTC
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGTGAAAGCATCCTC
* * * * *
589795 AGGTAGTGTAAATTCAAAGTTGGGAAAATAAT-AACCCCTTGGGGTAGGGTAGGGCCACAATGGG
65 AGGTAGTGTAGATTCAAAGTTGTGAAAAT-ATGAGCCCC-GGGGGTAGGGTGGGGCCACAAT-GG
* * *
589859 GGGTCGAAGTTTTACATAGAAATACATAGAGTAAATCT
127 GGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCT
*
589897 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGAAAGCATCCTCA
1 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
*
589962 GGTAGTGTAGATACAAAGT
66 GGTAGTGTAGATTCAAAGT
589981 ATGTATTATG
Statistics
Matches: 669, Mismatches: 48, Indels: 45
0.88 0.06 0.06
Matches are distributed among these distances:
161 35 0.05
162 146 0.22
163 112 0.17
164 10 0.01
165 192 0.29
166 165 0.25
167 9 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (164 bp):
TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
GGTAGTGTAGATTCAAAGTTGTGAAAATATGAGCCCCGGGGGTAGGGTGGGGCCACAATGGGGGT
CGAAGTTTAACATAGGAATATATAGAGTAAATCT
Found at i:589863 original size:328 final size:328
Alignment explanation
Indices: 589076--589980 Score: 1530
Period size: 328 Copynumber: 2.8 Consensus size: 328
589066 AACAACATCC
* * * * *
589076 TTAAAGATCTTTTTCTCAGAAACTAATCAGCCAGG-GAAGCTGACACTTGTGTGAAAGCATCCTC
1 TTAAAAATCTTCTTCTCAGAAACTAACCAGCC-GGCAAAGCTGAAACTTGTGTGAAAGCATCCTC
*
589140 AGGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATTGGG
65 AGGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGG
*
589205 GTCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCATCTCAGAAACTAATCA
130 GTCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA
589270 GCCAGGAAAGCTGACACTTGTGTTGAAGCATCTTCAGGTAGTGAAGATTCAAAGTTGTGAAAATG
195 GCCAGGAAAGCTGACACTTGTGTTGAAGCATCTTCAGGTAGTGAAGATTCAAAGTTGTGAAAATG
589335 GCCCTCGGGGGTAGGGTGGGGCCACAATGGGGTGTCAAAGTTTAACATAGGAATATATAGAGTAA
260 GCCCTCGGGGGTAGGGTGGGGCCACAATGGGGTGTCAAAGTTTAACATAGGAATATATAGAGTAA
589400 ATCT
325 ATCT
589404 TTAAAAATCTTCTTCTCAGAAACTAACCAGCCGGCAAAGCTGAAACTTGTGTGAAAGCATCCTCA
1 TTAAAAATCTTCTTCTCAGAAACTAACCAGCCGGCAAAGCTGAAACTTGTGTGAAAGCATCCTCA
*
589469 GGTAGTGTAGATTCAAAATTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
66 GGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
589534 TCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
131 TCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
589599 CCAGGAAAGCTGACACTTGTGTTGAAGCATCTTCAGGTAGTGAAGATTCAAAGTTGTGAAAATGG
196 CCAGGAAAGCTGACACTTGTGTTGAAGCATCTTCAGGTAGTGAAGATTCAAAGTTGTGAAAATGG
589664 CCCTC-GGGGTAGGGTGGGGCCACAATGGGGTGTCAAAGTTTAACATAGGAATATATAGAGTAAA
261 CCCTCGGGGGTAGGGTGGGGCCACAATGGGGTGTCAAAGTTTAACATAGGAATATATAGAGTAAA
589728 TCT
326 TCT
589731 TTAAAAATCTTCTTCTCAGAAACTAACCAGCCGGCAAAGCTGAAACTTGTGTGAAAGCATCCTCA
1 TTAAAAATCTTCTTCTCAGAAACTAACCAGCCGGCAAAGCTGAAACTTGTGTGAAAGCATCCTCA
* * * * * *
589796 GGTAGTGTAAATTCAAAGTTGGGAAAATAAT-AACCCCTTGGGGTAGGGTAGGGCCACAATGGGG
66 GGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCC-GGGGGTAGGGTGGGGCCACAAT-GGG
* * * * *
589860 GGTCGAAGTTTTACATAGAAATACATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
129 GGTCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* * * * *
589925 AGCCAGGAAAGCTTAAACTTGTG-TGAAAGCATCCTCAGGTAGTGTAGATACAAAGT
194 AGCCAGGAAAGCTGACACTTGTGTTG-AAGCATCTTCAGGTAGTGAAGATTCAAAGT
589981 ATGTATTATG
Statistics
Matches: 548, Mismatches: 25, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
326 5 0.01
327 178 0.32
328 365 0.67
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (328 bp):
TTAAAAATCTTCTTCTCAGAAACTAACCAGCCGGCAAAGCTGAAACTTGTGTGAAAGCATCCTCA
GGTAGTGTAGATTCAAAATTGGGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
TCGAAGTTTAATATAGGAATATATATAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
CCAGGAAAGCTGACACTTGTGTTGAAGCATCTTCAGGTAGTGAAGATTCAAAGTTGTGAAAATGG
CCCTCGGGGGTAGGGTGGGGCCACAATGGGGTGTCAAAGTTTAACATAGGAATATATAGAGTAAA
TCT
Found at i:599560 original size:21 final size:21
Alignment explanation
Indices: 599536--599608 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
599526 AATCCTATCG
599536 TATCGTGCGTGTAAACTGTTC
1 TATCGTGCGTGTAAACTGTTC
* * *
599557 TATCGTGCGT-TAATTCTATCC
1 TATCGTGCGTGTAA-ACTGTTC
* *
599578 TATCGTGCGTGTATATTGTTC
1 TATCGTGCGTGTAAACTGTTC
*
599599 TAACGTGCGT
1 TATCGTGCGT
599609 TTATCCTATC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (21 bp):
TATCGTGCGTGTAAACTGTTC
Found at i:599576 original size:42 final size:42
Alignment explanation
Indices: 599524--599629 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
599514 GTATCGTGTA
* *
599524 TTAATCCTATCGTATCGTGCGTGTAAACTGTTCTATCGTGCG
1 TTAATCCTATCCTATCGTGCGTGTAAACTGTTCTAACGTGCG
* * *
599566 TTAATTCTATCCTATCGTGCGTGTATATTGTTCTAACGTGCG
1 TTAATCCTATCCTATCGTGCGTGTAAACTGTTCTAACGTGCG
* *
599608 TTTATCCTATCCTGTCGTGCGT
1 TTAATCCTATCCTATCGTGCGT
599630 AAATCCTATC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (42 bp):
TTAATCCTATCCTATCGTGCGTGTAAACTGTTCTAACGTGCG
Found at i:615747 original size:166 final size:165
Alignment explanation
Indices: 615468--616630 Score: 1144
Period size: 166 Copynumber: 7.1 Consensus size: 165
615458 GGTATTTTTC
* * * * *
615468 AAAAATCTTCTTCTCAAAAACTATTCGGCCAGAAAAGCTTAAACTT-GTGTGGAGGCATCCTCGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAGAGTGGAAGCATCCTCAG
**
615532 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCATGGGTAGGGTGGGGCCACAATAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGG
* * *
615597 ATCAAGTTTTACATAGGAATATATAGATAAAATCTTT
129 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
615634 AAAAATCTTCTTCTCAGATACTATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGG
* *
615699 TTGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGAAGGGTGGGGCCACAATAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGA
* *
615764 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 TGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
615800 AAAAA---TCTTCTCAAAAACTATTTGGCCAGAAAAGCTAAAATTAAAAT-GAGAGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGA-AGCATCCTCAG
* * * * *
615861 GTAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTATGGCGGGGCCACAGTGGGGGA
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGG-
* * *
615926 ATGGATTTTTACATAGGAATATATAGAGAATACCTTT
129 ATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
615963 AAAAATCTTTTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGACTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGG
* *
616028 TAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGTA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TGGGGGA
* * *
616093 TGAATTTTTATACAGGAATATTTAGAGAAAATCTTT
130 TGAATTTTTACATAGGAATATATAGAGAAAATCTTT
** * * * * * * * * * * *
616129 AAATTTTTTTTTTTTTAAACTACCGGTATTAGGCTAGGAAAGCTCAAATTGGCGTGTAAGTATCC
1 AAA-AATCTTCTTCTCAAA--AAC--TATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCC
* ** * *
616194 TTATATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGG
61 TCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGG
* *
616259 GGGAT-AAATTTT---T----ATATAGAGAGAAAATCTTT
126 GGGATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * * *
616291 AAAACTCTTCTTCT-GAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCATCCCCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGG
* ** * * * ** * *
616355 TCGCATGGATTCAAGTTTGTTTAAATCATAGT-CCC-GGGGTACAGTGAGGCCACAATGGGGAAT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGAT
* * * *
616418 GAATTTTTATATAAGAATATGTAGAGAAAATATTT
131 GAATTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * * * *
616453 AAAAATCTT-TTTTTAAAAACTATTTGGCCAGAAAAGCTGAAACTT-GTGTAG-AGACACCCTCA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAGAGTGGAAG-CATCCTCA
* * * * * ** * *
616515 TGTAGTGTATAAATTCAAGTTTG--CAAAATCATAGTCCCTGGAGGTAGGGCAGGGACGCAATGG
64 GGTAGTG--TAGATTCAAGTTTGTTC-AAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGG
*
616578 CGGGTTGAATTTTTACATAGGAATATATAGAGAAAATCTTT
126 -GGGATGAATTTTTACATAGGAATATATAGAGAAAATCTTT
*
616619 AAAAATATTCTT
1 AAAAATCTTCTT
616631 GGAAAGTTTT
Statistics
Matches: 827, Mismatches: 139, Indels: 61
0.81 0.14 0.06
Matches are distributed among these distances:
154 23 0.03
155 8 0.01
156 60 0.07
158 3 0.00
160 2 0.00
161 11 0.01
162 87 0.11
163 151 0.18
164 14 0.02
165 17 0.02
166 328 0.40
167 19 0.02
169 8 0.01
170 7 0.01
171 89 0.11
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGAT
GAATTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:615915 original size:329 final size:325
Alignment explanation
Indices: 615476--616630 Score: 1192
Period size: 329 Copynumber: 3.5 Consensus size: 325
615466 TCAAAAATCT
* * * *
615476 TCTTCTCAAAAACTATTCGGCCAGAAAAGCTTAAACTT-GTGTGGAGGCATCCTCGGGTAGTGTA
1 TCTTCTCAAAAACTATTTGGCCAGAAAAGC-TAAAATTGGTGTAGA-GCATCCTCAGGTAGTGTA
* *** * * *
615540 GATTCAAGTTTGTTCAAATCATGGTCCCCATGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTT
64 GATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGCGGGGCCACAAT-GGGGGATGAATTT
* * *
615605 TTACATAGGAATATATAGATAAAATCTTTAAAAATCTTCTTCTCAGATACTATTTGGCCAGAAAA
128 TTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCA-AAACTATTAGGCCAGAAAA
** *
615670 GCTCAAATTAAAATGGAAGCATCCTCAGGTTGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
192 GCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
* * * *
615735 GGGGGAAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
257 GGGGGAAGGGTGGGGCCACAAT-GGGGAATGAATTTTTATATAGGAATATATAGAGAAAATCTTT
615800 AAAAA
321 AAAAA
**
615805 TCTTCTCAAAAACTATTTGGCCAGAAAAGCTAAAATTAAAATG-AGAGCATCCTCAGGTAGTGTA
1 TCTTCTCAAAAACTATTTGGCCAGAAAAGCTAAAATT--GGTGTAGAGCATCCTCAGGTAGTGTA
* * *
615869 GATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTATGGCGGGGCCACAGTGGGGGAATGGATTT
64 GATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGG-ATGAATTT
* * *
615934 TTACATAGGAATATATAGAGAATACCTTTAAAAATCTTTTTCTCAAAAACTATTAGGCCAGAAAA
128 TTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTC-AAAACTATTAGGCCAGAAAA
* * *
615999 GCTCAAATTTGACTGGAAGCATCCTCAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
192 GCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
* * * *
616064 GGGGGTAGGGTGGGGCCACAATTGGGGTATGAATTTTTATACAGGAATATTTAGAGAAAATCTTT
257 GGGGGAAGGGTGGGGCCACAA-TGGGGAATGAATTTTTATATAGGAATATATAGAGAAAATCTTT
**
616129 AAATTTTTT
321 AAA----AA
* * * * * * * * * * **
616138 TTTTTTTAAACTACCGGTATTAGGCTAGGAAAGCTCAAATTGGCGTGTA-AGTATCCTTATATAG
1 TCTTCTCAAA--AAC--TATTTGGCCAGAAAAGCTAAAATT-G-GTGTAGAGCATCCTCAGGTAG
*
616202 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGAT-AA
60 TGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATGAA
* * * * *
616266 ATTTT---T----ATATAGAGAGAAAATCTTTAAAACTCTTCTTCTGAAAACTATTAGGCCAGGA
125 TTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAGAA
* * * * ** * * *
616324 AAGCCCAAATTTGAGTGGAAGCATCCCCAGGTCGCATGGATTCAAGTTTGTTTAAATCATAGT-C
190 AAGCTCAAATTTGAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCC
* * * * *
616388 CCGGGGTACA--GTGAGGCCACAATGGGGAATGAATTTTTATATAAGAATATGTAGAGAAAATAT
255 CCGGGGGA-AGGGTGGGGCCACAATGGGGAATGAATTTTTATATAGGAATATATAGAGAAAATCT
616451 TTAAAAA
319 TTAAAAA
* * * * *
616458 TCTTTTTTTAAAAACTATTTGGCCAGAAAAGCTGAAACTT-GTGTAGAGACACCCTCATGTAGTG
1 TC--TTCTCAAAAACTATTTGGCCAGAAAAGCT-AAAATTGGTGTAGAG-CATCCTCAGGTAGTG
* * * * * *
616522 TATAAATTCAAGTTTG--CAAAATCATAGTCCCTGGAGGTAGGGCAGGGACGCAATGGCGGGTTG
62 --TAGATTCAAGTTTGTTC-AAATCATAGTCCCTGGGGGTAGGGCGGGGCCACAATGG-GGGATG
*
616585 AATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATATTCTT
123 AATTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
616631 GGAAAGTTTT
Statistics
Matches: 686, Mismatches: 106, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
316 5 0.01
317 2 0.00
318 27 0.04
319 37 0.05
320 20 0.03
321 6 0.01
322 8 0.01
324 42 0.06
325 11 0.02
326 7 0.01
327 70 0.10
328 67 0.10
329 270 0.39
330 4 0.01
331 2 0.00
332 1 0.00
333 7 0.01
335 7 0.01
336 2 0.00
337 90 0.13
338 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (325 bp):
TCTTCTCAAAAACTATTTGGCCAGAAAAGCTAAAATTGGTGTAGAGCATCCTCAGGTAGTGTAGA
TTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATGAATTTTTA
CATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAGAAAAGCTC
AAATTTGAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGG
GAAGGGTGGGGCCACAATGGGGAATGAATTTTTATATAGGAATATATAGAGAAAATCTTTAAAAA
Found at i:616821 original size:99 final size:98
Alignment explanation
Indices: 616650--616842 Score: 359
Period size: 99 Copynumber: 2.0 Consensus size: 98
616640 TCAGTCCAAA
*
616650 ACTCAGTACTTTGTTTGAAACCTCAGGTTATGCAGATTTAAGTTTGATGAAACCATGATTCCCTA
1 ACTCAGTACTTTGTTTGAAACCTCAGGTTATGCAGATTTAAGTTTAATGAAACCATGATTCCCTA
*
616715 GAGAAAAGTGGGGCCACAAAATGGGGGGGGGGG
66 GAGAAAAGTGGGGCAACAAAATGGGGGGGGGGG
616748 NACTCAGTACTTTGTTTGAAACCTCAGGTTATGCAGATTTAAGTTTAATGAAACCATGATTCCCT
1 -ACTCAGTACTTTGTTTGAAACCTCAGGTTATGCAGATTTAAGTTTAATGAAACCATGATTCCCT
616813 AGAGAAAAGTGGGGCAACAAAATGGGGGGG
65 AGAGAAAAGTGGGGCAACAAAATGGGGGGG
616843 TATATAGGAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (98 bp):
ACTCAGTACTTTGTTTGAAACCTCAGGTTATGCAGATTTAAGTTTAATGAAACCATGATTCCCTA
GAGAAAAGTGGGGCAACAAAATGGGGGGGGGGG
Found at i:619053 original size:29 final size:30
Alignment explanation
Indices: 618998--619149 Score: 91
Period size: 30 Copynumber: 5.1 Consensus size: 30
618988 ATTGCTGAAC
* *
618998 TGTCTGAAAAATCTGAATTGTTCTG-AATT
1 TGTCTGAAAAATCTGAACTGTTCTGAAAAT
619027 TGTCTGAAAAATCTGAACTGCTT-TGAAAAT
1 TGTCTGAAAAATCTGAACTG-TTCTGAAAAT
* * * * *
619057 TG-CTGAAACAGTCTGAACTCTATCTGTATAG
1 TGTCTGAAA-AATCTGAACTGT-TCTGAAAAT
* * * *
619088 TG-CTTAAACAGTCTGAACTATTCTGAATAT
1 TGTCTGAAA-AATCTGAACTGTTCTGAAAAT
* *
619118 TG-CTGAAACAGTCTGAACTATTCT-AAATAT
1 TGTCTGAAA-AATCTGAACTGTTCTGAAA-AT
619148 TG
1 TG
619150 CTGTAATACT
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
29 30 0.29
30 51 0.49
31 23 0.22
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (30 bp):
TGTCTGAAAAATCTGAACTGTTCTGAAAAT
Found at i:619074 original size:30 final size:30
Alignment explanation
Indices: 619018--619152 Score: 150
Period size: 30 Copynumber: 4.5 Consensus size: 30
619008 ATCTGAATTG
*
619018 TTCTGAAT-TTGTCTGAAA-AATCTGAACTGC
1 TTCTGAATATTG-CTGAAACAGTCTGAACT-C
*
619048 TT-TGAAAATTGCTGAAACAGTCTGAACTC
1 TTCTGAATATTGCTGAAACAGTCTGAACTC
* * * *
619077 TATCTGTATAGTGCTTAAACAGTCTGAACTA
1 T-TCTGAATATTGCTGAAACAGTCTGAACTC
*
619108 TTCTGAATATTGCTGAAACAGTCTGAACTA
1 TTCTGAATATTGCTGAAACAGTCTGAACTC
*
619138 TTCTAAATATTGCTG
1 TTCTGAATATTGCTG
619153 TAATACTCTA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.13
30 55 0.61
31 23 0.26
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (30 bp):
TTCTGAATATTGCTGAAACAGTCTGAACTC
Found at i:630772 original size:18 final size:18
Alignment explanation
Indices: 630739--630773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
630729 ATTTGTATAA
* *
630739 CAACAACGTCAGCGACAT
1 CAACAACGACAACGACAT
630757 CAACAACGACAACGACA
1 CAACAACGACAACGACA
630774 AACAAAGAAT
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:0.46, C:0.34, G:0.14, T:0.06
Consensus pattern (18 bp):
CAACAACGACAACGACAT
Found at i:634210 original size:13 final size:13
Alignment explanation
Indices: 634181--634209 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
634171 GTGTTGGTTG
634181 TTTTGGGTTTTTT
1 TTTTGGGTTTTTT
634194 TTTT-GGTTTTTT
1 TTTTGGGTTTTTT
634206 TTTT
1 TTTT
634210 TTTTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (13 bp):
TTTTGGGTTTTTT
Found at i:636099 original size:165 final size:165
Alignment explanation
Indices: 635849--636256 Score: 441
Period size: 165 Copynumber: 2.5 Consensus size: 165
635839 CGGTATATAT
* * * * *
635849 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTC
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTA-GGC
* * * *
635913 -AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCCGT-G-ATCTCAATCTAATACTGGG
64 AAGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA-CCGTAGCA-CTCAA-CTAATACTGGG
* * *
635974 GCCCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
126 GCCCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * *
636014 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTAGGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGCAA
* ** ** *
636079 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCACTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTCAACTAATACTGGGGCCCC
* *
636144 AAGAGGGGTTCAAAGTTTAACATAGAAAGATATAT
131 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * *
636179 TGAAAATGTTTTTAAAAA-GTTTTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTACTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGC
*
636243 AAGGATCCTCAAAT
64 AAGCATCCTCAAAT
636257 TGTGTAAACT
Statistics
Matches: 201, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
164 5 0.02
165 128 0.64
166 60 0.30
167 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (165 bp):
GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGCAA
GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTCAACTAATACTGGGGCCCC
AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
Found at i:642599 original size:2 final size:2
Alignment explanation
Indices: 642592--642633 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
642582 ATACATATTC
642592 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
642634 TTGGGGGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:648101 original size:20 final size:20
Alignment explanation
Indices: 648076--648153 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
648066 TTGAGGACAG
*
648076 ACGACTTTTATTTCGTGGGC
1 ACGACTTTTATTTCGTGGCC
648096 ACGACTTTTATTTCGTGGCC
1 ACGACTTTTATTTCGTGGCC
648116 ACGACTTTTATTTCGTGGCC
1 ACGACTTTTATTTCGTGGCC
648136 ACGACTTTTATTTCGTGG
1 ACGACTTTTATTTCGTGG
648154 NTGGCCACGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
ACGACTTTTATTTCGTGGCC
Found at i:651997 original size:2 final size:2
Alignment explanation
Indices: 651990--652054 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
651980 TTCCGGTGTT
*
651990 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TNC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC
652033 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
652055 AGATTGCTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:654202 original size:29 final size:28
Alignment explanation
Indices: 654119--654281 Score: 153
Period size: 29 Copynumber: 5.9 Consensus size: 28
654109 CCTCTTAGAA
*
654119 TAAATAAACACTCCTAATATCCCCTCCCC
1 TAAATAAACACTCCCAATATCCCC-CCCC
* *
654148 AATAAATAAACGCTCCAAATAT--CCCCCC
1 --TAAATAAACACTCCCAATATCCCCCCCC
*
654176 -AAATAAACACTCCCAATATCCACCCCCAA
1 TAAATAAACACTCCCAATATCC-CCCCC-C
654205 TAAATAAACACTCCCAATAT-----CCC
1 TAAATAAACACTCCCAATATCCCCCCCC
*
654228 TAAAATAAACACTCCAAATATCCCCCCCC
1 T-AAATAAACACTCCCAATATCCCCCCCC
*
654257 ATAAATAAACACTCCAAATATCCCC
1 -TAAATAAACACTCCCAATATCCCC
654282 TAAAATAAAC
Statistics
Matches: 113, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
23 1 0.01
24 20 0.18
25 17 0.15
28 9 0.08
29 28 0.25
30 20 0.18
31 18 0.16
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.19
Consensus pattern (28 bp):
TAAATAAACACTCCCAATATCCCCCCCC
Found at i:654220 original size:17 final size:17
Alignment explanation
Indices: 654176--654223 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
654166 ATATCCCCCC
654176 AAATAAACACTCCCAAT
1 AAATAAACACTCCCAAT
* *
654193 --AT--CCACCCCCAAT
1 AAATAAACACTCCCAAT
654206 AAATAAACACTCCCAAT
1 AAATAAACACTCCCAAT
654223 A
1 A
654224 TCCCTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 8
0.66 0.11 0.23
Matches are distributed among these distances:
13 9 0.39
15 4 0.17
17 10 0.43
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAACACTCCCAAT
Found at i:654256 original size:54 final size:55
Alignment explanation
Indices: 654120--654296 Score: 268
Period size: 54 Copynumber: 3.2 Consensus size: 55
654110 CTCTTAGAAT
* * **
654120 AAATAAACACTCCTAATATCCCCTCCCCAATAAATAAACGCTCCAAATATCCCCCC
1 AAATAAACACTCCAAATATCCCC-CCCCAATAAATAAACACTCCAAATATCCCCTA
* * *
654176 AAATAAACACTCCCAATATCCACCCCCAATAAATAAACACTCCCAATAT-CCCTA
1 AAATAAACACTCCAAATATCCCCCCCCAATAAATAAACACTCCAAATATCCCCTA
654230 AAATAAACACTCCAAATATCCCCCCCC-ATAAATAAACACTCCAAATATCCCCTA
1 AAATAAACACTCCAAATATCCCCCCCCAATAAATAAACACTCCAAATATCCCCTA
654284 AAATAAACACTCC
1 AAATAAACACTCC
654297 CAANNNNNNN
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
53 20 0.18
54 46 0.41
55 24 0.22
56 21 0.19
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.19
Consensus pattern (55 bp):
AAATAAACACTCCAAATATCCCCCCCCAATAAATAAACACTCCAAATATCCCCTA
Found at i:654289 original size:29 final size:29
Alignment explanation
Indices: 654117--654296 Score: 179
Period size: 25 Copynumber: 6.6 Consensus size: 29
654107 GCCCTCTTAG
*
654117 AATAAATAAACACTCCTAATATCCCCTCCCC
1 AATAAATAAACACTCCAAATATCCCCT--CC
*
654148 AATAAATAAACGCTCCAAATATCCCC-CC
1 AATAAATAAACACTCCAAATATCCCCTCC
* *
654176 ---AAATAAACACTCCCAATATCCACCCCC
1 AATAAATAAACACTCCAAATATCC-CCTCC
*
654203 AATAAATAAACACTCCCAATAT-CCCT--
1 AATAAATAAACACTCCAAATATCCCCTCC
*
654229 -A-AAATAAACACTCCAAATATCCCCCCC
1 AATAAATAAACACTCCAAATATCCCCTCC
*
654256 CATAAATAAACACTCCAAATATCCCCT--
1 AATAAATAAACACTCCAAATATCCCCTCC
654283 -A-AAATAAACACTCC
1 AATAAATAAACACTCC
654297 CAANNNNNNN
Statistics
Matches: 131, Mismatches: 8, Indels: 26
0.79 0.05 0.16
Matches are distributed among these distances:
24 18 0.14
25 36 0.27
26 3 0.02
27 2 0.02
28 5 0.04
29 24 0.18
30 19 0.15
31 24 0.18
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.19
Consensus pattern (29 bp):
AATAAATAAACACTCCAAATATCCCCTCC
Found at i:656371 original size:18 final size:19
Alignment explanation
Indices: 656348--656384 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
656338 GTGACTTCCG
656348 GTATCTGTACAAGA-CTCT
1 GTATCTGTACAAGATCTCT
656366 GTATCTGTACAAGATCTCT
1 GTATCTGTACAAGATCTCT
656385 CTGAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (19 bp):
GTATCTGTACAAGATCTCT
Found at i:662910 original size:2 final size:2
Alignment explanation
Indices: 662903--662953 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
662893 GGATGGATGT
662903 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
662945 TC TC TC TC T
1 TC TC TC TC T
662954 GAGTTTTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:664393 original size:2 final size:2
Alignment explanation
Indices: 664386--664429 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
664376 ACGAATATTT
664386 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
664428 TC
1 TC
664430 ATATTTGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:665358 original size:2 final size:2
Alignment explanation
Indices: 665351--665411 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
665341 AAAGTCTTTG
* * *
665351 CT CT CT CT CT TT CT CT TT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
665393 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
665412 AAGGTCACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:668926 original size:2 final size:2
Alignment explanation
Indices: 668919--668944 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
668909 GGTATTTAGA
668919 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
668945 ATGTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:671965 original size:2 final size:2
Alignment explanation
Indices: 671958--672000 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
671948 TTTACAAGAC
671958 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
672000 C
1 C
672001 ATAATTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:673436 original size:2 final size:2
Alignment explanation
Indices: 673429--673483 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
673419 TTACCGAAAA
673429 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
673471 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
673484 TAAGTTGCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:673958 original size:2 final size:2
Alignment explanation
Indices: 673951--674001 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
673941 TTGGTCGAGA
673951 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
673993 CT CT CT CT C
1 CT CT CT CT C
674002 AAAAGAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:675125 original size:17 final size:17
Alignment explanation
Indices: 675103--675207 Score: 112
Period size: 17 Copynumber: 6.4 Consensus size: 17
675093 CCCATTGGCC
*
675103 TGGCCTGGCCTCAAAGT
1 TGGCCTGGCCTCAAAAT
*
675120 TGGCCTGGCCTC--ACT
1 TGGCCTGGCCTCAAAAT
*
675135 T---TTGGCCTCAAAAT
1 TGGCCTGGCCTCAAAAT
*
675149 TGGCCTGGCCCCAAAATT
1 TGGCCTGGCCTCAAAA-T
675167 TGGCCTGGCCTCAAAAAT
1 TGGCCTGGCCTC-AAAAT
*
675185 TGGCCTGGCCTCAAATT
1 TGGCCTGGCCTCAAAAT
675202 TGGCCT
1 TGGCCT
675208 CTACCAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
12 7 0.09
14 3 0.04
15 3 0.04
17 32 0.43
18 25 0.34
19 4 0.05
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (17 bp):
TGGCCTGGCCTCAAAAT
Found at i:675178 original size:35 final size:35
Alignment explanation
Indices: 675137--675207 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
675127 GCCTCACTTT
675137 TGGCCTC-AAAATTGGCCTGGCCCCAAAATTTGGCC
1 TGGCCTCAAAAATTGGCCTGGCCCC-AAATTTGGCC
*
675172 TGGCCTCAAAAATTGGCCTGGCCTCAAATTTGGCC
1 TGGCCTCAAAAATTGGCCTGGCCCCAAATTTGGCC
675207 T
1 T
675208 CTACCAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (35 bp):
TGGCCTCAAAAATTGGCCTGGCCCCAAATTTGGCC
Found at i:675403 original size:18 final size:17
Alignment explanation
Indices: 675371--675475 Score: 103
Period size: 18 Copynumber: 6.4 Consensus size: 17
675361 ATTTTTGAAG
*
675371 AGGCCAAACTTGAGGCC
1 AGGCCAAATTTGAGGCC
675388 AGGCCAAAATTTGAGGCC
1 AGGCC-AAATTTGAGGCC
*
675406 AGGCCAAAATTTGGGGCC
1 AGGCC-AAATTTGAGGCC
*
675424 AGGCCAATTTTGAGG-C
1 AGGCCAAATTTGAGGCC
* *
675440 ---CTAAA-GTGAGGCC
1 AGGCCAAATTTGAGGCC
*
675453 AGGCCAACTTTGAGGCC
1 AGGCCAAATTTGAGGCC
675470 AGGCCA
1 AGGCCA
675476 GGCCAGGCCA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
12 5 0.07
13 4 0.06
16 4 0.06
17 26 0.36
18 33 0.46
ACGTcount: A:0.29, C:0.25, G:0.30, T:0.16
Consensus pattern (17 bp):
AGGCCAAATTTGAGGCC
Found at i:675656 original size:2 final size:2
Alignment explanation
Indices: 675649--675682 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
675639 AATATGATAT
675649 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
675683 AATGACGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:678339 original size:2 final size:2
Alignment explanation
Indices: 678332--678367 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
678322 TGGCTGCTAA
678332 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
678368 CAAAAAGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:679169 original size:2 final size:2
Alignment explanation
Indices: 679162--679200 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
679152 NNNNNNNNNN
679162 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
679201 AATCAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:682154 original size:23 final size:23
Alignment explanation
Indices: 682138--682181 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
682128 TTATGAATAT
682138 TACATGTAGATGTTTATACATAA
1 TACATGTAGATGTTTATACATAA
682161 TACATGTAGATGTTTAT-CATA
1 TACATGTAGATGTTTATACATA
682182 GTATCGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
TACATGTAGATGTTTATACATAA
Found at i:693203 original size:1 final size:1
Alignment explanation
Indices: 693167--693191 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
693157 TTGTCTTTAA
693167 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
693192 AAATCTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:693332 original size:3 final size:3
Alignment explanation
Indices: 693309--693349 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
693299 ATTTAAAGCC
* *
693309 CCA CCC CCA CC- CCA ACA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
693350 AGACAGAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:694669 original size:6 final size:7
Alignment explanation
Indices: 694650--694674 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
694640 CATATTTTGC
694650 AATTTTT
1 AATTTTT
694657 AATTTTT
1 AATTTTT
694664 AATTTTT
1 AATTTTT
694671 AATT
1 AATT
694675 GCACAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:697526 original size:2 final size:2
Alignment explanation
Indices: 697519--697585 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
697509 AATGTTCGAG
697519 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
697561 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
697586 NNNNNNNNNN
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:697846 original size:28 final size:28
Alignment explanation
Indices: 697810--697876 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
697800 AATATTTTAG
697810 TGTACTTAAAAATATATGTT-ATATTCAA
1 TGTACTTAAAAATAT-TGTTGATATTCAA
*
697838 TGTACTT-AAAATATTTTTGATATTCAA
1 TGTACTTAAAAATATTGTTGATATTCAA
*
697865 TGTACCTAAAAA
1 TGTACTTAAAAA
697877 ATCATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 21 0.60
28 11 0.31
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (28 bp):
TGTACTTAAAAATATTGTTGATATTCAA
Found at i:698960 original size:19 final size:19
Alignment explanation
Indices: 698936--698972 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
698926 TTACTGTGAA
698936 GAATGTGTCAACAACACAG
1 GAATGTGTCAACAACACAG
698955 GAATGTGTCAACAACACA
1 GAATGTGTCAACAACACA
698973 CAATGCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (19 bp):
GAATGTGTCAACAACACAG
Found at i:699206 original size:2 final size:2
Alignment explanation
Indices: 699199--699246 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
699189 ATAATTATTT
699199 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
699241 TC TC TC
1 TC TC TC
699247 ATATCTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:717783 original size:45 final size:45
Alignment explanation
Indices: 717731--717973 Score: 387
Period size: 45 Copynumber: 5.4 Consensus size: 45
717721 CACGAGGACT
717731 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
1 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
*
717776 TGCAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
1 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
* * *
717821 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATG
1 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
* *
717866 TACAGAAAAAGTTATACCTTTTGAACTACGTGTACTAGTATTCCATG
1 TACAGAAAAAGGTATACC--TTAAACTACGTGTACTAGTATTCCATG
* * *
717913 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATG
1 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
717958 TACAGAAAAAGGTATA
1 TACAGAAAAAGGTATA
717974 ACCCAAACTA
Statistics
Matches: 180, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 140 0.78
47 40 0.22
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (45 bp):
TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATG
Found at i:717937 original size:92 final size:90
Alignment explanation
Indices: 717731--717973 Score: 414
Period size: 92 Copynumber: 2.7 Consensus size: 90
717721 CACGAGGACT
* * * *
717731 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATGTGCAGAAAAAGGTATACCTT
1 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATACCTT
717796 AAACTACGTGTACTAGTATTCCATG
66 AAACTACGTGTACTAGTATTCCATG
*
717821 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGTTATACCTT
1 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATACC--
*
717886 TTGAACTACGTGTACTAGTATTCCATG
64 TTAAACTACGTGTACTAGTATTCCATG
717913 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATA
1 TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATA
717974 ACCCAAACTA
Statistics
Matches: 144, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
90 58 0.40
92 86 0.60
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (90 bp):
TACAGAAACAGGTATACCTTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATACCTT
AAACTACGTGTACTAGTATTCCATG
Found at i:717982 original size:137 final size:135
Alignment explanation
Indices: 717731--717986 Score: 406
Period size: 137 Copynumber: 1.9 Consensus size: 135
717721 CACGAGGACT
*
717731 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATGTGCAGAAAAAGGTATACCTT
1 TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATGTACAGAAAAAGGTATACCTT
* * * *
717796 AAACTACGTGTACTAGTATTCCATGTACAGAAACAGGTATACCTTAAACTACATGTACTAATATT
66 AAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATACCTCAAACTACATGTACTAATATT
717861 CCATG
131 CCATG
* * *
717866 TACAGAAAAAGTTATACCTTTTGAACTACGTGTACTAGTATTCCATGTACAGAAACAGGTATACC
1 TACAGAAAAAGGTATACC--TTAAACTACGTGTACTAGTATTCCATGTACAGAAAAAGGTATACC
717931 TTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATAACC-CAAACTACAT
64 TTAAACTACATGTACTAATATTCCATGTACAGAAAAAGGTAT-ACCTCAAACTACAT
717987 TTATTTCACG
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
135 17 0.15
137 90 0.82
138 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (135 bp):
TACAGAAAAAGGTATACCTTAAACTACGTGTACTAGTATTCCATGTACAGAAAAAGGTATACCTT
AAACTACATGTACTAATATTCCATGTACAGAAAAAGGTATACCTCAAACTACATGTACTAATATT
CCATG
Found at i:718026 original size:38 final size:39
Alignment explanation
Indices: 717957--718033 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
717947 AATATTCCAT
717957 GTACAGAAAAAGGTATAACCCAAACTACATTTATTTCAC
1 GTACAGAAAAAGGTATAACCCAAACTACATTTATTTCAC
*
717996 GTACAGAAAAA-TTAT-ACCCAAAACTACATTTATTTCAC
1 GTACAGAAAAAGGTATAACCC-AAACTACATTTATTTCAC
718034 ATAAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 4 0.11
38 21 0.58
39 11 0.31
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (39 bp):
GTACAGAAAAAGGTATAACCCAAACTACATTTATTTCAC
Found at i:721085 original size:2 final size:2
Alignment explanation
Indices: 721080--721135 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
721070 AAAATATATG
721080 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
721122 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
721136 ATTTGTCGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:731104 original size:12 final size:12
Alignment explanation
Indices: 731087--731112 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
731077 ATCATATCAC
731087 ACGTGTTGAAAT
1 ACGTGTTGAAAT
731099 ACGTGTTGAAAT
1 ACGTGTTGAAAT
731111 AC
1 AC
731113 CAAAGGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (12 bp):
ACGTGTTGAAAT
Found at i:733730 original size:3 final size:3
Alignment explanation
Indices: 733722--733779 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
733712 TTATTGGATA
* * * *
733722 GAT GAT GAT AAT GAT GAT GAT GGT GAT TAT GAT GAT TAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
733770 GAT GAT GAT G
1 GAT GAT GAT G
733780 TTACGTTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:755020 original size:16 final size:16
Alignment explanation
Indices: 754999--755030 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
754989 CCGGAATGCT
754999 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
755015 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
755031 ATTTACCCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:755561 original size:16 final size:17
Alignment explanation
Indices: 755535--755567 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
755525 ACCCTAGAGA
755535 TTGGTTACGTTTTCTCC
1 TTGGTTACGTTTTCTCC
755552 TTGG-TACGTTTTCTCC
1 TTGGTTACGTTTTCTCC
755568 GGATACCCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (17 bp):
TTGGTTACGTTTTCTCC
Found at i:756197 original size:13 final size:13
Alignment explanation
Indices: 756179--756203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
756169 ACTATTGAAG
756179 GTTTTACATACAT
1 GTTTTACATACAT
756192 GTTTTACATACA
1 GTTTTACATACA
756204 GTACATGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
GTTTTACATACAT
Found at i:771249 original size:16 final size:17
Alignment explanation
Indices: 771228--771260 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
771218 TTTAATGTCA
771228 TTCAGGTCT-TTAGTAT
1 TTCAGGTCTCTTAGTAT
771244 TTCAGGTCTCTTAGTAT
1 TTCAGGTCTCTTAGTAT
771261 GTCACGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (17 bp):
TTCAGGTCTCTTAGTAT
Found at i:784136 original size:2 final size:2
Alignment explanation
Indices: 784129--784174 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
784119 AAAATCAAAA
**
784129 TC TC TC TC AA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
784171 TC TC
1 TC TC
784175 GTAAATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:798163 original size:184 final size:183
Alignment explanation
Indices: 797832--798251 Score: 488
Period size: 184 Copynumber: 2.3 Consensus size: 183
797822 TGAGATAACT
* * * * * **
797832 GGCAGGCGTGTAC-TCTTCTCGGCAGGCGTATGCATTCTGCGTAAGAGTTATCTATTTTACCGAT
1 GGCAGGCGTATACATTTTCTCGGCAGGCGTATG-ATTCTACGTAAGAGCTATCCAGCTTACCGAT
* * * * *
797896 TTTTACTAATTTTGTGTTAATTAACGAATTTAAAGTCAAGTTTTTATTTCTGTTATCAATTACTA
65 TTTTACTAATTTTGTGTTAATTAACGAATATAAAATCAACTTTTGATTTCTATTATCAATTACTA
*** * * *
797961 AGCTAGGTAAACTAAAATATCAAAGAAATAATTAAAATAATCCATCAAATAAAC
130 AGCTAAAAAAAATAAAATATCAAAGAAAAAAGTAAAATAATCCATCAAATAAAC
* * *
798015 GGCAGGCGTATACATTTTCTTGGCAGGCGTATGATTTCTTCGTAAGAGCTA-CCAGCTTACCCTA
1 GGCAGGCGTATACATTTTCTCGGCAGGCGTATGA-TTCTACGTAAGAGCTATCCAGCTTA-CCGA
* ** *
798079 TTTTTACTTATTTTGTGTTAATTAATTAATATAAAATCAACTTTTGATTTCTATTATC-ATCTAT
64 TTTTTACTAATTTTGTGTTAATTAACGAATATAAAATCAACTTTTGATTTCTATTATCAAT-TAC
*
798143 TTAG-TAAAAAGAAATAAAATATCAAAGAAAAAAGTAAAATAATCCATCAAATAAAC
128 TAAGCTAAAAA-AAATAAAATATCAAAGAAAAAAGTAAAATAATCCATCAAATAAAC
* * * *
798199 GGCAGGCGTCTAGATTTCCTCGGCAGGCGTATGAATTCTACGTAAGAGTTATC
1 GGCAGGCGTATACATTTTCTCGGCAGGCGTATG-ATTCTACGTAAGAGCTATC
798252 TATCTTTACC
Statistics
Matches: 199, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
183 23 0.12
184 174 0.87
185 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (183 bp):
GGCAGGCGTATACATTTTCTCGGCAGGCGTATGATTCTACGTAAGAGCTATCCAGCTTACCGATT
TTTACTAATTTTGTGTTAATTAACGAATATAAAATCAACTTTTGATTTCTATTATCAATTACTAA
GCTAAAAAAAATAAAATATCAAAGAAAAAAGTAAAATAATCCATCAAATAAAC
Found at i:803162 original size:2 final size:2
Alignment explanation
Indices: 803155--803201 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
803145 AAAACTCAAA
*
803155 CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
803197 CT CT C
1 CT CT C
803202 ATCAAATCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:809618 original size:15 final size:15
Alignment explanation
Indices: 809598--809627 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
809588 TACTATCGGT
809598 ACGAACATATAAACA
1 ACGAACATATAAACA
809613 ACGAACATATAAACA
1 ACGAACATATAAACA
809628 TTTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.13
Consensus pattern (15 bp):
ACGAACATATAAACA
Found at i:819374 original size:179 final size:179
Alignment explanation
Indices: 819070--819490 Score: 700
Period size: 179 Copynumber: 2.4 Consensus size: 179
819060 CATATTTGGG
819070 ATAACTGTATTATAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAT
1 ATAACTGTATTATAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAT
* *
819135 ACCCAATTCCTTTTGAGGGTCGACTGGGCTGTCCCGGGGCCCCATCCCCACCAGATATGAAGGCC
66 ACCAAATTCCTTTTGAGGGTCGACTGGGCTGTCCCGGGGCCCCATCCCCACCAAATATGAAGGCC
*
819200 CAAATATGGGATACAGGGTGTAAGCCAGCCCCTTGGAA-GATATCCCATT
131 CAAATATGGGATACAGGGTGTAAGCCAGCCCCTT-GAATGAAATCCCATT
*
819249 ATAACTGTATTAAAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAT
1 ATAACTGTATTATAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAT
* * *
819314 ACCAAATTTCTTTTGGGGGTCGACTGGGCTGTCCCGGGGTCCCATCCCCACCAAATATGAAGGCC
66 ACCAAATTCCTTTTGAGGGTCGACTGGGCTGTCCCGGGGCCCCATCCCCACCAAATATGAAGGCC
* *
819379 CAAATATGGGATACAGGGTGTTAGCCTGCCCCTTGAATGAAATCCCATT
131 CAAATATGGGATACAGGGTGTAAGCCAGCCCCTTGAATGAAATCCCATT
* * * **
819428 ATAACTGTATTGTTGGAAATGTCGCATTTTCGCCAGGCTAGCTAAATCTCTTACTGGTCGTGT
1 ATAACTGTATTATAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGT
819491 TTATTATGTC
Statistics
Matches: 226, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
178 3 0.01
179 223 0.99
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (179 bp):
ATAACTGTATTATAGCAAATGTCGCATTTTCGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAT
ACCAAATTCCTTTTGAGGGTCGACTGGGCTGTCCCGGGGCCCCATCCCCACCAAATATGAAGGCC
CAAATATGGGATACAGGGTGTAAGCCAGCCCCTTGAATGAAATCCCATT
Found at i:821294 original size:24 final size:24
Alignment explanation
Indices: 821262--821311 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
821252 TAATTATAAA
821262 ATATTTGGTTTCAGTAACAACTTG
1 ATATTTGGTTTCAGTAACAACTTG
821286 ATATTTGGTTTCAGTAACAACTTG
1 ATATTTGGTTTCAGTAACAACTTG
821310 AT
1 AT
821312 TGTTGTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (24 bp):
ATATTTGGTTTCAGTAACAACTTG
Found at i:823882 original size:471 final size:470
Alignment explanation
Indices: 822999--823940 Score: 1875
Period size: 471 Copynumber: 2.0 Consensus size: 470
822989 CCCCTGTTAG
822999 GTTGAAACAAACACATGGTCGAAAAGGAAGATAAAGTAGATGTAAAAAATGACCAAAGAATAATA
1 GTTGAAACAAACACATGGTCGAAAAGGAAGATAAAGTAGATGTAAAAAATGACCAAAGAATAATA
823064 TTTGAAGAAATATTGACTGATCATGCCTCAACATCTGGCCTTCTTCTGTAGTCTTCTTCCTTGAC
66 TTTGAAGAAATATTGACTGATCATGCCTCAACATCTGGCCTTCTTCTGTAGTCTTCTTCCTTGAC
823129 TACTCATTACTGATAGCCTGAATACCGCTTAACATTCCTGAACATCATTGTGAACACTCATCTTT
131 TACTCATTACTGATAGCCTGAATACCGCTTAACATTCCTGAACATCATTGTGAACACTCATCTTT
823194 GACTCATTCTCTTTTATTGCATGCCAGCGGTGGTCAGGAACACACCTTTACCTTCTGAACCTTTT
196 GACTCATTCTCTTTTATTGCATGCCAGCGGTGGTCAGGAACACACCTTTACCTTCTGAACCTTTT
823259 CTTCCAAAAATTACCTGGTTCTTTTTATCACCATGGAAGCCTATCCCTTTGTTTGCCAATTGGAA
261 CTTCCAAAAATTACCTGGTTCTTTTTATCACCATGGAAGCCTATCCCTTTGTTTGCCAATTGGAA
823324 TTTTCATTAAAGGCGAAACGTTGTTCTTTTTCACCCCACTAACATTGCTAATTAATGCTGTAGAG
326 TTTTCATTAAAGGCGAAACGTTGTTCTTTTTCACCCCACTAACATTGCTAATTAATGCTGTAGAG
823389 CATGTTTACTAACTGTTTAGTCTGAGTCGTTCCATTAAAGCTAAGAAACGAAGTGTTCAAATAAC
391 CATGTTTACTAACTGTTTAGTCTGAGTCGTTCCATTAAAGCTAAGAAACGAAGTGTTCAAATAAC
823454 TTTCTTCAGTGAAGA
456 TTTCTTCAGTGAAGA
823469 GNTTGAAACAAACACATGGTCGAAAAGGAAGATAAAGTAGATGTAAAAAATGACCAAAGAATAAT
1 G-TTGAAACAAACACATGGTCGAAAAGGAAGATAAAGTAGATGTAAAAAATGACCAAAGAATAAT
823534 ATTTGAAGAAATATTGACTGATCATGCCTCAACATCTGGCCTTCTTCTGTAGTCTTCTTCCTTGA
65 ATTTGAAGAAATATTGACTGATCATGCCTCAACATCTGGCCTTCTTCTGTAGTCTTCTTCCTTGA
823599 CTACTCATTACTGATAGCCTGAATACCGCTTAACATTCCTGAACATCATTGTGAACACTCATCTT
130 CTACTCATTACTGATAGCCTGAATACCGCTTAACATTCCTGAACATCATTGTGAACACTCATCTT
823664 TGACTCATTCTCTTTTATTGCATGCCAGCGGTGGTCAGGAACACACCTTTACCTTCTGAACCTTT
195 TGACTCATTCTCTTTTATTGCATGCCAGCGGTGGTCAGGAACACACCTTTACCTTCTGAACCTTT
823729 TCTTCCAAAAATTACCTGGTTCTTTTTATCACCATGGAAGCCTATCCCTTTGTTTGCCAATTGGA
260 TCTTCCAAAAATTACCTGGTTCTTTTTATCACCATGGAAGCCTATCCCTTTGTTTGCCAATTGGA
823794 ATTTTCATTAAAGGCGAAACGTTGTTCTTTTTCACCCCACTAACATTGCTAATTAATGCTGTAGA
325 ATTTTCATTAAAGGCGAAACGTTGTTCTTTTTCACCCCACTAACATTGCTAATTAATGCTGTAGA
823859 GCATGTTTACTAACTGTTTAGTCTGAGTCGTTCCATTAAAGCTAAGAAACGAAGTGTTCAAATAA
390 GCATGTTTACTAACTGTTTAGTCTGAGTCGTTCCATTAAAGCTAAGAAACGAAGTGTTCAAATAA
823924 CTTTCTTCAGTGAAGA
455 CTTTCTTCAGTGAAGA
823940 G
1 G
823941 GTCCTTGAGA
Statistics
Matches: 471, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
470 1 0.00
471 470 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (470 bp):
GTTGAAACAAACACATGGTCGAAAAGGAAGATAAAGTAGATGTAAAAAATGACCAAAGAATAATA
TTTGAAGAAATATTGACTGATCATGCCTCAACATCTGGCCTTCTTCTGTAGTCTTCTTCCTTGAC
TACTCATTACTGATAGCCTGAATACCGCTTAACATTCCTGAACATCATTGTGAACACTCATCTTT
GACTCATTCTCTTTTATTGCATGCCAGCGGTGGTCAGGAACACACCTTTACCTTCTGAACCTTTT
CTTCCAAAAATTACCTGGTTCTTTTTATCACCATGGAAGCCTATCCCTTTGTTTGCCAATTGGAA
TTTTCATTAAAGGCGAAACGTTGTTCTTTTTCACCCCACTAACATTGCTAATTAATGCTGTAGAG
CATGTTTACTAACTGTTTAGTCTGAGTCGTTCCATTAAAGCTAAGAAACGAAGTGTTCAAATAAC
TTTCTTCAGTGAAGA
Found at i:824202 original size:20 final size:20
Alignment explanation
Indices: 824173--824218 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
824163 GGGATCAGTA
*
824173 TGTCCGTCCGTCCGTCTTTC
1 TGTCCGTCCGTCCGTCTGTC
*
824193 TGTCCTTCCGTCCGTCTGTC
1 TGTCCGTCCGTCCGTCTGTC
824213 TGTCCG
1 TGTCCG
824219 AGATCGCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTCCGTCCGTCCGTCTGTC
Found at i:826605 original size:82 final size:82
Alignment explanation
Indices: 826458--826671 Score: 252
Period size: 82 Copynumber: 2.6 Consensus size: 82
826448 GATAGAATAC
* * * *
826458 TAACTCCTGGTTAGTCTCTGCTATCTCAATCGCATTTCCACCTTACCGAGATAATAGTATGAAAC
1 TAACACCTGCTTAGTCTCGGCTATCTCAATCACATTTCCACCTTACCGAGATAATAGTATGAAAC
* * *
826523 GTTTGGATGATTGAGAG
66 GATCGGATAATTGAGAG
* ** *
826540 TAACACCTGCTTAGTCTCGGCTATCTCAATCACATTTCGACCTTGTCGAGATTATAGTATGAAAC
1 TAACACCTGCTTAGTCTCGGCTATCTCAATCACATTTCCACCTTACCGAGATAATAGTATGAAAC
826605 GATCGGATAATTGAGAG
66 GATCGGATAATTGAGAG
* * ** *
826622 TAACACCTGCTAAG-C-CATGCATATCTCAATTGCATTTCGACCTTACCGAG
1 TAACACCTGCTTAGTCTC-GGC-TATCTCAATCACATTTCCACCTTACCGAG
826672 GTTACAGCAT
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 3 0.03
82 109 0.96
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (82 bp):
TAACACCTGCTTAGTCTCGGCTATCTCAATCACATTTCCACCTTACCGAGATAATAGTATGAAAC
GATCGGATAATTGAGAG
Found at i:837794 original size:42 final size:42
Alignment explanation
Indices: 837747--837870 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 42
837737 TACCTGCAGG
* *
837747 TTAGTTTGTTAAAATATAAAACGAAAACTAAATATCTTTCCT
1 TTAGTTTGTTGAAATATAAAACGAAAACTAAATATCTTTCCA
*
837789 TTAGTTTGTTGAACTATAAAACGAAAACTAAATAT-TTTCCA
1 TTAGTTTGTTGAAATATAAAACGAAAACTAAATATCTTTCCA
** * * * * *
837830 CAAGTATGTTGAATTATAAAACAAAAAATAGATATCTTTCC
1 TTAGTTTGTTGAAATATAAAACGAAAACTAAATATCTTTCC
837871 GAGAGTCACA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 33 0.46
42 38 0.54
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (42 bp):
TTAGTTTGTTGAAATATAAAACGAAAACTAAATATCTTTCCA
Found at i:837840 original size:41 final size:42
Alignment explanation
Indices: 837761--837870 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 42
837751 TTTGTTAAAA
*** *
837761 TATAAAACGAAAACTAAATATCTTTCCTTTAGTTTGTTGAAC
1 TATAAAACGAAAACTAAATATCTTTCCACAAGTATGTTGAAC
*
837803 TATAAAACGAAAACTAAATAT-TTTCCACAAGTATGTTGAAT
1 TATAAAACGAAAACTAAATATCTTTCCACAAGTATGTTGAAC
* * *
837844 TATAAAACAAAAAATAGATATCTTTCC
1 TATAAAACGAAAACTAAATATCTTTCC
837871 GAGAGTCACA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 33 0.56
42 26 0.44
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (42 bp):
TATAAAACGAAAACTAAATATCTTTCCACAAGTATGTTGAAC
Found at i:838852 original size:2 final size:2
Alignment explanation
Indices: 838845--838874 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
838835 ACCATTATCG
838845 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
838875 TTAAATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:841592 original size:12 final size:12
Alignment explanation
Indices: 841575--841601 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
841565 TGATACGACT
841575 AATTTTACTATG
1 AATTTTACTATG
841587 AATTTTACTATG
1 AATTTTACTATG
841599 AAT
1 AAT
841602 ATTATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
AATTTTACTATG
Found at i:861364 original size:2 final size:2
Alignment explanation
Indices: 861357--861435 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
861347 GAGTGCGTAT
861357 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
861399 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
861436 TCAGTCTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.