Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold76
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1973630
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 106294 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:415049 original size:41 final size:40
Alignment explanation
Indices: 414992--415188 Score: 241
Period size: 41 Copynumber: 4.8 Consensus size: 40
414982 AAGCCCCCAA
414992 CATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAG
1 CATTAGCGGCGCTTTTT-AAAAACGCCGCTAAAACCCCGAG
* * *
415033 CATTAGCGGCACTTTTTAGAAAACGCCGCTAAAGCCCCCAG
1 CATTAGCGGCGCTTTTTA-AAAACGCCGCTAAAACCCCGAG
** *
415074 CATTAGTAGCGCTTTTTAAGAAACGCCGCTAAAGCCCCGAG
1 CATTAGCGGCGCTTTTTAA-AAACGCCGCTAAAACCCCGAG
* * *
415115 CATTAGCGGCGCTTTTTCAAAAACACGGCTAAAACCCAGAG
1 CATTAGCGGCGCTTTTT-AAAAACGCCGCTAAAACCCCGAG
* * *
415156 CATTACCGGCACTTTTTAGAAAACGCAGCTAAA
1 CATTAGCGGCGCTTTTTA-AAAACGCCGCTAAA
415189 GCCCTAAAAG
Statistics
Matches: 135, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 130 0.96
42 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (40 bp):
CATTAGCGGCGCTTTTTAAAAACGCCGCTAAAACCCCGAG
Found at i:421187 original size:51 final size:50
Alignment explanation
Indices: 421068--421205 Score: 172
Period size: 50 Copynumber: 2.7 Consensus size: 50
421058 TTATCATTCA
* *
421068 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATTAAACTTTCTG
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGATTAAACTATCTG
* * * *
421118 GTTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCGTT-ATCTATC-G
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGA---TTAAACTATCTG
*
421169 ATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTG
421206 TTTACAGGCA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 34 0.45
51 34 0.45
52 5 0.07
53 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (50 bp):
ATACACGTAGTAGCCTGCACATAGTACTACACACGTGATTAAACTATCTG
Found at i:424087 original size:49 final size:49
Alignment explanation
Indices: 424028--424162 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 49
424018 CGCCAATCTG
* *
424028 GTTAGCAACTAACATGCCCTACTAGTGGCCCATCATATACTTCCA-CCTA
1 GTTAGCAACTAACATGCCCTACTAGTGGCTCATCATAT-CTGCCATCCTA
* * * * * * * * *
424077 GTTAGTAACTAGCATGCCCTACCAGTGGTTTAGCACATCTGCCATTCTG
1 GTTAGCAACTAACATGCCCTACTAGTGGCTCATCATATCTGCCATCCTA
*
424126 GTTTGCAACTAACATGCCCTACTAGTGGCTCATCATA
1 GTTAGCAACTAACATGCCCTACTAGTGGCTCATCATA
424163 ATTGGGCACA
Statistics
Matches: 66, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
48 5 0.08
49 61 0.92
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (49 bp):
GTTAGCAACTAACATGCCCTACTAGTGGCTCATCATATCTGCCATCCTA
Found at i:424546 original size:2 final size:2
Alignment explanation
Indices: 424539--424563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
424529 AGTTTCACTG
424539 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
424564 GTTCACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:425138 original size:19 final size:20
Alignment explanation
Indices: 425097--425138 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
425087 AGTGTTAAAA
*
425097 GTAAATCTTTAAAAATGTTG
1 GTAAATCATTAAAAATGTTG
*
425117 GTAAATCATTAGAAAT-TTG
1 GTAAATCATTAAAAATGTTG
425136 GTA
1 GTA
425139 TGACGGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAAATCATTAAAAATGTTG
Found at i:425224 original size:20 final size:20
Alignment explanation
Indices: 425184--425297 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
425174 CAGAAAATTT
*
425184 TTAGAAATTTTGAG-AAATCC
1 TTAGAAATTTTG-GTAATTCC
*
425204 TTAAAAATTTTGGTAATTCC
1 TTAGAAATTTTGGTAATTCC
* * *
425224 TTAGATATTTTAGT-ATAACC
1 TTAGAAATTTTGGTAAT-TCC
* **
425244 ATAGAAATTTTAATAAATT-C
1 TTAGAAATTTTGGT-AATTCC
* *
425264 TTAGATATTTTGGTAAATCC
1 TTAGAAATTTTGGTAATTCC
* *
425284 TTAAAAATATTGGT
1 TTAGAAATTTTGGT
425298 TTCATTTTTT
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
19 6 0.08
20 63 0.89
22 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
TTAGAAATTTTGGTAATTCC
Found at i:425931 original size:16 final size:16
Alignment explanation
Indices: 425884--425934 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
425874 TAAAATTAAA
425884 AATTTTTATTATAATATT
1 AATTTTTA-TATAA-ATT
* * *
425902 AAATTTGATTTAAATT
1 AATTTTTATATAAATT
425918 AATTTTTATATAAATT
1 AATTTTTATATAAATT
425934 A
1 A
425935 CGAATATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 17 0.63
17 4 0.15
18 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTTTATATAAATT
Found at i:436629 original size:1 final size:1
Alignment explanation
Indices: 436623--436647 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
436613 GCTCATCTCA
436623 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
436648 AAACCAAAAA
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:444152 original size:13 final size:13
Alignment explanation
Indices: 444116--444145 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
444106 AGGTGATTTA
444116 TATATATCTA-TC
1 TATATATCTATTC
444128 TATATATCTATTC
1 TATATATCTATTC
444141 TATAT
1 TATAT
444146 TATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATCTATTC
Found at i:445376 original size:40 final size:40
Alignment explanation
Indices: 445279--445376 Score: 178
Period size: 40 Copynumber: 2.5 Consensus size: 40
445269 ACTGTTCATG
* *
445279 CCACGTCAGCAAATCGCATCCTAGAGGGCGCTATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGAGGGCACTATTTGTGT
445319 CCACGTCAGCAAATCGCGTCCTAGAGGGCACTATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGAGGGCACTATTTGTGT
445359 CCACGTCAGCAAATCGCG
1 CCACGTCAGCAAATCGCG
445377 CTGACGTGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.22
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTAGAGGGCACTATTTGTGT
Found at i:447701 original size:19 final size:20
Alignment explanation
Indices: 447677--447715 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
447667 TTTTCCGGAA
*
447677 ATTTCT-GAAAATGATTTAC
1 ATTTCTGGAAAATGACTTAC
447696 ATTTCTGGAAAATGACTTAC
1 ATTTCTGGAAAATGACTTAC
447716 TGAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
ATTTCTGGAAAATGACTTAC
Found at i:447839 original size:20 final size:20
Alignment explanation
Indices: 447814--447852 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
447804 GTTATTACAT
447814 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
447834 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
447853 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:448977 original size:32 final size:32
Alignment explanation
Indices: 448931--448991 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
448921 TGTCAACCAT
448931 TTCAATAACCAACAAGCTTAAAACATAATAAA
1 TTCAATAACCAACAAGCTTAAAACATAATAAA
* *
448963 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATAACCAACAAGCTTAAAACATAAT
448992 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATAACCAACAAGCTTAAAACATAATAAA
Found at i:448998 original size:27 final size:30
Alignment explanation
Indices: 448931--449004 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
448921 TGTCAACCAT
* *
448931 TTCAATAACCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
448963 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
448991 -TCAATATCTAACAA
1 TTCAATATCTAACAA
449005 ATTCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 2 0.05
32 22 0.55
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:449015 original size:27 final size:27
Alignment explanation
Indices: 448964--449018 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
448954 CATAATAAAT
*
448964 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
448991 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
449018 T
1 T
449019 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:462416 original size:6 final size:6
Alignment explanation
Indices: 462354--462417 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
462344 AAAAGGGAAG
* * * * * *
462354 AAAAAG AAAAAT AAAAAT AAAAGT CAAAAT GAAAAT GAAAAT -GAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
462400 AAAAAT CAAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAA
462418 AAACAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 6 0.12
6 36 0.75
7 6 0.12
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:462450 original size:15 final size:15
Alignment explanation
Indices: 462391--462426 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
462381 AATGAAAATG
462391 AAAATGAAAAAAAATCA
1 AAAAT-AAAAAAAA-CA
462408 AAAATAAAAAAAACA
1 AAAATAAAAAAAACA
462423 AAAA
1 AAAA
462427 AGAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.83, C:0.06, G:0.03, T:0.08
Consensus pattern (15 bp):
AAAATAAAAAAAACA
Found at i:469401 original size:97 final size:103
Alignment explanation
Indices: 469235--469505 Score: 401
Period size: 97 Copynumber: 2.6 Consensus size: 103
469225 NNNNNNNNNN
469235 AAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
1 AAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
*
469300 TGTCGATTTTTCTCGTTCAACC-A-A-C-TA-GTTTC-
66 TGTCGATTTTTCTCGTTCAACCAATAGCATACCTTTCA
*
469332 AAAATTACAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
1 AAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
469397 TGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTCA
66 TGTCGATTTTTCTCGTTCAACC-AATAGC---ATA-CCTTTCA
* * * *
469440 AAAATTACAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGGG
1 AAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
469505 T
66 T
469506 TTTGATTTCT
Statistics
Matches: 156, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
97 86 0.55
99 1 0.01
100 1 0.01
101 1 0.01
105 2 0.01
107 4 0.03
108 61 0.39
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (103 bp):
AAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGG
TGTCGATTTTTCTCGTTCAACCAATAGCATACCTTTCA
Found at i:471854 original size:265 final size:257
Alignment explanation
Indices: 471362--471883 Score: 882
Period size: 265 Copynumber: 2.0 Consensus size: 257
471352 ATCAGGAATT
* *
471362 TTATGCGTGTAAAGGTACTGATCATTCGTGTTCCTTTGAAATGACAAAAAAATCATTTTAACATA
1 TTATGCGTGTAAAGGTACTAATCATTCGTGTTCCTTTGAAACGACAAAAAAATCATTTTAACATA
*
471427 TGGGGATCAAGGTTAATGCAAAATTTAAATATAAGTTTTCCTTGTTTTGCTTTACTTGTGGTCGA
66 TGGGGATCAAGGTTAATGCAAAATTTAAATATAAGTTTTCCTTGCTTTGCTTTACTTGTGGTCGA
*
471492 TTGGGTCATAGGGATAGCTTCTGTCCAACGAGGCTGTATAATAGAGGGTTGAATGTGGTTCTTGT
131 TTGGGTCATAGGGATAGCTTCTGTCCAACGAGGCTGTATAATAGAGGGTTGAATATGGTTCTTGT
* *
471557 ATCACGGGCTAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGACGATCCGTTTGCTCCAAA
196 ATCACAGGCTAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGACGATCCGTTTACTCCAAA
*
471619 TTATGCGTGTAAAGGTACTAATCGTTGTTCGTGTTCCTTTGAAACGACAAAAAAAAATCATTTTA
1 TTATGCGTGTAAAGGTACTAATC---ATTCGTGTTCCTTTGAAACGAC--AAAAAAATCATTTTA
*
471684 ACATATGGGGATCAAGGTTAATGCAAAATTTAAATATGAGAAGTTTTCCTTGCTTTGCTTTGCTT
61 ACATATGGGGATCAAGGTTAATGCAAAATTTAAATAT---AAGTTTTCCTTGCTTTGCTTTACTT
471749 GTGGTCGATTGGGTCATAGGGATAGCTTCTGTCCAACGAGGCTGTATAATAGAGGGTTGAATATG
123 GTGGTCGATTGGGTCATAGGGATAGCTTCTGTCCAACGAGGCTGTATAATAGAGGGTTGAATATG
* *
471814 GTTCTTGTATCACAGGCTAGACCTTTCGTCTCGCAATCCGTGCGGCCTTAGACGATCTGTTTACT
188 GTTCTTGTATCACAGGCTAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGACGATCCGTTTACT
471879 CCAAA
253 CCAAA
471884 CTCGCCTAAG
Statistics
Matches: 247, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
257 22 0.09
260 20 0.08
262 52 0.21
265 153 0.62
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (257 bp):
TTATGCGTGTAAAGGTACTAATCATTCGTGTTCCTTTGAAACGACAAAAAAATCATTTTAACATA
TGGGGATCAAGGTTAATGCAAAATTTAAATATAAGTTTTCCTTGCTTTGCTTTACTTGTGGTCGA
TTGGGTCATAGGGATAGCTTCTGTCCAACGAGGCTGTATAATAGAGGGTTGAATATGGTTCTTGT
ATCACAGGCTAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGACGATCCGTTTACTCCAAA
Found at i:480192 original size:21 final size:21
Alignment explanation
Indices: 480154--480194 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
480144 ATTTTAGCTA
*
480154 TTTTAAAATAAATTAATAAAT
1 TTTTAAAATAAATAAATAAAT
480175 TTTTAAAAT-AATCAAATAAA
1 TTTTAAAATAAAT-AAATAAA
480195 AATGGCGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTTAAAATAAATAAATAAAT
Found at i:482184 original size:33 final size:33
Alignment explanation
Indices: 482147--482231 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
482137 TACTCTATAT
*
482147 TTGGTGTGTTGGTTGGATTAGCTCTTA-TGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTC-GAGTGAGCA
* * *
482180 TTGGTGTGATGGATGGATTGGCTCGAGTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
*
482213 TCTGGTATGTTTGGTTGGA
1 T-TGGTGTG-TTGGTTGGA
482232 CTAATGATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 1 0.02
33 28 0.67
34 6 0.14
35 7 0.17
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.39
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCGAGTGAGCA
Found at i:485282 original size:11 final size:11
Alignment explanation
Indices: 485264--485298 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
485254 CTGCCCATAC
485264 TAATTTTTATA
1 TAATTTTTATA
*
485275 TTATTTTTATA
1 TAATTTTTATA
*
485286 TAATTTTAATA
1 TAATTTTTATA
485297 TA
1 TA
485299 TATAATACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:485531 original size:22 final size:22
Alignment explanation
Indices: 485506--485548 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
485496 TATCCAAATA
485506 ATAACAATAAAAT-AGTAGCAAC
1 ATAACAATAAAATGA-TAGCAAC
* *
485528 ATAATAGTAAAATGATAGCAA
1 ATAACAATAAAATGATAGCAA
485549 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATGATAGCAAC
Found at i:490767 original size:36 final size:36
Alignment explanation
Indices: 490727--490802 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
490717 AGCATTGATA
490727 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
*
490763 GCTATCTTGAGTATCATTTGTTAAACCTGATGTAAT
1 GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
490799 GCTA
1 GCTA
490803 AACGATGTAC
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:0.14, G:0.16, T:0.41
Consensus pattern (36 bp):
GCTATCTTGAGTATCATTTATTAAACCTGATGTAAT
Found at i:490817 original size:36 final size:35
Alignment explanation
Indices: 490734--490817 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 35
490724 ATAGCTATCT
* *
490734 TGAGTATCATTTATTAAACCTGATGTAATGCTATC
1 TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
* *
490769 TTGAGTATCATTTGTTAAACCTGATGTAATGCTAAAC
1 -TGAGTACCATTTATTAAACCTGATGTAATGCT-AAC
490806 -GATGTACCATTT
1 TGA-GTACCATTT
490818 CACATGTGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 2 0.05
36 39 0.91
37 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (35 bp):
TGAGTACCATTTATTAAACCTGATGTAATGCTAAC
Found at i:496705 original size:60 final size:60
Alignment explanation
Indices: 496612--496726 Score: 230
Period size: 60 Copynumber: 1.9 Consensus size: 60
496602 ATGGGTTGAT
496612 TCCAGTGTGATCGGTTTGTCATAGGTATTGCTTTCGACATGATTGATTTGTCATACTGAC
1 TCCAGTGTGATCGGTTTGTCATAGGTATTGCTTTCGACATGATTGATTTGTCATACTGAC
496672 TCCAGTGTGATCGGTTTGTCATAGGTATTGCTTTCGACATGATTGATTTGTCATA
1 TCCAGTGTGATCGGTTTGTCATAGGTATTGCTTTCGACATGATTGATTTGTCATA
496727 AGTATTGGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (60 bp):
TCCAGTGTGATCGGTTTGTCATAGGTATTGCTTTCGACATGATTGATTTGTCATACTGAC
Found at i:496732 original size:32 final size:32
Alignment explanation
Indices: 496626--496733 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 32
496616 GTGTGATCGG
*
496626 TTTGTCATAGGTATTGCTTTCGACATGATTGA
1 TTTGTCATAAGTATTGCTTTCGACATGATTGA
* * * ** * *
496658 TTTGTCAT-ACTGACTCCAGT-G---TGATCGG
1 TTTGTCATAAGT-ATTGCTTTCGACATGATTGA
*
496686 TTTGTCATAGGTATTGCTTTCGACATGATTGA
1 TTTGTCATAAGTATTGCTTTCGACATGATTGA
496718 TTTGTCATAAGTATTG
1 TTTGTCATAAGTATTG
496734 GTTTTTTTTG
Statistics
Matches: 53, Mismatches: 17, Indels: 12
0.65 0.21 0.15
Matches are distributed among these distances:
28 17 0.32
29 2 0.04
31 2 0.04
32 32 0.60
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (32 bp):
TTTGTCATAAGTATTGCTTTCGACATGATTGA
Found at i:496795 original size:22 final size:22
Alignment explanation
Indices: 496763--496814 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
496753 CCTTTTTAGG
* *
496763 TATTTTCTTAATAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
496785 TATTTTTTTAACAGTTAAAAAA
1 TATTTTTTTAACAGTTAAAAAA
496807 TATTTTTT
1 TATTTTTT
496815 AACTGGTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTTTAACAGTTAAAAAA
Found at i:504272 original size:15 final size:15
Alignment explanation
Indices: 504248--504279 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
504238 TATGCATGAA
*
504248 AAATATAAAAGACAT
1 AAATACAAAAGACAT
504263 AAATACAAAAGACAT
1 AAATACAAAAGACAT
504278 AA
1 AA
504280 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:508506 original size:27 final size:27
Alignment explanation
Indices: 508476--508719 Score: 190
Period size: 27 Copynumber: 9.1 Consensus size: 27
508466 ACACAACATC
*
508476 AAAGAATAGCCTTTGTGGCGAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* *
508503 AAAGAATAGTCTTTGTGG-AAAATCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * *
508529 AAAGAATAGTCTTTTTAGCGAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * *
508556 GAAGGATAGCCTTTGTGGAAAACTCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * * *
508583 AAAGGATAACCTTTCTGGCAAACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* * ** *
508610 AAAGAATAACCTTAGTGAAAAACTTTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
** * *
508637 AAAGGAAT-GCCTCAGTGGCGAACTCTAA
1 AAA-GAATAGCCTTTGTGGCAAACTCT-G
*
508665 AAAGAAT-GCCTTAGTGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTG
* *
508691 AAAGGGAT-GCCTTTGTGGCAAATTCTG
1 AAA-GAATAGCCTTTGTGGCAAACTCTG
508718 AA
1 AA
508720 TGGAACGATT
Statistics
Matches: 174, Mismatches: 39, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
26 25 0.14
27 142 0.82
28 7 0.04
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCAAACTCTG
Found at i:508709 original size:54 final size:55
Alignment explanation
Indices: 508479--508719 Score: 224
Period size: 54 Copynumber: 4.5 Consensus size: 55
508469 CAACATCAAA
* *
508479 GAATAGCCTTTGTGGCGAACTCTGAAAGAATAGTCTTTGTGGAAAA-TCTGAAA-
1 GAATAGCCTTTGTGGCGAACTCTGAAAGAATAGCCTTAGTGGAAAACTCTGAAAG
* * * * * * *
508532 GAATAGTCTTTTTAGCGAACTCTGGAAGGATAGCCTTTGTGGAAAACTCTAAAAG
1 GAATAGCCTTTGTGGCGAACTCTGAAAGAATAGCCTTAGTGGAAAACTCTGAAAG
* * * * * * *
508587 G-ATAACCTTTCTGGCAAACTTTGAAAGAATAACCTTAGTGAAAAACTTTGAAAG
1 GAATAGCCTTTGTGGCGAACTCTGAAAGAATAGCCTTAGTGGAAAACTCTGAAAG
** * *
508641 GAAT-GCCTCAGTGGCGAACTCTAAAAAGAAT-GCCTTAGTGGCAAACTCTGAAAG
1 GAATAGCCTTTGTGGCGAACTCT-GAAAGAATAGCCTTAGTGGAAAACTCTGAAAG
* * *
508695 GGAT-GCCTTTGTGGCAAATTCTGAA
1 GAATAGCCTTTGTGGCGAACTCTGAA
508720 TGGAACGATT
Statistics
Matches: 147, Mismatches: 37, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
53 42 0.29
54 95 0.65
55 10 0.07
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (55 bp):
GAATAGCCTTTGTGGCGAACTCTGAAAGAATAGCCTTAGTGGAAAACTCTGAAAG
Found at i:524839 original size:109 final size:109
Alignment explanation
Indices: 524652--525178 Score: 691
Period size: 109 Copynumber: 4.8 Consensus size: 109
524642 TTAAAAAACG
* *
524652 AGGCGATATATTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGTGCTGGGTTTCGATTTTT
1 AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAA--TGTGCTGGGTTTCGATTTTT
* * *
524717 CTAGTTCGACCAAATAGCCAAATATCCTTTTAAAAAATTCAAAATA
64 CTCGCTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATA
* * * * *
524763 AGGCAATGTTTTGCATCTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
* *
524828 TGCTCAACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATA
66 CGCTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATA
* * ** *
524872 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATACGCTGCGTTTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
* **
524937 CGCTCGACCAAATAGCCAAATAT-CTTTTCAAAAATTTTAAAAGG
66 CGCTCGACCAAATAGCCAAATATCCTTTT-AAAAATTTCAAAATA
* *
524981 AGGCGATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTTGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
* * **
525046 CGCTCGACCAAATAGCCAAATATCCTTTCAAAAATTTTAAAACG
66 CGCTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATA
* * * * * * *
525090 AGGCAATATTTTGTGTTTGGAAACTAGAGAAAACGTTCCCTAATGCGTTGGGTTTCGA-TTTT-T
1 AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
* *
525153 CGTTGGACCAAATAGCCAAATATCCT
66 CGCTCGACCAAATAGCCAAATATCCT
525179 CTTATATCTT
Statistics
Matches: 372, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
107 25 0.07
108 9 0.02
109 298 0.80
110 4 0.01
111 36 0.10
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
AGGCAATATTTTGCGTTTGGAAAGTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
CGCTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATA
Found at i:526363 original size:7 final size:7
Alignment explanation
Indices: 526351--526401 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
526341 TGGATTACTA
526351 TTTAGGG
1 TTTAGGG
526358 TTTAGGG
1 TTTAGGG
*
526365 TTTACGG
1 TTTAGGG
*
526372 TATA-GG
1 TTTAGGG
*
526378 TTTAGTG
1 TTTAGGG
**
526385 TTTTTGG
1 TTTAGGG
526392 TTTAGGG
1 TTTAGGG
526399 TTT
1 TTT
526402 GAGAGTTTGG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.14, C:0.02, G:0.33, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:526536 original size:7 final size:7
Alignment explanation
Indices: 526526--526603 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
526516 AGAGTTTTGA
526526 GTTTAGG
1 GTTTAGG
*
526533 GTTTATG
1 GTTTAGG
* *
526540 ATGTAGG
1 GTTTAGG
* *
526547 TTTTGGTG
1 GTTTAG-G
526555 GTTT-GG
1 GTTTAGG
526561 GTTTAGG
1 GTTTAGG
*
526568 GTTTAGAA
1 GTTTAG-G
526576 GTTTAGG
1 GTTTAGG
* *
526583 ATTTAAG
1 GTTTAGG
*
526590 GTTTGGG
1 GTTTAGG
526597 GTTTAGG
1 GTTTAGG
526604 CTGCTTTAGT
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
6 5 0.10
7 37 0.71
8 10 0.19
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:531997 original size:21 final size:21
Alignment explanation
Indices: 531971--532060 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
531961 CTACAACTTA
*
531971 AAGCAGAGGCGGTAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
*
531992 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
* * * *
532013 AAGCAGAGGCTGCAACAAGAG
1 AAGCAGAGGCGGCAGCGAGGG
* * *
532034 AAGCAAAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGGG
532055 AAGCAG
1 AAGCAG
532061 CGAGAGAAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.36, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:532062 original size:12 final size:12
Alignment explanation
Indices: 532045--532072 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
532035 AGCAAAGGCT
532045 GCAGCGAGAGAA
1 GCAGCGAGAGAA
532057 GCAGCGAGAGAA
1 GCAGCGAGAGAA
532069 GCAG
1 GCAG
532073 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:532610 original size:42 final size:41
Alignment explanation
Indices: 532447--532721 Score: 207
Period size: 42 Copynumber: 6.4 Consensus size: 41
532437 AATCCCAAAA
* * *
532447 TTAGTGGCGTTTTTTTATAAAAGCGCCGCTAAA-AGTCATGTTCT
1 TTAGCGGCG-TTTTTTAT--AAGCGCCGCTAAAGA-ACATGATCT
* **
532491 ATAGCGGCGTTTGTGAAGTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTT-TTTA-TAAGCGCCGCTAAAGAACATGATCT
* * * * * *
532534 GTAGCGGCGTTTTTTACCAAGTGCCACTATAGAACATTA-CTT
1 TTAGCGGCGTTTTTTA-TAAGCGCCGCTAAAGAACATGATC-T
*
532576 TTAGCGGCGTTTCTGTT-TAAGCGCCGCTAAAGAACATGATCA
1 TTAGCGGCGTTT-T-TTATAAGCGCCGCTAAAGAACATGATCT
* *
532618 TTAGCGGCGTCTTTTTTTAAGCGATAAGCACCGCTAAAGGACATGATCT
1 TTAGCGGCG---TTTTTT-----ATAAGCGCCGCTAAAGAACATGATCT
* *
532667 TTAGCGGCGTTTTTTGT-AGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTTTATAAGCGCCGCTAAAGAACATGATCT
532707 TTAGCGGCGTTTTTT
1 TTAGCGGCGTTTTTT
532722 TTTGTAAACG
Statistics
Matches: 186, Mismatches: 29, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
40 35 0.19
41 2 0.01
42 57 0.31
43 38 0.20
44 13 0.07
45 4 0.02
46 6 0.03
49 31 0.17
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTATAAGCGCCGCTAAAGAACATGATCT
Found at i:534874 original size:26 final size:26
Alignment explanation
Indices: 534836--535058 Score: 216
Period size: 26 Copynumber: 8.6 Consensus size: 26
534826 CCTGAATAGA
*
534836 AGGCCTTGAGCCGGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
534862 ATGCCTTGAGCCGGTGTTTGTTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
534888 AGGCTTTGAGCCAGTGATTACTTAGT
1 AGGCTTTGAGCCGGTGTTTATTTAGC
** * *
534914 AGGCTTTGAGCTAGTGATTACTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
534940 AGGCTATGAGTCTGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * * *
534966 AGGCTTTGAGCTGATGATTATTTAAC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
534992 AGGCTTTGAGCCGATGTTTA-TTAGA
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
535017 AGACTTTGAGTCGGTGTTTATCTT-GC
1 AGGCTTTGAGCCGGTGTTTAT-TTAGC
535043 AGGCTTTGAGCCGGTG
1 AGGCTTTGAGCCGGTG
535059 AATGTTTATC
Statistics
Matches: 161, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
25 20 0.12
26 139 0.86
27 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.29, T:0.37
Consensus pattern (26 bp):
AGGCTTTGAGCCGGTGTTTATTTAGC
Found at i:541377 original size:65 final size:63
Alignment explanation
Indices: 541255--541452 Score: 218
Period size: 70 Copynumber: 3.0 Consensus size: 63
541245 AAGTGATAAA
* * * *
541255 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACACTTTCATAT
1 TTCTTCACTATTTTCATTAAAAAAGTTAATTTTAA-CCACATTGACTAGAGAATACTTTCATAT
*
541318 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTTGTAA
1 TTCTTCACTATTTTCATTAAAAAAGTTAATTTTAAC-C-ACATTGACTAGAGAATAC--TT-T--
*
541383 CTTAT
59 CATAT
* * *
541388 TTCTTCACTATTTTCATTAAACACGCTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCACTATTTTCATTAAAAAAGTTAATTTTAACCA--CATTGACTAGAGAATACTTTCATAT
541453 CTCACTTTTT
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
63 17 0.15
64 16 0.14
65 20 0.18
67 3 0.03
68 4 0.04
69 1 0.01
70 53 0.46
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (63 bp):
TTCTTCACTATTTTCATTAAAAAAGTTAATTTTAACCACATTGACTAGAGAATACTTTCATAT
Found at i:541407 original size:70 final size:66
Alignment explanation
Indices: 541255--541482 Score: 205
Period size: 70 Copynumber: 3.4 Consensus size: 66
541245 AAGTGATAAA
* * * * * *
541255 TTCTTCATTATTTTCATT-AAAAAGTTAATTTTAATTCACATTGATTAGAGAACAC--TTT-CAT
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAA-CCACATTGACTAGAGAATACTTTTTACTT
541316 AT
65 AT
541318 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACGCTACATTGACTAGAGAATACTTTTGTAA
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAAC-C-ACATTGACTAGAGAATACTTTT-T-A
541383 CTTAT
62 CTTAT
* *** *
541388 TTCTTCACTATTTTCATTAAACACGCTAATTTTAACCACCCATTGACTAGAGAATACTTTCATAT
1 TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCA--CATTGACTAGAGAATACTTT-TTA-
*
541453 CTCACT
62 CTTA-T
* *
541459 TT-TTTACTATTTTTATTAAAAAAA
1 TTCTTCACTATTTTCATTAAAAAAA
541483 AGTTAAATTT
Statistics
Matches: 135, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
63 17 0.13
64 16 0.12
65 16 0.12
67 2 0.01
68 2 0.01
69 2 0.01
70 77 0.57
71 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (66 bp):
TTCTTCACTATTTTCATTAAAAAAATTAATTTTAACCACATTGACTAGAGAATACTTTTTACTTA
T
Found at i:541784 original size:94 final size:93
Alignment explanation
Indices: 541568--541789 Score: 236
Period size: 94 Copynumber: 2.4 Consensus size: 93
541558 TTTAATCTTC
* * * *
541568 TTAAAAAGTTAATTTTAATTCCTCATTTG-CTAGAGAACATTCTCATGCTCACACTTATCTTATA
1 TTAAAAAGTTGATTTTAATTCCTCA-TTGACTAGAAAACACTCTCATGCTCACACTTACCTTATA
*
541632 AATAAGTGCCAATTTCTTCACTATTTTAA
65 AATAAGTGACAATTTCTTCACTATTTTAA
* * * * * *
541661 TTAAAAAAATTGAATTCAATCCCAT-ATTGACTAGAAAACACTCTCATATCTC-CATTTACCTTA
1 TT-AAAAAGTTGATTTTAATTCC-TCATTGACTAGAAAACACTCTCAT-GCTCACACTTACCTTA
*
541724 -AAAGTAAGTGACAATTTCTTCACTATTTTTTA
63 TAAA-TAAGTGACAATTTCTTCACTA-TTTTAA
* *
541756 TTAAAAAGTTGATTTTAGTTCCTCATTGATTAGA
1 TTAAAAAGTTGATTTTAATTCCTCATTGACTAGA
541790 GAGTATCCTC
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
93 9 0.09
94 84 0.81
95 11 0.11
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (93 bp):
TTAAAAAGTTGATTTTAATTCCTCATTGACTAGAAAACACTCTCATGCTCACACTTACCTTATAA
ATAAGTGACAATTTCTTCACTATTTTAA
Found at i:542342 original size:9 final size:9
Alignment explanation
Indices: 542328--542358 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
542318 GTTAAACAAA
542328 TCGAGTTAT
1 TCGAGTTAT
*
542337 TCGAGTTAA
1 TCGAGTTAT
542346 TCGAGTTAT
1 TCGAGTTAT
542355 TCGA
1 TCGA
542359 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:542429 original size:9 final size:9
Alignment explanation
Indices: 542412--542448 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
542402 TGAGTTTTTG
542412 AATTCGAAT
1 AATTCGAAT
*
542421 AACTCGAAT
1 AATTCGAAT
542430 AATTCGAAT
1 AATTCGAAT
542439 AATTCGAAT
1 AATTCGAAT
542448 A
1 A
542449 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:543258 original size:5 final size:5
Alignment explanation
Indices: 543248--543273 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
543238 CTCGAAAATT
543248 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
543274 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:547053 original size:18 final size:18
Alignment explanation
Indices: 547030--547064 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
547020 TAATGCTTAT
547030 TGAGCCATCACATATCCG
1 TGAGCCATCACATATCCG
*
547048 TGAGCCATCATATATCC
1 TGAGCCATCACATATCC
547065 ATCCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (18 bp):
TGAGCCATCACATATCCG
Found at i:558709 original size:24 final size:24
Alignment explanation
Indices: 558654--558703 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
558644 CACCCAATGA
558654 ATGTAGTGGTATTAAGTCCACGAG
1 ATGTAGTGGTATTAAGTCCACGAG
*
558678 ATGTAGTGGTTTTAAGTCCACGAG
1 ATGTAGTGGTATTAAGTCCACGAG
558702 AT
1 AT
558704 AGAGTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (24 bp):
ATGTAGTGGTATTAAGTCCACGAG
Found at i:560854 original size:43 final size:43
Alignment explanation
Indices: 560662--560834 Score: 258
Period size: 43 Copynumber: 4.0 Consensus size: 43
560652 ATGCCGTTAT
* * *
560662 AGAACATGACCTTTAGCGGTGC-TTTACCCACAAACGCCGCTAA
1 AGAACATGATCTTTAGCGGCGCTTTTA-TCACAAACGCCGCTAA
* *
560705 AGAACATGATCTTTAGCGGAGCTTTTATCACAAATGCCGCTAA
1 AGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* *
560748 AGAACATGACCTGTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
*
560791 AGAACATGTTCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
560834 A
1 A
560835 AGTACCGTTC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 114 0.97
44 4 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
AGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
Found at i:561029 original size:21 final size:21
Alignment explanation
Indices: 561005--561067 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
560995 TAACTGAAGT
561005 ATAATTTAAAATATTATTACA
1 ATAATTTAAAATATTATTACA
*
561026 ATAATTTTAAA-ATTA--ACA
1 ATAATTTAAAATATTATTACA
* * *
561044 AT-GTTAAAAATATTCTTACA
1 ATAATTTAAAATATTATTACA
561064 ATAA
1 ATAA
561068 GAAAACAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.16
18 8 0.25
20 9 0.28
21 10 0.31
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATTTAAAATATTATTACA
Found at i:562565 original size:42 final size:43
Alignment explanation
Indices: 562514--562609 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
562504 TGAGATTTAT
* *
562514 GTGTAAGACCATGTCTAAGACATTGGCGTC-GTATGTGATTAC
1 GTGTAAGACCATGTCTAAGACAGTGGCATCAGTATGTGATTAC
* ** * *
562556 GTGTAAGACCCTGTCTGGGACAGTGGCATCATTATTTGATTAC
1 GTGTAAGACCATGTCTAAGACAGTGGCATCAGTATGTGATTAC
*
562599 ATGTAAGACCA
1 GTGTAAGACCA
562610 CGTCCGGGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTAAGACAGTGGCATCAGTATGTGATTAC
Found at i:563222 original size:2 final size:2
Alignment explanation
Indices: 563215--563240 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
563205 TGATGCAAAG
563215 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
563241 GGTATGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:563483 original size:44 final size:44
Alignment explanation
Indices: 563420--563585 Score: 253
Period size: 44 Copynumber: 3.8 Consensus size: 44
563410 TGAAGTAAAT
563420 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
1 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
* **
563464 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGTTGCCCAAA
1 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
* * * *
563508 TGTTGATTGAATGTTGTCCGATTGTTGATTAAATGCTTTTCAAA
1 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
*
563552 TGTT-ATTGAATGTTGTCCAATTGTTGATTAAATG
1 TGTTGATTGAATGCTGTCCAATTGTTGATTAAATG
563586 TTGTTCGAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 29 0.26
44 83 0.74
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (44 bp):
TGTTGATTGAATGCTGTCCAATTGTTGATTAAATGCTATCCAAA
Found at i:563586 original size:22 final size:22
Alignment explanation
Indices: 563417--563589 Score: 197
Period size: 22 Copynumber: 7.9 Consensus size: 22
563407 AAGTGAAGTA
* *
563417 AATTGTTGATTGAATGCTGTCC
1 AATTGTTGATTAAATGTTGTCC
* *
563439 AATTGTTGATTAAATGCTATCC
1 AATTGTTGATTAAATGTTGTCC
* * *
563461 AAATGTTGATTGAATGCTGTCC
1 AATTGTTGATTAAATGTTGTCC
*
563483 AATTGTTGATTAAATGTTGCCC
1 AATTGTTGATTAAATGTTGTCC
* *
563505 AAATGTTGATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCC
* *
563527 GATTGTTGATTAAATGCTT-TTC
1 AATTGTTGATTAAATG-TTGTCC
* *
563549 AAATGTT-ATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCC
563570 AATTGTTGATTAAATGTTGT
1 AATTGTTGATTAAATGTTGT
563590 TCGAATGTTG
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.02
21 15 0.12
22 107 0.85
23 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (22 bp):
AATTGTTGATTAAATGTTGTCC
Found at i:565646 original size:3 final size:3
Alignment explanation
Indices: 565638--565678 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
565628 AAAGTATTTC
*
565638 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
565679 TTAATGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:566382 original size:21 final size:21
Alignment explanation
Indices: 566356--566397 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
566346 GTTTGCAAAG
*
566356 TTAGGGGTTTCGGGGGGGAAA
1 TTAGGGGTTTCAGGGGGGAAA
*
566377 TTAGGGGTTTTAGGGGGGAAA
1 TTAGGGGTTTCAGGGGGGAAA
566398 ATTTGGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.02, G:0.50, T:0.26
Consensus pattern (21 bp):
TTAGGGGTTTCAGGGGGGAAA
Found at i:566399 original size:22 final size:21
Alignment explanation
Indices: 566356--566405 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
566346 GTTTGCAAAG
* *
566356 TTAGGGGTTTCGGGGGGGAAA
1 TTAGGGGTTTAGGGGGGAAAA
566377 TTAGGGGTTTTAGGGGGGAAAA
1 TTAGGGG-TTTAGGGGGGAAAA
*
566399 TTTGGGG
1 TTAGGGG
566406 ATAAAACGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.20, C:0.02, G:0.50, T:0.28
Consensus pattern (21 bp):
TTAGGGGTTTAGGGGGGAAAA
Found at i:567317 original size:7 final size:7
Alignment explanation
Indices: 567307--567460 Score: 66
Period size: 7 Copynumber: 21.6 Consensus size: 7
567297 CATAAAATAG
567307 AAACCCT
1 AAACCCT
567314 AAACCCCT
1 AAA-CCCT
*
567322 AACCCCT
1 AAACCCT
567329 -AACCCTT
1 AAACCC-T
567336 AAACACC-
1 AAAC-CCT
*
567343 -AACTCTT
1 AAAC-CCT
*
567350 AAACCAT
1 AAACCCT
*
567357 AAACCAT
1 AAACCCT
*
567364 AAACCAT
1 AAACCCT
*
567371 AATCCCT
1 AAACCCT
567378 AAACCCAT
1 AAACCC-T
* *
567386 AATCCAT
1 AAACCCT
*
567393 AAACCTT
1 AAACCCT
*
567400 AAA--AT
1 AAACCCT
567405 AGTAACTCCT
1 A--AAC-CCT
*
567415 AAACCAT
1 AAACCCT
*
567422 AAAACCT
1 AAACCCT
*
567429 AAACCAT
1 AAACCCT
*
567436 ATACCCT
1 AAACCCT
*
567443 AAACCAT
1 AAACCCT
567450 AAACCCT
1 AAACCCT
567457 AAAC
1 AAAC
567461 TATAATGATA
Statistics
Matches: 111, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
5 2 0.02
6 8 0.07
7 77 0.69
8 20 0.18
9 2 0.02
10 2 0.02
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:567361 original size:50 final size:50
Alignment explanation
Indices: 567263--567368 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
567253 TAATATATAG
* * *
567263 TAAACCCCTAACCCATATCCCTTAAACCCTAAATCATAAAATAGAAACCC
1 TAAACCCCTAACCCATAACCCTTAAACCCTAAATCATAAAACAGAAACCA
* * * * *
567313 TAAACCCCTAACCCCTAACCCTTAAACACC-AACTCTTAAACCATAAACCA
1 TAAACCCCTAACCCATAACCCTTAAAC-CCTAAATCATAAAACAGAAACCA
567363 TAAACC
1 TAAACC
567369 ATAATCCCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.43, C:0.37, G:0.01, T:0.19
Consensus pattern (50 bp):
TAAACCCCTAACCCATAACCCTTAAACCCTAAATCATAAAACAGAAACCA
Found at i:567366 original size:14 final size:14
Alignment explanation
Indices: 567349--567465 Score: 87
Period size: 14 Copynumber: 8.2 Consensus size: 14
567339 CACCAACTCT
567349 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
567363 TAAACCATAATCCC
1 TAAACCATAAACCA
*
567377 TAAACCCATAATCCA
1 TAAA-CCATAAACCA
*
567392 TAAACCTTAAA--A
1 TAAACCATAAACCA
*
567404 TAGTAACTCCTAAACCA
1 TA--AAC-CATAAACCA
567421 TAAAACC-TAAACCA
1 T-AAACCATAAACCA
* *
567435 TATACCCTAAACCA
1 TAAACCATAAACCA
* *
567449 TAAACCCTAAACTA
1 TAAACCATAAACCA
567463 TAA
1 TAA
567466 TGATAATTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
12 3 0.03
13 4 0.05
14 54 0.63
15 19 0.22
16 3 0.03
17 2 0.02
18 1 0.01
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:567937 original size:40 final size:41
Alignment explanation
Indices: 567882--567987 Score: 144
Period size: 40 Copynumber: 2.6 Consensus size: 41
567872 TTTTTACGGG
* *
567882 GTTTTTCAAAAAGCGCCGCTAATGCTCAATCT-ATAGCTG-C
1 GTTTTTCAAAAAGCGCCGCTAATGCTCAACCTAATAAC-GAC
*
567922 GTTTTTCAAGAAGCGCCGCTAATGCTCAACCTAATAACGAC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCAACCTAATAACGAC
* *
567963 GATTTTCAAAAAGCGCCGTTAATGC
1 GTTTTTCAAAAAGCGCCGCTAATGC
567988 CACTAAAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 31 0.53
41 27 0.47
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (41 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCAACCTAATAACGAC
Found at i:568056 original size:154 final size:155
Alignment explanation
Indices: 567809--568102 Score: 362
Period size: 154 Copynumber: 1.9 Consensus size: 155
567799 ATATAGCGGC
* * *
567809 ATTTTACAAAAAGCGTCGTTAATGCCACTAAAGCTCAACATAAAACGACAGTGTCTTACTGAATT
1 ATTTTACAAAAAGCGCCGTTAATGCCACTAAAGATCAACATAAAACGACAGCGTCTTACTGAATT
* * * * *
567874 TTTACGGGGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGCTGCGTTTTTCAAGAAGCGCC
66 TTTACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCATTTTTCAAAAAGCGCC
567939 GCTAATGCTCAACCTAATAACGACG
131 GCTAATGCTCAACCTAATAACGACG
* * * * *
567964 ATTTT-CAAAAAGCGCCGTTAATGCCACTAAA-ATGAACATAAAATGACGGCGT-TGTGCTTAAT
1 ATTTTACAAAAAGCGCCGTTAATGCCACTAAAGATCAACATAAAACGACAGCGTCT-TACTGAA-
* * * * *
568026 TTTTTTGCGGCGTTTTT-AAAAGGCGCCGCTAATGGTCGACCTATAGCGGCATTTTTCAAAAAGT
64 -TTTTTACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCATTTTTCAAAAAGC
*
568090 GTCGCTAATGCTC
128 GCCGCTAATGCTC
568103 GATCTATAGA
Statistics
Matches: 117, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
152 1 0.01
153 21 0.18
154 76 0.65
155 19 0.16
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (155 bp):
ATTTTACAAAAAGCGCCGTTAATGCCACTAAAGATCAACATAAAACGACAGCGTCTTACTGAATT
TTTACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCATTTTTCAAAAAGCGCC
GCTAATGCTCAACCTAATAACGACG
Found at i:568075 original size:39 final size:39
Alignment explanation
Indices: 568032--568122 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
568022 TAATTTTTTT
* * *
568032 GCGGCGTTTTTAAAAGGCGCCGCTAATGGTCGACCTATA
1 GCGGCATTTTTAAAAAGCGCCGCTAATGCTCGACCTATA
* * *
568071 GCGGCATTTTTCAAAAAGTGTCGCTAATGCTCGATCTATA
1 GCGGCATTTTT-AAAAAGCGCCGCTAATGCTCGACCTATA
* *
568111 GAGGCTTTTTTA
1 GCGGCATTTTTA
568123 TCCAAACACC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 11 0.26
40 32 0.74
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (39 bp):
GCGGCATTTTTAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:577404 original size:30 final size:30
Alignment explanation
Indices: 577370--577429 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
577360 GAGTGAATGA
577370 GAGATAGAATTAAATCTTATCGAGTCTATT
1 GAGATAGAATTAAATCTTATCGAGTCTATT
577400 GAGATAGAATTAAATCTTATCGAGTCTATT
1 GAGATAGAATTAAATCTTATCGAGTCTATT
577430 TTCACATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (30 bp):
GAGATAGAATTAAATCTTATCGAGTCTATT
Found at i:584061 original size:37 final size:37
Alignment explanation
Indices: 583967--584085 Score: 109
Period size: 37 Copynumber: 3.2 Consensus size: 37
583957 CCAACTGAAG
*
583967 CACGCCAATTGCT-TGTAAGAGCTAATCCAACCGATAA
1 CACGCCAATTGCTCAG-AAGAGCTAATCCAACCGATAA
* * * *
584004 CACCCCTGA-TACTCATAAGAGCTAATCC-ACACGATAA
1 CACGCC-AATTGCTCAGAAGAGCTAATCCAAC-CGATAA
* * *
584041 CACGCCAATTGCTCCGAAGAGCTAGTCCAACCGAAAA
1 CACGCCAATTGCTCAGAAGAGCTAATCCAACCGATAA
*
584078 CACACCAA
1 CACGCCAA
584086 AACAAAGAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
36 3 0.05
37 58 0.91
38 3 0.05
ACGTcount: A:0.37, C:0.32, G:0.14, T:0.17
Consensus pattern (37 bp):
CACGCCAATTGCTCAGAAGAGCTAATCCAACCGATAA
Found at i:593551 original size:20 final size:21
Alignment explanation
Indices: 593526--593566 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
593516 TTTATCATAC
593526 ATGTC-AAATCTTTTA-GATTT
1 ATGTCAAAAT-TTTTAGGATTT
593546 ATGTCAAAATTTTTAGGATTT
1 ATGTCAAAATTTTTAGGATTT
593567 CAATTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (21 bp):
ATGTCAAAATTTTTAGGATTT
Found at i:593572 original size:27 final size:27
Alignment explanation
Indices: 593542--593593 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
593532 AATCTTTTAG
*
593542 ATTTATGTCAAAATTTTTAGGATTTCA
1 ATTTATGTCAAAATTTTAAGGATTTCA
* * *
593569 ATTTGTTTTAAAATTTTAAGGATTT
1 ATTTATGTCAAAATTTTAAGGATTT
593594 AAAATATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.52
Consensus pattern (27 bp):
ATTTATGTCAAAATTTTAAGGATTTCA
Found at i:604777 original size:25 final size:25
Alignment explanation
Indices: 604731--604779 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
604721 CTATTTTTGA
* *
604731 TAGTATATCCTAAAACTGCTATAGG
1 TAGTATATACTAAAACTACTATAGG
* *
604756 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTAAAACTACTATAG
604780 ATAGACTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (25 bp):
TAGTATATACTAAAACTACTATAGG
Found at i:613243 original size:23 final size:24
Alignment explanation
Indices: 613209--613253 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
613199 ATAACATAGC
*
613209 TAAATTATATATAATATTTTTTCA
1 TAAATTATATATAATAATTTTTCA
613233 TAAA-TATATATAATAATTTTT
1 TAAATTATATATAATAATTTTT
613254 GCTCCCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTATATATAATAATTTTTCA
Found at i:615740 original size:14 final size:13
Alignment explanation
Indices: 615721--615750 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
615711 TGATAAAGTT
615721 TATATAAATATAAA
1 TATATAAAT-TAAA
615735 TATATAAATTAAA
1 TATATAAATTAAA
615748 TAT
1 TAT
615751 GAATGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATAAATTAAA
Found at i:620578 original size:5 final size:5
Alignment explanation
Indices: 620568--620599 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
620558 TGACATGTAT
620568 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
620600 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:621514 original size:121 final size:121
Alignment explanation
Indices: 621383--621616 Score: 468
Period size: 121 Copynumber: 1.9 Consensus size: 121
621373 TATCATGAGT
621383 GTAGTAAAATGACATATTATATATTTTTGTATGTGTATTTGAAATATTTCACTTATAAACATAAT
1 GTAGTAAAATGACATATTATATATTTTTGTATGTGTATTTGAAATATTTCACTTATAAACATAAT
621448 GATATTTGAAATATTTCATGTCACATACCGAAAATCGAGTTAGAAGAATCCATATC
66 GATATTTGAAATATTTCATGTCACATACCGAAAATCGAGTTAGAAGAATCCATATC
621504 GTAGTAAAATGACATATTATATATTTTTGTATGTGTATTTGAAATATTTCACTTATAAACATAAT
1 GTAGTAAAATGACATATTATATATTTTTGTATGTGTATTTGAAATATTTCACTTATAAACATAAT
621569 GATATTTGAAATATTTCATGTCACATACCGAAAATCGAGTTAGAAGAA
66 GATATTTGAAATATTTCATGTCACATACCGAAAATCGAGTTAGAAGAA
621617 ATTGGGTTAG
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (121 bp):
GTAGTAAAATGACATATTATATATTTTTGTATGTGTATTTGAAATATTTCACTTATAAACATAAT
GATATTTGAAATATTTCATGTCACATACCGAAAATCGAGTTAGAAGAATCCATATC
Found at i:624878 original size:43 final size:43
Alignment explanation
Indices: 624815--624961 Score: 149
Period size: 43 Copynumber: 3.4 Consensus size: 43
624805 TCCTGAGGTG
*
624815 TGATTTCATGTAAGACCATGTTTGGGACATTTGCATCGATATGA
1 TGATTACATGTAAGACCATGTTTGGGACA-TTGCATCGATATGA
* * *
624859 -GATTACGTGTAAGATCATGTCTGGGACATTGACATC-ATAT-A
1 TGATTACATGTAAGACCATGTTTGGGACATTG-CATCGATATGA
* * * *
624900 TGATTTCATATAAGACCTTGTTTGGGACAGTGGCATCGATATG-
1 TGATTACATGTAAGACCATGTTTGGGACA-TTGCATCGATATGA
* *
624943 TGATAACAAGTAAGACCAT
1 TGATTACATGTAAGACCAT
624962 ATCTAGGATA
Statistics
Matches: 82, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 33 0.40
43 48 0.59
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTTTGGGACATTGCATCGATATGA
Found at i:626840 original size:14 final size:14
Alignment explanation
Indices: 626821--626854 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
626811 TGATGATGAA
626821 TGTATCAAATGTGT
1 TGTATCAAATGTGT
626835 TGTATCAAATGTGT
1 TGTATCAAATGTGT
626849 TGTATC
1 TGTATC
626855 TTTTTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (14 bp):
TGTATCAAATGTGT
Found at i:632798 original size:10 final size:10
Alignment explanation
Indices: 632755--632789 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
632745 ATGCATTAAC
*
632755 CACATATAGT
1 CACATATAAT
*
632765 CACAAATAAT
1 CACATATAAT
632775 CACATATAAT
1 CACATATAAT
632785 CACAT
1 CACAT
632790 TTAGTCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (10 bp):
CACATATAAT
Found at i:635109 original size:26 final size:27
Alignment explanation
Indices: 635052--635184 Score: 103
Period size: 27 Copynumber: 5.0 Consensus size: 27
635042 TAAAATTATT
* * * *
635052 GAAATACCCTTGAAGGGTAAAATAATC
1 GAAATACCCTCGATGGGTAAAATGACC
*
635079 AAAATACCCTCGATGGGT-AAATGACC
1 GAAATACCCTCGATGGGTAAAATGACC
*
635105 GAAATACCTTCGATGGGTAAAATGACC
1 GAAATACCCTCGATGGGTAAAATGACC
* **
635132 GTAATGGTCCT-G-TAGGGTAAAATGACC
1 GAAAT-ACCCTCGAT-GGGTAAAATGACC
* * *
635159 GTAATGCCC-CTATAGGGTAAAATGAC
1 GAAATACCCTCGAT-GGGTAAAATGAC
635185 TGTAACACCC
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
26 26 0.30
27 60 0.68
28 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (27 bp):
GAAATACCCTCGATGGGTAAAATGACC
Found at i:635149 original size:27 final size:27
Alignment explanation
Indices: 635119--635319 Score: 276
Period size: 27 Copynumber: 7.4 Consensus size: 27
635109 TACCTTCGAT
** *
635119 GGGTAAAATGACCGTAATGGTCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
635146 GGGTAAAATGACCGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
* ** *
635173 GGGTAAAATGACTGTAACACCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
*
635200 GGGTAAAATGACCGTAATGCACCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
*
635227 GGGTAAAATAACCGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
* * *
635254 GGGTAAAATAACTGTAATGCCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTATA
**
635281 GGGTAAAATGATTGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTATA
635308 GGGTAAAATGAC
1 GGGTAAAATGAC
635320 TATTTTGCCC
Statistics
Matches: 154, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 154 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATGCCCCTATA
Found at i:635331 original size:81 final size:81
Alignment explanation
Indices: 635119--635319 Score: 312
Period size: 81 Copynumber: 2.5 Consensus size: 81
635109 TACCTTCGAT
** * *
635119 GGGTAAAATGACCGTAATGGTCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGA
1 GGGTAAAATGACCGTAATGCACCTATAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATAA
635184 CTGTAACACCCCTGTA
66 CTGTAACACCCCTGTA
*
635200 GGGTAAAATGACCGTAATGCACCTATAGGGTAAAATAACCGTAATGCCCCTATAGGGTAAAATAA
1 GGGTAAAATGACCGTAATGCACCTATAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATAA
**
635265 CTGTAATGCCCCTGTA
66 CTGTAACACCCCTGTA
** *
635281 GGGTAAAATGATTGTAATGCCCCTATAGGGTAAAATGAC
1 GGGTAAAATGACCGTAATGCACCTATAGGGTAAAATGAC
635320 TATTTTGCCC
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (81 bp):
GGGTAAAATGACCGTAATGCACCTATAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATAA
CTGTAACACCCCTGTA
Found at i:635371 original size:24 final size:24
Alignment explanation
Indices: 635336--635444 Score: 96
Period size: 24 Copynumber: 4.6 Consensus size: 24
635326 GCCCCTTGGG
*
635336 GTAAA-GATTGATTTGTCTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
* * ***
635359 GTAAATAAATGATTTGTCCAAGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
635383 GTAAATGACTGATTTGTTTGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
635407 TTAAATGACTGATTT-TCCTGTGAT
1 GTAAATGACTGATTTGT-CTGTGAT
* **
635431 TTGTATGACTGATT
1 GTAAATGACTGATT
635445 CCGTGCATGG
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
23 6 0.09
24 63 0.91
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.43
Consensus pattern (24 bp):
GTAAATGACTGATTTGTCTGTGAT
Found at i:635546 original size:27 final size:27
Alignment explanation
Indices: 635508--635578 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
635498 ATGGAAGAAG
*
635508 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTAGCT-TGGCCACATA
635533 TCACTGTTACTGGTAGCTTGGCCACATA
1 T-ACTGTTACTGGTAGCTTGGCCACATA
*
635561 TACTGTTACTGGCAGCTT
1 TACTGTTACTGGTAGCTT
635579 TGCTACGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 1 0.03
26 5 0.12
27 32 0.80
28 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTAGCTTGGCCACATA
Found at i:635644 original size:32 final size:32
Alignment explanation
Indices: 635593--635779 Score: 221
Period size: 32 Copynumber: 5.8 Consensus size: 32
635583 ACGATGCTAT
* * * *
635593 TGATGGCTTTCTGCAGATCATATTACCATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * *
635625 TGGTGGCTATGTGCCGATCATATTACCATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * * *
635657 TGATGGTTGTCTGCCGATTATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
635689 TGATGGCTTTGTGCCGATCATACTACTATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
635721 TGATGGTTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
635753 TGATGGCTTTGTGCCAATCATATTACT
1 TGATGGCTGTGTGCCGATCATATTACT
635780 GTACTTATGG
Statistics
Matches: 131, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 131 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.38
Consensus pattern (32 bp):
TGATGGCTGTGTGCCGATCATATTACTATTAC
Found at i:635680 original size:64 final size:64
Alignment explanation
Indices: 635593--635778 Score: 266
Period size: 64 Copynumber: 2.9 Consensus size: 64
635583 ACGATGCTAT
* * * * *
635593 TGATGGCTT-TCTGCAGATCATATTACCATTACTGGTGGCTATGTGCCGATCATATTACCATTAC
1 TGATGG-TTGTCTGCCGATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
* * *
635657 TGATGGTTGTCTGCCGATTATATTACTACTACTGATGGCTTTGTGCCGATCATACTACTATTAC
1 TGATGGTTGTCTGCCGATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
* *
635721 TGATGGTTGTGTGCCGATCATATTACTACTACTGATGGCTTTGTGCCAATCATATTAC
1 TGATGGTTGTCTGCCGATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTAC
635779 TGTACTTATG
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
63 2 0.02
64 107 0.98
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (64 bp):
TGATGGTTGTCTGCCGATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTAC
Found at i:635757 original size:96 final size:95
Alignment explanation
Indices: 635593--635792 Score: 249
Period size: 96 Copynumber: 2.1 Consensus size: 95
635583 ACGATGCTAT
* * *
635593 TGATGGCTTTCTGCAGATCATATTACCATTACTGGTGGCTATGTGCCGATCATATTACCATTACT
1 TGATGGCTTTCTGCAGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
* *
635658 GATGG-TTGTCTGCCGATTATATTACTACTAC
66 GATGGCTT-TCTGCCAATCATATTACT-CTAC
* * * * * *
635689 TGATGGCTTTGTGCCGATCATACTACTATTACTGATGGTTGTGTGCCGATCATATTACTACTACT
1 TGATGGCTTTCTGCAGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
* *
635754 GATGGCTTTGTGCCAATCATATTACTGTAC
66 GATGGCTTTCTGCCAATCATATTACTCTAC
*
635784 TTATGGCTT
1 TGATGGCTT
635793 GTAGCCATTC
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
95 11 0.12
96 76 0.85
97 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (95 bp):
TGATGGCTTTCTGCAGATCATACTACCATTACTGATGGCTATGTGCCGATCATATTACCACTACT
GATGGCTTTCTGCCAATCATATTACTCTAC
Found at i:635809 original size:22 final size:21
Alignment explanation
Indices: 635784--635857 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
635774 ATTACTGTAC
635784 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* * *
635806 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
* *
635828 TTATGGCTCTTAACCATTCTGG
1 TTATGGCT-TTAGCCATTCTGT
635850 TTACTGGC
1 TTA-TGGC
635858 AGCTTTGCTG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 36 0.88
23 5 0.12
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:637307 original size:50 final size:50
Alignment explanation
Indices: 637187--637324 Score: 145
Period size: 50 Copynumber: 2.8 Consensus size: 50
637177 ACTGCCAATA
* * * * *
637187 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATACCGGTACCCATG
1 CCATGTCCCTGATATGGTCTTACATGGGACTTCTCATACCGGTACCAACG
* * ** *
637237 CCATGT-CCTAGACATAGTCTTACGGGGGACTTCTCAT-CTCGGTGCCAACG
1 CCATGTCCCT-GATATGGTCTTACATGGGACTTCTCATAC-CGGTACCAACG
*
637287 CCATGTCCCTGATATGGTCTTACATGGGACCTCTCATA
1 CCATGTCCCTGATATGGTCTTACATGGGACTTCTCATA
637325 ACCTCAATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
49 3 0.04
50 63 0.91
51 3 0.04
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
CCATGTCCCTGATATGGTCTTACATGGGACTTCTCATACCGGTACCAACG
Found at i:644506 original size:27 final size:27
Alignment explanation
Indices: 644468--644524 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
644458 TCTGAGAGAT
644468 ATGGAACCTAAGCTCTGATACCACCAA
1 ATGGAACCTAAGCTCTGATACCACCAA
644495 ATGGAACCTAAGCTCTGATACCACCAA
1 ATGGAACCTAAGCTCTGATACCACCAA
644522 ATG
1 ATG
644525 TAACACCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGGAACCTAAGCTCTGATACCACCAA
Found at i:645445 original size:49 final size:50
Alignment explanation
Indices: 645370--645465 Score: 167
Period size: 49 Copynumber: 1.9 Consensus size: 50
645360 TGCAACTACT
645370 TTACAAAGGATAAAATGGAGTAGGGGAGCTTAACAAGCTCTGTGAATGCC
1 TTACAAAGGATAAAATGGAGTAGGGGAGCTTAACAAGCTCTGTGAATGCC
* *
645420 TTAC-AAGGATACAATGGAGTGGGGGAGCTTAACAAGCTCTGTGAAT
1 TTACAAAGGATAAAATGGAGTAGGGGAGCTTAACAAGCTCTGTGAAT
645466 ACCTAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 40 0.91
50 4 0.09
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (50 bp):
TTACAAAGGATAAAATGGAGTAGGGGAGCTTAACAAGCTCTGTGAATGCC
Found at i:645686 original size:10 final size:10
Alignment explanation
Indices: 645643--645677 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
645633 ATGCATTAAC
645643 CACATATAAT
1 CACATATAAT
*
645653 CACAAATAAT
1 CACATATAAT
645663 CACATATAAT
1 CACATATAAT
645673 CACAT
1 CACAT
645678 CTAGTCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (10 bp):
CACATATAAT
Found at i:646107 original size:21 final size:21
Alignment explanation
Indices: 646081--646129 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
646071 TTACAACAGG
646081 CATCACAACAT-ATTCATATTT
1 CATCACAACATAATTC-TATTT
* *
646102 CATCACATCATAATTCTCTTT
1 CATCACAACATAATTCTATTT
646123 -ATCACAA
1 CATCACAA
646130 TTCATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 14 0.58
22 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (21 bp):
CATCACAACATAATTCTATTT
Found at i:649563 original size:50 final size:50
Alignment explanation
Indices: 649490--649589 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
649480 ATTGAAATGG
* *
649490 ATAATATATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTGATTA
1 ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
*
649540 ATAATACATGTATATGAGATATAATTATATGTTGTGTTCATTCTTAATTA
1 ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
649590 CATAGCCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (50 bp):
ATAATACATGTATAAGAGATATAATTATATGTTGTGTTCATTCTTAATTA
Found at i:671055 original size:41 final size:41
Alignment explanation
Indices: 670997--671203 Score: 245
Period size: 41 Copynumber: 5.0 Consensus size: 41
670987 AAAGTATATC
* * *
670997 CAAGGGTACGGAAGTACAAATAGGGGCATGTATGTGCAATT
1 CAAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
* * * * * *
671038 TAAGGGTACTGAAGTAC-AACTAGGGGCAAGGATGTGGAACT
1 CAAGGGTACCGAAGTACAAAC-AGGGGCACGTATGTGCAATT
* *
671079 CAGGGGTACCGAAGTACAAACAGGGGCACGTATCTGCAATT
1 CAAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
* * *
671120 CAAGGGTACCGAATTACAAACAAGGGCACGTATATGCAATT
1 CAAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
* * *
671161 CAAGGGTACTGAAGTACAAACAGGGTCACGTATGTCCAATT
1 CAAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
671202 CA
1 CA
671204 TCATTATACC
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 2 0.01
41 134 0.96
42 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
CAAGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATT
Found at i:671166 original size:21 final size:20
Alignment explanation
Indices: 671102--671166 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
671092 GTACAAACAG
671102 GGGCACGTATCTGCAATTCAA
1 GGGCACGTAT-TGCAATTCAA
* * * *
671123 GGGTACCGAATTACAA-ACAA
1 GGGCA-CGTATTGCAATTCAA
671143 GGGCACGTATATGCAATTCAA
1 GGGCACGTAT-TGCAATTCAA
671164 GGG
1 GGG
671167 TACTGAAGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 14 0.42
22 4 0.12
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
GGGCACGTATTGCAATTCAA
Found at i:673423 original size:27 final size:25
Alignment explanation
Indices: 673365--673433 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
673355 GCTCATACAT
*
673365 GCTGAATATCGATAAGCTCTCTCGA
1 GCTGAATATCGATAAGCTCTCTCAA
673390 GCTGAATATC-AGTAAGCTCTCTCAA
1 GCTGAATATCGA-TAAGCTCTCTCAA
*
673415 GCT-AAGAATCGATAA-CTCT
1 GCTGAA-TATCGATAAGCTCT
673434 AATGACATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.18
25 31 0.79
26 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (25 bp):
GCTGAATATCGATAAGCTCTCTCAA
Found at i:674834 original size:20 final size:20
Alignment explanation
Indices: 674787--674835 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
674777 CATTTTGCAC
*
674787 ATATGACCAAGACATCATAA
1 ATATGACCAAAACATCATAA
*
674807 ACAT-ACCAAAACATACAT-A
1 ATATGACCAAAACAT-CATAA
674826 ATATGACCAA
1 ATATGACCAA
674836 TTCAAATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.18
Consensus pattern (20 bp):
ATATGACCAAAACATCATAA
Found at i:676705 original size:138 final size:136
Alignment explanation
Indices: 676440--676708 Score: 315
Period size: 137 Copynumber: 2.0 Consensus size: 136
676430 CGAGCCATAA
* * * * * **
676440 ATGGGTCTGTTAACACAAGCTGACGGTCAAAATATAGCTACATGATGTCGCTTACACAAGCTGGC
1 ATGGGTCTGCTAACACAAGCTAACAGTCAAAATATAGCTACACGATGTCGCTCACACAAGCTAAC
* * * *
676505 GATTATCCATAAAAAATGTCGATCTCAGCAATCGGTAGGACATTCAAGTCCAGCACCTGAAACAT
66 GAGTATCCACAAAAAATGTCGAACTCAGCAATCGGTAGGACATTCAAGACCAGCACCTGAAACAT
676570 GGTAAC
131 GGTAAC
* * * *
676576 ATGGGTCTGCTCACACAAGCTAATAGTCAAAATTTAAGCTACACGATGTTGCTCACACAAGCTAA
1 ATGGGTCTGCTAACACAAGCTAACAGTCAAAATAT-AGCTACACGATGTCGCTCACACAAGCTAA
* * * * * *
676641 TGAGTATCCGCAACAAATGCTGGAACTCAGCCATCGGTAGGATATTCAAGACCAGCA-CTCGAAA
65 CGAGTATCCACAAAAAATG-TCGAACTCAGCAATCGGTAGGACATTCAAGACCAGCACCT-GAAA
676705 CATG
128 CATG
676709 AAAACCCTAA
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
136 29 0.27
137 40 0.37
138 40 0.37
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (136 bp):
ATGGGTCTGCTAACACAAGCTAACAGTCAAAATATAGCTACACGATGTCGCTCACACAAGCTAAC
GAGTATCCACAAAAAATGTCGAACTCAGCAATCGGTAGGACATTCAAGACCAGCACCTGAAACAT
GGTAAC
Found at i:676881 original size:30 final size:30
Alignment explanation
Indices: 676847--676914 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
676837 ATATATATTG
676847 ATTCATTTACATTAGAACAACACATTAAGC
1 ATTCATTTACATTAGAACAACACATTAAGC
676877 ATTCATTTACATTAGAACAACACATTAAGC
1 ATTCATTTACATTAGAACAACACATTAAGC
676907 ATTCATTT
1 ATTCATTT
676915 TAATCAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (30 bp):
ATTCATTTACATTAGAACAACACATTAAGC
Found at i:678455 original size:26 final size:26
Alignment explanation
Indices: 678419--678485 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
678409 TACATCATTA
*
678419 CTCACACGAGCTGTGAAATGGGCCTG
1 CTCACACGAGCTGTGAAATAGGCCTG
*
678445 CTCACACGAGCTATGAAATAGGCCTG
1 CTCACACGAGCTGTGAAATAGGCCTG
*
678471 CTCACACGAGTTGTG
1 CTCACACGAGCTGTG
678486 GAGAGTCCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (26 bp):
CTCACACGAGCTGTGAAATAGGCCTG
Found at i:679377 original size:260 final size:260
Alignment explanation
Indices: 678916--679440 Score: 924
Period size: 260 Copynumber: 2.0 Consensus size: 260
678906 AGGACAATAG
*
678916 TTTTAGGACCACAAATCTGACAAGCAAATTATTATTATTTATGATTTTAATGTTTATGAGATGTT
1 TTTTAGGACCACAAATCTGACAAGCAAATTATTATTATTTATGAGTTTAATGTTTATGAGATGTT
678981 AGTAAGGTCGTATTAATGTTTGCATGACTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
66 AGTAAGGTCGTATTAATGTTTGCATGACTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
*
679046 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTATAGTGAGAGGACTTATAT
131 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
* *
679111 GGTAATTAGACCATTTGTGTGGTTAGGGGATATTCATGGAAAGGTTTGTTTGAAATTTTTAATGC
196 GGTAATTAGACCATTTGTGTGGTTAAGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
** * * * *
679176 TTTTAGGACCACAAATCTGATGAGTAAATTATTATTTTTTATTAGTTTAATGTTTATGGGATGTT
1 TTTTAGGACCACAAATCTGACAAGCAAATTATTATTATTTATGAGTTTAATGTTTATGAGATGTT
* * * *
679241 AGTAAGGTCGTATTGATGTTTGCATGATTAATTAAGTAAAAAGGACTAAATTGTAAAAGGTTCAA
66 AGTAAGGTCGTATTAATGTTTGCATGACTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
679306 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
131 AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
679371 GGTAATTAGACCATTTGTGTGGTTAAGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
196 GGTAATTAGACCATTTGTGTGGTTAAGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
679436 TTTTA
1 TTTTA
679441 AAGGTTAAAA
Statistics
Matches: 251, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
260 251 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (260 bp):
TTTTAGGACCACAAATCTGACAAGCAAATTATTATTATTTATGAGTTTAATGTTTATGAGATGTT
AGTAAGGTCGTATTAATGTTTGCATGACTAATTAAGTAAAAAGAACTAAATCGTAAAAGGTTCAA
AAGTAGAGTTCTATTAGTTAAAGGTGTCAAATGGCTATGAAACTTTAAAGTGAGAGGACTTATAT
GGTAATTAGACCATTTGTGTGGTTAAGGGATATTCATGGAAAGGTTTGTTTGAAATTTTGAATGC
Found at i:685186 original size:50 final size:50
Alignment explanation
Indices: 685118--685306 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 50
685108 ATTATTATCA
* * * *
685118 TTCGATACATGTAGTAGCCTTCACATAGTACTACACAGGTGATCAAACTT
1 TTCGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
* * *
685168 TTCGATTCACGTAATAGCCTGCACATAGTACTACACATGTGACCAAAGCCT
1 TTCGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAA-CTT
* * * * * *
685219 TCCGGTGCACATAGTAACCTGCACATAGTACTACACATGTGACCATTA-TCT
1 TTCGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-AACT-T
* *
685270 ATCGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 TTCGATACACGTAGTAGCCTGCACATAGTACTACACA
685307 CGTCTTTATA
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
50 41 0.36
51 72 0.63
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
Found at i:692913 original size:51 final size:51
Alignment explanation
Indices: 692785--692962 Score: 173
Period size: 51 Copynumber: 3.5 Consensus size: 51
692775 TAAACGTAGT
* * * * *
692785 AGCCTTCACATAGTACTACACACGTGATC-AAACTTTCTGGTTCACGTAGC
1 AGCCTACACATAGTACTACACACGTGACCAAAACTTTCCGGTACACATAGC
692835 AGCCTACACATAGTACTACACACGTGACCAAAGAC-TTCCGGTACACATAGC
1 AGCCTACACATAGTACTACACACGTGACCAAA-ACTTTCCGGTACACATAGC
** * * * * * * * *
692886 AGCCTGGACATAGTACTCCACATGTGACCATTATCTAT-CGATACACGTAGT
1 AGCCTACACATAGTACTACACACGTGACCA-AAACTTTCCGGTACACATAGC
*
692937 AGCCTACACTTAGTACTACACACGTG
1 AGCCTACACATAGTACTACACACGTG
692963 TTTATAGGCA
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
50 27 0.26
51 73 0.70
52 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
AGCCTACACATAGTACTACACACGTGACCAAAACTTTCCGGTACACATAGC
Found at i:694588 original size:27 final size:27
Alignment explanation
Indices: 694551--694604 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
694541 AATATTTACC
*
694551 CCTTAAATTCT-TTTTAACAGAATCAA
1 CCTTAAATTCTGTTATAACAGAATCAA
*
694577 CCTTAAAATTCTGTTATAACATAATCAA
1 CCTT-AAATTCTGTTATAACAGAATCAA
694605 TTGAAGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 7 0.29
28 13 0.54
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (27 bp):
CCTTAAATTCTGTTATAACAGAATCAA
Found at i:702036 original size:9 final size:8
Alignment explanation
Indices: 702023--702047 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
702013 AACAAAAATT
702023 TAAAAAAA
1 TAAAAAAA
702031 TAAAAAAA
1 TAAAAAAA
702039 TAAAAAAA
1 TAAAAAAA
702047 T
1 T
702048 TGAAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:705489 original size:16 final size:16
Alignment explanation
Indices: 705468--705501 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
705458 AGATAGATTA
705468 TTTCCACCATTATTTC
1 TTTCCACCATTATTTC
* *
705484 TTTCCACCTTTCTTTC
1 TTTCCACCATTATTTC
705500 TT
1 TT
705502 CTTCCCCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTCCACCATTATTTC
Found at i:709500 original size:15 final size:15
Alignment explanation
Indices: 709469--709506 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
709459 AATTAGTAAC
709469 TTAAAATTAAATAAAA
1 TTAAAA-TAAATAAAA
*
709485 TTAAAATAACTAAAA
1 TTAAAATAAATAAAA
709500 TTAAAAT
1 TTAAAAT
709507 TCGTATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAATAAATAAAA
Found at i:710471 original size:133 final size:135
Alignment explanation
Indices: 710219--710489 Score: 528
Period size: 133 Copynumber: 2.0 Consensus size: 135
710209 TAATTCCTCC
710219 ATTAATTATTCCCACATCTGGTCGTTAATCTCCCTAAGGAAATTAGCCACTCATGGATCTAGATG
1 ATTAATTATTCCCACATCTGGTCGTTAATCTCCCTAAGGAAATTAGCCACTCATGGATCTAGATG
710284 CAATTTTCCCTGGTTTCATATTGAACATGCAAAGCAAATAATTAAACAAAAAATGGGAATAAGAA
66 CAATTTTCCCTGGTTTCATATTGAACATGCAAAGCAAATAATTAAACAAAAAATGGGAATAAGAA
710349 AATTG
131 AATTG
710354 ATTAATTATT-CC-CATCTGGTCGTTAATCTCCCTAAGGAAATTAGCCACTCATGGATCTAGATG
1 ATTAATTATTCCCACATCTGGTCGTTAATCTCCCTAAGGAAATTAGCCACTCATGGATCTAGATG
710417 CAATTTTCCCTGGTTTCATATTGAACATGCAAAGCAAATAATTAAACAAAAAATGGGAATAAGAA
66 CAATTTTCCCTGGTTTCATATTGAACATGCAAAGCAAATAATTAAACAAAAAATGGGAATAAGAA
710482 AATTG
131 AATTG
710487 ATT
1 ATT
710490 CATTTAGGTA
Statistics
Matches: 136, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 124 0.91
134 2 0.01
135 10 0.07
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (135 bp):
ATTAATTATTCCCACATCTGGTCGTTAATCTCCCTAAGGAAATTAGCCACTCATGGATCTAGATG
CAATTTTCCCTGGTTTCATATTGAACATGCAAAGCAAATAATTAAACAAAAAATGGGAATAAGAA
AATTG
Found at i:714891 original size:27 final size:26
Alignment explanation
Indices: 714803--714883 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 26
714793 CACGATATAT
*
714803 AAAGAAAGCTTTTGTGACATAAT-AT-A
1 AAAGAAAGC-TTTGTGGCA-AATAATGA
714829 AAAGAAAGCCTTTGTGGCAAATAATGA
1 AAAGAAAG-CTTTGTGGCAAATAATGA
*
714856 AAAGAAAGCTTATGTGGCAAATCATGA
1 AAAGAAAGCTT-TGTGGCAAATAATGA
714883 A
1 A
714884 CTAAAAGCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
25 3 0.06
26 21 0.43
27 25 0.51
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (26 bp):
AAAGAAAGCTTTGTGGCAAATAATGA
Found at i:725984 original size:8 final size:9
Alignment explanation
Indices: 725957--725981 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
725947 CAAGCTTGTT
725957 TTATTTTTA
1 TTATTTTTA
725966 TTATTTTTA
1 TTATTTTTA
725975 TTATTTT
1 TTATTTT
725982 ATTTTTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTTA
Found at i:728261 original size:17 final size:17
Alignment explanation
Indices: 728239--728271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
728229 GTTAGTGCAC
*
728239 ATTGTCATTGCATTTTT
1 ATTGTCATCGCATTTTT
728256 ATTGTCATCGCATTTT
1 ATTGTCATCGCATTTT
728272 AATCTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
ATTGTCATCGCATTTTT
Found at i:730021 original size:13 final size:13
Alignment explanation
Indices: 730000--730032 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
729990 CGTGTTGTGG
730000 TTGTATTTACTTA
1 TTGTATTTACTTA
*
730013 TTGTGTTTACTTA
1 TTGTATTTACTTA
730026 TT-TATTT
1 TTGTATTT
730033 TAGTTTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (13 bp):
TTGTATTTACTTA
Found at i:757519 original size:15 final size:15
Alignment explanation
Indices: 757501--757530 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
757491 TAGGTAGAAA
757501 TTAAATTAAACAAAT
1 TTAAATTAAACAAAT
*
757516 TTAAATTAAGCAAAT
1 TTAAATTAAACAAAT
757531 GGAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TTAAATTAAACAAAT
Found at i:758762 original size:42 final size:43
Alignment explanation
Indices: 758715--758800 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
758705 AGGGTAAATC
* * *
758715 CAACAACCCATGTTTATCTTCTCTTC-TTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
758757 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
758800 C
1 C
758801 TAGGATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 23 0.57
43 17 0.43
ACGTcount: A:0.23, C:0.26, G:0.02, T:0.49
Consensus pattern (43 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
Found at i:767096 original size:19 final size:19
Alignment explanation
Indices: 767074--767119 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
767064 TGTCAACTAT
* *
767074 ACTTGCATCGACAGTGTAC
1 ACTTGCACCAACAGTGTAC
767093 ACTTGCACCAACAGTGTAC
1 ACTTGCACCAACAGTGTAC
767112 ACTTGCAC
1 ACTTGCAC
767120 ATTATTGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (19 bp):
ACTTGCACCAACAGTGTAC
Found at i:774306 original size:14 final size:14
Alignment explanation
Indices: 774287--774314 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
774277 AGAATTGTTT
774287 GCTGTAGTATTTGC
1 GCTGTAGTATTTGC
774301 GCTGTAGTATTTGC
1 GCTGTAGTATTTGC
774315 TTTTGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
GCTGTAGTATTTGC
Found at i:777061 original size:21 final size:20
Alignment explanation
Indices: 777036--777092 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
777026 GTGCCCCTAT
777036 TTGTACTTCGGTACCCCTGAA
1 TTGTACTTCGGTACCCCTG-A
* * *
777057 TTGTACATAC-GTGCCCCTGT
1 TTGTAC-TTCGGTACCCCTGA
*
777077 TTATACTTCGGTACCC
1 TTGTACTTCGGTACCC
777093 TTAAATTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 14 0.50
22 2 0.07
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTACTTCGGTACCCCTGA
Found at i:777071 original size:41 final size:41
Alignment explanation
Indices: 777009--777156 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
776999 GTTAATTATT
777009 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * *
777050 CCCTGAATTGTACATACGTGCCCCTGTTTATACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * **
777091 CCTTAAATTGCACATATGTGCCCCTATTTGTACTTTAGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* *
777132 CCATGAATTGCACATACGTGCCCCT
1 CCCTAAATTGCACATACGTGCCCCT
777157 GTTTACACTC
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
Found at i:780971 original size:4 final size:4
Alignment explanation
Indices: 780962--781048 Score: 165
Period size: 4 Copynumber: 21.8 Consensus size: 4
780952 AGGTGCCGTT
780962 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
781010 ATAA ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
781049 ACCACAAATG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:781637 original size:16 final size:15
Alignment explanation
Indices: 781609--781652 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
781599 ACCTATGCAT
*
781609 AGACTCATCATGTAG
1 AGACTCATCATGTAA
781624 AGACTCATTCATGTAA
1 AGACTCA-TCATGTAA
781640 AGACTCCATCATG
1 AGACT-CATCATG
781653 CTTTTAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (15 bp):
AGACTCATCATGTAA
Found at i:784820 original size:21 final size:21
Alignment explanation
Indices: 784796--784836 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
784786 TCATAAGCCA
784796 ATTTCATCATCAAAT-GCATAT
1 ATTTCAT-ATCAAATGGCATAT
*
784817 ATTTCATATCATATGGCATA
1 ATTTCATATCAAATGGCATA
784837 CCGCATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTCATATCAAATGGCATAT
Found at i:786685 original size:6 final size:6
Alignment explanation
Indices: 786666--786698 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
786656 AGGACTTAAG
*
786666 TCTGTA TCTCTA TCTGTA TCTGTA TCTGT- TCTG
1 TCTGTA TCTGTA TCTGTA TCTGTA TCTGTA TCTG
786699 CATATGAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.12, C:0.21, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGTA
Found at i:798308 original size:66 final size:66
Alignment explanation
Indices: 798202--798325 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
798192 TTTCTGCACT
* *
798202 AATGTCGCTACATGAGTTAATTCCAGATTGTGTCATGAATTGTCGCTATAGTTGACAGATATTCG
1 AATGTCGCTACATGAGTTAATTCCAGATGGTGTCATGAATTGTCGCCATAGTTGACAGATATTCG
798267 C
66 C
* *
798268 AATGTCGCTGCATGAGTTAATTCCAGATGGCAT-TCA-GAATTTTCGCCATAGTTGACAG
1 AATGTCGCTACATGAGTTAATTCCAGATGG--TGTCATGAATTGTCGCCATAGTTGACAG
798326 TTGTCAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
66 48 0.92
67 3 0.06
68 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (66 bp):
AATGTCGCTACATGAGTTAATTCCAGATGGTGTCATGAATTGTCGCCATAGTTGACAGATATTCG
C
Found at i:817652 original size:18 final size:18
Alignment explanation
Indices: 817629--817688 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
817619 TTGAACCATG
817629 TTTTATATTTTTTTAATA
1 TTTTATATTTTTTTAATA
*
817647 TTTTATATTTTTTAAAT-
1 TTTTATATTTTTTTAATA
* *
817664 TTTTATGAATTATTTAATA
1 TTTTAT-ATTTTTTTAATA
*
817683 ATTTAT
1 TTTTAT
817689 TTAATAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 6 0.17
18 24 0.69
19 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTTTTAATA
Found at i:822415 original size:19 final size:20
Alignment explanation
Indices: 822391--822435 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
822381 CCAAATTTTT
* *
822391 ATTTTAA-GTTATTTTGTAC
1 ATTTTAATGTTATTATGCAC
*
822410 ATTTTAATTTTATTATGCAC
1 ATTTTAATGTTATTATGCAC
822430 ATTTTA
1 ATTTTA
822436 TTAACTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTAATGTTATTATGCAC
Done.