Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015310.1 Kokia drynarioides strain JFW-HI SEQ_130355, whole genome shotgun sequence
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: 579475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 305 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:383229 original size:30 final size:28
Alignment explanation
Indices: 383189--383378 Score: 134
Period size: 29 Copynumber: 6.5 Consensus size: 28
383179 TTCGAGAGTG
*
383189 AAAATATAATTTTGGAGAAATTTAGGGTC
1 AAAATGTAATTTTGGA-AAATTTAGGGTC
*
383218 AAAGATGTAATTTTGGAAAGA-TT-GGAGAC
1 AAA-ATGTAATTTTGGAAA-ATTTAGG-GTC
*
383247 AAAAATGTAATTTTTGGAAAATTCGAGGGTC
1 -AAAATGTAA-TTTTGGAAAATT-TAGGGTC
* * * *
383278 AAAATATGATTTTTGAAAATTTTAGGGGTT
1 AAAATGTAATTTTGGAAAA-TTTA-GGGTC
* *
383308 AAAATGTAATTTTTGGAAAGTTTGGGGTC
1 AAAATGTAA-TTTTGGAAAATTTAGGGTC
* * * *
383337 AAAATATAATTTTTGAAAGTTCGAGGG-C
1 AAAATGTAATTTTGGAAAATT-TAGGGTC
383365 AAAAATGTAATTTT
1 -AAAATGTAATTTT
383379 TGTGAAGTTT
Statistics
Matches: 128, Mismatches: 20, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
28 14 0.11
29 53 0.41
30 49 0.38
31 10 0.08
32 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAATTTAGGGTC
Found at i:383304 original size:29 final size:29
Alignment explanation
Indices: 383189--383410 Score: 130
Period size: 30 Copynumber: 7.5 Consensus size: 29
383179 TTCGAGAGTG
*
383189 AAAATATAATTTTGGAGAAA-TTTAGGGTC
1 AAAATATAATTTTTGA-AAATTTTAGGGTC
* * *
383218 AAAGATGTAATTTTGGAAAGA--TT-GGAGAC
1 AAA-ATATAATTTTTGAAA-ATTTTAGG-GTC
* **
383247 AAAAATGTAATTTTTGGAAAATTCGAGGGTC
1 -AAAATATAATTTTT-GAAAATTTTAGGGTC
* *
383278 AAAATATGATTTTTGAAAATTTTAGGGGTT
1 AAAATATAATTTTTGAAAATTTTA-GGGTC
* * * *
383308 AAAATGTAATTTTTGGAAAGTTTGGGGTC
1 AAAATATAATTTTTGAAAATTTTAGGGTC
* **
383337 AAAATATAATTTTTGAAAGTTCGAGGG-C
1 AAAATATAATTTTTGAAAATTTTAGGGTC
* * * * * *
383365 AAAAATGTAATTTTTGTGAAGTTTGAGTGTA
1 -AAAATATAATTTTTG-AAAATTTTAGGGTC
383396 AAAATATAATTTTTG
1 AAAATATAATTTTTG
383411 TGAAGTTCAG
Statistics
Matches: 151, Mismatches: 30, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
28 3 0.02
29 66 0.44
30 78 0.52
31 2 0.01
32 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAATTTTAGGGTC
Found at i:383406 original size:30 final size:29
Alignment explanation
Indices: 383247--383417 Score: 146
Period size: 30 Copynumber: 5.8 Consensus size: 29
383237 GATTGGAGAC
* * *
383247 AAAAATGTAATTTTTGGAAAATTCGAGGGT
1 AAAAATATAATTTTTGG-AAGTTTGAGGGT
* * * * *
383277 CAAAATATGATTTTTGAAAATTTTAGGGGT
1 AAAAATATAATTTTTGGAAGTTTGA-GGGT
* *
383307 TAAAATGTAATTTTTGGAAAGTTTG-GGGT
1 AAAAATATAATTTTTGG-AAGTTTGAGGGT
* * * *
383336 CAAAATATAATTTTTGAAAGTTCGAGGGC
1 AAAAATATAATTTTTGGAAGTTTGAGGGT
* *
383365 AAAAATGTAATTTTTGTGAAGTTTGAGTGT
1 AAAAATATAATTTTTG-GAAGTTTGAGGGT
383395 AAAAATATAATTTTTGTGAAGTT
1 AAAAATATAATTTTTG-GAAGTT
383418 CAGGTGCAAA
Statistics
Matches: 113, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
28 6 0.05
29 41 0.36
30 61 0.54
31 5 0.04
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.39
Consensus pattern (29 bp):
AAAAATATAATTTTTGGAAGTTTGAGGGT
Found at i:383429 original size:59 final size:58
Alignment explanation
Indices: 383189--383439 Score: 204
Period size: 59 Copynumber: 4.2 Consensus size: 58
383179 TTCGAGAGTG
* * * * * * * *
383189 AAAATATAA-TTTTGGAGAAATTTAGGGTCAAAGATGTAATTTTGGAAAGATTGGA-GACA
1 AAAATGTAATTTTTGGA-AAGTTTGGGGT-AAAAATATAATTTTTGAAAG-TTCGAGGGCA
* * * * * ** **
383248 AAAATGTAATTTTTGGAAAATTCGAGGGTCAAAATATGATTTTTGAAAATTTTAGGGGTT
1 AAAATGTAATTTTTGGAAAGTTTG-GGGTAAAAATATAATTTTTGAAAGTTCGA-GGGCA
*
383308 AAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATATAATTTTTGAAAGTTCGAGGGCA
1 AAAATGTAATTTTTGGAAAGTTTGGGGTAAAAATATAATTTTTGAAAGTTCGAGGGCA
* *
383366 AAAATGTAATTTTTGTG-AAGTTTGAGTGTAAAAATATAATTTTTGTGAAGTTC-AGGTGCA
1 AAAATGTAATTTTTG-GAAAGTTTG-GGGTAAAAATATAATTTTTG-AAAGTTCGAGG-GCA
*
383426 AAATTGTAATTTTT
1 AAAATGTAATTTTT
383440 AAAAAATTTA
Statistics
Matches: 158, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
58 28 0.18
59 74 0.47
60 56 0.35
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAAGTTTGGGGTAAAAATATAATTTTTGAAAGTTCGAGGGCA
Found at i:383436 original size:30 final size:30
Alignment explanation
Indices: 383308--383439 Score: 114
Period size: 30 Copynumber: 4.5 Consensus size: 30
383298 TTTAGGGGTT
* *
383308 AAAATGTAATTTTTG-GAAAGTT-TGGGGTC-
1 AAAATGTAATTTTTGTG-AAGTTCAGGTG-CA
* *
383337 AAAATATAATTTTTG-AAAGTTCGAGG-GCA
1 AAAATGTAATTTTTGTGAAGTTC-AGGTGCA
* *
383366 AAAATGTAATTTTTGTGAAGTT-TGAGTGTA
1 AAAATGTAATTTTTGTGAAGTTCAG-GTGCA
*
383396 AAAATATAATTTTTGTGAAGTTCAGGTGCA
1 AAAATGTAATTTTTGTGAAGTTCAGGTGCA
*
383426 AAATTGTAATTTTT
1 AAAATGTAATTTTT
383440 AAAAAATTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
28 7 0.08
29 30 0.36
30 46 0.55
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTTGTGAAGTTCAGGTGCA
Found at i:385177 original size:11 final size:10
Alignment explanation
Indices: 385141--385182 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
385131 TGGACTTTTT
385141 AATTTAAATA
1 AATTTAAATA
385151 AATTTAAACTTA
1 AATTTAAA--TA
385163 AATTTATAATA
1 AATTTA-AATA
385174 AATTTAAAT
1 AATTTAAAT
385183 TTTGTTGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 11 0.38
11 8 0.28
12 8 0.28
13 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTAAATA
Found at i:387080 original size:11 final size:11
Alignment explanation
Indices: 387064--387105 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
387054 TCATGTTTTT
387064 AAAAAAATTTG
1 AAAAAAATTTG
**
387075 AAAAAAAAAT-
1 AAAAAAATTTG
387085 AAAAAAATTTG
1 AAAAAAATTTG
387096 AAAAAAATTT
1 AAAAAAATTT
387106 AGTTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:387089 original size:21 final size:21
Alignment explanation
Indices: 387063--387102 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
387053 TTCATGTTTT
387063 TAAAAAAATTTGAAAAAAAAA
1 TAAAAAAATTTGAAAAAAAAA
387084 TAAAAAAATTTGAAAAAAA
1 TAAAAAAATTTGAAAAAAA
387103 TTTAGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
TAAAAAAATTTGAAAAAAAAA
Found at i:387130 original size:6 final size:6
Alignment explanation
Indices: 387112--387170 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
387102 ATTTAGTTTA
* ** *
387112 TTTATT TTCATT TTTATT TTTAGC TTT-GT TTTA-T TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
387157 TTTAAT TTTATT TT
1 TTTATT TTTATT TT
387171 ATTATGCACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 14 0.32
6 30 0.68
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:387148 original size:5 final size:5
Alignment explanation
Indices: 387103--387173 Score: 54
Period size: 5 Copynumber: 13.2 Consensus size: 5
387093 TTGAAAAAAA
* * *
387103 TTTAG TTTA- TTTAT TTTCATT TTTATT TTTAGC TTTGT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTT-A-T TTTA-T TTTA-T TTTAT TTTAT TTTAT
387151 TTTATT TTTAAT TTTAT TTTAT T
1 TTTA-T TTT-AT TTTAT TTTAT T
387174 ATGCACTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.07
5 28 0.50
6 19 0.34
7 5 0.09
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:387164 original size:17 final size:17
Alignment explanation
Indices: 387112--387173 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
387102 ATTTAGTTTA
*
387112 TTTATTTTCATTTTTATT
1 TTTATTTT-ATTTTTAAT
* *
387130 TTTAGCTTT-GTTTT-AT
1 TTTA-TTTTATTTTTAAT
387146 TTTATTTTATTTTTAAT
1 TTTATTTTATTTTTAAT
387163 TTTATTTTATT
1 TTTATTTTATT
387174 ATGCACTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.08
16 9 0.25
17 17 0.47
18 4 0.11
19 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTTTAAT
Found at i:388147 original size:13 final size:13
Alignment explanation
Indices: 388131--388164 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
388121 TCGAAAAAAT
388131 AAAAAAAAAATTC
1 AAAAAAAAAATTC
*
388144 AAAAAACAAATTC
1 AAAAAAAAAATTC
388157 AAAAAAAA
1 AAAAAAAA
388165 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:389220 original size:23 final size:25
Alignment explanation
Indices: 389194--389239 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
389184 CCAATTAGGG
389194 AATTA-TTGTTTAG-ATTTAATTCA
1 AATTATTTGTTTAGAATTTAATTCA
*
389217 AATTATTTTTTTAGAATTTAATT
1 AATTATTTGTTTAGAATTTAATT
389240 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATTTGTTTAGAATTTAATTCA
Found at i:397086 original size:19 final size:19
Alignment explanation
Indices: 397063--397115 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
397053 AAATTACAAA
397063 AAAAATTCAAAATGATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
397082 TAAAATACAAAATATTTAT
1 AAAAATTCAAAATATTTAT
397101 AAAAATTCTAAAATA
1 AAAAATTC-AAAATA
397116 AAATCTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:397982 original size:21 final size:21
Alignment explanation
Indices: 397958--398033 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
397948 GAAATTTAAA
397958 ACAAACATAATGAGAAGAGTT
1 ACAAACATAATGAGAAGAGTT
* * **
397979 ACAAAACATTATGAGGAGAGGA
1 AC-AAACATAATGAGAAGAGTT
398001 ACAAACATAATGAGGAA-AGTT
1 ACAAACATAATGA-GAAGAGTT
398022 ACAAACATAATG
1 ACAAACATAATG
398034 TTTTGTAGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 26 0.58
22 19 0.42
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.17
Consensus pattern (21 bp):
ACAAACATAATGAGAAGAGTT
Found at i:399677 original size:18 final size:17
Alignment explanation
Indices: 399647--399680 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
399637 GTTATAAATC
*
399647 AATTTAAATTAATAATG
1 AATTTAAAATAATAATG
399664 AATTTAAAAATAATAAT
1 AATTT-AAAATAATAAT
399681 TCTTACAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAAATAATAATG
Found at i:402119 original size:24 final size:24
Alignment explanation
Indices: 402087--402132 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
402077 TCATTTAACT
*
402087 TAATCGAACTTGTTCATGAACATA
1 TAATCGAACTTGTTCACGAACATA
*
402111 TAATTGAACTTGTTCACGAACA
1 TAATCGAACTTGTTCACGAACA
402133 ATGTTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (24 bp):
TAATCGAACTTGTTCACGAACATA
Found at i:405258 original size:19 final size:19
Alignment explanation
Indices: 405234--405281 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
405224 GAATATATTT
405234 AAATATTA-TTATATTTGAA
1 AAATATTATTTA-ATTTGAA
* *
405253 AAATATAAATTTAATTTGAT
1 AAATAT-TATTTAATTTGAA
405273 AAATATTAT
1 AAATATTAT
405282 AAATATGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
AAATATTATTTAATTTGAA
Found at i:407632 original size:23 final size:23
Alignment explanation
Indices: 407558--407817 Score: 200
Period size: 23 Copynumber: 11.6 Consensus size: 23
407548 TAAACGGAAC
* * *
407558 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
407580 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
407602 GGGCAACAGAGAGCACACAAAGCGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
407628 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
** *
407648 ----ATTGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
407667 AATCAGAGAGCACACACAA-TGCT
1 AAACAGAGAGCACACA-AAGTGCT
* *
407690 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
407713 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
407736 AATCAGAGAGCACGCGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
407759 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
407782 AATCAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
*
407805 AATCAGAGAGCAC
1 AAACAGAGAGCAC
407818 GAGACGTGCT
Statistics
Matches: 192, Mismatches: 31, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.05
18 1 0.01
19 1 0.01
20 1 0.01
21 1 0.01
22 20 0.10
23 137 0.71
24 2 0.01
25 13 0.07
26 6 0.03
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:407720 original size:46 final size:46
Alignment explanation
Indices: 407651--407838 Score: 258
Period size: 46 Copynumber: 4.1 Consensus size: 46
407641 ACAAAGTATT
* *
407651 GAGCACAC-ACAGTGCTAATCAGAGAGCACACACAATGCTAATCAGA
1 GAGCACACGA-AGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
407697 GAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
*
407743 GAGCACGCGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
* * *
407789 GAGCACGA-GACGTGCTAATCAGAGAGCACGAGAC-GTGCTAAAT-AGA
1 GAGCAC-ACGAAGTGCTAAACAGAGAGCAC-ACACAGTGCT-AATCAGA
407835 GAGC
1 GAGC
407839 GCGCTAGTGT
Statistics
Matches: 131, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
46 124 0.95
47 7 0.05
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
Found at i:407818 original size:23 final size:22
Alignment explanation
Indices: 407651--407838 Score: 198
Period size: 23 Copynumber: 8.2 Consensus size: 22
407641 ACAAAGTATT
*
407651 GAGCACACACAGTGCTAATCAGA
1 GAGCACAGAC-GTGCTAATCAGA
* *
407674 GAGCACACACAATGCTAATCAGA
1 GAGCACAGAC-GTGCTAATCAGA
* *
407697 GAGCACACGAAGTGCTAAACAGA
1 GAGCACA-GACGTGCTAATCAGA
*
407720 GAGCACACACAGTGCTAATCAGA
1 GAGCACAGAC-GTGCTAATCAGA
* * *
407743 GAGCACGCGAAGTGCTAAACAGA
1 GAGCAC-AGACGTGCTAATCAGA
*
407766 GAGCACACACAGTGCTAATCAGA
1 GAGCACAGAC-GTGCTAATCAGA
407789 GAGCACGAGACGTGCTAATCAGA
1 GAGCAC-AGACGTGCTAATCAGA
407812 GAGCACGAGACGTGCTAAAT-AGA
1 GAGCAC-AGACGTGCT-AATCAGA
407835 GAGC
1 GAGC
407839 GCGCTAGTGT
Statistics
Matches: 142, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.01
23 132 0.93
24 8 0.06
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (22 bp):
GAGCACAGACGTGCTAATCAGA
Found at i:407818 original size:69 final size:69
Alignment explanation
Indices: 407651--407838 Score: 256
Period size: 69 Copynumber: 2.7 Consensus size: 69
407641 ACAAAGTATT
* * *
407651 GAGCACACACAGTGCTAATCAGAGAGCACAC-ACAATGCTAATCAGAGAGCACACGAAGTGCTAA
1 GAGCACACACAGTGCTAATCAGAGAGCACGCGA-AGTGCTAAACAGAGAGCACACGAAGTGCTAA
407715 ACAGA
65 ACAGA
407720 GAGCACACACAGTGCTAATCAGAGAGCACGCGAAGTGCTAAACAGAGAGCACAC-ACAGTGCTAA
1 GAGCACACACAGTGCTAATCAGAGAGCACGCGAAGTGCTAAACAGAGAGCACACGA-AGTGCTAA
*
407784 TCAGA
65 ACAGA
* * * *
407789 GAGCACGAGAC-GTGCTAATCAGAGAGCACGAGACGTGCTAAATAGAGAGC
1 GAGCAC-ACACAGTGCTAATCAGAGAGCACGCGAAGTGCTAAACAGAGAGC
407839 GCGCTAGTGT
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
68 1 0.01
69 103 0.95
70 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (69 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGCGAAGTGCTAAACAGAGAGCACACGAAGTGCTAAA
CAGA
Found at i:407939 original size:24 final size:26
Alignment explanation
Indices: 407901--407948 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
407891 TCTACATGGG
407901 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
407927 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
407949 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:408089 original size:14 final size:14
Alignment explanation
Indices: 408070--408102 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
408060 TATTTCACAT
408070 ATATATTGT-TCATC
1 ATATA-TGTATCATC
408084 ATATATGTATCATC
1 ATATATGTATCATC
408098 ATATA
1 ATATA
408103 CCTCTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (14 bp):
ATATATGTATCATC
Found at i:409119 original size:25 final size:23
Alignment explanation
Indices: 409071--409120 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
409061 NNNNNNNNNN
409071 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
409094 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
409117 GAGC
1 GAGC
409121 GCGCTAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:416902 original size:24 final size:23
Alignment explanation
Indices: 416863--416908 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
416853 TATTACAAGC
416863 AAAAAAAATTAGTATTAAAAATT
1 AAAAAAAATTAGTATTAAAAATT
* *
416886 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
416909 CCGGGCAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATT
Found at i:427459 original size:28 final size:28
Alignment explanation
Indices: 427420--427474 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
427410 AAATTTAAGT
*
427420 TTACTTATTAACATTATAAAAAAAATAC
1 TTACTTATTAACAATATAAAAAAAATAC
* *
427448 TTACTT-TGTAACAATGTAACAAAAATA
1 TTACTTAT-TAACAATATAAAAAAAATA
427475 ATGATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (28 bp):
TTACTTATTAACAATATAAAAAAAATAC
Found at i:428857 original size:16 final size:18
Alignment explanation
Indices: 428826--428859 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
428816 TTATTATAAG
428826 TTTTGATTATATATGTTT
1 TTTTGATTATATATGTTT
428844 TTTTGA-TATA-ATGTTT
1 TTTTGATTATATATGTTT
428860 AGAATTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGATTATATATGTTT
Found at i:436173 original size:29 final size:29
Alignment explanation
Indices: 436138--436573 Score: 235
Period size: 29 Copynumber: 14.9 Consensus size: 29
436128 TGGATACCGG
* *
436138 GGGTAAAATGGTAATTTTGGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGAAAGTTCGA
* *
436167 GGGTAAAAAT-GTACTTTTTTAGAAAATT--A
1 GGGT-AAAATGGTA-ATTTTT-GAAAGTTCGA
*
436196 GGGTCAAAATGG-AATTTTTGAAAGTT-TA
1 GGGT-AAAATGGTAATTTTTGAAAGTTCGA
* *
436224 GGGATAAAATGGTAATTTTATAAAAATT-G-
1 GGG-TAAAATGGTAATTTT-TGAAAGTTCGA
* **
436253 GGGTCAAAAT-GAAATTTTTGAAAGTTTAA
1 GGGT-AAAATGGTAATTTTTGAAAGTTCGA
**
436282 GGGTAAAATGGTAATTTTTGGAAAAATC-A
1 GGGTAAAATGGTAATTTTT-GAAAGTTCGA
*
436311 GGGTCGAAAAT-G-AATTTTTTGGAAGTTCGA
1 GGGT--AAAATGGTAA-TTTTTGAAAGTTCGA
* **
436341 GGGTAAAATAGTAATTTTTGAAAAAAAAATC-A
1 GGGTAAAATGGTAATTTTTG----AAAGTTCGA
* *
436373 AGGTCAAAAATGG-AATTTTTAGAAAGTTTGA
1 GGGT--AAAATGGTAATTTTT-GAAAGTTCGA
* *
436404 GGGTAAAATGGTAATTTTACGAAA-ATCGA
1 GGGTAAAATGGTAATTTT-TGAAAGTTCGA
* * *
436433 -GGTCAAAAT-GAAATTTTTTAAAAGTTCAA
1 GGGT-AAAATGGTAA-TTTTTGAAAGTTCGA
*
436462 GGGTAAAATGGTAATTTTTGGAAAATT-GA
1 GGGTAAAATGGTAATTTTT-GAAAGTTCGA
* * *
436491 GGTTAAAATAG-AATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGAAAGTTCGA
** **
436519 GGGTAAAATGGTAATTTCAGGAAAAATCGA
1 GGGTAAAATGGTAATTT-TTGAAAGTTCGA
* *
436549 GGTTAAAATAG-AATTTTTGAAAGTT
1 GGGTAAAATGGTAATTTTTGAAAGTT
436574 TTGGTGTAAA
Statistics
Matches: 310, Mismatches: 59, Indels: 77
0.70 0.13 0.17
Matches are distributed among these distances:
27 17 0.05
28 66 0.21
29 116 0.37
30 75 0.24
31 14 0.05
32 4 0.01
33 11 0.04
34 7 0.02
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGAAAGTTCGA
Found at i:436232 original size:58 final size:57
Alignment explanation
Indices: 436138--436573 Score: 300
Period size: 58 Copynumber: 7.5 Consensus size: 57
436128 TGGATACCGG
* * *
436138 GGGT-AAAATGGTAATTTTGGGAAGTTCGAGGGTAAAAAT-GTACTTTTTTAGAAAATTA
1 GGGTCAAAATGG-AATTTTTGAAAGTTCTAGGGT-AAAATGGTA-TTTTTTAGAAAATTA
* *
436196 GGGTCAAAATGGAATTTTTGAAAGTT-TAGGGATAAAATGGTAATTTTATA-AAAATTG
1 GGGTCAAAATGGAATTTTTGAAAGTTCTAGGG-TAAAATGGT-ATTTTTTAGAAAATTA
* * * *
436253 GGGTCAAAATGAAATTTTTGAAAGTT-TAAGGGTAAAATGGTAATTTTTGGAAAAATCA
1 GGGTCAAAATGGAATTTTTGAAAGTTCT-AGGGTAAAATGGTATTTTTTAG-AAAATTA
* * * * * *
436311 GGGTCGAAAAT-GAATTTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAAAAATCA
1 GGGTC-AAAATGGAA-TTTTTGAAAGTTCTAGGGTAAAATGGT-ATTTTT---TAGAAAATTA
* * *
436373 AGGTCAAAAATGGAATTTTTAGAAAGTT-TGAGGGTAAAATGGTA-ATTTTACGAAAA-TC
1 GGGTC-AAAATGGAATTTTT-GAAAGTTCT-AGGGTAAAATGGTATTTTTTA-GAAAATTA
* * * * *
436431 GAGGTCAAAATGAAATTTTTTAAAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAATT-
1 G-GGTCAAAATGGAA-TTTTTGAAAGTTCTAGGGTAAAATGGTATTTTTTAGAAAATTA
* * * * * * * *
436489 GAGGTTAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGGTA-ATTTCAGGAAAAATC
1 G-GGTCAAAATGGAATTTTTGAAAGTTCTAGGGTAAAATGGTATTTTTTA-GAAAATTA
* *
436547 GAGGTTAAAATAGAATTTTTGAAAGTT
1 G-GGTCAAAATGGAATTTTTGAAAGTT
436574 TTGGTGTAAA
Statistics
Matches: 307, Mismatches: 46, Indels: 50
0.76 0.11 0.12
Matches are distributed among these distances:
56 8 0.03
57 81 0.26
58 113 0.37
59 54 0.18
60 5 0.02
61 3 0.01
62 22 0.07
63 21 0.07
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (57 bp):
GGGTCAAAATGGAATTTTTGAAAGTTCTAGGGTAAAATGGTATTTTTTAGAAAATTA
Found at i:436585 original size:29 final size:29
Alignment explanation
Indices: 436550--436655 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 29
436540 AAAAATCGAG
436550 GTTAAAATAGAATTTTTGAAAGTTTTGGT
1 GTTAAAATAGAATTTTTGAAAGTTTTGGT
* * *
436579 GTAAAAAT-GTACTTTTTGGAAAGTTTAGG-
1 GTTAAAATAG-AATTTTT-GAAAGTTTTGGT
* * * *
436608 GTTAAAATATAATTTTAGAGAGGTTTGAGT
1 GTTAAAATAGAATTTTTGAAAGTTTTG-GT
*
436638 GTTAAAATATAATTTTTG
1 GTTAAAATAGAATTTTTG
436656 GACAGTTTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 8 0.13
29 26 0.43
30 27 0.44
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (29 bp):
GTTAAAATAGAATTTTTGAAAGTTTTGGT
Found at i:436600 original size:58 final size:56
Alignment explanation
Indices: 436197--436600 Score: 370
Period size: 58 Copynumber: 6.9 Consensus size: 56
436187 AGAAAATTAG
* *
436197 GGTCAAAATGGAATTTTTGAAAGTTTAGGGATAAAATGGTAATTTTAT--AAAAATTGG
1 GGTCAAAAT-GAATTTTTGAAAGTTTAGGG-TAAAATGGTAATTTT-TGGAAAAATCGA
436254 GGTCAAAATGAAATTTTTGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATC-A
1 GGTCAAAATG-AATTTTTGAAAGTTT-AGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * * * *
436311 GGGTCGAAAATGAATTTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAAAAATCAA
1 -GGTC-AAAATGAA-TTTTTGAAAGTT-TAGGGTAAAATGGTAATTTTTG---GAAAAATCGA
**
436374 GGTCAAAAATGGAATTTTTAGAAAGTTTGAGGGTAAAATGGTAATTTTACG-AAAATCGA
1 GGTC-AAAAT-GAATTTTT-GAAAGTTT-AGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * *
436433 GGTCAAAATGAAATTTTTTAAAAGTTCAAGGGTAAAATGGTAATTTTTGG-AAAATTGA
1 GGTCAAAATG-AA-TTTTTGAAAGTT-TAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * * **
436491 GGTTAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTCAGGAAAAATCGA
1 GGTCAAAAT-GAATTTTTGAAAGTT-TAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * *
436549 GGTTAAAATAGAATTTTTGAAAGTTTTGGTGTAAAAAT-GTACTTTTTGGAAA
1 GGTCAAAAT-GAATTTTTGAAAGTTTAGG-GT-AAAATGGTAATTTTTGGAAA
436601 GTTTAGGGTT
Statistics
Matches: 293, Mismatches: 32, Indels: 43
0.80 0.09 0.12
Matches are distributed among these distances:
56 2 0.01
57 73 0.25
58 110 0.38
59 59 0.20
62 21 0.07
63 28 0.10
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (56 bp):
GGTCAAAATGAATTTTTGAAAGTTTAGGGTAAAATGGTAATTTTTGGAAAAATCGA
Found at i:436663 original size:59 final size:58
Alignment explanation
Indices: 436549--436667 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 58
436539 GAAAAATCGA
* * * *
436549 GGTTAAAATAGAATTTTTGAAAGTTTTGGTGTAAAAATGTACTTTTTGGAAAGTTTAG
1 GGTTAAAATAGAATTTTAGAAAGGTTTGGTGTAAAAATATAATTTTTGGAAAGTTTAG
* * * *
436607 GGTTAAAATATAATTTTAGAGAGGTTTGAGTGTTAAAATATAATTTTTGGACAGTTTAG
1 GGTTAAAATAGAATTTTAGAAAGGTTTG-GTGTAAAAATATAATTTTTGGAAAGTTTAG
436666 GG
1 GG
436668 ACCTTCAGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 24 0.46
59 28 0.54
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (58 bp):
GGTTAAAATAGAATTTTAGAAAGGTTTGGTGTAAAAATATAATTTTTGGAAAGTTTAG
Found at i:437740 original size:3 final size:3
Alignment explanation
Indices: 437732--437790 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
437722 ATCATTAATG
* * *
437732 TTA TTA TTA ATA TTA TTTA TTA TTA TTA TTG TTA TTA ATA TTAA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* *
437779 TCA TTT TTA TTA
1 TTA TTA TTA TTA
437791 CTACCAATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:437766 original size:28 final size:28
Alignment explanation
Indices: 437720--437789 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
437710 TTTTCCTTTT
* * * *
437720 TTATCATTAATGTTATTATTAATATTAT
1 TTATCATTATTATTGTTATTAATATTAA
*
437748 TTATTATTATTATTGTTATTAATATTAA
1 TTATCATTATTATTGTTATTAATATTAA
*
437776 TTATCATTTTTATT
1 TTATCATTATTATT
437790 ACTACCAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TTATCATTATTATTGTTATTAATATTAA
Found at i:438579 original size:17 final size:17
Alignment explanation
Indices: 438527--438577 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
438517 TATTTCAAAT
438527 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
438544 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
438561 TTTAAATTTTAAAATAA
1 TTTAAA-TTTAAAATAA
438578 TTCTAAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:439489 original size:25 final size:25
Alignment explanation
Indices: 439455--439506 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
439445 TCCAACACTT
439455 TCGATAAAAACACATATTAAAACCG
1 TCGATAAAAACACATATTAAAACCG
*
439480 TCGATAAAAACACATATTAAAATCG
1 TCGATAAAAACACATATTAAAACCG
439505 TC
1 TC
439507 CGGGCCCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (25 bp):
TCGATAAAAACACATATTAAAACCG
Found at i:444300 original size:118 final size:118
Alignment explanation
Indices: 444103--444562 Score: 418
Period size: 119 Copynumber: 3.8 Consensus size: 118
444093 GGTCATGCTT
* * * * **
444103 TTTTTGTCAGATAAAAAATTTAATTTTTTTGGTGTGGGTCATTGCATG-GCGACGTCCCCTTTTT
1 TTTTTATCAGATAAAAAATTTAATTTTTTTAGTGTTGGTCATTGCATGATCGACACCCCCTTTTT
** * *
444167 TATCTGGTAAAAAATCAATTTTTTGTGTTAATCATTACATGGCCGACACCTCT
66 TATCTGGTAAAAAATCAATTTTTTGTGTTAGCCATTGCATGGCCGACACCTCC
444220 TTTTTATCAGATAAAAAATTTAAATTTTTTT-GTGTTGGTCATTGCATGATCGACACCCCCTTTT
1 TTTTTATCAGATAAAAAATTT-AATTTTTTTAGTGTTGGTCATTGCATGATCGACACCCCCTTTT
* *
444284 TTATCTGGTGAAAAATCAATTTTTTTTTGTTAGCCATTGCATGGCCGACA-CTCCC
65 TTATCTGGTAAAAAATCAA-TTTTTTGTGTTAGCCATTGCATGGCCGACACCT-CC
* * * * * * *
444339 TTTTTGTCAGATAAAAAATTTAATTTTTTTAGTGTT-GACTGTTGCAAGACCGACACCACC--TA
1 TTTTTATCAGATAAAAAATTTAATTTTTTTAGTGTTGGTC-ATTGCATGATCGACACCCCCTTTT
* * *
444401 TTATTTGATAAAAAAAATCAAATTTTTTG-GTGTAGGCCATTGCATGGCCGACACCACC
65 TTATCTGGT--AAAAAATC-AATTTTTTGTGT-TA-GCCATTGCATGGCCGACACCTCC
* * * * * *
444459 TTTCTATCTGATAAAACAATTTAAATATTTTTT-GTGTTGGCCA-TGCATTGGTCGACA-CCACA
1 TTTTTATCAGATAAAA-AATTT-AAT-TTTTTTAGTGTTGGTCATTGCA-TGATCGACACCCCCT
** *
444521 TTTTTATCTGAAAAATAAAATAAAATTTTTTGGTGTTAGCCA
62 TTTTTATCTG-GTAA-AAAAT-CAATTTTTT-GTGTTAGCCA
444563 ATGCTTAGCG
Statistics
Matches: 282, Mismatches: 37, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
117 44 0.16
118 54 0.19
119 83 0.29
120 35 0.12
121 12 0.04
122 16 0.06
123 32 0.11
124 4 0.01
125 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (118 bp):
TTTTTATCAGATAAAAAATTTAATTTTTTTAGTGTTGGTCATTGCATGATCGACACCCCCTTTTT
TATCTGGTAAAAAATCAATTTTTTGTGTTAGCCATTGCATGGCCGACACCTCC
Found at i:444334 original size:59 final size:59
Alignment explanation
Indices: 444114--444474 Score: 245
Period size: 60 Copynumber: 6.1 Consensus size: 59
444104 TTTTGTCAGA
* ** **
444114 TAAAAAATTTAATTTTTTTGGTGTGGGTCATTGCATGG-CGACGTCCCCTTTTTTATCTGG
1 TAAAAAA-TCAATTTTTTT-GTGTTAGTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
* * * * *
444174 TAAAAAATCAA-TTTTTTGTGTTAATCATTACATGGCCGACA-CCTCTTTTTTATCAGA
1 TAAAAAATCAATTTTTTTGTGTTAGTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
* * **
444231 TAAAAAATTTAAATTTTTTTGTGTTGGTCATTGCATGATCGACACCCCCTTTTTTATCTGG
1 TAAAAAA--TCAATTTTTTTGTGTTAGTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
* * * * * * *
444292 TGAAAAATCAATTTTTTTTTGTTAGCCATTGCATGGCCGACACTCCC-TTTTTGTCAGA
1 TAAAAAATCAATTTTTTTGTGTTAGTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
* * * * * * * * *
444350 TAAAAAATTTAATTTTTTTAGTGTT-GACTGTTGCAAGACCGACACCACC--TATTATTTGA
1 TAAAAAA-TCAATTTTTTT-GTGTTAGTC-ATTGCATGGCCGACACCCCCTTTTTTATCTGG
* * * * *
444409 TAAAAAAAATCAAATTTTTTG-GTGTAGGCCATTGCATGGCCGACACCACC-TTTCTATCTGA
1 T--AAAAAATCAATTTTTTTGTGT-TA-GTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
444470 TAAAA
1 TAAAA
444475 CAATTTAAAT
Statistics
Matches: 236, Mismatches: 51, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
57 34 0.14
58 26 0.11
59 64 0.27
60 77 0.33
61 35 0.15
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (59 bp):
TAAAAAATCAATTTTTTTGTGTTAGTCATTGCATGGCCGACACCCCCTTTTTTATCTGG
Found at i:444578 original size:61 final size:60
Alignment explanation
Indices: 444401--444579 Score: 168
Period size: 61 Copynumber: 2.9 Consensus size: 60
444391 ACACCACCTA
* * * * *
444401 TTATTTGATAAAAAAAATCAAATTTTTTGGTG-TAGGCCATTGCATGGCCGACACCACCTTT
1 TTATCTGATAAAAAAAATAAAATTTTTTGGTGTTA-GCCAATGCTTGG-CGACACCACATTT
* ** *
444462 CTATCTGATAAAACAATTTAAATATTTTTT-GTGTTGGCC-ATGCATTGGTCGACACCACATTT
1 TTATCTGATAAAA-AAAATAAA-ATTTTTTGGTGTTAGCCAATGC-TTGG-CGACACCACATTT
*
444524 TTATCTGA-AAAATAAAATAAAATTTTTTGGTGTTAGCCAATGCTTAGCGGACACCA
1 TTATCTGATAAAA-AAAATAAAATTTTTTGGTGTTAGCCAATGCTTGGC-GACACCA
444580 ACTTTCTCTC
Statistics
Matches: 95, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
60 8 0.08
61 42 0.44
62 37 0.39
63 8 0.08
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (60 bp):
TTATCTGATAAAAAAAATAAAATTTTTTGGTGTTAGCCAATGCTTGGCGACACCACATTT
Found at i:445466 original size:30 final size:30
Alignment explanation
Indices: 445417--445591 Score: 230
Period size: 30 Copynumber: 5.9 Consensus size: 30
445407 AAAAAATAAT
*
445417 AATTAGAAA-TAAAATTTAAAATATAAACGA
1 AATTACAAATTAAAA-TTAAAATATAAACGA
* *
445447 AATTACAAATTAAAATTAAAATATACAGGA
1 AATTACAAATTAAAATTAAAATATAAACGA
* *
445477 AATTAGAAATTAAATTTAAAATATAAACGA
1 AATTACAAATTAAAATTAAAATATAAACGA
* *
445507 AATTACAAATTAAAATTAAAATATACAGGA
1 AATTACAAATTAAAATTAAAATATAAACGA
* *
445537 AATTAGAAATTAAATTTAAAATATAAAC-A
1 AATTACAAATTAAAATTAAAATATAAACGA
*
445566 AATTACAAATT-AAATTAAAAAATAAA
1 AATTACAAATTAAAATTAAAATATAAA
445592 TAGAAAAAAA
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.10
29 11 0.09
30 97 0.77
31 5 0.04
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (30 bp):
AATTACAAATTAAAATTAAAATATAAACGA
Found at i:445589 original size:60 final size:60
Alignment explanation
Indices: 445417--445585 Score: 315
Period size: 60 Copynumber: 2.9 Consensus size: 60
445407 AAAAAATAAT
*
445417 AATTAGAAATAAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAATATACAGGA
1 AATTAGAAATTAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAATATACAGGA
445477 AATTAGAAATTAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAATATACAGGA
1 AATTAGAAATTAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAATATACAGGA
445537 AATTAGAAATTAAATTTAAAATATAAAC-AAATTACAAATT-AAATTAAAA
1 AATTAGAAATTAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAA
445586 AATAAATAGA
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
58 9 0.08
59 12 0.11
60 87 0.81
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (60 bp):
AATTAGAAATTAAATTTAAAATATAAACGAAATTACAAATTAAAATTAAAATATACAGGA
Found at i:446722 original size:13 final size:13
Alignment explanation
Indices: 446704--446728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
446694 ATTTCGAAAA
446704 TGTAAAAAATATT
1 TGTAAAAAATATT
446717 TGTAAAAAATAT
1 TGTAAAAAATAT
446729 CAAAATTTTA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTAAAAAATATT
Found at i:446899 original size:19 final size:19
Alignment explanation
Indices: 446875--446918 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
446865 TTTTATTTTT
*
446875 TAAAAA-ATTTGAAAATATA
1 TAAAAACATTTCAAAA-ATA
446894 TAAAAACATTTCAAAAATA
1 TAAAAACATTTCAAAAATA
*
446913 GAAAAA
1 TAAAAA
446919 TATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAACATTTCAAAAATA
Found at i:450270 original size:61 final size:60
Alignment explanation
Indices: 450197--450363 Score: 185
Period size: 62 Copynumber: 2.7 Consensus size: 60
450187 GTGTCGGCCA
*
450197 ATGC-ATGACCAACACCAAAAAAATTGAATATTTTTATCAGATAAAAAGGT-GATGCCGACC
1 ATGCAATGGCCAACACCAAAAAAATTGAAT-TTTTTATCAGATAAAAAGGTAG-TGCCGACC
* * * * **
450257 ATGTAATGGCCAACACAAAAAAAAATTGAATTTTTTGTCAGATTAAAAAGGTAGTGTCGGTC
1 ATGCAATGGCCAACAC-CAAAAAAATTGAATTTTTTATCAGA-TAAAAAGGTAGTGCCGACC
* * *
450319 ATGCAATGGCCAACACCAAAAAATTTGATTTTTTTTATAAGATAA
1 ATGCAATGGCCAACACCAAAAAAATTGA-ATTTTTTATCAGATAA
450364 TAGGTGTTGG
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
60 3 0.03
61 33 0.37
62 52 0.58
63 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (60 bp):
ATGCAATGGCCAACACCAAAAAAATTGAATTTTTTATCAGATAAAAAGGTAGTGCCGACC
Found at i:450327 original size:62 final size:60
Alignment explanation
Indices: 450126--450463 Score: 225
Period size: 61 Copynumber: 5.8 Consensus size: 60
450116 GGGAAAGTTG
* * * *
450126 GTGTCGGCCAATGC-ATGGCCAACAC--AAAAAATT-ATTATTTTTTATCTGACAACAAATAGT
1 GTGTCGGCC-ATGCAATGGCCAACACAAAAAAAATTGAATA-TTTTTATCAGATAA-AAA-GGT
* *
450186 GGTGTCGGCCAATGC-ATGACCAACACCAAAAAAATTGAATATTTTTATCAGATAAAAAGGT
1 -GTGTCGGCC-ATGCAATGGCCAACACAAAAAAAATTGAATATTTTTATCAGATAAAAAGGT
* * * *
450247 GATGCCGACCATGTAATGGCCAACACAAAAAAAAATTGAAT-TTTTTGTCAGATTAAAAAGGT
1 G-TGTCGGCCATGCAATGGCCAACAC-AAAAAAAATTGAATATTTTTATCAGA-TAAAAAGGT
* * * * * * *
450309 AGTGTCGGTCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTTATAAGAT-AATAGGT
1 -GTGTCGGCCATGCAATGGCCAACACAAAAAAAATTGAATATTTTTATCAGATAAAAAGGT
*
450369 GT-T-GG-C---CAA----C-AC-C-AAAAAATTTGAA-ATTTTTATCAGATTAAAAAGGT
1 GTGTCGGCCATGCAATGGCCAACACAAAAAAAATTGAATATTTTTATCAGA-TAAAAAGGT
* * *
450416 GGTGTCGGCCATACAATGGCCAACAGAAAAAAATTTGAAT-TTTTTATC
1 -GTGTCGGCCATGCAATGGCCAACACAAAAAAAATTGAATATTTTTATC
450464 TGACAAACCG
Statistics
Matches: 225, Mismatches: 26, Indels: 52
0.74 0.09 0.17
Matches are distributed among these distances:
45 10 0.04
46 12 0.05
47 7 0.03
48 4 0.02
49 2 0.01
50 2 0.01
51 1 0.00
53 3 0.01
54 3 0.01
56 1 0.00
57 2 0.01
58 2 0.01
59 4 0.02
60 10 0.04
61 84 0.37
62 54 0.24
63 21 0.09
64 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (60 bp):
GTGTCGGCCATGCAATGGCCAACACAAAAAAAATTGAATATTTTTATCAGATAAAAAGGT
Found at i:450450 original size:107 final size:108
Alignment explanation
Indices: 450263--450460 Score: 299
Period size: 107 Copynumber: 1.8 Consensus size: 108
450253 GACCATGTAA
* * * *
450263 TGGCCAACACAAAAAAAAATTGAATTTTTTGTCAGATTAAAAAGGTAGTGTCGGTCATGCAATGG
1 TGGCCAACACAAAAAAAAATTGAAATTTTTATCAGATTAAAAAGGTAGTGTCGGCCATACAATGG
* *
450328 CCAACACCAAAAAATTTGATTTTTTTTATAAGATAATAGGTGT
66 CCAACACAAAAAAATTTGAATTTTTTTATAAGATAATAGGTGT
* * *
450371 TGGCCAACAC-CAAAAAATTTGAAATTTTTATCAGATTAAAAAGGTGGTGTCGGCCATACAATGG
1 TGGCCAACACAAAAAAAAATTGAAATTTTTATCAGATTAAAAAGGTAGTGTCGGCCATACAATGG
*
450435 CCAACAGAAAAAAATTTGAATTTTTT
66 CCAACACAAAAAAATTTGAATTTTTT
450461 ATCTGACAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 70 0.88
108 10 0.12
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (108 bp):
TGGCCAACACAAAAAAAAATTGAAATTTTTATCAGATTAAAAAGGTAGTGTCGGCCATACAATGG
CCAACACAAAAAAATTTGAATTTTTTTATAAGATAATAGGTGT
Found at i:450542 original size:96 final size:97
Alignment explanation
Indices: 450377--450563 Score: 286
Period size: 96 Copynumber: 1.9 Consensus size: 97
450367 GTGTTGGCCA
** * *
450377 ACACCAAAAAATTTGAAATTTTTATCAGATTAAAAAGGTGGTGTCGGCCATACAATGGCCAACAG
1 ACACCAAAAAATTTGAAATTTTTATCAGACAAAAAAGGTGGTGTCGACCATACAATGACCAACAG
450442 AAAAAAATTTGAATTTTTTATCTGACAAACCG
66 AAAAAAATTTGAATTTTTTATCTGACAAACCG
* * * * *
450474 ACACCAAAGAATTTGAATTTTTTATCTGACAAAAAAGG-GGTGTCGACCATGCAATGACCAACAT
1 ACACCAAAAAATTTGAAATTTTTATCAGACAAAAAAGGTGGTGTCGACCATACAATGACCAACAG
450538 AAAAAAATTTGAATTTTTTATCTGAC
66 AAAAAAATTTGAATTTTTTATCTGAC
450564 GAAAAGAGGG
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 48 0.59
97 33 0.41
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (97 bp):
ACACCAAAAAATTTGAAATTTTTATCAGACAAAAAAGGTGGTGTCGACCATACAATGACCAACAG
AAAAAAATTTGAATTTTTTATCTGACAAACCG
Found at i:450547 original size:60 final size:60
Alignment explanation
Indices: 450483--450683 Score: 257
Period size: 60 Copynumber: 3.4 Consensus size: 60
450473 GACACCAAAG
* *
450483 AATTTGAATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGCAATGACCAACATAAAAA
1 AATTTGAATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGCAATGGCTAACATAAAAA
*
450543 AATTTGAATTTTTTATCTGAC-GAAAAGAGGGTGTC-AGCCATGCAATGGCTAACACTAAAAA
1 AATTTGAATTTTTTATCTGACAAAAAAG-GGGTGTCGA-CCATGCAATGGCTAACA-TAAAAA
* * * * *
450604 AA-TTG-ATTTTTTACCAGATAAAAAAGGAGGTGTCGATCATGCAATGGCTAACACAAAAA
1 AATTTGAATTTTTTATCTGACAAAAAAGG-GGTGTCGACCATGCAATGGCTAACATAAAAA
*
450663 AATTTAAATTTTTTATCTGAC
1 AATTTGAATTTTTTATCTGAC
450684 CCAAAATTTT
Statistics
Matches: 120, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
59 25 0.21
60 75 0.62
61 20 0.17
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (60 bp):
AATTTGAATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGCAATGGCTAACATAAAAA
Found at i:452136 original size:5 final size:5
Alignment explanation
Indices: 452128--452155 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
452118 TCTCTTCTAC
452128 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
452156 TGACAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:452192 original size:3 final size:3
Alignment explanation
Indices: 452177--452208 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
452167 TCTCTTCATA
*
452177 TCC TCC TCT TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
452209 ATTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:452295 original size:12 final size:12
Alignment explanation
Indices: 452277--452310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
452267 TTATCTGTTC
452277 GACATACATACA
1 GACATACATACA
*
452289 TACATACATACA
1 GACATACATACA
*
452301 GACAAACATA
1 GACATACATA
452311 TAGGAGTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (12 bp):
GACATACATACA
Found at i:455876 original size:29 final size:30
Alignment explanation
Indices: 455830--455891 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
455820 AAAAAGGTAA
*
455830 TTTTGGACACTTCAGGGGCGAAATAATAAT
1 TTTTGGACACTTCAGGGGCAAAATAATAAT
* **
455860 TTTTGGACAC-TCGGGGGCAAAATGGTAAT
1 TTTTGGACACTTCAGGGGCAAAATAATAAT
455889 TTT
1 TTT
455892 CAAATGTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (30 bp):
TTTTGGACACTTCAGGGGCAAAATAATAAT
Found at i:455939 original size:30 final size:30
Alignment explanation
Indices: 455903--456257 Score: 216
Period size: 30 Copynumber: 11.9 Consensus size: 30
455893 AAATGTTCGA
**
455903 GGGTAAAACGGTAATTTTTAGAAAGTTTAG
1 GGGTAAAAATGTAATTTTTAGAAAGTTTAG
* *
455933 GGGT-AAAATAGTAATTTTTAGAAAGTTCAA
1 GGGTAAAAAT-GTAATTTTTAGAAAGTTTAG
* * *
455963 GGTTAAAAAATG-ATATTTTT-GGAAGTTTGG
1 GGGT-AAAAATGTA-ATTTTTAGAAAGTTTAG
* *
455993 GGGT-AAAATGGCAATTTTTAG-AAG-TTCG
1 GGGTAAAAAT-GTAATTTTTAGAAAGTTTAG
* ** *
456021 AGGGCAAAAATGTAATTTCCATAAAGTTTA-
1 -GGGTAAAAATGTAATTTTTAGAAAGTTTAG
** * *
456051 GGAAAAAAATGTAATTTCTATAAAGTTT-G
1 GGGTAAAAATGTAATTTTTAGAAAGTTTAG
*
456080 GGGTTAAAAATGTAATTTTT-GTAAAGTTTAA
1 GGG-TAAAAATGTAATTTTTAG-AAAGTTTAG
*
456111 GGG-AAAAATGTAATTTTT-GTGAAGTTTAG
1 GGGTAAAAATGTAATTTTTAG-AAAGTTTAG
* * * *
456140 GGGTCAAAATATGA-TTTTGGAAAAGTTTGAG
1 GGGTAAAAATGTAATTTTTAG-AAAGTTT-AG
* * *
456171 GGTTAAAATATG--ATTTTTGGAAAATTTAG
1 GGGTAAAA-ATGTAATTTTTAGAAAGTTTAG
* * * * *
456200 GGGTTAAAATATAATTTTTGGAAAATTTGG
1 GGGTAAAAATGTAATTTTTAGAAAGTTTAG
* *
456230 GGGTCAAAATATAATTTTTAGAAAGTTT
1 GGGTAAAAATGTAATTTTTAGAAAGTTT
456258 GAGGCTCGAA
Statistics
Matches: 260, Mismatches: 43, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
28 10 0.04
29 89 0.34
30 128 0.49
31 26 0.10
32 7 0.03
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTAGAAAGTTTAG
Found at i:456077 original size:59 final size:59
Alignment explanation
Indices: 456014--456126 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
456004 CAATTTTTAG
456014 AAGTTCGAGGG-CAAAAATGTAATTTCCATAAAGTTT-AGGAAAAAAATGTAATTTCTATA
1 AAGTTCG-GGGTCAAAAATGTAATTTCCATAAAGTTTAAGG-AAAAAATGTAATTTCTATA
* * *** *
456073 AAGTTTGGGGTTAAAAATGTAATTTTTGTAAAGTTTAAGGGAAAAATGTAATTT
1 AAGTTCGGGGTCAAAAATGTAATTTCCATAAAGTTTAAGGAAAAAATGTAATTT
456127 TTGTGAAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 3 0.07
59 40 0.87
60 3 0.07
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
AAGTTCGGGGTCAAAAATGTAATTTCCATAAAGTTTAAGGAAAAAATGTAATTTCTATA
Found at i:456136 original size:59 final size:59
Alignment explanation
Indices: 456026--456219 Score: 164
Period size: 59 Copynumber: 3.3 Consensus size: 59
456016 GTTCGAGGGC
*** * * * *
456026 AAAAATGTAATTTCCATAAAGTTTAGGAAAAAAATGTAATTTCTATAAAGTTT-GGGGTT
1 AAAAATGTAATTTTTGTAAAGTTTAGG-GAAAAATGTAATTTTTGTGAAGTTTAGGGGTT
*
456085 AAAAATGTAATTTTTGTAAAGTTTAAGGGAAAAATGTAATTTTTGTGAAGTTTAGGGGTC
1 AAAAATGTAATTTTTGTAAAGTTT-AGGGAAAAATGTAATTTTTGTGAAGTTTAGGGGTT
* * * * * *
456145 AAAATATG--ATTTTGGAAAAGTTTGAGGGTTAAAATATGATTTTTG-GAAAATTTAGGGGTT
1 AAAA-ATGTAATTTTTGTAAAGTTT-AGGG-AAAAATGTAATTTTTGTG-AAGTTTAGGGGTT
*
456205 -AAAATATAATTTTTG
1 AAAAATGTAATTTTTG
456220 GAAAATTTGG
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
58 2 0.02
59 63 0.57
60 42 0.38
61 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (59 bp):
AAAAATGTAATTTTTGTAAAGTTTAGGGAAAAATGTAATTTTTGTGAAGTTTAGGGGTT
Found at i:456275 original size:90 final size:90
Alignment explanation
Indices: 456115--456286 Score: 204
Period size: 90 Copynumber: 1.9 Consensus size: 90
456105 GTTTAAGGGA
* * * * * * *
456115 AAAATGTAATTTTTGTGAAGTTTAGGGGTCAAAATATGATTTTGGAAAAGTTTGAGGGTTAAAAT
1 AAAATATAATTTTTGTGAAATTTAGGGGTCAAAATATAATTTTAGAAAAGTTTGAGGCTCAAAAC
* *
456180 ATGATTTTTGGAAAATTTAGGGGTT
66 ATGATTTCTAGAAAATTTAGGGGTT
* *
456205 AAAATATAATTTTTG-GAAAATTTGGGGGTCAAAATATAATTTTTAG-AAAGTTTGAGGCTCGAA
1 AAAATATAATTTTTGTG-AAATTTAGGGGTCAAAATATAA-TTTTAGAAAAGTTTGAGGCTCAAA
*
456268 ACGTGATTTCTAGAAAATT
64 ACATGATTTCTAGAAAATT
456287 CAAGAACCTC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 1 0.01
90 62 0.91
91 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (90 bp):
AAAATATAATTTTTGTGAAATTTAGGGGTCAAAATATAATTTTAGAAAAGTTTGAGGCTCAAAAC
ATGATTTCTAGAAAATTTAGGGGTT
Found at i:457403 original size:3 final size:3
Alignment explanation
Indices: 457395--457421 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
457385 TTTTTCTTTT
457395 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
457422 ATGATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:458096 original size:6 final size:6
Alignment explanation
Indices: 458087--458178 Score: 86
Period size: 6 Copynumber: 15.7 Consensus size: 6
458077 ATATTTAGGA
458087 TAAATT TAAATT TGATAA-- TAAATT TAAACTT TAAA-T TAAATT TAAATT
1 TAAATT TAAATT T-A-AATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
* * * *
458135 TAAA-A TAAATT TAAACT TAAACT TAAA-A TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
458179 AACAAATTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.19
6 48 0.66
7 7 0.10
8 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:458154 original size:23 final size:23
Alignment explanation
Indices: 458118--458178 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
458108 ATTTAAACTT
*
458118 TAAA-TTAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAACTTAAAA
*
458140 TAAATTTAAACTTAAACTTAAAA
1 TAAATTTAAATTTAAACTTAAAA
458163 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
458179 AACAAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 4 0.11
23 31 0.89
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTAAATTTAAACTTAAAA
Found at i:458180 original size:18 final size:17
Alignment explanation
Indices: 458072--458207 Score: 101
Period size: 17 Copynumber: 7.5 Consensus size: 17
458062 GGAATTTATT
* **
458072 AATTTATATTTAGGATA
1 AATTTAAATTTAAAATA
*
458089 AATTTAAATTTGATAATA
1 AATTTAAATTT-AAAATA
*
458107 AATTTAAACTTTAAATTA
1 AATTTAAA-TTTAAAATA
458125 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
458142 AATTTAAACTTAAACTTAAAATA
1 AATTTAAA--T----TTAAAATA
*
458165 AATTTAAATTTAAAAACA
1 AATTTAAATTT-AAAATA
* * *
458183 AATTCAAACTTAAGATA
1 AATTTAAATTTAAAATA
*
458200 AATCTAAA
1 AATTTAAA
458208 ACAAAAATGT
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
17 38 0.39
18 38 0.39
19 4 0.04
21 1 0.01
23 16 0.16
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:458186 original size:41 final size:41
Alignment explanation
Indices: 458105--458195 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
458095 AATTTGATAA
* * *
458105 TAAATTTAAACTTTAAATTAAATTTAAATTTAAAATAAATT
1 TAAACTTAAACTTTAAAATAAATTTAAATTTAAAACAAATT
458146 TAAACTTAAAC-TTAAAATAAATTTAAATTTAAAAACAAATT
1 TAAACTTAAACTTTAAAATAAATTTAAATTT-AAAACAAATT
*
458187 CAAACTTAA
1 TAAACTTAA
458196 GATAAATCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 18 0.40
41 27 0.60
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (41 bp):
TAAACTTAAACTTTAAAATAAATTTAAATTTAAAACAAATT
Found at i:460797 original size:33 final size:33
Alignment explanation
Indices: 460760--460830 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
460750 GATGCAACGT
460760 GAAATAAAATT-AATTATAGTAAATAAGATAAAA
1 GAAAT-AAATTGAATTATAGTAAATAAGATAAAA
* *
460793 GAAATTAGTTGAATTATAGTAAATAAGATAAAA
1 GAAATAAATTGAATTATAGTAAATAAGATAAAA
*
460826 TAAAT
1 GAAAT
460831 TAGTTGAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (33 bp):
GAAATAAATTGAATTATAGTAAATAAGATAAAA
Found at i:460831 original size:33 final size:33
Alignment explanation
Indices: 460771--460838 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
460761 AAATAAAATT
460771 AATTATAGTAAATAAGATAAAAGAAATTAGTTG
1 AATTATAGTAAATAAGATAAAAGAAATTAGTTG
*
460804 AATTATAGTAAATAAGATAAAATAAATTAGTTG
1 AATTATAGTAAATAAGATAAAAGAAATTAGTTG
460837 AA
1 AA
460839 GGGGTGTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (33 bp):
AATTATAGTAAATAAGATAAAAGAAATTAGTTG
Found at i:462394 original size:29 final size:28
Alignment explanation
Indices: 462362--462531 Score: 153
Period size: 29 Copynumber: 5.9 Consensus size: 28
462352 TAAGACATCC
* *
462362 GGGGGTAAAATGGTAATTTTTTGATGTTT
1 GGGGGTAAAAT-GTAATTTTTAGAAGTTT
462391 GGGGGTAAAATGTTAA-TTTTAGAAAGTTT
1 GGGGGTAAAATG-TAATTTTTAG-AAGTTT
* * * *
462420 AGGGTTAAAATGTGATTTTTGGAAGTTT
1 GGGGGTAAAATGTAATTTTTAGAAGTTT
* * *
462448 AGGGGTAAAAATGAAATTTTTGAGAAGCTT
1 GGGGGT-AAAATGTAATTTTT-AGAAGTTT
* * * *
462478 GAGGGTTAAAATGTGATTTATGGAAGTTT
1 G-GGGGTAAAATGTAATTTTTAGAAGTTT
462507 GGGGGTAAAATGTAATTTTTGAGAA
1 GGGGGTAAAATGTAATTTTT-AGAA
462532 AGTTAAGAGT
Statistics
Matches: 112, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
28 35 0.31
29 56 0.50
30 17 0.15
31 4 0.04
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.38
Consensus pattern (28 bp):
GGGGGTAAAATGTAATTTTTAGAAGTTT
Found at i:462459 original size:58 final size:57
Alignment explanation
Indices: 462367--462637 Score: 240
Period size: 59 Copynumber: 4.6 Consensus size: 57
462357 CATCCGGGGG
* * * * *
462367 TAAAATGGTAATTTTTTGATGTTTGGGGGTAAAATGTTAATTTTAGAAAG-TTTAGGGT
1 TAAAAT-GTGATTTTTGGAAGTTTAGGGGTAAAATG-TAATTTTAGAAAGCTTGAGGGT
* *
462425 TAAAATGTGATTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTTGAGAAGCTTGAGGGT
1 TAAAATGTGATTTTTGGAAGTTTAGGGGT-AAAATGTAATTTTAGA-AAGCTTGAGGGT
* * * *
462484 TAAAATGTGATTTATGGAAGTTTGGGGGTAAAATGTAATTTTTGAGAAAG-TTAAGAGT
1 TAAAATGTGATTTTTGGAAGTTTAGGGGTAAAATGTAA-TTTT-AGAAAGCTTGAGGGT
* * * * * * *
462542 TAAAATATAATTTTTGGAAAGTTTAAGGGTTAAAATATGATTTTTGAAATGCTCGAGGGT
1 TAAAATGTGATTTTTGG-AAGTTT-AGGGGTAAAATGTAATTTTAGAAA-GCTTGAGGGT
* * *
462602 CAAAATATAGTTTTTTGGAAGTTTAGGGGTTAAAAT
1 TAAAATGT-GATTTTTGGAAGTTTAGGGG-TAAAAT
462638 ATGATTTTTG
Statistics
Matches: 174, Mismatches: 28, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
57 27 0.16
58 47 0.27
59 56 0.32
60 37 0.21
61 7 0.04
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.38
Consensus pattern (57 bp):
TAAAATGTGATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTAGAAAGCTTGAGGGT
Found at i:462546 original size:30 final size:30
Alignment explanation
Indices: 462396--462674 Score: 207
Period size: 30 Copynumber: 9.4 Consensus size: 30
462386 TGTTTGGGGG
*
462396 TAAAATGTTAATTTTAGA-AAGTTT-AGGGT
1 TAAAATG-TAATTTTTGAGAAGTTTAAGGGT
* *
462425 TAAAATGTGATTTTTG-GAAGTTTAGGGGT
1 TAAAATGTAATTTTTGAGAAGTTTAAGGGT
* * * *
462454 AAAAATGAAATTTTTGAGAAGCTTGAGGGT
1 TAAAATGTAATTTTTGAGAAGTTTAAGGGT
* * * *
462484 TAAAATGTGATTTATG-GAAGTTT-GGGGG
1 TAAAATGTAATTTTTGAGAAGTTTAAGGGT
*
462512 TAAAATGTAATTTTTGAGAAAG-TTAAGAGT
1 TAAAATGTAATTTTTGAG-AAGTTTAAGGGT
*
462542 TAAAATATAATTTTTG-GAAAGTTTAAGGGT
1 TAAAATGTAATTTTTGAG-AAGTTTAAGGGT
* * * **
462572 TAAAATATGATTTTTGA-AATGCTCGAGGGT
1 TAAAATGTAATTTTTGAGAA-GTTTAAGGGT
* * * *
462602 CAAAATATAGTTTTTTG-GAAGTTTAGGGGT
1 TAAAATGTA-ATTTTTGAGAAGTTTAAGGGT
* * *
462632 TAAAATATGATTTTTGAAAAGTTTAAGGGT
1 TAAAATGTAATTTTTGAGAAGTTTAAGGGT
* *
462662 CAAACTGTAATTT
1 TAAAATGTAATTT
462675 CTAGACATTT
Statistics
Matches: 195, Mismatches: 43, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
28 30 0.15
29 46 0.24
30 111 0.57
31 8 0.04
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
TAAAATGTAATTTTTGAGAAGTTTAAGGGT
Found at i:462665 original size:60 final size:59
Alignment explanation
Indices: 462420--462661 Score: 258
Period size: 60 Copynumber: 4.1 Consensus size: 59
462410 TAGAAAGTTT
* * *
462420 AGGGTTAAAATGTGATTTTTGGAAGTTTAGGGG-TAAAA-ATGAAATTTTTGAGAAGCTTG
1 AGGGTTAAAATATGATTTTTGGAAGTTTAGGGGTTAAAATATG--ATTTTTGAAAAGCTTA
* * * * *
462479 AGGGTTAAAATGTGATTTATGGAAGTTT-GGGGGTAAAATGTAATTTTTGAGAAAG-TTA
1 AGGGTTAAAATATGATTTTTGGAAGTTTAGGGGTTAAAATATGATTTTTGA-AAAGCTTA
* * * * **
462537 AGAGTTAAAATATAATTTTTGGAAAGTTTAAGGGTTAAAATATGATTTTTGAAATGCTCG
1 AGGGTTAAAATATGATTTTTGG-AAGTTTAGGGGTTAAAATATGATTTTTGAAAAGCTTA
* * *
462597 AGGGTCAAAATATAGTTTTTTGGAAGTTTAGGGGTTAAAATATGATTTTTGAAAAGTTTA
1 AGGGTTAAAATAT-GATTTTTGGAAGTTTAGGGGTTAAAATATGATTTTTGAAAAGCTTA
462657 AGGGT
1 AGGGT
462662 CAAACTGTAA
Statistics
Matches: 151, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
58 32 0.21
59 44 0.29
60 68 0.45
61 7 0.05
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (59 bp):
AGGGTTAAAATATGATTTTTGGAAGTTTAGGGGTTAAAATATGATTTTTGAAAAGCTTA
Found at i:463631 original size:18 final size:21
Alignment explanation
Indices: 463612--463659 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
463602 TTTATTACTA
463612 TTATTCATA-TTA-TATTTAT
1 TTATTCATAGTTATTATTTAT
*
463631 TTATTTAATAGTTATTATTTAT
1 TTA-TTCATAGTTATTATTTAT
463653 TTATTCA
1 TTATTCA
463660 AAACATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 5 0.21
21 6 0.25
22 10 0.42
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTCATAGTTATTATTTAT
Found at i:463635 original size:22 final size:23
Alignment explanation
Indices: 463599--463657 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
463589 CTTTATTGTT
*
463599 TTATTTATTACTATTATTCATA-TTA
1 TTATTTATT--TATT-TTAATAGTTA
463624 -TATTTATTTA-TTTAATAGTTA
1 TTATTTATTTATTTTAATAGTTA
463645 TTATTTATTTATT
1 TTATTTATTTATT
463658 CAAAACATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 5 0.17
21 4 0.13
22 12 0.40
23 1 0.03
24 8 0.27
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATTTATTTATTTTAATAGTTA
Found at i:464428 original size:17 final size:17
Alignment explanation
Indices: 464402--464505 Score: 75
Period size: 17 Copynumber: 6.1 Consensus size: 17
464392 GGAGCTTCTT
* *
464402 TTTAATTTTTAATTAAA
1 TTTAAATTTTAAATAAA
464419 TTTAAATTTTAAATAAA
1 TTTAAATTTTAAATAAA
* * *
464436 TTCAAATTTAAAATGAA
1 TTTAAATTTTAAATAAA
** **
464453 CCTAAATTCAAAATAAA
1 TTTAAATTTTAAATAAA
*
464470 TTTAAA-TTTATACTAAA
1 TTTAAATTTTA-AATAAA
* * *
464487 TTCAAACTTAAAATAAA
1 TTTAAATTTTAAATAAA
464504 TT
1 TT
464506 AAAAATGGGT
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
16 2 0.03
17 62 0.93
18 3 0.04
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTTAAATAAA
Found at i:464470 original size:28 final size:28
Alignment explanation
Indices: 464439--464492 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
464429 AAATAAATTC
464439 AAATTTAAAATGA-ACCTAAATTCAAAAT
1 AAATTTAAAATGATA-CTAAATTCAAAAT
* *
464467 AAATTTAAATTTATACTAAATTCAAA
1 AAATTTAAAATGATACTAAATTCAAA
464493 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (28 bp):
AAATTTAAAATGATACTAAATTCAAAAT
Found at i:465278 original size:209 final size:207
Alignment explanation
Indices: 464905--465550 Score: 828
Period size: 209 Copynumber: 3.1 Consensus size: 207
464895 TCAGGAAGAA
* ** * *
464905 GACCACTTTATTGCTTCGACCTGCTTCTCT-GTATCTCATCAATAAGATGGTGTTTGATGTTTCG
1 GACCATTTTATTGCTTCGACCTGCTTCT-TAGTATCTCATCAGGAAGATGG-GTTCGAAGTTTCG
* * * * * * * *
464969 CTCACATTGAGCTTTGTTTTATTTATTTGGTATAGTTCTCTGTATTTTATTAAGAAGATGATCAC
64 CTCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAAGAAGATGACCAC
* * *
465034 CTCACTTGTTTTAATCCGCTTCTCTGTATCTCATCACGAAGATGAATTTGCTCCACTTCTCAGTA
129 CTCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTTG-TCCACTTCTCAGTA
465099 TCTCATCAGAAAGCT
193 TCTCATCAGAAAGCT
** *
465114 GTTCATTTTATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGATGAGGTTCGAAGTTTCGC
1 GACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGATG-GGTTCGAAGTTTCGC
* * *
465179 TCGCATTGAGCTTTGTTTCATTGAGTTGGTATATTTCTCTGTATCTCATCAAGAAGATGACCATC
65 TCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAAGAAGATGACCACC
* *
465244 TCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAAACGGTTTTGGTCCACTTCTCAGTAT
130 TCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTT-GTCCACTTCTCAGTAT
* *
465309 CTCATTAGGAAGCT
194 CTCATCAGAAAGCT
* * * *
465323 GACCATTTTATTGCTTCGACTTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGC
1 GACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGAT-GGGTTCGAAGTTTCGC
* **
465388 TCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAGGAAGATGACTGCC
65 TCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAAGAAGATGACCACC
* ** * *
465453 TCACTTATTTTAATTTGCTTCTCTGTATCTTATCAGGAAGACGGATTTAGTCCACTTCTCTGTAT
130 TCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTT-GTCCACTTCTCAGTAT
* *
465518 CTCATTAGGAAGAC-
194 CTCATCAGAAAG-CT
**
465532 GACCGCTTTATTGCTTCGA
1 GACCATTTTATTGCTTCGA
465551 TAATTGCAAT
Statistics
Matches: 384, Mismatches: 48, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
208 1 0.00
209 379 0.99
210 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (207 bp):
GACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGATGGGTTCGAAGTTTCGCT
CGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAAGAAGATGACCACCT
CACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTTGTCCACTTCTCAGTATCT
CATCAGAAAGCT
Found at i:466094 original size:50 final size:49
Alignment explanation
Indices: 466040--466151 Score: 117
Period size: 50 Copynumber: 2.3 Consensus size: 49
466030 GCCATTGCTA
*
466040 CCTCAATCCTTCCCATTT-CATCTTCTTT-GGTATCA-AGTTCGCCGTTGCGG
1 CCTCAATCCTTCCC-TTTACATCTT-TTTAGGTATCAGA-TTCACC-TTGCGG
*
466090 CCTCAA-CCTTTCCCTTTACATCTTTTTAAGGTATCGGATTCACCTTGCGG
1 CCTCAATCC-TTCCCTTTACATCTTTTT-AGGTATCAGATTCACCTTGCGG
466140 CCTCAAT-CTTCC
1 CCTCAATCCTTCC
466152 TCTGTCATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
49 12 0.22
50 30 0.56
51 11 0.20
52 1 0.02
ACGTcount: A:0.16, C:0.33, G:0.13, T:0.38
Consensus pattern (49 bp):
CCTCAATCCTTCCCTTTACATCTTTTTAGGTATCAGATTCACCTTGCGG
Found at i:466180 original size:100 final size:101
Alignment explanation
Indices: 466076--466328 Score: 241
Period size: 100 Copynumber: 2.5 Consensus size: 101
466066 TTGGTATCAA
* *
466076 GTTCGCCGTTGCGGCCTCAACCTTTCCCTTTACATCTTTTTAAGGTATCGGATTCAC-CTTGCGG
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTTTAAGGTATCGGATTCACTCTTGCGA
* * **
466140 CCTCAATC-TTCCTCTGTCATC-TCTTCAT-GGTACTGG
66 CCTCAACCTTTCC-CT-TCA-CATCTTCATAGGAACCAG
** * * * * * * * *
466176 GTTCGTTGTTGCGGCCTCAACTTTTCACATCACATCTTCTT-AGGTATCGGGTTCGCTGTTGTGA
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTTTAAGGTATCGGATTCACTCTTGCGA
**
466240 CCTCAACCTTTCCCTTCACATCTTTTTAGGAACCAG
66 CCTCAACCTTTCCCTTCACATCTTCATAGGAACCAG
* * *
466276 GTTAGCCGTTGCGACCTCAACCTTTCCCTTCA-ATC-TTTTAAGGTACCGGATTC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTTTAAGGTATCGGATTC
466329 GTCGACGCAG
Statistics
Matches: 120, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
98 4 0.03
99 35 0.29
100 77 0.64
101 4 0.03
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (101 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTTTAAGGTATCGGATTCACTCTTGCGA
CCTCAACCTTTCCCTTCACATCTTCATAGGAACCAG
Found at i:466228 original size:50 final size:50
Alignment explanation
Indices: 466058--466301 Score: 154
Period size: 50 Copynumber: 4.9 Consensus size: 50
466048 CTTCCCATTT
* ** * * * * *
466058 CATCTTCTTTGGTATCAAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
1 CATCTTCTTAGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTCACATCA
* * * * * * * * **
466108 CATCTTTTTAAGGTATCGGATTCAC-CTTGCGGCCTCAATCTTCCTC-TGT
1 CATCTTCTT-AGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTCACATCA
* * *
466157 CATC-TCTTCATGGTA-CTGGGTTCGTTGTTGCGGCCTCAACTTTTCACATCA
1 CATCTTCTT-A-GGTATC-GGGTTCGCTGTTGCGACCTCAACCTTTCACATCA
* * *
466208 CATCTTCTTAGGTATCGGGTTCGCTGTTGTGACCTCAACCTTTCCCTTCA
1 CATCTTCTTAGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTCACATCA
* * * * * *
466258 CATCTTTTTAGGAACCAGGTTAGCCGTTGCGACCTCAACCTTTC
1 CATCTTCTTAGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTC
466302 CCTTCAATCT
Statistics
Matches: 150, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
48 5 0.03
49 14 0.09
50 110 0.73
51 17 0.11
52 4 0.03
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.37
Consensus pattern (50 bp):
CATCTTCTTAGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTCACATCA
Found at i:466302 original size:50 final size:50
Alignment explanation
Indices: 466183--466314 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 50
466173 TGGGTTCGTT
* * * * * * * * * *
466183 GTTGCGGCCTCAACTTTTCACATCACATCTTCTTAGGTATCGGGTTCGCT
1 GTTGCGACCTCAACCTTTCCCTTCACATCTTTTTAGGAACCAGGTTAGCC
*
466233 GTTGTGACCTCAACCTTTCCCTTCACATCTTTTTAGGAACCAGGTTAGCC
1 GTTGCGACCTCAACCTTTCCCTTCACATCTTTTTAGGAACCAGGTTAGCC
466283 GTTGCGACCTCAACCTTTCCCTTCA-ATCTTTT
1 GTTGCGACCTCAACCTTTCCCTTCACATCTTTT
466315 AAGGTACCGG
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 7 0.10
50 63 0.90
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.36
Consensus pattern (50 bp):
GTTGCGACCTCAACCTTTCCCTTCACATCTTTTTAGGAACCAGGTTAGCC
Found at i:467222 original size:7 final size:7
Alignment explanation
Indices: 467210--467264 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
467200 TGACCTCTCA
467210 TTTTTCT
1 TTTTTCT
467217 TTTTTCT
1 TTTTTCT
467224 TTTTT-T
1 TTTTTCT
467230 GTTTTT-T
1 -TTTTTCT
467237 TGTTTTCT
1 T-TTTTCT
*
467245 TTTTCCT
1 TTTTTCT
467252 TTTTTCT
1 TTTTTCT
467259 ATTTTT
1 -TTTTT
467265 TATTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 2 0.05
7 33 0.79
8 7 0.17
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:467243 original size:28 final size:29
Alignment explanation
Indices: 467211--467265 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
467201 GACCTCTCAT
* *
467211 TTTTCTTTTTTCTTTTTT-TGTTTTTTTG
1 TTTTCTTTTTCCTTTTTTCTATTTTTTTG
467239 TTTTCTTTTTCCTTTTTTCTATTTTTT
1 TTTTCTTTTTCCTTTTTTCTATTTTTT
467266 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.84
Consensus pattern (29 bp):
TTTTCTTTTTCCTTTTTTCTATTTTTTTG
Found at i:472651 original size:28 final size:29
Alignment explanation
Indices: 472620--472834 Score: 86
Period size: 28 Copynumber: 7.3 Consensus size: 29
472610 GGACATCTGA
*
472620 GGGTAAAATGAAAATTTTGG-ATGTTCGG
1 GGGTAAAATGAAAATTTTGGAAAGTTCGG
** *
472648 GGGTAAAATGTTAATTTTGGAAAGTTTGG
1 GGGTAAAATGAAAATTTTGGAAAGTTCGG
* ** * * * *
472677 GGTTAAAATGTGATTTTTTG-AAGTTTGA
1 GGGTAAAATGAAAATTTTGGAAAGTTCGG
*
472705 GGGTAAAAAT-AAAATTTTTGAGAAGCTT--G
1 GGGT-AAAATGAAAATTTTGGA-AAG-TTCGG
* *
472734 GGGTAAAA--AATACGATTTATGG-AAGTTTGA
1 GGGTAAAATGAA-A--ATTT-TGGAAAGTTCGG
* * *
472764 GGGTAAAATGTAATTTTTGAGAAAGTTCGA
1 GGGTAAAATGAAAATTTTG-GAAAGTTCGG
*** *
472794 GGGTCAAAATGTATTTTTTTGGAAAGTTTGG
1 GGGT-AAAATG-AAAATTTTGGAAAGTTCGG
472825 GGGTTAAAAT
1 GGG-TAAAAT
472835 ATGATTTTTA
Statistics
Matches: 145, Mismatches: 24, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.01
28 44 0.30
29 38 0.26
30 26 0.18
31 27 0.19
32 8 0.06
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGAAAATTTTGGAAAGTTCGG
Found at i:472694 original size:29 final size:29
Alignment explanation
Indices: 472662--472933 Score: 194
Period size: 30 Copynumber: 9.1 Consensus size: 29
472652 AAAATGTTAA
* *
472662 TTTTGGAAAGTTTGGGGTTAAAATGTGAT
1 TTTTGGAAAGTTTGGGGTTAAAATATAAT
* * *
472691 TTTTTG-AAGTTTGAGGGTAAAAATAAAAT
1 TTTTGGAAAGTTTG-GGGTTAAAATATAAT
* *
472720 TTTT-GAGAAGCTTGGGG-TAAAAAATACGAT
1 TTTTGGA-AAGTTTGGGGTTAAAATATA--AT
* *
472750 TTATGG-AAGTTTGAGGG-TAAAATGTAAT
1 TTTTGGAAAGTTTG-GGGTTAAAATATAAT
* * * *
472778 TTTTGAGAAAGTTCGAGGGTCAAAATGTATTT
1 TTTTG-GAAAGTTTG-GGGTTAAAATATA-AT
*
472810 TTTTGGAAAGTTTGGGGGTTAAAATATGAT
1 TTTTGGAAAGTTT-GGGGTTAAAATATAAT
**
472840 TTTTAAAAAGTTTAGGGGTTTAAAATATAAT
1 TTTTGGAAAGTTT-GGGG-TTAAAATATAAT
* * *
472871 TTTTAGGAAGGTTAGGGGTTAAAATATGAT
1 TTTT-GGAAAGTTTGGGGTTAAAATATAAT
* * * *
472901 TTTTGAAAAGTTCGAGGTTAAAATGTAAT
1 TTTTGGAAAGTTTGGGGTTAAAATATAAT
472930 TTTT
1 TTTT
472934 AGACAGTTCA
Statistics
Matches: 192, Mismatches: 37, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
28 20 0.10
29 53 0.28
30 62 0.32
31 45 0.23
32 12 0.06
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.39
Consensus pattern (29 bp):
TTTTGGAAAGTTTGGGGTTAAAATATAAT
Found at i:472790 original size:30 final size:30
Alignment explanation
Indices: 472617--472941 Score: 164
Period size: 30 Copynumber: 11.0 Consensus size: 30
472607 TTAGGACATC
* * *
472617 TGAGGGTAAAATGAAAATTTTG-G-ATGTT
1 TGAGGGTAAAATGTAATTTTTGAGAAAGTT
* *
472645 CGGGGGTAAAATGTTAA-TTTTG-GAAAGTT
1 TGAGGGTAAAATG-TAATTTTTGAGAAAGTT
* *
472674 TG-GGGTTAAAATGTGATTTTT-TG-AAGTT
1 TGAGGG-TAAAATGTAATTTTTGAGAAAGTT
** *
472702 TGAGGGTAAAAATAAAATTTTTGAG-AAGCT
1 TGAGGGT-AAAATGTAATTTTTGAGAAAGTT
** *
472732 TG-GGGTAAAAAATACGATTTATG-G-AAGTT
1 TGAGGGTAAAATGTA--ATTTTTGAGAAAGTT
472761 TGAGGGTAAAATGTAATTTTTGAGAAAGTT
1 TGAGGGTAAAATGTAATTTTTGAGAAAGTT
* *
472791 CGAGGGTCAAAATGTATTTTTTTG-GAAAGTT
1 TGAGGGT-AAAATGTA-ATTTTTGAGAAAGTT
* * * *
472822 TGGGGGTTAAAATATGATTTTT-AAAAAGTT
1 TGAGGG-TAAAATGTAATTTTTGAGAAAGTT
* * *
472852 T-AGGGGTTTAAAATATAATTTTT-AGGAAGGT
1 TGA-GGG--TAAAATGTAATTTTTGAGAAAGTT
* *
472883 T-AGGGGTTAAAATATGATTTTTGA-AAAGTT
1 TGA-GGG-TAAAATGTAATTTTTGAGAAAGTT
* * *
472913 CGAGGTTAAAATGTAATTTTT-AGACAGTT
1 TGAGGGTAAAATGTAATTTTTGAGAAAGTT
472942 CAGGGGCCTT
Statistics
Matches: 236, Mismatches: 39, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
28 43 0.18
29 63 0.27
30 70 0.30
31 53 0.22
32 7 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
TGAGGGTAAAATGTAATTTTTGAGAAAGTT
Found at i:472803 original size:59 final size:57
Alignment explanation
Indices: 472648--472790 Score: 157
Period size: 58 Copynumber: 2.5 Consensus size: 57
472638 GGATGTTCGG
* ** * *
472648 GGGTAAAATGTTAA-TTTTG-GAAAGTTTGGGGTTAAAATGTGATTTTTTGAAGTTTGA
1 GGGTAAAATG-TAATTTTTGAGAAAG-TTGGGGTAAAAATACGATTTATGGAAGTTTGA
**
472705 GGGTAAAAATAAAATTTTTGAG-AAGCTTGGGGTAAAAAATACGATTTATGGAAGTTTGA
1 GGGT-AAAATGTAATTTTTGAGAAAG-TTGGGGT-AAAAATACGATTTATGGAAGTTTGA
472764 GGGTAAAATGTAATTTTTGAGAAAGTT
1 GGGTAAAATGTAATTTTTGAGAAAGTT
472791 CGAGGGTCAA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
57 6 0.08
58 37 0.52
59 28 0.39
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGAGAAAGTTGGGGTAAAAATACGATTTATGGAAGTTTGA
Found at i:472850 original size:61 final size:60
Alignment explanation
Indices: 472749--472935 Score: 200
Period size: 61 Copynumber: 3.1 Consensus size: 60
472739 AAAAATACGA
* * * * * *
472749 TTTATGGAAGTTTGAGGG-TAAAATGTAATTTTTGAGAAAGTTCGAGGGTCAAAATGTATTT
1 TTTA-GGAAGTTTGGGGGTTAAAATATGATTTTT-AAAAAGTTCGAGGGTTAAAATGTAATT
* * *
472810 TTTTGGAAAGTTTGGGGGTTAAAATATGATTTTTAAAAAGTT-TAGGGGTTTAAAATATAATT
1 TTTAGG-AAGTTTGGGGGTTAAAATATGATTTTTAAAAAGTTCGA-GGG-TTAAAATGTAATT
* * *
472872 TTTAGGAAGGTTAGGGGTTAAAATATGATTTTTGAAAAGTTCGA-GGTTAAAATGTAATT
1 TTTAGGAAGTTTGGGGGTTAAAATATGATTTTTAAAAAGTTCGAGGGTTAAAATGTAATT
472931 TTTAG
1 TTTAG
472936 ACAGTTCAGG
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
59 17 0.16
60 5 0.05
61 55 0.52
62 29 0.27
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.40
Consensus pattern (60 bp):
TTTAGGAAGTTTGGGGGTTAAAATATGATTTTTAAAAAGTTCGAGGGTTAAAATGTAATT
Found at i:473898 original size:18 final size:21
Alignment explanation
Indices: 473877--473920 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
473867 TATTTATTAC
473877 TATTATT-AAT-ATTA-TATT
1 TATTATTAAATAATTATTATT
473895 TATTTATTAAATAATTATTATT
1 TA-TTATTAAATAATTATTATT
473917 TATT
1 TATT
473921 TATTCAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 5 0.23
20 3 0.14
21 6 0.27
22 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTAAATAATTATTATT
Found at i:474819 original size:12 final size:12
Alignment explanation
Indices: 474806--474886 Score: 74
Period size: 12 Copynumber: 6.7 Consensus size: 12
474796 AAAATAGTAG
*
474806 CAAAAATAACAG
1 CAAAAATAACAA
*
474818 C-AAAACAACAA
1 CAAAAATAACAA
474829 CAAAAATAACAA
1 CAAAAATAACAA
*
474841 CAAAAATAGCAA
1 CAAAAATAACAA
* *
474853 TAAAAACAACAATA
1 CAAAAATAAC-A-A
*
474867 AAAAAATAACAA
1 CAAAAATAACAA
*
474879 TAAAAATA
1 CAAAAATA
474887 GTACCAAAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
11 9 0.16
12 36 0.64
13 2 0.04
14 9 0.16
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (12 bp):
CAAAAATAACAA
Found at i:474821 original size:23 final size:21
Alignment explanation
Indices: 474803--474887 Score: 63
Period size: 23 Copynumber: 4.1 Consensus size: 21
474793 TCCAAAATAG
*
474803 TAGCAAAAATAACAGCAAAACAA
1 TAGCAAAAATAACAAC-AAA-AA
* *
474826 CAACAAAAATAACAACAAAAA
1 TAGCAAAAATAACAACAAAAA
474847 TAGCAATAAA-AACAAC---AA
1 TAGCAA-AAATAACAACAAAAA
* *
474865 TA-AAAAAATAACAATAAAAA
1 TAGCAAAAATAACAACAAAAA
474885 TAG
1 TAG
474888 TACCAAAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 4 0.08
20 4 0.08
21 12 0.24
22 6 0.12
23 13 0.27
ACGTcount: A:0.71, C:0.14, G:0.05, T:0.11
Consensus pattern (21 bp):
TAGCAAAAATAACAACAAAAA
Found at i:479295 original size:2 final size:2
Alignment explanation
Indices: 479288--479312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
479278 CATACTACTG
479288 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
479313 TCATGCATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:482405 original size:31 final size:30
Alignment explanation
Indices: 482370--482469 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
482360 AAAGCTTAAG
482370 TACCAAATTAGGAAAAAATGTCAAGTTCAAA
1 TACCAAATTAGGAAAAAATGTCAA-TTCAAA
* * *
482401 TACCAAATTAAGTTAAAAAA-AT-AATTTAAA
1 TACCAAATT-AG-GAAAAAATGTCAATTCAAA
* ** *
482431 TGCCAAATTAGGAAAACGTGTCAACTTCATA
1 TACCAAATTAGGAAAAAATGTCAA-TTCAAA
482462 TACCAAAT
1 TACCAAAT
482470 GCTATATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 15 0.28
31 22 0.42
32 3 0.06
33 6 0.11
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (30 bp):
TACCAAATTAGGAAAAAATGTCAATTCAAA
Found at i:483249 original size:19 final size:19
Alignment explanation
Indices: 483189--483250 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
483179 AAGGAAATTG
*
483189 TTTTA-TATAAATTTTATG
1 TTTTATTATAAATTTTATT
* *
483207 ATTTATTAATTAATTTTAATT
1 TTTTATT-ATAAATTTT-ATT
*
483228 TTTTCTTATAAATTTTATT
1 TTTTATTATAAATTTTATT
483247 TTTT
1 TTTT
483251 TATGTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.11
19 8 0.23
20 16 0.46
21 7 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATTATAAATTTTATT
Found at i:486605 original size:29 final size:30
Alignment explanation
Indices: 486557--486619 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
486547 TTTTGAATAG
486557 ATTT-ATGTAATATTATATA-TTTATTTAA
1 ATTTAATGTAATATTATATATTTTATTTAA
*
486585 ATTTAATGTAAATGTTA-ATATTTTATTTAA
1 ATTTAATGT-AATATTATATATTTTATTTAA
486615 ATTTA
1 ATTTA
486620 TTTGTATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 4 0.13
29 7 0.23
30 20 0.65
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
ATTTAATGTAATATTATATATTTTATTTAA
Found at i:493139 original size:11 final size:11
Alignment explanation
Indices: 493123--493147 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
493113 TCCCAACGGA
493123 ATTAATTAGGT
1 ATTAATTAGGT
493134 ATTAATTAGGT
1 ATTAATTAGGT
493145 ATT
1 ATT
493148 TTCCGATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTAATTAGGT
Found at i:496747 original size:2 final size:2
Alignment explanation
Indices: 496740--496766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
496730 TGAACCAAAA
496740 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 A
496767 AGATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:504955 original size:82 final size:83
Alignment explanation
Indices: 504849--505014 Score: 289
Period size: 82 Copynumber: 2.0 Consensus size: 83
504839 GCTTCAGTCA
* *
504849 TTGCACGAGTAATTTCTTTTAGTTGAATTTTTTATTTAATACGTTGAACATGATTGAAAATTTTG
1 TTGCACGAATAATTTCTTTTAGTTGAATTTTTTATTTAATACGTTGAACATGATTGAAAATTTTA
*
504914 AACTAAGAGAATTTTGTG
66 AACTAAAAGAATTTTGTG
*
504932 TTGCACGAATAATTT-TTTTAGTTGAATTTTTTATTTAATACGTTGAATATGATTGAAAATTTTA
1 TTGCACGAATAATTTCTTTTAGTTGAATTTTTTATTTAATACGTTGAACATGATTGAAAATTTTA
504996 AACTAAAAGAATTTTGTG
66 AACTAAAAGAATTTTGTG
505014 T
1 T
505015 GTTAGTATGA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 65 0.82
83 14 0.18
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (83 bp):
TTGCACGAATAATTTCTTTTAGTTGAATTTTTTATTTAATACGTTGAACATGATTGAAAATTTTA
AACTAAAAGAATTTTGTG
Found at i:505622 original size:6 final size:6
Alignment explanation
Indices: 505607--505640 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
505597 AACAATTTAA
* *
505607 AAAAAT AAATAT AAATAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
505641 TATTAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:505632 original size:12 final size:12
Alignment explanation
Indices: 505607--505649 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
505597 AACAATTTAA
505607 AAAAATAAATAT
1 AAAAATAAATAT
* *
505619 AAATATAAAAAT
1 AAAAATAAATAT
505631 AAAAATAAAATAT
1 AAAAAT-AAATAT
*
505644 TAAAAT
1 AAAAAT
505650 GATTAGTACG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAAATAT
Found at i:505641 original size:19 final size:18
Alignment explanation
Indices: 505607--505649 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
505597 AACAATTTAA
*
505607 AAAAATAAATATAAATAT
1 AAAAATAAAAATAAATAT
505625 AAAAATAAAAATAAAATAT
1 AAAAATAAAAAT-AAATAT
*
505644 TAAAAT
1 AAAAAT
505650 GATTAGTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAATAAATAT
Found at i:512940 original size:138 final size:138
Alignment explanation
Indices: 512764--513022 Score: 482
Period size: 138 Copynumber: 1.9 Consensus size: 138
512754 AAATATTTAT
* *
512764 AATGATTAACTTTTACAATTTAGTCCTTATATCTTAATTAACTCTCTAATTGACAAAATTAAAGG
1 AATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAAAATTAAAGG
512829 ACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTATAGACTTGA
66 ACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTATAGACTTGA
512894 GTATCGAC
131 GTATCGAC
*
512902 AATGATTAACTTTTACAATTTAGTCTTTATACCTTAATTAACTCTCCAATTGACAAAATTAAAGG
1 AATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAAAATTAAAGG
*
512967 ATCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
66 ACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
513023 CAGGCTCGAA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 117 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.37
Consensus pattern (138 bp):
AATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAAAATTAAAGG
ACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTATAGACTTGA
GTATCGAC
Found at i:513044 original size:138 final size:138
Alignment explanation
Indices: 512755--513044 Score: 481
Period size: 138 Copynumber: 2.1 Consensus size: 138
512745 TAATTAATTA
* * *
512755 AATATTTATAATGATTAACTTTTACAATTTAGTCCTTATATCTTAATTAACTCTCTAATTGACAA
1 AATATTGATAATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAA
512820 AATTAAAGGACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
66 AATTAAAGGACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
* *
512885 TAGACTTG
131 CAGACTCG
* * * *
512893 AGTATCGACAATGATTAACTTTTACAATTTAGTCTTTATACCTTAATTAACTCTCCAATTGACAA
1 AATATTGATAATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAA
*
512958 AATTAAAGGATCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
66 AATTAAAGGACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
*
513023 CAGGCTCG
131 CAGACTCG
513031 AATATTGATAATGA
1 AATATTGATAATGA
513045 GGTTTCGAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (138 bp):
AATATTGATAATGATTAACTTTTACAATTTAGTCCTTATACCTTAATTAACTCTCCAATTGACAA
AATTAAAGGACCAAACTTCAATTAAACTTTATACTAACATCGTAAATATTAAATAATAATATTTA
CAGACTCG
Found at i:531155 original size:22 final size:22
Alignment explanation
Indices: 531107--531156 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
531097 TGCTTGAAGG
* * *
531107 AAGCTGTCTTGCATCCCACGCC
1 AAGCTGTCTTGCACCCCACACA
*
531129 TAGCTGTCTTGCACCCCACACA
1 AAGCTGTCTTGCACCCCACACA
531151 AAGCTG
1 AAGCTG
531157 GTCAACCCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (22 bp):
AAGCTGTCTTGCACCCCACACA
Found at i:533740 original size:53 final size:53
Alignment explanation
Indices: 533675--533780 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
533665 TCAAGTCCAC
533675 TAATCTTAGTTGAGTTAAGTCTTTGGTGTTCTCCAAAGAAGCAATTGTTGCTT
1 TAATCTTAGTTGAGTTAAGTCTTTGGTGTTCTCCAAAGAAGCAATTGTTGCTT
533728 TAATCTTAGTTGAGTTAAGTCTTTGGTGTTCTCCAAAGAAGCAATTGTTGCTT
1 TAATCTTAGTTGAGTTAAGTCTTTGGTGTTCTCCAAAGAAGCAATTGTTGCTT
533781 CATACTTCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.42
Consensus pattern (53 bp):
TAATCTTAGTTGAGTTAAGTCTTTGGTGTTCTCCAAAGAAGCAATTGTTGCTT
Found at i:549237 original size:33 final size:33
Alignment explanation
Indices: 549152--549218 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
549142 AGATAGTTGC
549152 AAGTAAAATAATAGTTAAAACATAAGTTCTACA
1 AAGTAAAATAATAGTTAAAACATAAGTTCTACA
*
549185 AAGTAAAATAATAGTTAAAACATACGTTCTACA
1 AAGTAAAATAATAGTTAAAACATAAGTTCTACA
549218 A
1 A
549219 TATCGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (33 bp):
AAGTAAAATAATAGTTAAAACATAAGTTCTACA
Found at i:549858 original size:13 final size:13
Alignment explanation
Indices: 549827--549861 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
549817 GGAATTTTTG
* *
549827 AAAGAAAGTCGTA
1 AAAGAGAGTCATA
549840 AAAGAGAGTCATA
1 AAAGAGAGTCATA
549853 AAAGAGAGT
1 AAAGAGAGT
549862 TAGTAGACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.06, G:0.26, T:0.14
Consensus pattern (13 bp):
AAAGAGAGTCATA
Found at i:550981 original size:23 final size:22
Alignment explanation
Indices: 550955--551032 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
550945 ACACTAGCGC
550955 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
*
550978 GCTTACTATTTCGCACTTTGTGT
1 GCTTACTGTTTCGCAC-TTGTGT
* *
551001 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
551023 GCTTACTGTT
1 GCTTACTGTT
551033 AAGTACTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
21 1 0.02
22 17 0.36
23 27 0.57
24 2 0.04
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:552821 original size:18 final size:19
Alignment explanation
Indices: 552785--552821 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
552775 TTCCATTTTT
*
552785 ATCTGTTAACATTTGTTTG
1 ATCTGTTAACATCTGTTTG
552804 ATCTGTTAACA-CTGTTTG
1 ATCTGTTAACATCTGTTTG
552822 GGATTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (19 bp):
ATCTGTTAACATCTGTTTG
Found at i:552828 original size:29 final size:29
Alignment explanation
Indices: 552795--552856 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
552785 ATCTGTTAAC
552795 ATTTGTTTGATCTGTTAACACTGTTTGGG
1 ATTTGTTTGATCTGTTAACACTGTTTGGG
552824 ATTTGTTTGATCTGTTAACACTGTTTGGG
1 ATTTGTTTGATCTGTTAACACTGTTTGGG
552853 ATTT
1 ATTT
552857 AGGGTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.18, C:0.10, G:0.23, T:0.50
Consensus pattern (29 bp):
ATTTGTTTGATCTGTTAACACTGTTTGGG
Found at i:553129 original size:22 final size:22
Alignment explanation
Indices: 553101--553155 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
553091 ACAGAAATGG
* *
553101 TTAAATGTTTGCATGTGTTGTA
1 TTAAATGTTTGCAGGTGTCGTA
*
553123 TTAAATGTTTTCAGGTGTCGTA
1 TTAAATGTTTGCAGGTGTCGTA
553145 TTAAATGTTTG
1 TTAAATGTTTG
553156 TTCCTGGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (22 bp):
TTAAATGTTTGCAGGTGTCGTA
Found at i:555815 original size:21 final size:21
Alignment explanation
Indices: 555783--555831 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
555773 GGAAAGACCC
* *
555783 CAACTCAGCAAGTGAGTAGCA
1 CAACTCAACAAGTGAGCAGCA
*
555804 CATCTCAACAAGTGAGCAGCA
1 CAACTCAACAAGTGAGCAGCA
555825 CAACTCA
1 CAACTCA
555832 GTTGCAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (21 bp):
CAACTCAACAAGTGAGCAGCA
Found at i:557592 original size:24 final size:24
Alignment explanation
Indices: 557560--557607 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
557550 TTAAAAAGTA
*
557560 AAAAAATAAAAATAGCTGTTAAGG
1 AAAAAATAAAAATAGCCGTTAAGG
557584 AAAAAATAAAAATAGCCGTTAAGG
1 AAAAAATAAAAATAGCCGTTAAGG
557608 TTGTGTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (24 bp):
AAAAAATAAAAATAGCCGTTAAGG
Found at i:575965 original size:17 final size:17
Alignment explanation
Indices: 575913--575967 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
575903 ATATAAAATT
* *
575913 TTTTAGATTTTAAGATTA
1 TTTTA-ATTTAAATATTA
* *
575931 TTTTAATTTAATTTTTA
1 TTTTAATTTAAATATTA
*
575948 TTTTTATTTAAATATTA
1 TTTTAATTTAAATATTA
575965 TTT
1 TTT
575968 GTAAAAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTTAATTTAAATATTA
Found at i:578669 original size:29 final size:29
Alignment explanation
Indices: 578597--578825 Score: 250
Period size: 30 Copynumber: 7.8 Consensus size: 29
578587 ATACCCGAGG
* ** *
578597 AAAATGGTAATTTTGGGAAAATTCGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCG-GGGTA
*
578628 AAAATGGGATTTTTGGAAG-TTCGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
578656 AAAATAGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
*
578686 AAAAT-GAGATTTTTGGAAGTTTAGGGGT-
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTA
578714 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* *
578743 AAAATGGAATTTTTGGGAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
578773 AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
578802 CAAAATGGAATTTTTGGACAGTTT
1 -AAAATGGAATTTTTGGA-AGTTT
578826 AGGGACCTCC
Statistics
Matches: 173, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.02
28 41 0.24
29 38 0.22
30 79 0.46
31 12 0.07
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:578685 original size:58 final size:58
Alignment explanation
Indices: 578623--578829 Score: 260
Period size: 58 Copynumber: 3.5 Consensus size: 58
578613 GAAAATTCGA
* * *
578623 GGTTAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAAATAGAATTTTTGGAAGTTTTGG
1 GGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAG-TTTGG
*
578681 GGTTAAAAAT-GAGATTTTTGGAAGTTTAGGGGT-AAAATGGAATTTTTGGAAGTTCGAG
1 GGTTAAAAATGGA-ATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTG-G
* * *
578739 GG-TAAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGG
1 GGTTAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTGG
*
578797 GGGTACAAAATGGAATTTTTGGACAGTTTAGGG
1 GGTTA-AAAATGGAATTTTTGGA-AGTTTAGGG
578830 ACCTCCGGGC
Statistics
Matches: 130, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
57 29 0.22
58 47 0.36
59 30 0.23
60 16 0.12
61 8 0.06
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.35
Consensus pattern (58 bp):
GGTTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTGG
Done.