Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 2 of 313
Found at i:199851 original size:30 final size:30
Alignment explanation
Indices: 199815--199907 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
199805 GTCCCAGAGC
*
199815 AGTTCATATAACCCGGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
199845 AGTTCATATCACCCGGACATGGGTGGTTCA
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* * *
199875 AGTTTATATCACCCGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
199905 AGT
1 AGT
199908 CTAATTGACC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:203440 original size:31 final size:34
Alignment explanation
Indices: 203386--203452 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 34
203376 TATGATATAT
203386 TTTTTATAAATATTAAAAATATATTTTCAA-ATTA
1 TTTTTATAAATATT-AAAATATATTTTCAATATTA
*
203420 TTTTT-TAAATATT-AAATATATTTTTAATATTA
1 TTTTTATAAATATTAAAATATATTTTCAATATTA
203452 T
1 T
203453 AAAACATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 13 0.42
32 5 0.16
33 8 0.26
34 5 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTTTATAAATATTAAAATATATTTTCAATATTA
Found at i:203501 original size:9 final size:9
Alignment explanation
Indices: 203422--203520 Score: 65
Period size: 10 Copynumber: 10.4 Consensus size: 9
203412 TCAAATTATT
203422 TTTTAAATA
1 TTTTAAATA
*
203431 -TTAAATATA
1 TTTTAA-ATA
*
203440 TTTTTAATA
1 TTTTAAATA
* *
203449 TTATAAAACA
1 TT-TTAAATA
*
203459 TTTAAAATGA
1 TTTTAAAT-A
*
203469 TTTAAAATGA
1 TTTTAAAT-A
*
203479 TTTAAAATA
1 TTTTAAATA
*
203488 TTTTTTAATA
1 -TTTTAAATA
203498 TTTTAAATGA
1 TTTTAAAT-A
203508 TTTTAAATA
1 TTTTAAATA
203517 TTTT
1 TTTT
203521 TTAAATTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
8 4 0.05
9 26 0.35
10 44 0.59
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (9 bp):
TTTTAAATA
Found at i:203548 original size:29 final size:29
Alignment explanation
Indices: 203468--203530 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
203458 ATTTAAAATG
* *
203468 ATTTAAAATGATTTAAAATATTTTTTAAT
1 ATTTTAAATGATTTTAAATATTTTTTAAT
203497 ATTTTAAATGATTTTAAATATTTTTTAA-
1 ATTTTAAATGATTTTAAATATTTTTTAAT
203525 ATTTTA
1 ATTTTA
203531 CATAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTTTAAATGATTTTAAATATTTTTTAAT
Found at i:204270 original size:37 final size:35
Alignment explanation
Indices: 204200--204270 Score: 106
Period size: 37 Copynumber: 2.0 Consensus size: 35
204190 AAATAATTAT
*
204200 TTTTTTAAAATTTTAAAAATTAATTTGAAAAATAC
1 TTTTTTAAAATTTTAAAAATTAATTTCAAAAATAC
*
204235 TTTTTTAAAATTTATAAATAATTAATTTCACAAATA
1 TTTTTTAAAATTT-TAAA-AATTAATTTCAAAAATA
204271 TATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 13 0.41
36 4 0.12
37 15 0.47
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (35 bp):
TTTTTTAAAATTTTAAAAATTAATTTCAAAAATAC
Found at i:204318 original size:22 final size:23
Alignment explanation
Indices: 204290--204379 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
204280 AGTTAAAAAT
204290 ATTTTTAAAAATAATAAT-TAAA
1 ATTTTTAAAAATAATAATATAAA
*
204312 ATTTTTAAAAA-AATATTATAAA
1 ATTTTTAAAAATAATAATATAAA
* * * *
204334 ACATTTTAAATAT-ATATTACAAA
1 A-TTTTTAAAAATAATAATATAAA
*
204357 ATTTTTAAAATTAATAATATAAA
1 ATTTTTAAAAATAATAATATAAA
204380 TTAAATAAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.09
22 24 0.44
23 26 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTTTTAAAAATAATAATATAAA
Found at i:204340 original size:23 final size:22
Alignment explanation
Indices: 204290--204366 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
204280 AGTTAAAAAT
*
204290 ATTTTTAAAAATAATAAT-TAAA
1 ATTTTTAAAAA-AATATTATAAA
204312 ATTTTTAAAAAAATATTATAAA
1 ATTTTTAAAAAAATATTATAAA
* * * *
204334 ACATTTTAAATATATATTACAAA
1 A-TTTTTAAAAAAATATTATAAA
204357 ATTTTTAAAA
1 ATTTTTAAAA
204367 TTAATAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 5 0.11
22 23 0.50
23 18 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTTTAAAAAAATATTATAAA
Found at i:204414 original size:18 final size:18
Alignment explanation
Indices: 204364--204415 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
204354 AAAATTTTTA
*
204364 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
204382 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
204400 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
204416 ACTCAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:204466 original size:7 final size:8
Alignment explanation
Indices: 204448--204477 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
204438 AGAAAGAGAC
204448 AAAAAGTA
1 AAAAAGTA
204456 AAAAAGTAA
1 AAAAAGT-A
204465 AAAAAGTA
1 AAAAAGTA
204473 AAAAA
1 AAAAA
204478 AAATATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAGTA
Found at i:204479 original size:10 final size:9
Alignment explanation
Indices: 204448--204478 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
204438 AGAAAGAGAC
204448 AAAAAGT-A
1 AAAAAGTAA
204456 AAAAAGTAA
1 AAAAAGTAA
204465 AAAAAGTAA
1 AAAAAGTAA
204474 AAAAA
1 AAAAA
204479 AATATAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAGTAA
Found at i:205080 original size:31 final size:32
Alignment explanation
Indices: 205006--205085 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
204996 CTTGTTCTAT
* * * * * *
205006 TTATTTTGAACTCTAATCATTTTAACTTTAAG
1 TTATTTAGAATTCAAATCATTTTAAATATAAA
205038 TTATTTAGAATT-AAATCATTTTAAATATAAA
1 TTATTTAGAATTCAAATCATTTTAAATATAAA
* *
205069 TTGTTTTGAATTCAAAT
1 TTATTTAGAATTCAAAT
205086 TAATTTAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (32 bp):
TTATTTAGAATTCAAATCATTTTAAATATAAA
Found at i:212013 original size:26 final size:26
Alignment explanation
Indices: 211983--212766 Score: 1568
Period size: 26 Copynumber: 30.2 Consensus size: 26
211973 TGAAATGCCC
211983 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212009 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212035 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212061 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212087 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212113 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212139 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212165 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212191 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212217 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212243 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212269 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212295 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212321 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212347 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212373 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212399 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212425 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212451 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212477 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212503 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212529 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212555 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212581 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212607 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212633 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212659 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212685 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212711 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212737 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
212763 ATCA
1 ATCA
212767 ATTTTTATCA
Statistics
Matches: 758, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 758 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:219323 original size:25 final size:27
Alignment explanation
Indices: 219286--219338 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
219276 TCAAACATGC
219286 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
219312 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
219338 A
1 A
219339 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:227370 original size:26 final size:26
Alignment explanation
Indices: 227341--227393 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
227331 CCAAACATGC
227341 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
227367 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
227393 A
1 A
227394 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:227714 original size:8 final size:8
Alignment explanation
Indices: 227673--227716 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
227663 AAAATACTAA
227673 TTTTCGGC
1 TTTTCGGC
*
227681 ATTTCGGC
1 TTTTCGGC
*
227689 ATTTCGGC
1 TTTTCGGC
*
227697 TTTTCAGC
1 TTTTCGGC
227705 TTTTCGGC
1 TTTTCGGC
227713 TTTT
1 TTTT
227717 GCCGATCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (8 bp):
TTTTCGGC
Found at i:233619 original size:53 final size:49
Alignment explanation
Indices: 233498--233620 Score: 140
Period size: 50 Copynumber: 2.4 Consensus size: 49
233488 ACATTTAATA
* **
233498 AAGTTATGCATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATAAAT
1 AAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCATCATAAAT
* *
233547 AATGACATGCATTATGTAACTCCCATGTTAGTTAACGTTTGCATCTTTAAAATT
1 AA-GTCATGCATTATGTAACTCCCATGTTAGTTAA-GTTTGCATC-AT-AAA-T
233601 AAGTCATGCATTCA-GTAACT
1 AAGTCATGCATT-ATGTAACT
233621 TATTTGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
49 2 0.03
50 28 0.45
51 9 0.15
52 1 0.02
53 18 0.29
54 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (49 bp):
AAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCATCATAAAT
Found at i:237837 original size:31 final size:31
Alignment explanation
Indices: 237802--237866 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
237792 ATATGTTAAA
* * * *
237802 GTTAGTTTATGTATGTGTGTTATTTAATTTG
1 GTTAGTTTATGTAGGAGTGCTATTTAATATG
237833 GTTAGTTTATGTAGGAGTGCTATTTAATATG
1 GTTAGTTTATGTAGGAGTGCTATTTAATATG
237864 GTT
1 GTT
237867 GTTATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.02, G:0.25, T:0.52
Consensus pattern (31 bp):
GTTAGTTTATGTAGGAGTGCTATTTAATATG
Found at i:239436 original size:28 final size:29
Alignment explanation
Indices: 239390--239444 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
239380 ACCAATCTCT
*
239390 TTCATATGACCCATTAGGCCCAAATCATA
1 TTCATATGACCCACTAGGCCCAAATCATA
*
239419 TTCATATG-GCCACTAGGCCCAAATCA
1 TTCATATGACCCACTAGGCCCAAATCA
239445 CATTTACAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (29 bp):
TTCATATGACCCACTAGGCCCAAATCATA
Found at i:241185 original size:28 final size:29
Alignment explanation
Indices: 241120--241226 Score: 112
Period size: 28 Copynumber: 3.8 Consensus size: 29
241110 TTCACATACT
* * *
241120 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
241148 T-TCAGATGGCCCATTAGGCCCATATCAC-
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
* *
241176 TGTATGTGGCCTATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
241205 TTTATATGGCCCATTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
241227 GTTACATTCA
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 38 0.60
29 24 0.38
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:241215 original size:57 final size:56
Alignment explanation
Indices: 241120--241226 Score: 151
Period size: 57 Copynumber: 1.9 Consensus size: 56
241110 TTCACATACT
*
241120 TGTATCTGGCCCATTAAGCCCAATCATATTCAGATGGCCCATTAGGCCCATATCAC
1 TGTATCTGGCCCATTAAGCCCAATCACATTCAGATGGCCCATTAGGCCCATATCAC
* * * * *
241176 TGTATGTGGCCTATTAGGCCCAAATCACATTTATATGGCCCATTAGGCCCA
1 TGTATCTGGCCCATTAAGCCC-AATCACATTCAGATGGCCCATTAGGCCCA
241227 GTTACATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 18 0.41
57 26 0.59
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (56 bp):
TGTATCTGGCCCATTAAGCCCAATCACATTCAGATGGCCCATTAGGCCCATATCAC
Found at i:242967 original size:16 final size:16
Alignment explanation
Indices: 242942--242972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
242932 AAATTTGAGA
*
242942 TTTCGGGATTTTTGGG
1 TTTCGAGATTTTTGGG
242958 TTTCGAGATTTTTGG
1 TTTCGAGATTTTTGG
242973 AGCGTTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.32, T:0.52
Consensus pattern (16 bp):
TTTCGAGATTTTTGGG
Found at i:251114 original size:50 final size:48
Alignment explanation
Indices: 251001--251322 Score: 235
Period size: 46 Copynumber: 6.8 Consensus size: 48
250991 CATGGGTAAA
* * *
251001 GTGCCGATGCCATGTCGCAGACATGGTCTTACACTGGCTATCATCTTC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
* *
251049 GAGGCCGATGCCATGTCCCAGGA-ATGGTCTTACACTAGCTCTCA-CATAACC
1 G-TGCCGATGCCATGTCCCA-GACATGGTCTTACACTAGCTATCATC-T--CC
* *
251100 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAAC-A-CATCT-T
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
* * *
251145 GTAGCCGATG-CATGTCCCAGACAT-GTCTTATACTGGCT-TACGTC-CC
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCC
* * * * *
251191 GAGGCTGAT-ACATGTCCCAGATAT-GTCTTACACTAGC-ATTAGTCTCC
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCA-TCTCC
* * * * * *
251238 ATGTCGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT--
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCAT-CTCC
*
251285 GTGGCCGGTG-CATGTCCCAGACAT-GTCTTACACTAGCT
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
251323 CACACAAATG
Statistics
Matches: 216, Mismatches: 36, Indels: 46
0.72 0.12 0.15
Matches are distributed among these distances:
44 10 0.05
45 16 0.07
46 60 0.28
47 30 0.14
48 22 0.10
49 42 0.19
50 34 0.16
51 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
Found at i:255020 original size:5 final size:5
Alignment explanation
Indices: 255010--255034 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
255000 TTTGACTAAG
255010 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
255035 AATAAACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:257199 original size:5 final size:5
Alignment explanation
Indices: 257189--257213 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
257179 CATATGCTCT
257189 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
257214 ACGAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:266845 original size:85 final size:85
Alignment explanation
Indices: 266702--266897 Score: 268
Period size: 85 Copynumber: 2.3 Consensus size: 85
266692 TAAAACATCG
* * * * *
266702 TGTAAGACCGTGTCTGGGACATAGGCCTCGATTGAGATTTATGTATAAGATCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGATACAGGCCTCGATTAAGATTTACGTATAAGACCATGTCTGGGACAT
266767 CGACATCATATCTAATTTCA
66 CGACATCATATCTAATTTCA
* *
266787 TGTAAGACCGTGTCTGGGATACAGTCCTTGATTAAGATTTACGTATAAGACCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGATACAGGCCTCGATTAAGATTTACGTATAAGACCATGTCTGGGACAT
* * *
266852 CGACATCGTATCTTATTTCG
66 CGACATCATATCTAATTTCA
* *
266872 TGTAAGATCC-TATCTGGGATAGAGGC
1 TGTAAGA-CCGTGTCTGGGATACAGGC
266898 ATTAATATTG
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
85 95 0.98
86 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (85 bp):
TGTAAGACCGTGTCTGGGATACAGGCCTCGATTAAGATTTACGTATAAGACCATGTCTGGGACAT
CGACATCATATCTAATTTCA
Found at i:266921 original size:85 final size:85
Alignment explanation
Indices: 266745--266942 Score: 220
Period size: 85 Copynumber: 2.3 Consensus size: 85
266735 GAGATTTATG
* *
266745 TATAAGATCATGTCTGGGACATCGACATCATATCTAATTTCATGTAAGACCGTGTCTGGGATACA
1 TATAAGACCATGTCTGGGACATCGACATCATATCTAATTTCATGTAAGACCGTATCTGGGATACA
* * * * *
266810 GTCCTTGATTAAGATTTACG
66 GGCATTAATTAAGAATTACA
* * * *
266830 TATAAGACCATGTCTGGGACATCGACATCGTATCTTATTTCGTGTAAGATCC-TATCTGGGATAG
1 TATAAGACCATGTCTGGGACATCGACATCATATCTAATTTCATGTAAGA-CCGTATCTGGGATAC
*
266894 AGGCATTAA-TATTGAATTACA
65 AGGCATTAATTA-AGAATTACA
* ** *
266915 TGTAAGACCACATTTGGGACATCGACAT
1 TATAAGACCATGTCTGGGACATCGACAT
266943 TGTACTTGTT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 2 0.02
85 91 0.96
86 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (85 bp):
TATAAGACCATGTCTGGGACATCGACATCATATCTAATTTCATGTAAGACCGTATCTGGGATACA
GGCATTAATTAAGAATTACA
Found at i:274197 original size:16 final size:16
Alignment explanation
Indices: 274176--274208 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
274166 AAGACAGGGG
274176 AGCATGAAATCACTCT
1 AGCATGAAATCACTCT
274192 AGCATGAAATCACTCT
1 AGCATGAAATCACTCT
274208 A
1 A
274209 ACCCTCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
AGCATGAAATCACTCT
Found at i:274837 original size:48 final size:47
Alignment explanation
Indices: 274797--274967 Score: 182
Period size: 48 Copynumber: 3.6 Consensus size: 47
274787 TATCGGTGCT
*
274797 GATGCCATGTCCCAAATATGGTCTTACACTAGCACACATATCATCGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAT-GCC
* * * **
274845 GATGCCATGTTCCAGACATGGTCTTACACTGGCACACATATCAACACC
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATC-ATGCC
* * *
274893 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA-ACTCGGATGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATA-TC--ATGCC
* * *
274942 AACGCCATGTCCCAGACATGGTCTTA
1 GATGCCATGTCCCAAACATGGTCTTA
274968 GACAGGATCT
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.01
48 76 0.73
49 27 0.26
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (47 bp):
GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCATGCC
Found at i:286370 original size:34 final size:34
Alignment explanation
Indices: 286331--286397 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
286321 TATGAAAAGT
*
286331 ATGAATTCAAATATGTTATGTTCATGAAATCTAC
1 ATGAATTCAAATATGCTATGTTCATGAAATCTAC
*
286365 ATGAATTCAAATGTGCTATGTTCATGAAATCTA
1 ATGAATTCAAATATGCTATGTTCATGAAATCTA
286398 TATTACCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (34 bp):
ATGAATTCAAATATGCTATGTTCATGAAATCTAC
Found at i:288360 original size:16 final size:16
Alignment explanation
Indices: 288339--288371 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
288329 GGGATATTTG
288339 ATAAATGATAAAACTA
1 ATAAATGATAAAACTA
288355 ATAAATGATAAAACTA
1 ATAAATGATAAAACTA
288371 A
1 A
288372 CATAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAAATGATAAAACTA
Found at i:291356 original size:79 final size:81
Alignment explanation
Indices: 291220--291404 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
291210 TTGAATGATG
*
291220 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
291284 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
291299 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
291361 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
291379 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
291405 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:291418 original size:40 final size:40
Alignment explanation
Indices: 291221--291404 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
291211 TGAATGATGT
* * * *
291221 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
291261 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
291301 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
291339 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
291380 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
291405 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:291426 original size:79 final size:79
Alignment explanation
Indices: 291273--291437 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
291263 GGACTAAGAT
* **
291273 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
291338 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
291352 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
291415 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
291431 CCGAAGG
1 CCGAAGG
291438 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:299256 original size:40 final size:39
Alignment explanation
Indices: 299212--299316 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
299202 AGTGACCATA
*
299212 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
299252 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
299290 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
299317 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:299273 original size:39 final size:40
Alignment explanation
Indices: 299172--299335 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
299162 TTGAATGATG
* *
299172 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
299212 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
299251 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
299291 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
299331 TCCGG
1 TCCGG
299336 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:299335 original size:79 final size:80
Alignment explanation
Indices: 299172--299322 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
299162 TTGAATGATG
*
299172 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
299237 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
299252 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
299314 TTGAACGAG
64 TTGAACGAG
299323 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:301973 original size:12 final size:12
Alignment explanation
Indices: 301956--301981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
301946 ATCATATAGA
301956 TTGGTTTAACTC
1 TTGGTTTAACTC
301968 TTGGTTTAACTC
1 TTGGTTTAACTC
301980 TT
1 TT
301982 TTTTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGGTTTAACTC
Found at i:302804 original size:16 final size:16
Alignment explanation
Indices: 302783--302814 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
302773 CTAATTACTG
302783 TAAATTGAAGTCTTTT
1 TAAATTGAAGTCTTTT
302799 TAAATTGAAGTCTTTT
1 TAAATTGAAGTCTTTT
302815 CGAGTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TAAATTGAAGTCTTTT
Found at i:304902 original size:41 final size:41
Alignment explanation
Indices: 304839--304949 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
304829 GTTAATTATT
* * * *
304839 CCCTAAATTGAACATACATGCCCCCATTTGTACTTCAGTAC
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAC
* * *
304880 CCCTGAATTGCACATACGTGCCCTTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAC
*
304921 CCCTGAATTGCACACACGTGCCCCTATTT
1 CCCTGAATTGCACATACGTGCCCCTATTT
304950 ACACTCCGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (41 bp):
CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAC
Found at i:304960 original size:41 final size:41
Alignment explanation
Indices: 304876--304960 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 41
304866 TTGTACTTCA
* * * ** *
304876 GTACCCCTGAATTGCACATACGTGCCCTTGTTTGTACTTCG
1 GTACCCCTGAATTGCACACACGTGCCCCTATTTACACTCCG
304917 GTACCCCTGAATTGCACACACGTGCCCCTATTTACACTCCG
1 GTACCCCTGAATTGCACACACGTGCCCCTATTTACACTCCG
304958 GTA
1 GTA
304961 ACATTGAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (41 bp):
GTACCCCTGAATTGCACACACGTGCCCCTATTTACACTCCG
Found at i:304969 original size:41 final size:41
Alignment explanation
Indices: 304882--304969 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
304872 TTCAGTACCC
* * * ** * * *
304882 CTGAATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCC
1 CTGAATTGCACACACGTGCCCCTATTTACACTCCGGTAACA
304923 CTGAATTGCACACACGTGCCCCTATTTACACTCCGGTAACA
1 CTGAATTGCACACACGTGCCCCTATTTACACTCCGGTAACA
*
304964 TTGAAT
1 CTGAAT
304970 CGAGTAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (41 bp):
CTGAATTGCACACACGTGCCCCTATTTACACTCCGGTAACA
Found at i:310613 original size:17 final size:17
Alignment explanation
Indices: 310583--310623 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
310573 GGTTAGAATT
310583 TTATT-TTCTATTATTA
1 TTATTATTCTATTATTA
*
310599 TTATTATTCTTTTATTA
1 TTATTATTCTATTATTA
*
310616 GTATTATT
1 TTATTATT
310624 ATTCTTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TTATTATTCTATTATTA
Found at i:310620 original size:20 final size:20
Alignment explanation
Indices: 310591--310630 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
310581 TTTTATTTTC
*
310591 TATTATTATTATTATTCTTT
1 TATTAGTATTATTATTCTTT
310611 TATTAGTATTATTATTCTTT
1 TATTAGTATTATTATTCTTT
310631 GTACATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTAGTATTATTATTCTTT
Found at i:315622 original size:19 final size:19
Alignment explanation
Indices: 315598--315635 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
315588 TGAAAATTTT
315598 ACTCAAAACAGAGGACACA
1 ACTCAAAACAGAGGACACA
* *
315617 ACTCAAGATAGAGGACACA
1 ACTCAAAACAGAGGACACA
315636 CGTTCGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.18, T:0.08
Consensus pattern (19 bp):
ACTCAAAACAGAGGACACA
Found at i:316945 original size:40 final size:40
Alignment explanation
Indices: 316850--316991 Score: 160
Period size: 40 Copynumber: 3.5 Consensus size: 40
316840 TCGATATCTC
* * ** * **
316850 GCACACTAAGTGCCTTACATAGGTGAAGCTATCTCAGTCTT
1 GCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCGAATT
*
316891 GCACGCTAAGTGCCATATATAGCCGAAGCTATTCCGAATT
1 GCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAATT
* * *
316931 TCACACTAAGTGCCATATATAGTCGAAGCTA-TCTCGAATC
1 GCACACTAAGTGCCATATATAGCCGAAGCTATTC-CGAATT
316971 GCACACTAAGTGCCATATATA
1 GCACACTAAGTGCCATATATA
316992 TATCCGAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 58 0.67
41 27 0.31
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (40 bp):
GCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAATT
Found at i:320873 original size:41 final size:41
Alignment explanation
Indices: 320772--320866 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
320762 AGTTTTTCCT
* * * *
320772 TGAATTGCATATACGTGCCCCTGTTTGTACTTTAGTATCAT
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCAC
* * *
320813 TGAATAGCACATACGTGCCCGTGTTTGTACTTCAGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCAC
320854 TGAATTGCACATA
1 TGAATTGCACATA
320867 TATGCCCTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCAC
Found at i:325199 original size:25 final size:25
Alignment explanation
Indices: 325171--325256 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 25
325161 CAACTCGAGA
325171 GAGCTTACCAATATTCAGCTTGTAT
1 GAGCTTACCAATATTCAGCTTGTAT
* * *
325196 GAGCTTACCATTACTCAGCTCGTAT
1 GAGCTTACCAATATTCAGCTTGTAT
* * * *
325221 GAGTTTACCGAT-TACAGCTTGTAA
1 GAGCTTACCAATATTCAGCTTGTAT
*
325245 GAGCATACCAAT
1 GAGCTTACCAAT
325257 TCAGAGCTCG
Statistics
Matches: 48, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
24 17 0.35
25 31 0.65
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (25 bp):
GAGCTTACCAATATTCAGCTTGTAT
Found at i:329136 original size:27 final size:27
Alignment explanation
Indices: 329106--329283 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
329096 ATATTGAGTC
* * * *
329106 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
329133 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
329160 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
329188 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
329215 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
329242 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
329269 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
329284 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:329245 original size:82 final size:81
Alignment explanation
Indices: 329127--329282 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
329117 TGCTATATAA
* *
329127 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
329192 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
329209 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
329273 CACTTAGTGC
65 CACTTAGTGC
329283 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:349778 original size:40 final size:39
Alignment explanation
Indices: 349682--349822 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 39
349672 ATGATGTCCG
* * * *
349682 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTAAATCC
349721 GGACTAAGAT-CCG-AGGCATTTGTGTGAGTTACTAAATCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGTGAGTTACTAAATCC
* *
349760 AGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA-CC
1 -GGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTA-AATCC
*
349800 GGGCTATGTCCCGAAGGCATTTG
1 -GGCTAAGTCCCGAAGGCATTTG
349823 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
38 1 0.01
39 25 0.29
40 57 0.66
41 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAATCC
Found at i:358614 original size:12 final size:12
Alignment explanation
Indices: 358579--358616 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
358569 CTACACACGC
*
358579 CCGTGTGCCAGG
1 CCGTGTGCTAGG
358591 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
358603 CCGTGTGTTAGG
1 CCGTGTGCTAGG
358615 CC
1 CC
358617 ATGCCAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:362855 original size:40 final size:40
Alignment explanation
Indices: 362707--362857 Score: 187
Period size: 40 Copynumber: 3.7 Consensus size: 40
362697 ACTCGAATTC
** *
362707 TCGCACACTAAATGCCAATACATAGATGAAGCTAT-TTTAA
1 TCGCACACTAAATGCC-ATACATAGCCGAAGCTATCTTGAA
* * * *
362747 TCCTGCACATTAAGTGCCATACATAGCCAAAGCTGTCTTGAA
1 T-C-GCACACTAAATGCCATACATAGCCGAAGCTATCTTGAA
* *
362789 TCACACACTAAGTGCCATACATAGCCGAAGCTATCTTGAA
1 TCGCACACTAAATGCCATACATAGCCGAAGCTATCTTGAA
362829 TCGCACACTAAATGCCATACATAGCCGAA
1 TCGCACACTAAATGCCATACATAGCCGAA
362858 TTGTCATCCA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
40 62 0.65
41 16 0.17
42 17 0.18
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAATGCCATACATAGCCGAAGCTATCTTGAA
Found at i:371743 original size:19 final size:20
Alignment explanation
Indices: 371719--371756 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
371709 GGTACCACCA
371719 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
371738 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
371757 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:372096 original size:93 final size:93
Alignment explanation
Indices: 371986--372156 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
371976 GCCCCTAAGT
* *
371986 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAACGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAACGAACTCGGACTCAACTCAA
*
372051 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * **
372079 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAACGAACTCGGACTCAACTCAA
372144 CGAGTTCGGATGC
66 CGAGTTCGGATGC
372157 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAACGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:372153 original size:46 final size:46
Alignment explanation
Indices: 371981--372153 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
371971 AACCCGCCCC
* * * * *
371981 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * *
372027 TAAACGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
*
372075 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
372120 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
372154 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 58 0.55
47 29 0.28
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:372611 original size:31 final size:30
Alignment explanation
Indices: 372576--372636 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
372566 ATTTAATACG
372576 AACTTTAAAAAAAATTACACTTTTGCCCCTA
1 AACTTT-AAAAAAATTACACTTTTGCCCCTA
*** *
372607 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
372637 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:377092 original size:24 final size:24
Alignment explanation
Indices: 377065--377135 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
377055 TTGTCAGGAG
377065 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
377089 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
377113 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
377136 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:379767 original size:39 final size:39
Alignment explanation
Indices: 379723--379842 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
379713 ATTATATTAT
* *
379723 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
379762 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
379801 CAGCACGAAGCCTGGGGGACTTTAGCCCAGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
379840 CAG
1 CAG
379843 TGTCTTGCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:382353 original size:28 final size:27
Alignment explanation
Indices: 382266--382377 Score: 113
Period size: 27 Copynumber: 4.1 Consensus size: 27
382256 AGGAAGCGTC
*
382266 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
*
382293 CTGGTGGCTCTGCCACATATATCTAT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
* * *
382320 CTGGTGGTTTTGGCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
382348 CTGGTGACTCTGTCACATTATCTGT-T
1 CTGGTGGCTCTGCCACATTATCTGTAT
382374 CTGG
1 CTGG
382378 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
26 7 0.10
27 49 0.69
28 15 0.21
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:385688 original size:62 final size:61
Alignment explanation
Indices: 385615--385743 Score: 231
Period size: 62 Copynumber: 2.1 Consensus size: 61
385605 ATCCATGGTC
*
385615 ATACACACACACAATCAAAAATAAATACCAAAATTTTCATATCCTTTATGCCCTAAGCCGA
1 ATACACACACACAATAAAAAATAAATACCAAAATTTTCATATCCTTTATGCCCTAAGCCGA
*
385676 ATACACGACACACAATAAAAAATAAATACCAAAATTTTCATATCCTTTATGCCCTATGCCGA
1 ATACAC-ACACACAATAAAAAATAAATACCAAAATTTTCATATCCTTTATGCCCTAAGCCGA
385738 ATACAC
1 ATACAC
385744 TTGTCATGTT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 6 0.09
62 59 0.91
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.25
Consensus pattern (61 bp):
ATACACACACACAATAAAAAATAAATACCAAAATTTTCATATCCTTTATGCCCTAAGCCGA
Found at i:389614 original size:46 final size:46
Alignment explanation
Indices: 389564--389733 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
389554 GGCATTCGAA
389564 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAG
* ** *** * *
389610 CTCGTTGAGTTGCGTTTGAGTTCGAGAGATGTAACTAG-GCAT--CCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATGCCCGAG
* *
389657 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAG
*
389703 CTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
389734 GCGGGTTACA
Statistics
Matches: 98, Mismatches: 19, Indels: 14
0.75 0.15 0.11
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 59 0.60
47 29 0.30
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAG
Found at i:389711 original size:93 final size:93
Alignment explanation
Indices: 389552--389725 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
389542 CTAGGATGTT
* * *
389552 TAGGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTG
1 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTG
* *
389617 AGTTGCGTTTGAGTTCGAGAGATGTAAC
66 AGTTGAGTCTGAGTTCGAGAGATGTAAC
*
389645 TAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTG
1 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTG
389710 AGTTGAGTCTGAGTTC
66 AGTTGAGTCTGAGTTC
389726 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTG
AGTTGAGTCTGAGTTCGAGAGATGTAAC
Found at i:392700 original size:15 final size:15
Alignment explanation
Indices: 392680--392748 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
392670 GTATCTTGGG
392680 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
392695 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
392710 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
392725 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
392740 TTTCTTTAT
1 TTTCTTTAT
392749 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:392749 original size:30 final size:30
Alignment explanation
Indices: 392671--392758 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
392661 CATAGTATCG
* * * *
392671 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
392701 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
392731 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
392759 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:394870 original size:46 final size:46
Alignment explanation
Indices: 394813--394988 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
394803 TGTTTGGGCA
*
394813 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
394859 TCCGAAG-TCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCG-AGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
394906 TCCGAGCTCGTTGAGTTGACTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
394952 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
394989 GTGGGTCACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 30 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:394968 original size:93 final size:93
Alignment explanation
Indices: 394809--394980 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
394799 AGGATGTTTG
* *
394809 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAAGTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGACTCCGAGTTCACTTATGGATGCGAATGCCCGAAGTCGTTGAG
394874 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
394902 GGCATCCGAGCTCGTTGAGTTGACTCCGAGTTCACTTATGGATGCGAATGCCCG-AGCTTGTTGA
1 GGCATCCGAACTCGTTGAGTTGACTCCGAGTTCACTTATGGATGCGAATGCCCGAAG-TCGTTGA
394966 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
394981 ACTTATGGGT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGACTCCGAGTTCACTTATGGATGCGAATGCCCGAAGTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:395310 original size:14 final size:14
Alignment explanation
Indices: 395291--395319 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
395281 GTTATGTTAC
395291 TTGCTATTTGCATG
1 TTGCTATTTGCATG
395305 TTGCTATTTGCATG
1 TTGCTATTTGCATG
395319 T
1 T
395320 GAACTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (14 bp):
TTGCTATTTGCATG
Found at i:399745 original size:31 final size:30
Alignment explanation
Indices: 399707--399789 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
399697 TATTAATTAT
399707 TAAAATAAAAATAAAAATATAGAATCAAA-A
1 TAAAATAAAAATAAAAATATAG-ATCAAATA
*
399737 CTAAAATAAATAATAAAAAT-TAGATTAAATA
1 -TAAAATAAA-AATAAAAATATAGATCAAATA
*
399768 TAAAGATATAAAT-AAAATATAG
1 TAAA-ATAAAAATAAAAATATAG
399790 CAAGTATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 5 0.11
30 15 0.33
31 17 0.37
32 9 0.20
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (30 bp):
TAAAATAAAAATAAAAATATAGATCAAATA
Found at i:399755 original size:19 final size:19
Alignment explanation
Indices: 399710--399756 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
399700 TAATTATTAA
*
399710 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
399729 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
399748 AATAAAAAT
1 AATAAAAAT
399757 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:400291 original size:70 final size:69
Alignment explanation
Indices: 400216--400347 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 69
400206 ATGAAACATC
* * * *
400216 TCAATTTTCAGCAACTAAACACTTCAATTTGTAGTACTTAAAACA-CTTCAATTTACAACATTTA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTT-AAACATC-TCAATTAACAACATTTA
400280 AGTACT
64 AGTACT
* ** * *
400286 TCAATTTACAGTATTTAAACATTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTT
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATCTCAATTAACAACATTT
400348 GTACAACTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
69 19 0.37
70 33 0.63
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (69 bp):
TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATCTCAATTAACAACATTTAAG
TACT
Found at i:400311 original size:23 final size:23
Alignment explanation
Indices: 400216--400512 Score: 203
Period size: 23 Copynumber: 12.9 Consensus size: 23
400206 ATGAAACATC
* **
400216 TCAATTTTCAGCAACTAAACACT
1 TCAATTTACAGCATTTAAACACT
** * *
400239 TCAATTTGTAGTACTTAAAACACT
1 TCAATTTACAGCA-TTTAAACACT
* **
400263 TCAATTTACAACATTTAAGTACT
1 TCAATTTACAGCATTTAAACACT
* *
400286 TCAATTTACAGTATTTAAACATT
1 TCAATTTACAGCATTTAAACACT
*
400309 TCAATTTGCAGCACTTT-AACA-T
1 TCAATTTACAGCA-TTTAAACACT
* * **
400331 CTCAATTAACAACATTTGTACAAC-
1 -TCAATTTACAGCATTTAAAC-ACT
*
400355 TCAA-TTACA--ATGATAAA-ACAT
1 TCAATTTACAGCAT-TTAAACAC-T
* **
400376 CTCAATTTCCAGCAACTAAACACT
1 -TCAATTTACAGCATTTAAACACT
* *** *
400400 TCAATTTGCAGTGCTTCAACACT
1 TCAATTTACAGCATTTAAACACT
* *
400423 TCAATTTACAGTACTTAAACACT
1 TCAATTTACAGCATTTAAACACT
*
400446 TCAATTTACAACATTTAAACACT
1 TCAATTTACAGCATTTAAACACT
*
400469 TCAATTTACAGCATTCAAACACT
1 TCAATTTACAGCATTTAAACACT
*
400492 TCAATTTGCAGCATTTAAACA
1 TCAATTTACAGCATTTAAACA
400513 ACAGCAGCCA
Statistics
Matches: 213, Mismatches: 47, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.01
20 2 0.01
21 2 0.01
22 12 0.06
23 167 0.78
24 25 0.12
25 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
TCAATTTACAGCATTTAAACACT
Found at i:401931 original size:7 final size:7
Alignment explanation
Indices: 401917--401951 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
401907 AATTCTATTG
401917 TGAGTTA
1 TGAGTTA
*
401924 TAAGTTA
1 TGAGTTA
401931 TGAGTTA
1 TGAGTTA
401938 TGAGTTA
1 TGAGTTA
401945 TGAGTTA
1 TGAGTTA
401952 AGGCACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (7 bp):
TGAGTTA
Found at i:402916 original size:80 final size:80
Alignment explanation
Indices: 402778--402937 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
402768 ATGATCTTTT
402778 CGTTACTTCTATATGAAAATAGACTCATCGAACTTCGATGACATAATTTATTCATCAATTAATTC
1 CGTTACTTCTATATGAAAATAGACTCATCGAACTTCGATGACATAATTTATTCATCAATTAATTC
402843 CACTCCTACTATTTG
66 CACTCCTACTATTTG
* *
402858 CGTTGCTTCTATATGAAAATAGACTCATCGAGCTTCGAAT-ACATAATTTATTCATCAATTAATT
1 CGTTACTTCTATATGAAAATAGACTCATCGAACTTCG-ATGACATAATTTATTCATCAATTAATT
402922 CCACTCCTACTATTTG
65 CCACTCCTACTATTTG
402938 TTTAGTGATT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
80 75 0.97
81 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (80 bp):
CGTTACTTCTATATGAAAATAGACTCATCGAACTTCGATGACATAATTTATTCATCAATTAATTC
CACTCCTACTATTTG
Found at i:403861 original size:421 final size:421
Alignment explanation
Indices: 403077--403918 Score: 1513
Period size: 421 Copynumber: 2.0 Consensus size: 421
403067 TTTACATACT
*
403077 AAAGTTCAAACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAA
1 AAAGTTCAAACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCAACTAAGAAGAA
* *
403142 AGTACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCCGACCACGCAAAAAGAGATGT
66 AGTACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCCGACCACGCAAAAAGAGACGA
403207 GTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAA
131 GTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAA
* *
403272 GCTATGCACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATGGAACGAGGCTAATTA
196 GCAATACACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATGGAACGAGGCTAATTA
* * * ***
403337 CTCCATCCATTCCGAACCATACCATAGTTCCTCCGACCTATCGGTTTAATTTCATACCAATTTAT
261 CTCCATCCATACCGAACCATACCATAGTTCCTCCGACCTATCGGTTCAATCTCATACCAAACCAT
* *
403402 GCATTCACAATCCACATACTCATCAATAGGATATTCGAGGCATTTTCATAAATCATTTTATTTTC
326 GCATTCACAATCCACATACTCATCAATAGAATATTCGAGGCATTTTCATAAATCATTTCATTTTC
403467 GTTACAAACATACAACTAAACGGCCTTTCAC
391 GTTACAAACATACAACTAAACGGCCTTTCAC
403498 AAAGTTCAAACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCAACTAAGAAGAA
1 AAAGTTCAAACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCAACTAAGAAGAA
403563 AGTACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCCGACCACGCAAAAAGAGACGA
66 AGTACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCCGACCACGCAAAAAGAGACGA
403628 GTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAA
131 GTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAA
* * *
403693 GCAATACACTACCATCCATTAATAACATTATCACAAGAGGAAACAAAATGGAACGAGGCTAGTTA
196 GCAATACACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATGGAACGAGGCTAATTA
403758 CTCCATCCATACCGAACCATACCATAGTTCCTCCGACCTATCGGTTCAATCTCATACCAAACCAT
261 CTCCATCCATACCGAACCATACCATAGTTCCTCCGACCTATCGGTTCAATCTCATACCAAACCAT
* *
403823 GCATTCACATTCCATATACTCATCAATAGAATATTCGAGGCATTTTCATAAATCATTTCATTTTC
326 GCATTCACAATCCACATACTCATCAATAGAATATTCGAGGCATTTTCATAAATCATTTCATTTTC
*
403888 GTTACAATCATACAACTAAACGGCCTTTCAC
391 GTTACAAACATACAACTAAACGGCCTTTCAC
403919 CCATTCCACG
Statistics
Matches: 402, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
421 402 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (421 bp):
AAAGTTCAAACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCAACTAAGAAGAA
AGTACCAAAACTTGCTATCCGGTGTGATGACTTCGATGACGGCCCGACCACGCAAAAAGAGACGA
GTCCAAGAAACCTAGAATAGGTGACAAGGAAACACCGAGTGAGTTTATAACTCAGTAAGTCATAA
GCAATACACTACCATCCATCAATAACATTATCACAAGAGAAAACAAAATGGAACGAGGCTAATTA
CTCCATCCATACCGAACCATACCATAGTTCCTCCGACCTATCGGTTCAATCTCATACCAAACCAT
GCATTCACAATCCACATACTCATCAATAGAATATTCGAGGCATTTTCATAAATCATTTCATTTTC
GTTACAAACATACAACTAAACGGCCTTTCAC
Found at i:404178 original size:28 final size:27
Alignment explanation
Indices: 404117--404213 Score: 140
Period size: 27 Copynumber: 3.6 Consensus size: 27
404107 ATATTAAGTC
* * * *
404117 CGCATACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
404144 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
404172 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
404199 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
404214 GCACAATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 37 0.58
28 27 0.42
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:406819 original size:7 final size:7
Alignment explanation
Indices: 406799--406857 Score: 73
Period size: 7 Copynumber: 8.0 Consensus size: 7
406789 ATATAGACTA
*
406799 AAATATT
1 AAATTTT
*
406806 AATTTTT
1 AAATTTT
406813 AAATTTTT
1 AAA-TTTT
406821 AAATTTTT
1 AAA-TTTT
406829 AAATTTTT
1 AAA-TTTT
406837 AAATTTT
1 AAATTTT
406844 AAATTTT
1 AAATTTT
406851 AAATTTT
1 AAATTTT
406858 TTATTTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
7 25 0.52
8 23 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AAATTTT
Found at i:406819 original size:8 final size:8
Alignment explanation
Indices: 406806--406858 Score: 92
Period size: 8 Copynumber: 6.9 Consensus size: 8
406796 CTAAAATATT
406806 AATTTTTA
1 AATTTTTA
406814 AATTTTTA
1 AATTTTTA
406822 AATTTTTA
1 AATTTTTA
406830 AATTTTTA
1 AATTTTTA
406838 AA-TTTTA
1 AATTTTTA
406845 AA-TTTTA
1 AATTTTTA
406852 AATTTTT
1 AATTTTT
406859 TATTTTTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 14 0.32
8 30 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AATTTTTA
Found at i:407181 original size:22 final size:23
Alignment explanation
Indices: 407153--407205 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
407143 TTTAGGGCTT
407153 GGGGTTTAAGGGTTGG-GGTTTA
1 GGGGTTTAAGGGTTGGAGGTTTA
* *
407175 GGGGTTTAGGGGTTGGAGTTTTA
1 GGGGTTTAAGGGTTGGAGGTTTA
*
407198 AGGGTTTA
1 GGGGTTTA
407206 TGATTTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (23 bp):
GGGGTTTAAGGGTTGGAGGTTTA
Found at i:407195 original size:14 final size:14
Alignment explanation
Indices: 407143--407180 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
407133 TAAACATTGT
*
407143 TTTAGGGCTTGGGG
1 TTTAGGGGTTGGGG
*
407157 TTTAAGGGTTGGGG
1 TTTAGGGGTTGGGG
407171 TTTAGGGGTT
1 TTTAGGGGTT
407181 TAGGGGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.03, G:0.47, T:0.39
Consensus pattern (14 bp):
TTTAGGGGTTGGGG
Found at i:407284 original size:22 final size:22
Alignment explanation
Indices: 407194--407284 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
407184 GGGTTGGAGT
*
407194 TTTAAGGGTTTATGATTTGAGA
1 TTTAAGAGTTTATGATTTGAGA
* * *
407216 TTT-AGAGTTTAGGGTGTTGGGA
1 TTTAAGAGTTTATGAT-TTGAGA
*
407238 -TTAAG-GTTTATTG-TTTAGAGT
1 TTTAAGAGTTTA-TGATTT-GAGA
*
407259 TTTAAGAGTTTATGATTTGATA
1 TTTAAGAGTTTATGATTTGAGA
407281 TTTA
1 TTTA
407285 GGGTCTGGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
20 2 0.04
21 19 0.36
22 24 0.45
23 8 0.15
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.48
Consensus pattern (22 bp):
TTTAAGAGTTTATGATTTGAGA
Found at i:407337 original size:66 final size:66
Alignment explanation
Indices: 407249--407378 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
407239 TAAGGTTTAT
* * *
407249 TGTTTAGAGTTTTAAGAGTTTATGATTTGATATTTAGGGTCTGGTGTTTAAAGAGTTATTGATTA
1 TGTTTAGAGTTTTAAGAGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGATTA
407314 G
66 G
* * * * *
407315 TGTTTATAGTTTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGGGTTGTTGATT
1 TGTTTAGAGTTTTAAGAGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGATT
407379 TAAGGGGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (66 bp):
TGTTTAGAGTTTTAAGAGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGATTA
G
Found at i:407400 original size:66 final size:65
Alignment explanation
Indices: 407252--407402 Score: 153
Period size: 66 Copynumber: 2.3 Consensus size: 65
407242 GGTTTATTGT
* * * * * *
407252 TTAGAGTTTTAAGAGTTTATGATTTGATATTTAGGGTCTGGTGTTTAAAGAGTTATTGATTAGTG
1 TTAGAG-TTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGATTAGGG
*
407317 T
65 G
* * *
407318 TTATAGTTTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGGGTTGTTGATTTAAG
1 TTAGAG-TTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGA-TT-AG
407383 GGG
63 GGG
407386 TTAGGAG-TTA-GGGTTTA
1 TTA-GAGTTTAGGGGTTTA
407403 AAGAAAGCCA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
66 58 0.82
67 5 0.07
68 6 0.08
69 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (65 bp):
TTAGAGTTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGGGTTTAAAGAGTTATTGATTAGGGG
Found at i:408862 original size:90 final size:90
Alignment explanation
Indices: 408703--408867 Score: 215
Period size: 90 Copynumber: 1.8 Consensus size: 90
408693 CGCCATATCC
* * * * * *
408703 CAGATATGGTCTTACTTGGGATCACAACTCGATGCCAATGCCATGTCCTAGGCATGGTCTTACAT
1 CAGATATGGTCTTACATGAGAACACAACTCGATGCCAATGCCATATCCTAGACATGGTCTTACAC
*
408768 GGGATTTCATATCAACACCACATCT
66 GGGATCTCATATCAACACCACATCT
* * * *
408793 CAGATATGGTCTTACATGATAACACATAC-CGATGCCGATGCCATATCCTAGATATGGTCTTATA
1 CAGATATGGTCTTACATGAGAACACA-ACTCGATGCCAATGCCATATCCTAGACATGGTCTTACA
408857 CGGGATCTCAT
65 CGGGATCTCAT
408868 CAACCCAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
90 61 0.97
91 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (90 bp):
CAGATATGGTCTTACATGAGAACACAACTCGATGCCAATGCCATATCCTAGACATGGTCTTACAC
GGGATCTCATATCAACACCACATCT
Found at i:418379 original size:50 final size:50
Alignment explanation
Indices: 418304--418403 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
418294 AGGATCTATT
418304 CATGAAGAACGAAGGTTGCAAAGAGACAAGCTAGATGAATGGCGAACACA
1 CATGAAGAACGAAGGTTGCAAAGAGACAAGCTAGATGAATGGCGAACACA
418354 CATGAAGAACGAAGGTTGCAAAGAGACAAGCTAGATGAATGGCGAACACA
1 CATGAAGAACGAAGGTTGCAAAGAGACAAGCTAGATGAATGGCGAACACA
418404 TAAACCGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (50 bp):
CATGAAGAACGAAGGTTGCAAAGAGACAAGCTAGATGAATGGCGAACACA
Found at i:425546 original size:30 final size:30
Alignment explanation
Indices: 425507--425567 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
425497 ATTAATTTTC
* *
425507 AGGCATAGGGGTAAAATGGTTATTTTGCCA
1 AGGCATAGGGGCAAAATGGTCATTTTGCCA
*
425537 AGGCCTAGGGGCAAAATGGTCATTTTGCCA
1 AGGCATAGGGGCAAAATGGTCATTTTGCCA
425567 A
1 A
425568 AGTTGTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (30 bp):
AGGCATAGGGGCAAAATGGTCATTTTGCCA
Found at i:425961 original size:46 final size:46
Alignment explanation
Indices: 425908--426074 Score: 158
Period size: 46 Copynumber: 3.6 Consensus size: 46
425898 AATTTCTGCA
425908 CCAGTGTAAGACATGTTTGGGACATGCTTCGGCCACATTATGAGAG
1 CCAGTGTAAGACATGTTTGGGACATGCTTCGGCCACATTATGAGAG
* * * * * *
425954 CCAGTGTAAGACCATGTATGGGACATGGCATCGGCAACCA-GACGAGGG
1 CCAGTGTAAGA-CATGTTTGGGACAT-GCTTCGGCCA-CATTATGAGAG
* ** * *
426002 CTAGTGTAAGACATGTCTT-GGACATGCTTCAACCATATTATGAGTG
1 CCAGTGTAAGACATGT-TTGGGACATGCTTCGGCCACATTATGAGAG
* * *
426048 CCAGAGTAAGACATATTCGGGACATGC
1 CCAGTGTAAGACATGTTTGGGACATGC
426075 ATTAGCCTTG
Statistics
Matches: 95, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
45 2 0.02
46 43 0.45
47 24 0.25
48 24 0.25
49 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
CCAGTGTAAGACATGTTTGGGACATGCTTCGGCCACATTATGAGAG
Found at i:432914 original size:47 final size:46
Alignment explanation
Indices: 432843--433110 Score: 190
Period size: 47 Copynumber: 5.7 Consensus size: 46
432833 TGATTTGTGC
* *
432843 GCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCA-C-ATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CATCTA-GATGAGA
*
432889 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCTAGATGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCTAGATGAGA
* * ** * *
432937 GCTAGTGTAAGACATGTCTAGGACATGCATTAGC--CTGGACAGAGGTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCTAGA-TGA-G-A
* * * * * *
432984 GCCAATGTAAGACGTGTCTGGGACACGCATCGGC-T-AAGA-GTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCTAGATG-AGA
* * * * *
433028 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCACGCATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA-TC-TAGATGAGA
*
433076 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
433111 TAATTTATCC
Statistics
Matches: 170, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
44 32 0.19
45 4 0.02
46 19 0.11
47 58 0.34
48 36 0.21
49 15 0.09
50 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCTAGATGAGA
Found at i:445802 original size:28 final size:28
Alignment explanation
Indices: 445770--445834 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
445760 ATTTACTAGA
*
445770 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
445798 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
445826 ATACCCCTA
1 ATACCCCTA
445835 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:445998 original size:27 final size:28
Alignment explanation
Indices: 445940--446029 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
445930 AGGAAGCGTC
*
445940 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
445968 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
445995 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
446024 CTGGTG
1 CTGGTG
446030 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:446040 original size:29 final size:28
Alignment explanation
Indices: 445950--446040 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
445940 CTGGTGGCTA
* * *
445950 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
445978 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
446005 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
446034 TGTCACA
1 TGCCACA
446041 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:446048 original size:55 final size:56
Alignment explanation
Indices: 445940--446054 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
445930 AGGAAGCGTC
* * *
445940 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
445995 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
446051 CTGG
1 CTGG
446055 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:446516 original size:19 final size:19
Alignment explanation
Indices: 446494--446532 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
446484 TTTAATTATT
* *
446494 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
446513 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
446532 T
1 T
446533 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:449510 original size:110 final size:110
Alignment explanation
Indices: 449317--449535 Score: 393
Period size: 110 Copynumber: 2.0 Consensus size: 110
449307 AGAATAAGTA
* *
449317 CCCTCTGCCAAGGATTGACGATCTGTTCGACCAGCTTAAAGGAGCTTCTGTATTTTCCAAGATCG
1 CCCTCTGCCAAGGATTGACGATCTGTTCGACCAGCTTAAAGGAGCTTCTATATTTTCCAAGATCA
*
449382 ATCTTCGATCTGGATATCATTAGTTAAGGGTCAAGGAGGCAGATG
66 ATCTTCGATCTGGATATCATCAGTTAAGGGTCAAGGAGGCAGATG
* *
449427 CCCTCTGCCAAGGATTGACGATTTGTTCGACCAGCTTAAAGGAGCTTTTATATTTTCCAAGATCA
1 CCCTCTGCCAAGGATTGACGATCTGTTCGACCAGCTTAAAGGAGCTTCTATATTTTCCAAGATCA
449492 ATCTTCGATCTGGATATCATCAGTTAAGGGTCAAGGAGGCAGAT
66 ATCTTCGATCTGGATATCATCAGTTAAGGGTCAAGGAGGCAGAT
449536 ATTCATAAGA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 104 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (110 bp):
CCCTCTGCCAAGGATTGACGATCTGTTCGACCAGCTTAAAGGAGCTTCTATATTTTCCAAGATCA
ATCTTCGATCTGGATATCATCAGTTAAGGGTCAAGGAGGCAGATG
Found at i:453743 original size:28 final size:28
Alignment explanation
Indices: 453711--453775 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
453701 ATTTACTAGA
*
453711 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
453739 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
453767 ATACCCCTA
1 ATACCCCTA
453776 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:453939 original size:27 final size:27
Alignment explanation
Indices: 453881--453970 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
453871 AGGAAGCGTC
453881 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
453909 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
453936 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
453965 CTGGTG
1 CTGGTG
453971 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:457411 original size:6 final size:6
Alignment explanation
Indices: 457393--457537 Score: 88
Period size: 6 Copynumber: 23.8 Consensus size: 6
457383 AAGAAACATT
* *
457393 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
457442 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* * *
457493 A-CAGA ATCAG- -TCAGGTA A-CAGA ATCAAA ATGAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
457538 GTAATAGAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 32
0.70 0.10 0.21
Matches are distributed among these distances:
4 3 0.03
5 9 0.08
6 82 0.76
7 11 0.10
8 3 0.03
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:457438 original size:31 final size:31
Alignment explanation
Indices: 457377--457502 Score: 166
Period size: 31 Copynumber: 4.1 Consensus size: 31
457367 TAACCCATTA
* * *
457377 CAGAATAAGAAACATTATCA-G-AACTAGAAT
1 CAGAATCAGAATCAGTATCAGGTAAC-AGAAT
* * *
457407 CAGAATCAGAATCAGAATTAGGTGACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
457438 CAGAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
*
457469 CAAAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
457500 CAG
1 CAG
457503 TCAGGTAACA
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.18
31 66 0.80
32 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:457466 original size:25 final size:24
Alignment explanation
Indices: 457438--457518 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 24
457428 GTGACAGAAT
457438 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAG-ATCAGGTAA
* *
457463 CAGAATCAAAATCAGAATCA-GTAT
1 CAGAATCAGAATCAG-ATCAGGTAA
457487 CAGGTAA-CAGAATCAG-TCAGGTAA
1 CA-G-AATCAGAATCAGATCAGGTAA
457511 CAGAATCA
1 CAGAATCA
457519 AAATGAGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.04
23 6 0.13
24 10 0.21
25 27 0.57
26 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (24 bp):
CAGAATCAGAATCAGATCAGGTAA
Found at i:457508 original size:17 final size:18
Alignment explanation
Indices: 457444--457518 Score: 74
Period size: 19 Copynumber: 4.4 Consensus size: 18
457434 GAATCAGAAT
457444 CAGAATCAGTATCAGGTAA
1 CAGAATCAG-ATCAGGTAA
*
457463 CAGAATCA-A--A---AT
1 CAGAATCAGATCAGGTAA
457475 CAGAATCAGTATCAGGTAA
1 CAGAATCAG-ATCAGGTAA
457494 CAGAATCAG-TCAGGTAA
1 CAGAATCAGATCAGGTAA
457511 CAGAATCA
1 CAGAATCA
457519 AAATGAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
12 9 0.19
14 1 0.02
15 1 0.02
16 1 0.02
17 17 0.36
19 18 0.38
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (18 bp):
CAGAATCAGATCAGGTAA
Found at i:457520 original size:48 final size:49
Alignment explanation
Indices: 457444--457547 Score: 174
Period size: 48 Copynumber: 2.1 Consensus size: 49
457434 GAATCAGAAT
457444 CAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAG-ATCAGGTAACAGAATCAAAATCAGAATCAGTATCAGGTAA
*
457494 CAGAATCAG-TCAGGTAACAGAATCAAAATGAGAATCAGTATCAGGTAA
1 CAGAATCAGATCAGGTAACAGAATCAAAATCAGAATCAGTATCAGGTAA
*
457542 TAGAAT
1 CAGAAT
457548 AAAAAATCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 43 0.83
50 9 0.17
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20
Consensus pattern (49 bp):
CAGAATCAGATCAGGTAACAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:457528 original size:29 final size:30
Alignment explanation
Indices: 457495--457552 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
457485 ATCAGGTAAC
*
457495 AGAATCAG-TCAGGTAACAGAATCAAAATG
1 AGAATCAGATCAGGTAACAGAATAAAAATG
*
457524 AGAATCAGTATCAGGTAATAGAATAAAAA
1 AGAATCAG-ATCAGGTAACAGAATAAAAA
457553 ATCAGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (30 bp):
AGAATCAGATCAGGTAACAGAATAAAAATG
Found at i:457739 original size:27 final size:26
Alignment explanation
Indices: 457697--457791 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
457687 GCTCAGTTAT
* *
457697 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
457724 CAGATATTATGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
* *
457750 CAAATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
*
457778 CAGATAATGTGGCA
1 CAGATATTGTGGCA
457792 AATTCACTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.10
27 45 0.78
28 7 0.12
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:457985 original size:22 final size:22
Alignment explanation
Indices: 457957--458020 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
457947 GCAAATACGT
*
457957 TTGGCACACAGCCATAATTAAG
1 TTGGCACAAAGCCATAATTAAG
* *
457979 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-TAAG
*
458001 TTGACACAAAGCCATAATTA
1 TTGGCACAAAGCCATAATTA
458021 GAAGGCTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATTAAG
Found at i:458503 original size:27 final size:27
Alignment explanation
Indices: 458447--458606 Score: 182
Period size: 27 Copynumber: 6.0 Consensus size: 27
458437 GGGGCAAAAT
* * * *
458447 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
458473 GGTAATTCCACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
458500 GGTAATTCTACCCTAAAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
458526 TGGTAATTCTACCTTACAGGGGTATTTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
*
458554 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
458581 GAG-ATTTCTACCCTATAAGGGTATTT
1 G-GTAATTCTACCCTACAGGGGTATTT
458607 TGATAATTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
26 17 0.15
27 94 0.82
28 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:458570 original size:81 final size:81
Alignment explanation
Indices: 458465--458614 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
458455 TACCCCACAA
*
458465 GGTATCTCGGTAATTCCACCCTACAGGGGTATTTCG-GTAATTCTACCCTA-AAGGGGTATTCTG
1 GGTATCTCAGTAATTCCACCCTACAGGGGTATTTCGAG-AATTCTACCCTATAA-GGGTATTCTG
*
458528 GTAATTCTACCTTACAGG
64 ATAATTCTACCTTACAGG
* * * *
458546 GGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGAGATTTCTACCCTATAAGGGTATTTTGAT
1 GGTATCTCAGTAATTCCACCCTACAGGGGTATTTCGAGAATTCTACCCTATAAGGGTATTCTGAT
458611 AATT
66 AATT
458615 TTGTAAATCG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
81 58 0.95
82 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (81 bp):
GGTATCTCAGTAATTCCACCCTACAGGGGTATTTCGAGAATTCTACCCTATAAGGGTATTCTGAT
AATTCTACCTTACAGG
Found at i:458682 original size:27 final size:26
Alignment explanation
Indices: 458647--458887 Score: 180
Period size: 27 Copynumber: 9.0 Consensus size: 26
458637 TAATTCTGTA
* *
458647 AATCAAGGGTACTTTGGTAATTTTAC
1 AATCGAGGGTATTTTGGTAATTTTAC
***
458673 AAGTCGAGGGTATTTCAATAATTTTAC
1 AA-TCGAGGGTATTTTGGTAATTTTAC
* * *
458700 AGGTCGAGGGTATTTTAGTAATTTCAC
1 A-ATCGAGGGTATTTTGGTAATTTTAC
*
458727 AAAT-TAGGGATATTTTGGTAATTTTAC
1 -AATCGAGGG-TATTTTGGTAATTTTAC
* *
458754 TAA-CTAGGGGTATTTTGATAATTTTAC
1 -AATCGA-GGGTATTTTGGTAATTTTAC
* *
458781 AAACCAGGGATATTTTGGTAATTTTAC
1 AATCGAGGG-TATTTTGGTAATTTTAC
* * *
458808 AAACCAGGGGTATTTTGGTAATTTTAT
1 AATCGA-GGGTATTTTGGTAATTTTAC
* * * *
458835 AAACAAAAGGTATTTTAGTAATTTTAC
1 AATC-GAGGGTATTTTGGTAATTTTAC
* *
458862 AAACCAGGGGTATTTTGGTAATTTTA
1 AATCGA-GGGTATTTTGGTAATTTTA
458888 TAAACNNNNN
Statistics
Matches: 179, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
26 12 0.07
27 159 0.89
28 8 0.04
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (26 bp):
AATCGAGGGTATTTTGGTAATTTTAC
Found at i:458744 original size:81 final size:81
Alignment explanation
Indices: 458659--458885 Score: 235
Period size: 81 Copynumber: 2.8 Consensus size: 81
458649 TCAAGGGTAC
* * ** *
458659 TTTGGTAATTTTAC-AAGTCGAGGGTATTTCAATAATTTTACAGGTCGAGGG-TATTTTAGTAAT
1 TTTGGTAATTTTACTAACTAG-GGGTATTTCAATAATTTTACA-AACCAGGGATATTTTAGTAAT
**
458722 TTCACAAATTAGGGATAT
64 TTCACAAACCAGGGATAT
** *
458740 TTTGGTAATTTTACTAACTAGGGGTATTTTGATAATTTTACAAACCAGGGATATTTTGGTAATTT
1 TTTGGTAATTTTACTAACTAGGGGTATTTCAATAATTTTACAAACCAGGGATATTTTAGTAATTT
* *
458805 TACAAACCAGGGGTAT
66 CACAAACCAGGGATAT
* ** * * * *
458821 TTTGGTAATTTTA-TAAACAAAAGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATT
1 TTTGGTAATTTTACT-AACTAGGGGTATTTCAATAATTTTACAAACCAGGGATATTTTAGTAATT
458885 T
65 T
458886 TATAAACNNN
Statistics
Matches: 125, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
80 6 0.05
81 115 0.92
82 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (81 bp):
TTTGGTAATTTTACTAACTAGGGGTATTTCAATAATTTTACAAACCAGGGATATTTTAGTAATTT
CACAAACCAGGGATAT
Found at i:458892 original size:27 final size:27
Alignment explanation
Indices: 458707--458892 Score: 237
Period size: 27 Copynumber: 6.9 Consensus size: 27
458697 TACAGGTCGA
* * **
458707 GGGTATTTTAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
458734 GGATATTTTGGTAATTTTACTAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
458761 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
458788 GGATATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
458815 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
458842 AGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
458869 GGGTATTTTGGTAATTTTATAAAC
1 GGGTATTTTGGTAATTTTACAAAC
458893 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:461683 original size:26 final size:26
Alignment explanation
Indices: 461617--461684 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
461607 TCCGACCCAT
* **
461617 AGCTCGTGTGAGTAGGCCCATTTCAC
1 AGCTCGTGTGAGCATACCCATTTCAC
** *
461643 AGCTAATGTGAGCATACTCATTTCAC
1 AGCTCGTGTGAGCATACCCATTTCAC
461669 AGCTCGTGTGAGCATA
1 AGCTCGTGTGAGCATA
461685 AATCTTCAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (26 bp):
AGCTCGTGTGAGCATACCCATTTCAC
Found at i:468091 original size:42 final size:42
Alignment explanation
Indices: 468045--468132 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
468035 GTCTACGCCA
* *
468045 TGTGTGACACATGGTCAGCCCCATGGGCATGTCGTTCAGCTG
1 TGTGTGACACACGGTCAGCCCCATAGGCATGTCGTTCAGCTG
* * **
468087 TGTGTGACACACGGTCAGCCCTATAGGCGTGTCGTTTGGCTG
1 TGTGTGACACACGGTCAGCCCCATAGGCATGTCGTTCAGCTG
468129 TGTG
1 TGTG
468133 CCCCCTGCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28
Consensus pattern (42 bp):
TGTGTGACACACGGTCAGCCCCATAGGCATGTCGTTCAGCTG
Found at i:469353 original size:40 final size:40
Alignment explanation
Indices: 469276--469492 Score: 330
Period size: 40 Copynumber: 5.5 Consensus size: 40
469266 AAACCAAGTA
* * * *
469276 CCTTCGGGATTTAG-CCGGACATAGCT-ACCCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
469315 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
469355 CCTTCAGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
469395 CCTTCGGGACTTAGCCCGGATATATTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
469435 CATTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
469475 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
469493 AAATTATCAT
Statistics
Matches: 163, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.09
40 149 0.91
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:475504 original size:11 final size:12
Alignment explanation
Indices: 475472--475511 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
475462 AGGATCATCA
475472 AAGTGTAAGCTC
1 AAGTGTAAGCTC
475484 AAGTGTAAGCTC
1 AAGTGTAAGCTC
475496 AAG-GTAAGCTC
1 AAGTGTAAGCTC
475507 AAGTG
1 AAGTG
475512 CACATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (12 bp):
AAGTGTAAGCTC
Found at i:478733 original size:46 final size:45
Alignment explanation
Indices: 478680--478942 Score: 187
Period size: 46 Copynumber: 5.7 Consensus size: 45
478670 GATATTTGGG
*
478680 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGTGAA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTGAT-GATGTGAA
*
478726 CATCCGAACTCGTTGAGTTGAGT-TCGAGTTCA-TGA-GATGTAACTA
1 CATCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTGATGATGTGA--A
** * * *
478771 GGCATTTGAACTTGTTGAGTTGAGTCTGAGTTCACTTATAGATGCGAA
1 --CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTGAT-GATGTGAA
* * * * *
478819 CGTCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAATTA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTGATGATGTGA--A
* * * * *
478864 GGCATCCGAGCTCATTGAGTTGAGTCTAAGTTCACTTATGGATGCGAA
1 --CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTGAT-GATGTGAA
* * *
478912 C-GCTCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CATC-CGAACTCGTTGAGTTGAGTCTGAGTTC
478943 GCTTATGGGC
Statistics
Matches: 168, Mismatches: 32, Indels: 34
0.72 0.14 0.15
Matches are distributed among these distances:
43 11 0.07
45 8 0.05
46 80 0.48
47 52 0.31
48 7 0.04
50 10 0.06
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (45 bp):
CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTGATGATGTGAA
Found at i:478943 original size:93 final size:93
Alignment explanation
Indices: 478678--478943 Score: 381
Period size: 93 Copynumber: 2.9 Consensus size: 93
478668 CTGATATTTG
* * *
478678 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGTGAACATCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
* *
478743 TTGAGTTCGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
** * * *
478771 GGCATTTGAACTTGTTGAGTTGAGTCTGAGTTCACTTATAGATGCGAACGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
478836 TTGAGTCCGAGTTCGTGAGATGTAATTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
478864 GGCATCCGAGCTCATTGAGTTGAGTCTAAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGA
478928 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
478944 CTTATGGGCG
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
92 1 0.01
93 151 0.99
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:501904 original size:77 final size:77
Alignment explanation
Indices: 501777--501930 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
501767 TAAACCCATT
501777 TTGAGCCTAACAAGCCATTAATTGATTTACCCTCAATATTAACCCATAAACCATCATTGTTGAAA
1 TTGAGCCTAACAAGCCATTAATTGATTTACCCTCAATATTAACCCATAAACCATCATTGTTGAAA
501842 TCCCCTAATTTG
66 TCCCCTAATTTG
*
501854 TTGAGCCTAACAAGCCATTAATTGATTTACCCTCAATATTAACCCATAAACCATTATTGTTGAAA
1 TTGAGCCTAACAAGCCATTAATTGATTTACCCTCAATATTAACCCATAAACCATCATTGTTGAAA
*
501919 TCCCCTACTTTG
66 TCCCCTAATTTG
501931 ATCCCTATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (77 bp):
TTGAGCCTAACAAGCCATTAATTGATTTACCCTCAATATTAACCCATAAACCATCATTGTTGAAA
TCCCCTAATTTG
Found at i:506933 original size:39 final size:39
Alignment explanation
Indices: 506890--507042 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
506880 CCAGACATAT
* * *
506890 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
*
506929 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
* * *
506968 TTCCAACACATAGCCTGCGAACCCTAACTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
*
507007 TTCCAGCACATAGCCTGCAGACCCTAAGTCCGGATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
507043 AACATCACTG
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 104 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:506944 original size:78 final size:78
Alignment explanation
Indices: 506862--507034 Score: 213
Period size: 78 Copynumber: 2.2 Consensus size: 78
506852 ACTAGCTCGA
* * * * * * * *
506862 AGCCTGCGGGACTTTAA-CCCAGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTA
1 AGCCTGC-GGACCTTAAGCCCAGACATAATTCCAACACATAGCCTGCGAACCCTAACTCCGGATA
506926 TAATTCCAGCACAT
65 TAATTCCAGCACAT
* * *
506940 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAACACATAGCCTGCGAACCCTAACTCCGGATAT
1 AGCCTGCGGACCTTAAGCCCAGACATAATTCCAACACATAGCCTGCGAACCCTAACTCCGGATAT
507005 AATTCCAGCACAT
66 AATTCCAGCACAT
* *
507018 AGCCTGCAGACCCTAAG
1 AGCCTGCGGACCTTAAG
507035 TCCGGATAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 8 0.10
78 73 0.90
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (78 bp):
AGCCTGCGGACCTTAAGCCCAGACATAATTCCAACACATAGCCTGCGAACCCTAACTCCGGATAT
AATTCCAGCACAT
Found at i:509267 original size:149 final size:149
Alignment explanation
Indices: 508997--509294 Score: 560
Period size: 149 Copynumber: 2.0 Consensus size: 149
508987 GAGTCCTCTT
508997 GTACTATACCATGCATTATTCGACCCTCTAAATTCTTCCTATCACATTTTTAAGTTTTAACACAC
1 GTACTATACCATGCATTATTCGACCCTCTAAATTCTTCCTATCACATTTTTAAGTTTTAACACAC
* * *
509062 AAGTCCTTTTTAGCTATTTCCACATTCAAATGACAAAGTTAAGACACGATACTTTCACACATACA
66 AAGTCCTTTTTAGCTATTTCCACATTCAAATGACAAAGTTAAGAAAAGATACTTTCACACAGACA
*
509127 CTTTCACATATAATAAGCA
131 CTTCCACATATAATAAGCA
509146 GTACTATACCATGCATTATTCGACCCTCTAAATTCTTCCTATCACATTTTTAAGTTTTAACACAC
1 GTACTATACCATGCATTATTCGACCCTCTAAATTCTTCCTATCACATTTTTAAGTTTTAACACAC
509211 AAGTCCTTTTTAGCTATTTCCACATTCAAATGACAAAGTTAAGAAAAGATACTTTCACACAGACA
66 AAGTCCTTTTTAGCTATTTCCACATTCAAATGACAAAGTTAAGAAAAGATACTTTCACACAGACA
509276 CTTCCACATATAATAAGCA
131 CTTCCACATATAATAAGCA
509295 TAGATAATAA
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (149 bp):
GTACTATACCATGCATTATTCGACCCTCTAAATTCTTCCTATCACATTTTTAAGTTTTAACACAC
AAGTCCTTTTTAGCTATTTCCACATTCAAATGACAAAGTTAAGAAAAGATACTTTCACACAGACA
CTTCCACATATAATAAGCA
Found at i:517702 original size:40 final size:40
Alignment explanation
Indices: 517640--517856 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
517630 AAGCCAAGTA
* * *
517640 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
* *
517679 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* *
517719 CCTTCGGGACTTAGCCCGGACATAATAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * *
517759 CCTTCGGGAATTAGCCCGGGTATAATAACTCGCAC-AATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAA-TG
* * *
517799 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
517838 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
517857 TTATCATCCG
Statistics
Matches: 155, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 43 0.28
40 111 0.72
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:545149 original size:47 final size:47
Alignment explanation
Indices: 545081--545212 Score: 264
Period size: 47 Copynumber: 2.8 Consensus size: 47
545071 CTCGAACCGC
545081 CATACATATGTATGAATGCACTTAATTTGAACGAAATTAAGGGAAAA
1 CATACATATGTATGAATGCACTTAATTTGAACGAAATTAAGGGAAAA
545128 CATACATATGTATGAATGCACTTAATTTGAACGAAATTAAGGGAAAA
1 CATACATATGTATGAATGCACTTAATTTGAACGAAATTAAGGGAAAA
545175 CATACATATGTATGAATGCACTTAATTTGAACGAAATT
1 CATACATATGTATGAATGCACTTAATTTGAACGAAATT
545213 TTACGACTTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (47 bp):
CATACATATGTATGAATGCACTTAATTTGAACGAAATTAAGGGAAAA
Done.