Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008840.1 Hibiscus syriacus cultivar Beakdansim tig00112044_pilon, 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: 1122218
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:206958 original size:25 final size:25
Alignment explanation
Indices: 206924--206992 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
206914 ATTAATTATT
* * *
206924 TAATAATAATAATATAATATAATAA
1 TAATAATAATAATAAAACAAAATAA
*
206949 TAATAATAATATTAAAACAAAATAA
1 TAATAATAATAATAAAACAAAATAA
206974 TAATAAT-A-AATAAAACAAA
1 TAATAATAATAATAAAACAAA
206993 TGAAATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.26
24 1 0.03
25 28 0.72
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (25 bp):
TAATAATAATAATAAAACAAAATAA
Found at i:206993 original size:22 final size:22
Alignment explanation
Indices: 206925--206993 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
206915 TTAATTATTT
* *
206925 AATAATAATAATATAATATAA-T
1 AATAATAATAATA-AATAAAACA
*
206947 AATAATAATAAT-ATTAAAACAA
1 AATAATAATAATAAATAAAAC-A
206969 AATAATAATAATAAATAAAACA
1 AATAATAATAATAAATAAAACA
206991 AAT
1 AAT
206994 GAAATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.12
22 28 0.70
23 7 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAATAATAATAAATAAAACA
Found at i:211984 original size:21 final size:21
Alignment explanation
Indices: 211958--212009 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
211948 GGAGCGTGGG
211958 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
211979 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
212000 GGGAATCGGT
1 GGGAATCGGT
212010 TCCCTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:215422 original size:4 final size:4
Alignment explanation
Indices: 215413--218437 Score: 5897
Period size: 4 Copynumber: 760.8 Consensus size: 4
215403 CTTTTTTAAT
215413 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215461 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215509 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215557 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215605 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215653 ATAG ATAG ATAG ATAG ATAG AT-- ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215699 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215747 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215795 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215843 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215891 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215939 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
215987 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216035 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216083 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216131 ATAG --AG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216177 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
216225 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AGAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216273 AT-G ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216320 ATAG ATAG ATAG ATAG --AG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216366 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG --AG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216412 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216460 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216508 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216556 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG --AG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216602 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216650 ATAG ATAG ATAG ATAG AT-- ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216696 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216744 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216792 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216840 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216888 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216936 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
216984 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT-G ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217031 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217079 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217127 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217175 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217223 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
217271 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG CTAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217319 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217367 ATAG ATAG ATAG ATAG ATAG ATAG --AG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217413 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217461 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217509 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
217557 CTAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217605 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217653 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217701 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217749 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG --AG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217795 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217843 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217891 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217939 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
217987 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218035 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218083 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218131 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218179 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218227 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218275 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218323 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218371 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
218419 ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATA
218438 AGTTCCATCT
Statistics
Matches: 2997, Mismatches: 6, Indels: 36
0.99 0.00 0.01
Matches are distributed among these distances:
2 16 0.01
3 6 0.00
4 2975 0.99
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:220729 original size:17 final size:17
Alignment explanation
Indices: 220707--220741 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
220697 TAGGCTGCTT
* *
220707 TTATTTTTTTTTAATTA
1 TTATTTTTGTTGAATTA
220724 TTATTTTTGTTGAATTA
1 TTATTTTTGTTGAATTA
220741 T
1 T
220742 GCAAGGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTATTTTTGTTGAATTA
Found at i:230513 original size:31 final size:31
Alignment explanation
Indices: 230478--230555 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
230468 ATGACGATTG
* * *
230478 AGTGATTATTTTATTATAAATTGATAATGTC
1 AGTGATTATTTTATTATAAATTAATAATATA
230509 AGTGATTATTTTATTATAAATTAATAATATA
1 AGTGATTATTTTATTATAAATTAATAATATA
* *
230540 AATGATTAATTTATTA
1 AGTGATTATTTTATTA
230556 CTTTTAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (31 bp):
AGTGATTATTTTATTATAAATTAATAATATA
Found at i:232007 original size:17 final size:18
Alignment explanation
Indices: 231974--232007 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
231964 TCACTATTAG
231974 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
231992 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
232008 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:233406 original size:21 final size:21
Alignment explanation
Indices: 233380--233500 Score: 133
Period size: 21 Copynumber: 5.8 Consensus size: 21
233370 TTTCCAAATT
233380 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
233401 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
233424 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
233443 CGTTGAGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
233464 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
233485 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
233501 AATCGCAACG
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
19 24 0.29
21 32 0.38
23 28 0.33
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:233434 original size:44 final size:40
Alignment explanation
Indices: 233364--233444 Score: 126
Period size: 44 Copynumber: 1.9 Consensus size: 40
233354 ACTATCGCAA
233364 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
233404 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCG
1 TGCGA-TT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCG
233445 TTGAGATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
40 5 0.14
41 2 0.05
42 9 0.24
44 21 0.57
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:233447 original size:42 final size:41
Alignment explanation
Indices: 233364--233506 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 41
233354 ACTATCGCAA
233364 TGCGATT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTCGCGTTGCGATAGTCCAAGTT--CGT
233404 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
1 TGCGA-TTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
* * * * *
233446 TGAGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGATTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGT
* *
233488 TGCGA-TAGTCCAAAATCGC
1 TGCGATTATTCCAAATTCGC
233507 AACGACTGGT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
40 23 0.26
41 2 0.02
42 44 0.50
44 19 0.22
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
TGCGATTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
Found at i:233463 original size:63 final size:61
Alignment explanation
Indices: 233372--233501 Score: 206
Period size: 63 Copynumber: 2.1 Consensus size: 61
233362 AATGCGATTT
*
233372 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAG
* * *
233435 TCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
233496 TCCAAA
1 TCCAAA
233502 ATCGCAACGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 16 0.26
63 46 0.74
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (61 bp):
TCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:233623 original size:10 final size:11
Alignment explanation
Indices: 233592--233625 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
233582 GACACGTATT
233592 ACCACGACCACG
1 ACCACGACC-CG
233604 ACCACGACCCG
1 ACCACGACCCG
233615 ACC-CGACCCG
1 ACCACGACCCG
233625 A
1 A
233626 GACGAAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:234405 original size:21 final size:21
Alignment explanation
Indices: 234381--234580 Score: 147
Period size: 21 Copynumber: 9.8 Consensus size: 21
234371 TGCGATTTTG
234381 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
*
234402 GACTATCGCAA--CGAACTTA
1 GACTATCGCAACGCGAACTTC
*
234421 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* *
234444 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTC
* * *
234463 GAATAAATCGCAATGCGAACTTG
1 GACT--ATCGCAACGCGAACTTC
*
234486 GACTATCGCAA--CGAA-TTT
1 GACTATCGCAACGCGAACTTC
*
234504 GTAATAAATCGCAACGCGAACTTC
1 G-ACT--ATCGCAACGCGAACTTC
*
234528 GACTATCGCAATGCG-A-TT-
1 GACTATCGCAACGCGAACTTC
234546 ---TATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
*
234564 GACTATCGCAATGCGAA
1 GACTATCGCAACGCGAA
234581 TATGTAAATC
Statistics
Matches: 143, Mismatches: 16, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
15 11 0.08
16 1 0.01
17 2 0.01
18 3 0.02
19 27 0.19
20 1 0.01
21 69 0.48
23 26 0.18
24 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:234444 original size:42 final size:41
Alignment explanation
Indices: 234385--234574 Score: 255
Period size: 42 Copynumber: 4.7 Consensus size: 41
234375 ATTTTGGACT
234385 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTT-GAATAA
*
234427 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTT-GAATAA
* * *
234469 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTG-AATAA
* **
234511 ATCGCAACGCGAACTTCGACTATCGCAATG--C--G-ATTT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAATAA
234547 ATCGCAACGCGAACTTCGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
234575 TGCGAATATG
Statistics
Matches: 137, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
36 30 0.22
38 1 0.01
41 1 0.01
42 105 0.77
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAATAA
Found at i:234558 original size:36 final size:36
Alignment explanation
Indices: 234511--234579 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
234501 TTTGTAATAA
234511 ATCGCAACGCGAACTTCGACTATCGCAATGCGATTT
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGATTT
234547 ATCGCAACGCGAACTTCGACTATCGCAATGCGA
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGA
234580 ATATGTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (36 bp):
ATCGCAACGCGAACTTCGACTATCGCAATGCGATTT
Found at i:234614 original size:41 final size:41
Alignment explanation
Indices: 234569--234870 Score: 131
Period size: 41 Copynumber: 7.3 Consensus size: 41
234559 ACTTCGACTA
*
234569 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
* * * * * *
234610 TCGCATTGCGAATCTGGAAA-CTG-ATTTGCGATA-CCGGAGA
1 TCGCATTGCGAATATGTAAATC-GCA-ATGCGATAGTCGAAGT
* * * * * *
234650 TAGCGTTGCGAATTAT-CAACTATCGCAACGCGA-ACTTC-AACT
1 TCGCATTGCGAA-TATGTAA--ATCGCAATGCGATA-GTCGAAGT
*
234692 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 -TCGCATTGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
* * * * * * *
234734 TCGCGTTGCGAATCTGGAAA-CTG-ATTTGCGATACT-GGAGA
1 TCGCATTGCGAATATGTAAATC-GCA-ATGCGATAGTCGAAGT
* * * * * * *
234774 TCGCGTTGCGAATTATCG-ACTATCGCAACGCGA-ACTTGGACT
1 TCGCATTGCGAA-TAT-GTA-AATCGCAATGCGATAGTCGAAGT
*
234816 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 -TCGCATTGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
* *
234858 TCACGTTGCGAAT
1 TCGCATTGCGAAT
234871 CTGGAAACTG
Statistics
Matches: 188, Mismatches: 49, Indels: 48
0.66 0.17 0.17
Matches are distributed among these distances:
40 35 0.19
41 94 0.50
42 33 0.18
43 26 0.14
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (41 bp):
TCGCATTGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
Found at i:234690 original size:21 final size:21
Alignment explanation
Indices: 234665--234704 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
234655 TTGCGAATTA
234665 TCAACTATCGCAACGCGAACT
1 TCAACTATCGCAACGCGAACT
*
234686 TCAACTATCGCAATGCGAA
1 TCAACTATCGCAACGCGAA
234705 TATGTAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAACTATCGCAACGCGAACT
Found at i:234915 original size:124 final size:124
Alignment explanation
Indices: 234546--234916 Score: 670
Period size: 124 Copynumber: 3.0 Consensus size: 124
234536 CAATGCGATT
234546 TATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
1 TATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
* * *
234611 CGCATTGCGAATCTGGAAACTGATTTGCGATACCGGAGATAGCGTTGCGAATTATCAAC
66 CGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGAC
*
234670 TATCGCAACGCGAACTTCAACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
1 TATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
*
234735 CGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGTTGCGAATTATCGAC
66 CGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGAC
*
234794 TATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
1 TATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
* *
234859 CACGTTGCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTTGCGAATTATCGA
66 CGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGA
234917 TCGCATTGCG
Statistics
Matches: 237, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 237 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (124 bp):
TATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTT
CGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGAC
Found at i:239321 original size:18 final size:18
Alignment explanation
Indices: 239298--239349 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
239288 CAAAAAACAT
239298 ATTATATAGTAATTCATA
1 ATTATATAGTAATTCATA
* * *
239316 ATTATATA-T-TTTTATT
1 ATTATATAGTAATTCATA
*
239332 ATTAAATAGTAATTCATA
1 ATTATATAGTAATTCATA
239350 TTAAACTGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
16 11 0.44
17 2 0.08
18 12 0.48
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
ATTATATAGTAATTCATA
Found at i:240654 original size:23 final size:23
Alignment explanation
Indices: 240595--240654 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
240585 GAATATTTTC
*
240595 TAATTTAATTATAATTTTAGATTT
1 TAATTTAA-TATAATTTTAAATTT
240619 T--TTTCAATATAATTTTCAAATTT
1 TAATTT-AATATAATTTT-AAATTT
240642 TAATTTAAT-TAAT
1 TAATTTAATATAAT
240655 ATTATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 12 0.39
23 12 0.39
24 4 0.13
25 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATTTAATATAATTTTAAATTT
Found at i:241430 original size:16 final size:16
Alignment explanation
Indices: 241409--241449 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
241399 TTAAGCGCTG
*
241409 AATGATTCAAATATTA
1 AATGATTCAAATACTA
*
241425 AATGATTCAAATACTG
1 AATGATTCAAATACTA
241441 AATGATTCA
1 AATGATTCA
241450 GAGACTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (16 bp):
AATGATTCAAATACTA
Found at i:244286 original size:10 final size:10
Alignment explanation
Indices: 244271--244311 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
244261 TATTTAAATA
244271 ATAAACGAAC
1 ATAAACGAAC
244281 ATAAACGAAC
1 ATAAACGAAC
** *
244291 ACGAACGAAT
1 ATAAACGAAC
244301 ATAAACGAAC
1 ATAAACGAAC
244311 A
1 A
244312 CAATAAACGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:244299 original size:20 final size:20
Alignment explanation
Indices: 244274--244312 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
244264 TTAAATAATA
244274 AACGAACATAAACGAACACG
1 AACGAACATAAACGAACACG
*
244294 AACGAATATAAACGAACAC
1 AACGAACATAAACGAACAC
244313 AATAAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (20 bp):
AACGAACATAAACGAACACG
Found at i:244607 original size:14 final size:14
Alignment explanation
Indices: 244588--244654 Score: 88
Period size: 14 Copynumber: 5.1 Consensus size: 14
244578 GTCCTCTGTT
244588 CGAACATAAATGAA
1 CGAACATAAATGAA
244602 CGAACAT--A--AA
1 CGAACATAAATGAA
*
244612 CAAACATAAATGAA
1 CGAACATAAATGAA
244626 CGAACATAAATGAA
1 CGAACATAAATGAA
*
244640 CGAACATAAACGAA
1 CGAACATAAATGAA
244654 C
1 C
244655 ATATAATCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 8 0.17
12 2 0.04
14 36 0.78
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:244619 original size:24 final size:24
Alignment explanation
Indices: 244590--244635 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
244580 CCTCTGTTCG
244590 AACATAAATGAACGAACATAAACA
1 AACATAAATGAACGAACATAAACA
244614 AACATAAATGAACGAACATAAA
1 AACATAAATGAACGAACATAAA
244636 TGAACGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.63, C:0.15, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACA
Found at i:252813 original size:20 final size:20
Alignment explanation
Indices: 252790--252827 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
252780 CGGTACTAAC
252790 CCTTAAGTATCGATACTCCA
1 CCTTAAGTATCGATACTCCA
**
252810 CCTTGGGTATCGATACTC
1 CCTTAAGTATCGATACTC
252828 TACAACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (20 bp):
CCTTAAGTATCGATACTCCA
Found at i:254156 original size:7 final size:7
Alignment explanation
Indices: 254144--254170 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
254134 ATTAAATCAC
254144 AAAATTT
1 AAAATTT
254151 AAAATTT
1 AAAATTT
254158 AAAATTT
1 AAAATTT
254165 AAAATT
1 AAAATT
254171 AATTTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:257106 original size:64 final size:66
Alignment explanation
Indices: 257028--257183 Score: 185
Period size: 64 Copynumber: 2.4 Consensus size: 66
257018 CACACCCATT
* * * *
257028 TCGAGTGCATTTTGTGTACCGATGCACAAG-CTATGCATCGATGCACT-CTTGAAT-TTTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACCATGCATCGATGCACTAC-AGAATCATTTGAAA
257090 CA
65 CA
* *
257092 TCGAATGCATTTTGTGTACCGATGCA-TAGACCATGCATCGATGCACTACAGGATCATTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAAGACCATGCATCGATGCACTACAGAATCATTTGAAAC
257156 A
66 A
* * * *
257157 TCGAATGTAATTAGTGTATCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
257184 CCCTAGTGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 44 0.56
65 32 0.41
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (66 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGACCATGCATCGATGCACTACAGAATCATTTGAAAC
A
Found at i:259877 original size:15 final size:15
Alignment explanation
Indices: 259857--259888 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
259847 GTCAATTTTG
259857 TGATAAAGGATACAA
1 TGATAAAGGATACAA
259872 TGATAAAGGATACAA
1 TGATAAAGGATACAA
259887 TG
1 TG
259889 TCTTATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (15 bp):
TGATAAAGGATACAA
Found at i:262663 original size:18 final size:17
Alignment explanation
Indices: 262606--262666 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
262596 TGTCCCGAAT
262606 GACCACTATGTCCAGAAG
1 GACCACTATGTCCA-AAG
* *
262624 GATCACTATGTTTCGAAA-
1 GACCACTATG--TCCAAAG
262642 GACCACTATGTCCTAAAG
1 GACCACTATGTCC-AAAG
262660 GACCACT
1 GACCACT
262667 GATAATCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 25 0.71
19 2 0.06
20 3 0.09
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (17 bp):
GACCACTATGTCCAAAG
Found at i:269490 original size:21 final size:20
Alignment explanation
Indices: 269464--269525 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
269454 GAATGACCAC
269464 TATGTCTAGAAGGACCACTGA
1 TATGTCT-GAAGGACCACTGA
* *
269485 TATGTCCCGAATGACCACT-A
1 TATGT-CTGAAGGACCACTGA
*
269505 TAT-CCTGAAGGACCACTGA
1 TATGTCTGAAGGACCACTGA
269524 TA
1 TA
269526 ATCCCTCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.32
19 3 0.09
20 4 0.12
21 15 0.44
22 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
TATGTCTGAAGGACCACTGA
Found at i:269494 original size:39 final size:39
Alignment explanation
Indices: 269448--269525 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
269438 ACTGAATATT
*
269448 TGTCCCGAATGACCACTATGT-CTAGAAGGACCACTGATA
1 TGTCCCGAATGACCACTATATCCT-GAAGGACCACTGATA
269487 TGTCCCGAATGACCACTATATCCTGAAGGACCACTGATA
1 TGTCCCGAATGACCACTATATCCTGAAGGACCACTGATA
269526 ATCCCTCGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (39 bp):
TGTCCCGAATGACCACTATATCCTGAAGGACCACTGATA
Found at i:269520 original size:18 final size:18
Alignment explanation
Indices: 269458--269521 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
269448 TGTCCCGAAT
*
269458 GACCACTATGT-CTAGAAG
1 GACCACTATATCCT-GAAG
* *
269476 GACCACTGATATGTCCCGAAT
1 GACCACT-ATA--TCCTGAAG
269497 GACCACTATATCCTGAAG
1 GACCACTATATCCTGAAG
269515 GACCACT
1 GACCACT
269522 GATAATCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 20 0.54
19 2 0.05
20 3 0.08
21 11 0.30
22 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (18 bp):
GACCACTATATCCTGAAG
Found at i:270481 original size:22 final size:23
Alignment explanation
Indices: 270438--270486 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
270428 ATCTCACTCA
270438 AATTCCAACATGTTCTAAATC-T
1 AATTCCAACATGTTCTAAATCTT
* *
270460 AATTCTAACAT-TTCGTATATCTT
1 AATTCCAACATGTTC-TAAATCTT
270483 AATT
1 AATT
270487 AAGTCGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTCCAACATGTTCTAAATCTT
Found at i:272063 original size:23 final size:22
Alignment explanation
Indices: 271987--272066 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
271977 ACACTAGACA
*
271987 GTGCATTGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * *
272010 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
* *
272031 GTTCACCGATGCATTCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
*
272054 GCGCATCGATGCA
1 GTGCATCGATGCA
272067 CTCTGCTATG
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 16 0.37
23 27 0.63
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:277071 original size:24 final size:24
Alignment explanation
Indices: 277039--277085 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
277029 TCTACCAATT
**
277039 AAAGTTATGGTCAAAAATTAAAGA
1 AAAGTTATGACCAAAAATTAAAGA
*
277063 AAAGTTATGACCATAAATTAAAG
1 AAAGTTATGACCAAAAATTAAAG
277086 TTATAAGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAGTTATGACCAAAAATTAAAGA
Found at i:277169 original size:164 final size:164
Alignment explanation
Indices: 276883--277236 Score: 541
Period size: 164 Copynumber: 2.2 Consensus size: 164
276873 TATCGATATT
* *
276883 GTCATAAATTAAAGAAAAAGTTACGACCATAAATTAAAGTTATAAGTGAATTTTATTTAACTTTA
1 GTCATAAATTAAAG-AAAAGTTATGACCATAAATTAAAGTTATAAGTGAATTTTATGTAACTTTA
* * * *
276948 TGATTTACATTAATGGTGATAAAAATTGTATTCACTTCATATATAATTTCACATTAATAGTGATA
65 TGATTCACATTAATGGTGATAAAAACTATATTCACTTCATATATAATTTCACATTAATAATGATA
* *
277013 GATGAAAGGTTAATTT-TCTACCAATTAAAGTTATG
130 GATGAAAGGTCAATTTCT-TACAAATTAAAGTTATG
*
277048 GTCAAAAATTAAAGAAAAGTTATGACCATAAATTAAAGTTATAAGTGAATTTT-TCGTAACTTTA
1 GTCATAAATTAAAGAAAAGTTATGACCATAAATTAAAGTTATAAGTGAATTTTAT-GTAACTTTA
* *
277112 TGATTCACATTAATGGTGATAAGAACTATATTCACTTCATATATCATTTCACATTAATAATGATA
65 TGATTCACATTAATGGTGATAAAAACTATATTCACTTCATATATAATTTCACATTAATAATGATA
* *
277177 GGTGAAAGGTCAATTTCTTACAAATTAAAGTTGTG
130 GATGAAAGGTCAATTTCTTACAAATTAAAGTTATG
*
277212 GTCATAAATTAAAGAAAAGATATGA
1 GTCATAAATTAAAGAAAAGTTATGA
277237 TCATGAAGTT
Statistics
Matches: 172, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
163 1 0.01
164 157 0.91
165 14 0.08
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (164 bp):
GTCATAAATTAAAGAAAAGTTATGACCATAAATTAAAGTTATAAGTGAATTTTATGTAACTTTAT
GATTCACATTAATGGTGATAAAAACTATATTCACTTCATATATAATTTCACATTAATAATGATAG
ATGAAAGGTCAATTTCTTACAAATTAAAGTTATG
Found at i:277910 original size:43 final size:43
Alignment explanation
Indices: 277853--277961 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
277843 TTTTTAACTT
* *
277853 TATA-TTCACATTAATGGTGATAAAAATTGTATTCATTTTATA
1 TATATTTCACATTAATGGTGATAAAAATTGTATTCACTTCATA
* * * * *
277895 TATATTTCAAATTAATGGTGGTAAGAATTTTGTTCACTTCATA
1 TATATTTCACATTAATGGTGATAAAAATTGTATTCACTTCATA
*
277938 TATTATTTCACATTAATAGTGATA
1 TA-TATTTCACATTAATGGTGATA
277962 GGTGAAAGGG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 4 0.07
43 33 0.60
44 18 0.33
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (43 bp):
TATATTTCACATTAATGGTGATAAAAATTGTATTCACTTCATA
Found at i:278053 original size:206 final size:206
Alignment explanation
Indices: 277699--278310 Score: 711
Period size: 206 Copynumber: 3.0 Consensus size: 206
277689 ACCATCATAT
* * *
277699 ATTAATGGTGATAAGAATTATATTCACTTCATATATCATTTCACATCAATAATGGTAGGTGAAAG
1 ATTAATGGTGGTAAGAATTATATTCACTTCATATATCATTTCACATTAAT-ATGATAGGTGAAAG
* * * ** * * * *
277764 ATCAATTTCTTATTAACTAAAGTTGTTGTCATAAATTAAAGAAAAAATGATGACCGTAAATTAAA
65 GTCGATTTCCTACCAATTAAAGTTGTGGTCATAAATTAAAG-AAAAATTATGACCATAAATTAAA
* * * *
277829 GTTATGATTGAATTTTTTTAACTTTAT-ATTCACATTAATGGTGATAAAAATTGTATTCATTTTA
129 GTTATGAATGAATTTTTTTAACTTTATGATTCATATTAATGATGATAAAAATTGTATTCATTTCA
*
277893 TATAT-ATTTCAA
194 TATATCACTTCAA
* * *
277905 ATTAATGGTGGTAAGAATTTTGTTCACTTCATATATTATTTCACATTAATAGTGATAGGTGAAAG
1 ATTAATGGTGGTAAGAATTATATTCACTTCATATATCATTTCACATTAATA-TGATAGGTGAAAG
* ** * *
277970 GGCGATTTCCTACCAATTAAAGTCATGGTCATAAATTAAAGAAAAAGTTATGACTATAAAATAAA
65 GTCGATTTCCTACCAATTAAAGTTGTGGTCATAAATTAAAGAAAAA-TTATGACCATAAATTAAA
* * * * *
278035 ATTATGAATGGATTTTTTTAACTTTGTGATTCATGTTAATGATGATAAGAATTGTATTCATTTCA
129 GTTATGAATGAATTTTTTTAACTTTATGATTCATATTAATGATGATAAAAATTGTATTCATTTCA
278100 TATATCACTTCAA
194 TATATCACTTCAA
* * * * *
278113 ATTAATAGTAGTAACAATTGA-ATTCACTTCATATATCATTTCACATTAACA--AT-GGTAGCAA
1 ATTAATGGTGGTAAGAATT-ATATTCACTTCATATATCATTTCACATTAATATGATAGGT-GAAA
*
278174 GGTCGGTTT-CTACCAATTAAAGTTGTGGTCATAAATTAAAGAAAACATTATGACCATAAATTAA
64 GGTCGATTTCCTACCAATTAAAGTTGTGGTCATAAATTAAAGAAAA-ATTATGACCATAAATTAA
* * * *
278238 AGTTAT-AAGTGAATTTTCTTTAACTTTATGATTCATATTAATTATGATAAGAACTGTA-TCACT
128 AGTTATGAA-TGAATTTT-TTTAACTTTATGATTCATATTAATGATGATAAAAATTGTATTCATT
*
278301 TGATATATCA
191 TCATATATCA
278311 TTTTACATTA
Statistics
Matches: 345, Mismatches: 52, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
203 2 0.01
204 77 0.22
205 55 0.16
206 125 0.36
207 37 0.11
208 49 0.14
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (206 bp):
ATTAATGGTGGTAAGAATTATATTCACTTCATATATCATTTCACATTAATATGATAGGTGAAAGG
TCGATTTCCTACCAATTAAAGTTGTGGTCATAAATTAAAGAAAAATTATGACCATAAATTAAAGT
TATGAATGAATTTTTTTAACTTTATGATTCATATTAATGATGATAAAAATTGTATTCATTTCATA
TATCACTTCAA
Found at i:278485 original size:164 final size:160
Alignment explanation
Indices: 278108--278648 Score: 544
Period size: 164 Copynumber: 3.3 Consensus size: 160
278098 CATATATCAC
* * * * * * * *
278108 TTCAAATTAATAGTAGTAACAATTGAATTCACTTCATATATCATTTCACATTAACAATG-GTAGC
1 TTCACATTAATAGTAATAAGAATTGTATTCACTTTATATATCTTTTCACATTAATAATGAGT-GA
** * *
278172 AAGGTCGGTTTCTACCAATTAAAGTTGTGGTCATAAATTAAAGAAAACATTATGACCATAAATTA
65 AAGGTCATTTTCTATCAATTAAAGTTGTGGTCATAAATTAAAGAAAAAATTATGACCATAAATTA
*
278237 AAGTTATAAGTGAATTTTCTTTAACTTTATGA
130 AAG-TATGAGTGAATTTTCTTTAACTTTATGA
* * * *
278269 TTCATATTAATTA-TGATAAGAACTGTA-TCACTTGATATATCATTTT-ACATTAATAATGACAA
1 TTCACATTAA-TAGTAATAAGAATTGTATTCACTTTATATATC-TTTTCACATTAATAATG---A
* * * **
278331 GTGAAAGGTCAATTTTTTATCAATTAAAATTGTGGTCATAAAATAAAAGAAAAAATTATGATTAT
61 GTGAAAGGTC-ATTTTCTATCAATTAAAGTTGTGGTCAT-AAATTAAAGAAAAAATTATGACCAT
278396 AAATTAAAGT-TGAGTGAATTTTCTTTAACTTTATGA
124 AAATTAAAGTATGAGTGAATTTTCTTTAACTTTATGA
*
278432 TTCACAATAATAGTAATAAGAATTGTATTCACTTTATATATCTTTTCACATTAATAATGGTAGCT
1 TTCACATTAATAGTAATAAGAATTGTATTCACTTTATATATCTTTTCACATTAATAAT-G-AG-T
* * * *
278497 GAAAGGTCTATTTCCTATCAATTAAAGTTGTTGTCATAAATTAAA-ACAAAATTATTACCATAAA
63 GAAAGGTC-ATTTTCTATCAATTAAAGTTGTGGTCATAAATTAAAGAAAAAATTATGACCATAAA
* * *
278561 TTAAAATTATGAGTAAATTTTAC---AACTTTATTA
127 TT-AAAGTATGAGTGAATTTT-CTTTAACTTTATGA
* * * * * *
278594 TTCACATTAATGGTGATAAGAATTGTATTTATTTTACATAT-TATTTCAAATTAAT
1 TTCACATTAATAGTAATAAGAATTGTATTCACTTTATATATCT-TTTCACATTAAT
278649 GGTGATAAGA
Statistics
Matches: 317, Mismatches: 46, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
160 24 0.08
161 22 0.07
162 76 0.24
163 69 0.22
164 94 0.30
165 32 0.10
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (160 bp):
TTCACATTAATAGTAATAAGAATTGTATTCACTTTATATATCTTTTCACATTAATAATGAGTGAA
AGGTCATTTTCTATCAATTAAAGTTGTGGTCATAAATTAAAGAAAAAATTATGACCATAAATTAA
AGTATGAGTGAATTTTCTTTAACTTTATGA
Found at i:278684 original size:44 final size:44
Alignment explanation
Indices: 278594--278691 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
278584 AACTTTATTA
* * * *
278594 TTCACATTAATGGTGATAAGAATTGTATTTATTTTACATATTAT
1 TTCACATTAATGGTGATAAGAATTGTATTCACTTCACATATCAT
* * *
278638 TTCAAATTAATGGTGATAAGAATTGTGTTCACTTCATATATCAT
1 TTCACATTAATGGTGATAAGAATTGTATTCACTTCACATATCAT
278682 TTCACATTAA
1 TTCACATTAA
278692 AATTAGTAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (44 bp):
TTCACATTAATGGTGATAAGAATTGTATTCACTTCACATATCAT
Found at i:278818 original size:206 final size:205
Alignment explanation
Indices: 278447--278898 Score: 547
Period size: 206 Copynumber: 2.2 Consensus size: 205
278437 AATAATAGTA
* * * **
278447 ATAAGAATTGTATTCACTTTATATATCTTTTCACATTAATAATGGTAGCTGAAAGGTCTATTTCC
1 ATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAATAGTAGCTGAAAGGTAGATTTCC
* * * *
278512 TATCAATTAAAGTTGTTGTCATAAATTAAAACAAAATTATTACCATAAATTAAAATTATGAGTAA
66 TATCAATTAAAGTTGTGGCCATAAATCAAAACAAAATTATGACCATAAATTAAAATTATGAGTAA
* * * *
278577 ATTTTACAACTTTATTATTCACATTAATGGTGATAAGAATTGTATTTATTTTACATAT-TATTTC
131 ATTTTACAACTTTATGATTCACATTAATAGTGATAAGAATTATATTTA-CTT-CATATATATTTC
278641 AAATTAATGGTG
194 AAATTAATGGTG
* * * *
278653 ATAAGAATTGTGTTCACTTCATATATCATTTCACATTAA-AATTAGTAGGTGAAATGTAGATTTT
1 ATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAA-TAGTAGCTGAAAGGTAGATTTC
* *
278717 CTA-CAAATTAAAGTTGTGGCCATAAATC-AAACAAAAAGTTATGATC-TAAATT-AAGTTATGA
65 CTATC-AATTAAAGTTGTGGCCATAAATCAAAAC-AAAA-TTATGACCATAAATTAAAATTATGA
* ** *
278778 GTGAATTTTTTTAACTTTATGATTCATATTAATAGTGATAAGAATTATATTTACTTCATATATAT
127 GT-AAATTTTACAACTTTATGATTCACATTAATAGTGATAAGAATTATATTTACTTCATATATAT
278843 TTCAAATTAATGGTG
191 TTCAAATTAATGGTG
* * * * *
278858 GTAACAATTATATTCATTTCATATATCATCTCACATTAATA
1 ATAAGAATTGTATTCACTTCATATATCATTTCACATTAATA
278899 GTGATAGGTG
Statistics
Matches: 210, Mismatches: 29, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
204 5 0.02
205 70 0.33
206 129 0.61
207 6 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (205 bp):
ATAAGAATTGTATTCACTTCATATATCATTTCACATTAATAATAGTAGCTGAAAGGTAGATTTCC
TATCAATTAAAGTTGTGGCCATAAATCAAAACAAAATTATGACCATAAATTAAAATTATGAGTAA
ATTTTACAACTTTATGATTCACATTAATAGTGATAAGAATTATATTTACTTCATATATATTTCAA
ATTAATGGTG
Found at i:278853 original size:43 final size:44
Alignment explanation
Indices: 278800--278904 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
278790 AACTTTATGA
* * *
278800 TTCATATTAATAGTGATAAGAATTATATTTACTTCATATAT-AT
1 TTCAAATTAATAGTGATAACAATTATATTCACTTCATATATCAT
* * *
278843 TTCAAATTAATGGTGGTAACAATTATATTCATTTCATATATCAT
1 TTCAAATTAATAGTGATAACAATTATATTCACTTCATATATCAT
* *
278887 CTCACATTAATAGTGATA
1 TTCAAATTAATAGTGATA
278905 GGTGATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 35 0.69
44 16 0.31
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (44 bp):
TTCAAATTAATAGTGATAACAATTATATTCACTTCATATATCAT
Found at i:279213 original size:44 final size:45
Alignment explanation
Indices: 279151--279251 Score: 147
Period size: 44 Copynumber: 2.3 Consensus size: 45
279141 TAACTTTATG
*
279151 ATTT-ACATTAAT-AGTGATAAGAATTGTATTCACTTCATATATA
1 ATTTAACATTAATGAGTGATAAGAATTGAATTCACTTCATATATA
*
279194 ATTTCAA-ATTAATGA-TGATAAGAATTGAATTCACTTCATATATC
1 ATTT-AACATTAATGAGTGATAAGAATTGAATTCACTTCATATATA
279238 ATTTAACATTAATG
1 ATTTAACATTAATG
279252 GTGGTAGGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
43 6 0.12
44 44 0.85
45 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (45 bp):
ATTTAACATTAATGAGTGATAAGAATTGAATTCACTTCATATATA
Found at i:285902 original size:20 final size:21
Alignment explanation
Indices: 285866--285927 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
285856 AAAATTTTAA
* *
285866 TCATGAACCCCAAACTCTAAC
1 TCATTAACCCTAAACTCTAAC
*
285887 TC-TTAGCCCTAAACTCTAA-
1 TCATTAACCCTAAACTCTAAC
* *
285906 TCATTAACCTTAACCTCTAAC
1 TCATTAACCCTAAACTCTAAC
285927 T
1 T
285928 TAAAACCCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.85
21 3 0.09
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (21 bp):
TCATTAACCCTAAACTCTAAC
Found at i:286357 original size:36 final size:32
Alignment explanation
Indices: 286309--286409 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 32
286299 GTCTCCACCA
*
286309 ACCTTCTACCATTCCATGTTTCCTTTTCCACT
1 ACCTTCCACCATTCCATGTTTCCTTTTCCACT
286341 ACCTTCCTTCCACCATTCCATGTTTCCTTTTTCCACT
1 A----CCTTCCACCATTCCATGTTTCC-TTTTCCACT
286378 ACCTTCCACCATTCCATGTTTCCTTCTTCCAC
1 ACCTTCCACCATTCCATGTTTCCTT-TTCCAC
286410 CACAACAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
32 3 0.05
33 28 0.45
36 21 0.34
37 10 0.16
ACGTcount: A:0.15, C:0.41, G:0.03, T:0.42
Consensus pattern (32 bp):
ACCTTCCACCATTCCATGTTTCCTTTTCCACT
Found at i:286435 original size:2 final size:2
Alignment explanation
Indices: 286428--286484 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
286418 TTATTTCTAT
286428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
286469 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
286485 AATGTATTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:290863 original size:37 final size:36
Alignment explanation
Indices: 290822--290898 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
290812 CAAAGGGTCG
* *
290822 TCTCGCTCGAGACAAGTTTTCTTAAAAACAAATTTCA
1 TCTCGCTCGAGACAA-TTTTCTTAAAAACAAAATTAA
* * *
290859 TCTCGGTGGAGACAATTTTCTTTAAAACAAAATTAA
1 TCTCGCTCGAGACAATTTTCTTAAAAACAAAATTAA
290895 TCTC
1 TCTC
290899 ACTTGAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 22 0.63
37 13 0.37
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (36 bp):
TCTCGCTCGAGACAATTTTCTTAAAAACAAAATTAA
Found at i:291118 original size:29 final size:29
Alignment explanation
Indices: 291073--291151 Score: 133
Period size: 29 Copynumber: 2.7 Consensus size: 29
291063 TTTGTCTCTA
*
291073 TTGAGAGA-GTTTCCCTTGAAACATAAACT
1 TTGAGA-ACGTTTTCCTTGAAACATAAACT
291102 TTGAGAACGTTTTCCTTGAAACATAAACT
1 TTGAGAACGTTTTCCTTGAAACATAAACT
291131 TTGAGAACGTTTTCCTTGAAA
1 TTGAGAACGTTTTCCTTGAAA
291152 TGAATTATGT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (29 bp):
TTGAGAACGTTTTCCTTGAAACATAAACT
Found at i:291389 original size:76 final size:77
Alignment explanation
Indices: 291191--291436 Score: 301
Period size: 77 Copynumber: 3.3 Consensus size: 77
291181 CTTCAAACAA
* * * *
291191 AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAATAAGATTT-ATTTCACTCAAGATTG
1 AAGATTTTGTCTCGCTTGAGACAATTTTTACTCAAAACAA-GACATTTCATTTCACTCAAGATTG
*
291255 TTTTTCTTAAAAG
65 TTTTTCTTAAAAC
* * *
291268 AAGATTTTTTCTCGCTTGAGACAATTTTTACTGAAAACAAGACATTTCATTTCACTACATG-TTG
1 AAGATTTTGTCTCGCTTGAGACAATTTTTACTCAAAACAAGACATTTCATTTCACT-CAAGATTG
291332 TTTTTCTTAAAAC
65 TTTTTCTTAAAAC
* * *
291345 AAGA-TTTGTCTCGATTGAGACAATTTTTACTCAAAAGAAGACATTCCA-TTCACTCAAGATTG-
1 AAGATTTTGTCTCGCTTGAGACAATTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTGT
*
291407 -TTT-TT-AAAG
66 TTTTCTTAAAAC
*
291416 AAGATTTTATCTCGCTTGAGA
1 AAGATTTTGTCTCGCTTGAGA
291437 TAGTTTCTCT
Statistics
Matches: 148, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
71 7 0.05
72 16 0.11
73 3 0.02
74 3 0.02
75 9 0.06
76 44 0.30
77 63 0.43
78 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (77 bp):
AAGATTTTGTCTCGCTTGAGACAATTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTGT
TTTTCTTAAAAC
Found at i:292083 original size:39 final size:39
Alignment explanation
Indices: 291414--292081 Score: 778
Period size: 39 Copynumber: 17.3 Consensus size: 39
291404 TTGTTTTTAA
* * *
291414 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
291453 AGGAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
291492 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * **
291531 ATG-AGATTTTGTCTCGCTTGAGACAATTTTTACTC-AAA-
1 A-GAAGATTTTGTCTCGCTTGAGA-TAGTTTCCCTCGAAAC
** * ** ** * *
291569 AGAAGACATTTCATTTTACTCAAGATTGTTT---T--TAA-
1 AGAAG--ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
291604 AGAAGATTTTGTCTTGTTTGATATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
291643 AGAAGATTTTGTCTCGCTTGAGATAGTTCCCCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
291682 AGAATATTTTGTCTAGCTTGAGATAGTTTCTCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
291721 ATAAGATTTTGTCTCGCTTGAGATATTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
291760 AGAAGATTTTGTCACGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
291799 AGAAGATTTTGTCTTGCTTGAGATAGTTTCCCTCGAAAG
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
291838 AGAAGATTTTGTCTCGCTTGAGATAGTTTTCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
291877 AGAAGATTTTGTTTTGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
291916 AAAAGATTTTGTCTCGTTTGTGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
291955 AAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
291994 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
292033 AGAAGATTTTATCTCGATTGGGATAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
292072 AAAAGATTTT
1 AGAAGATTTT
292082 ATAAGAAACT
Statistics
Matches: 535, Mismatches: 83, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
33 15 0.03
35 7 0.01
36 2 0.00
37 1 0.00
38 5 0.01
39 487 0.91
40 18 0.03
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:293374 original size:21 final size:21
Alignment explanation
Indices: 293320--293375 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
293310 GTCCTTGTAC
*
293320 TTATTTTATTTTTATTTGTTAT
1 TTATATTA-TTTTATTTGTTAT
* *
293342 TTATGTTGTTTTATTTGTTAT
1 TTATATTATTTTATTTGTTAT
293363 TT-TAATTATTTTA
1 TTAT-ATTATTTTA
293376 AATAAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTATATTATTTTATTTGTTAT
Found at i:295788 original size:15 final size:15
Alignment explanation
Indices: 295755--295788 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
295745 AAAATAAAAG
**
295755 TATTAAAATAATTTT
1 TATTAAAATAATTAA
295770 TATTAAAATAATTAA
1 TATTAAAATAATTAA
295785 TATT
1 TATT
295789 TACTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAAATAATTAA
Found at i:295892 original size:35 final size:35
Alignment explanation
Indices: 295851--295929 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
295841 TAATGTTAGC
*
295851 AAATATTTTAAAAAAATTAAACTAGTAAACATATT
1 AAATATTTTAAAAAAATCAAACTAGTAAACATATT
*
295886 AAATATTTTAAAAAAATCAAACTAGTACACATATT
1 AAATATTTTAAAAAAATCAAACTAGTAAACATATT
295921 -AAT-TTTTAA
1 AAATATTTTAA
295930 TATATTGCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 6 0.14
34 3 0.07
35 33 0.79
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (35 bp):
AAATATTTTAAAAAAATCAAACTAGTAAACATATT
Found at i:296117 original size:31 final size:31
Alignment explanation
Indices: 296080--296150 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
296070 TCCAAGCGAC
* *
296080 CAAAACTTAATTAAACGATAACGTAAGTGA-
1 CAAAACTTAATAAAACAATAACGTAAGTGAT
*
296110 CACAAACTTAATAAAACAATAATGTAAGTGAT
1 CA-AAACTTAATAAAACAATAACGTAAGTGAT
296142 CAAAACTTA
1 CAAAACTTA
296151 TGTTTTTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 32 0.89
32 2 0.06
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (31 bp):
CAAAACTTAATAAAACAATAACGTAAGTGAT
Found at i:300657 original size:345 final size:346
Alignment explanation
Indices: 299827--300845 Score: 1967
Period size: 345 Copynumber: 3.0 Consensus size: 346
299817 TACTCCATGC
299827 TATTGGTTTAGTCTGTTA-TTTCTCAATCAT-CCGTTATTCACTGCAGAGGTTGTTAATTTATGG
1 TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
299890 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
66 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
299955 TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
131 TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
*
300020 AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCTTAGAATTTTATGTACTTAAAGATGGAAAGC
196 AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCATAGAATTTTATGTACTTAAAGATGGAAAGC
300085 TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
261 TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
*
300150 TTATGAACTTCATAGAATCTT
326 TTATGAACTGCATAGAATCTT
300171 TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
1 TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
300236 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
66 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
300301 TTCTG-TTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
131 TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
300365 AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCATAGAATTTTATGTACTTAAAGATGG-AAGC
196 AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCATAGAATTTTATGTACTTAAAGATGGAAAGC
300429 TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
261 TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
300494 TTATGAACTGCATAGAATCTT
326 TTATGAACTGCATAGAATCTT
300515 TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
1 TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
300580 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
66 TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
300645 TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
131 TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
*
300710 AAGATAAAGTTGAGGGATCATATGTCTGTGTAGCATAGAATTTTATGTACTTAAAGATGGAAAGC
196 AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCATAGAATTTTATGTACTTAAAGATGGAAAGC
*
300775 TACTGCAGAAACTATGCTCTAGTTGTG-CCTTTAATCTTTATGGGGATTGAAATGAACAGCTAGA
261 TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
300839 TTATGAA
326 TTATGAA
300846 TGGCAACAAA
Statistics
Matches: 667, Mismatches: 4, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
344 242 0.36
345 291 0.44
346 134 0.20
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (346 bp):
TATTGGTTTAGTCTGTTATTTTCTCAATCATCCCGTTATTCACTGCAGAGGTTGTTAATTTATGG
TGTTTCTCCTATGAATGGCTTACATAAAACTAGAGGTTAAATAATCTTGTGCTTAAGCCAAGTAA
TTCTGTTTTTTATTTGCCTATTGAAGCCATGCTAGAAGTCATTTCTTTCAGGATAGAAAAAATAA
AAGATAAAGTTGAGGGATCATATGTTTGTGTAGCATAGAATTTTATGTACTTAAAGATGGAAAGC
TACTGCAGAAACTATGCTCTAGTTGTGCCCTTTATTCTTTATGGGGATTGAAATGAACAGCTAGA
TTATGAACTGCATAGAATCTT
Found at i:304821 original size:21 final size:20
Alignment explanation
Indices: 304736--304892 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
304726 AATGACCAAT
** *
304736 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
304755 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
304775 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
304795 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
304816 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
304837 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
304858 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
304878 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
304893 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:304921 original size:20 final size:20
Alignment explanation
Indices: 304859--305103 Score: 246
Period size: 20 Copynumber: 12.2 Consensus size: 20
304849 CGATTTTCCA
* ** *
304859 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
304879 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
304899 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
304919 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
304939 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
304959 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
304979 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
304999 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
305019 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
305039 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
305059 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
305079 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
305099 AAATC
1 AAATC
305104 CGGTAGGGCA
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 188 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:305853 original size:24 final size:24
Alignment explanation
Indices: 305814--305860 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
305804 AAATTTGGTC
305814 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
305838 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
305861 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:306052 original size:12 final size:12
Alignment explanation
Indices: 306035--306059 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
306025 ATATAATCCT
306035 GAAGAAGAAAAA
1 GAAGAAGAAAAA
306047 GAAGAAGAAAAA
1 GAAGAAGAAAAA
306059 G
1 G
306060 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:308208 original size:14 final size:14
Alignment explanation
Indices: 308189--308278 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
308179 TTGAAATGAA
308189 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
308203 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
308222 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
308236 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
308255 AATCGCAACGAGAG
1 AATCGCAACGAGAG
308269 AATCGCAACG
1 AATCGCAACG
308279 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:308226 original size:33 final size:33
Alignment explanation
Indices: 308181--308295 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
308171 TCTTTGGGTT
308181 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
308214 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
308247 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
308280 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
308296 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:308227 original size:19 final size:19
Alignment explanation
Indices: 308203--308300 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
308193 GCAACGAGAG
*
308203 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
308222 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
308236 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
308255 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
308269 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
308288 AATCGCAATGCGA
1 AATCGCAACGCGA
308301 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:308366 original size:20 final size:20
Alignment explanation
Indices: 308319--308375 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
308309 TCGCGTTGCG
***
308319 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
308339 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
308360 ATTCTCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
308376 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:308727 original size:22 final size:22
Alignment explanation
Indices: 308673--308727 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
308663 TGGTTGTGAG
**
308673 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
** *
308695 GGAAATATTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
308717 GGATTTCTTCG
1 GGATTTCTTCG
308728 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:308901 original size:20 final size:20
Alignment explanation
Indices: 308874--309066 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
308864 CTTTAAATAT
*
308874 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
*
308894 CTCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
308915 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
308934 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
308954 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
308974 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
308994 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
309014 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
309034 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
309054 CGCGTTGCGATTT
1 CGCGTTGCGATTT
309067 TGGAAAATCG
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 146 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:309060 original size:60 final size:60
Alignment explanation
Indices: 308873--309188 Score: 196
Period size: 60 Copynumber: 5.2 Consensus size: 60
308863 GCTTTAAATA
* * * * ** * *
308873 TCGCGTTGCGATTTACGGATTCTCGTTGCGATTTACG-GATTATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTG-TTCGCGTTGCGATTTTCAGAT
* * **** * * *
308933 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCAGAT
* * * *
308993 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCAGAT
* * * * * * *
309053 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TGTACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGT-GT-TCGCGTTGCGATTTTC-AGAT
* * * * * *
309116 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGA-TTCTGGGTATCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATTTATGTGT-TCGCGTTGCGATTTTCAGAT
309175 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
309189 TATTGGTCAT
Statistics
Matches: 208, Mismatches: 39, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
59 16 0.08
60 116 0.56
61 31 0.15
62 26 0.12
63 19 0.09
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCAGAT
Found at i:309083 original size:21 final size:21
Alignment explanation
Indices: 309053--309135 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
309043 ATTTTCATAT
*
309053 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
309074 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
309095 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
309116 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
309136 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:309126 original size:42 final size:43
Alignment explanation
Indices: 309033--309131 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
309023 ATTTATGTGT
* *
309033 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
309074 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
309116 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
309132 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:318270 original size:24 final size:24
Alignment explanation
Indices: 318236--318308 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
318226 ATACATTACC
* *
318236 TGAATTCTGTTATGATTTCTGATA
1 TGAATTATGTTATGATTTCTAATA
* * * * *
318260 TGGATTTTGTTCTGATATCTTATA
1 TGAATTATGTTATGATTTCTAATA
*
318284 TGAATTATGTTTTGATTTCTAATA
1 TGAATTATGTTATGATTTCTAATA
318308 T
1 T
318309 CTCCATTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (24 bp):
TGAATTATGTTATGATTTCTAATA
Found at i:322283 original size:22 final size:22
Alignment explanation
Indices: 322255--322313 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
322245 ATGCCTTGTT
322255 TAAAGTTTAGGATTTTAGATTC
1 TAAAGTTTAGGATTTTAGATTC
322277 TAAAGTTTAGGATTTTAGATTC
1 TAAAGTTTAGGATTTTAGATTC
*
322299 TAAAGTTTAGAATTT
1 TAAAGTTTAGGATTT
322314 ATAAACTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (22 bp):
TAAAGTTTAGGATTTTAGATTC
Found at i:323066 original size:21 final size:21
Alignment explanation
Indices: 323041--323095 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
323031 AGGGTTAAGA
323041 CCTTTCGATGAAAGGACTTAAT
1 CCTTTCGATGAAAGGACTT-AT
* *
323063 -CTTTCAATTAAAGGACTTAT
1 CCTTTCGATGAAAGGACTTAT
*
323083 CCTTTTGATGAAA
1 CCTTTCGATGAAA
323096 AGTGTTTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (21 bp):
CCTTTCGATGAAAGGACTTAT
Found at i:326210 original size:38 final size:38
Alignment explanation
Indices: 326159--326236 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
326149 CAATCTTGCC
*
326159 TTTCTCTATCACCGAAAAGAACGAATTTGGAATGAATT
1 TTTCTCTATCACCGAAAAGAACGAATTTGGAAGGAATT
* *
326197 TTTCTCTATCACCGGAAAGAACGAGTTTGGAAGGAATT
1 TTTCTCTATCACCGAAAAGAACGAATTTGGAAGGAATT
326235 TT
1 TT
326237 CTAAGTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (38 bp):
TTTCTCTATCACCGAAAAGAACGAATTTGGAAGGAATT
Found at i:326365 original size:21 final size:21
Alignment explanation
Indices: 326341--326410 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
326331 AAAGGCTAAG
* *
326341 ACCTTTCGATGAAATGACTTA
1 ACCTTTTGATGAAAAGACTTA
* *
326362 ACCTTTTGATTAAAAGACTTC
1 ACCTTTTGATGAAAAGACTTA
* * *
326383 TCCTTTTGATGAAAGGGCTTA
1 ACCTTTTGATGAAAAGACTTA
*
326404 ACTTTTT
1 ACCTTTT
326411 TATAATAGGA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (21 bp):
ACCTTTTGATGAAAAGACTTA
Found at i:328707 original size:21 final size:21
Alignment explanation
Indices: 328683--328722 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
328673 TTTGTTTTTC
328683 TTTTTTAAAA-TATATATAAT
1 TTTTTTAAAATTATATATAAT
*
328703 TTTTTTAAAATTTTATATAA
1 TTTTTTAAAATTATATATAA
328723 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTTAAAATTATATATAAT
Found at i:329422 original size:2 final size:2
Alignment explanation
Indices: 329415--329447 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
329405 CAAGTTTTCC
329415 TA TA TA TA 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 TA TA TA TA T
329448 GAGTGAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:329773 original size:33 final size:34
Alignment explanation
Indices: 329700--329773 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
329690 AAGTTTTCAT
*
329700 AATATATATATATAATTTCAATGATTTTAAATATA
1 AATATATATATATAA-TTCAATGATTTTAAATAAA
*
329735 TATATATATATATAA-TCAATGATTTTACAA-AAA
1 AATATATATATATAATTCAATGATTTTA-AATAAA
329768 AATATA
1 AATATA
329774 AAAAATAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 19 0.54
34 2 0.06
35 14 0.40
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (34 bp):
AATATATATATATAATTCAATGATTTTAAATAAA
Found at i:330231 original size:24 final size:24
Alignment explanation
Indices: 330193--330239 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
330183 ATTATAAATA
* *
330193 TAAAAGTATTCAAATTTTCAAAAAG
1 TAAAAGTATACAAATATT-AAAAAG
330218 TAAAA-TATACAAATATTAAAAA
1 TAAAAGTATACAAATATTAAAAA
330240 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (24 bp):
TAAAAGTATACAAATATTAAAAAG
Found at i:338720 original size:23 final size:23
Alignment explanation
Indices: 338694--338769 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
338684 GGACATTATA
**
338694 TGGCACTACAGTGCATTTCTACG
1 TGGCACTATGGTGCATTTCTACG
* * *
338717 TGGCACTTTGGTGCAATCCTACG
1 TGGCACTATGGTGCATTTCTACG
*
338740 TGGCACTATGGTGCATTTCTAAG
1 TGGCACTATGGTGCATTTCTACG
*
338763 CGGCACT
1 TGGCACT
338770 TCGGTGTATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTATGGTGCATTTCTACG
Found at i:338775 original size:23 final size:23
Alignment explanation
Indices: 338694--338785 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
338684 GGACATTATA
* *
338694 TGGCACTACAGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
338717 TGGCACTTTGGTGCAATCCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
338740 TGGCACTAT-GGTGCATTTCTAAG
1 TGGCACT-TCGGTGCATTTCTACG
* * *
338763 CGGCACTTCGGTGTATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
338786 AGCTGTGGTG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:342537 original size:35 final size:34
Alignment explanation
Indices: 342456--342542 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
342446 AGAATAATTT
*
342456 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
342490 TAAATGATAACAAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
342528 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
342543 ACTGAAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.11
35 26 0.55
36 1 0.02
37 4 0.09
38 11 0.23
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:344902 original size:17 final size:18
Alignment explanation
Indices: 344861--344899 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
344851 ATTATATAAG
344861 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
344878 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
344896 TAAA
1 TAAA
344900 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:352929 original size:16 final size:16
Alignment explanation
Indices: 352910--352949 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
352900 CTTAACATTT
352910 TAAAATATTATAAGAA
1 TAAAATATTATAAGAA
*
352926 TAAAATATTATAATAA
1 TAAAATATTATAAGAA
352942 TAAAATAT
1 TAAAATAT
352950 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAATATTATAAGAA
Found at i:352978 original size:30 final size:30
Alignment explanation
Indices: 352942--353003 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
352932 ATTATAATAA
352942 TAAAATATATTTTATTTTTATCTTAACTTT
1 TAAAATATATTTTATTTTTATCTTAACTTT
*
352972 TAAAATATATTTTATTTTTATCTTAATTTT
1 TAAAATATATTTTATTTTTATCTTAACTTT
353002 TA
1 TA
353004 TTTAACTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (30 bp):
TAAAATATATTTTATTTTTATCTTAACTTT
Found at i:353051 original size:44 final size:43
Alignment explanation
Indices: 352972--353058 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 43
352962 TCTTAACTTT
* *
352972 TAAAATATATTTTATTTTTATCTTAATTTTTATTTAACTTAAA
1 TAAAATATATTTTATTTTTATCTTAATTTTAATTTAAATTAAA
353015 TAAAATATATTTTTATTTTTATCTTAATTTTAATTTAAATTAAA
1 TAAAATATA-TTTTATTTTTATCTTAATTTTAATTTAAATTAAA
353059 AATATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 9 0.22
44 32 0.78
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (43 bp):
TAAAATATATTTTATTTTTATCTTAATTTTAATTTAAATTAAA
Found at i:355894 original size:49 final size:49
Alignment explanation
Indices: 355823--355948 Score: 218
Period size: 49 Copynumber: 2.6 Consensus size: 49
355813 TCCAAATTTC
*
355823 TGAC-TTAGGTTGAATATTCTATTATTCAGGTTAATTCATGCAGAAGTG
1 TGACTTTAGGTTGAATCTTCTATTATTCAGGTTAATTCATGCAGAAGTG
*
355871 TGACTTTAGGTTGAATCTTCTATTATTCAGGTTAATTCATGCAGACGTG
1 TGACTTTAGGTTGAATCTTCTATTATTCAGGTTAATTCATGCAGAAGTG
*
355920 TGACTTTAGGTTGAAACTTCTATTATTCA
1 TGACTTTAGGTTGAATCTTCTATTATTCA
355949 TGTATTTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 4 0.05
49 70 0.95
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (49 bp):
TGACTTTAGGTTGAATCTTCTATTATTCAGGTTAATTCATGCAGAAGTG
Found at i:356791 original size:202 final size:202
Alignment explanation
Indices: 356445--356849 Score: 792
Period size: 202 Copynumber: 2.0 Consensus size: 202
356435 TTTAAAACAT
356445 ATATTTTATTTTTAATATTGTATTTATTTGAAAATTCAAAAACATACTTACAAAATATAATCATG
1 ATATTTTATTTTTAATATTGTATTTATTTGAAAATTCAAAAACATACTTACAAAATATAATCATG
356510 TGTTTATTTTTCATATAGAAAGACGGCAGTTTTATTAAAAATAGAAATATCCAAAATTACAATGA
66 TGTTTATTTTTCATATAGAAAGACGGCAGTTTTATTAAAAATAGAAATATCCAAAATTACAATGA
*
356575 AGATTTACGAGCATAACTATAAATGTAAACAAAATTATAATTAGTTCATTTTCTTATAACCATTA
131 AGATTTACGAGCATAACTATAAATGTAAACAAAATTATAATTAGTTCATTTTCCTATAACCATTA
356640 ACACAAA
196 ACACAAA
356647 ATATTTTATTTTTAATATTGTATTTATTTGAAAATTCAAAAACATACTTACAAAATATAATCATG
1 ATATTTTATTTTTAATATTGTATTTATTTGAAAATTCAAAAACATACTTACAAAATATAATCATG
*
356712 TGTTTATTTTTCATATAGAAAGACGGTAGTTTTATTAAAAATAGAAATATCCAAAATTACAATGA
66 TGTTTATTTTTCATATAGAAAGACGGCAGTTTTATTAAAAATAGAAATATCCAAAATTACAATGA
356777 AGATTTACGAGCATAACTATAAATGTAAACAAAATTATAATTAGTTCATTTTCCTATAACCATTA
131 AGATTTACGAGCATAACTATAAATGTAAACAAAATTATAATTAGTTCATTTTCCTATAACCATTA
356842 ACACAAA
196 ACACAAA
356849 A
1 A
356850 ACTAGCCACC
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
202 201 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (202 bp):
ATATTTTATTTTTAATATTGTATTTATTTGAAAATTCAAAAACATACTTACAAAATATAATCATG
TGTTTATTTTTCATATAGAAAGACGGCAGTTTTATTAAAAATAGAAATATCCAAAATTACAATGA
AGATTTACGAGCATAACTATAAATGTAAACAAAATTATAATTAGTTCATTTTCCTATAACCATTA
ACACAAA
Found at i:361719 original size:21 final size:21
Alignment explanation
Indices: 361695--361746 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
361685 ATACCAAAGA
361695 GAAGACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
*
361716 GAAGACCCTTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
361737 GAAGACCATT
1 GAAGACCATT
361747 TCGCATTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:368112 original size:34 final size:34
Alignment explanation
Indices: 367945--368145 Score: 219
Period size: 35 Copynumber: 5.9 Consensus size: 34
367935 AGCAAAGTCA
*
367945 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAG--AACC
* * * *
367981 ATCTTAAGCCTTCACGGGAGAGTAGTGAAACAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTG-AAGAACC
* * **
368016 ATCTTAAGCTTTCACAGAAGAATAGTGAAGCAGTC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAG-AACC
*
368051 ATCTTAAGCCTTCACAG-A-AGTAGTGAAGTACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGAACC
* *
368083 ATCTTAAGCCTTCACAGAGGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGAACC
*
368117 ATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAA
368146 TCAAATCCAT
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
32 18 0.13
33 9 0.06
34 43 0.31
35 46 0.33
36 22 0.16
37 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (34 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGAACC
Found at i:368748 original size:215 final size:215
Alignment explanation
Indices: 368152--369042 Score: 1419
Period size: 215 Copynumber: 4.1 Consensus size: 215
368142 TGAATCAAAT
*
368152 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
* *
368216 AGAAGATGAAAGTTTTGAAAACGAAGAATGCGATTTTCAAATTTTCACGATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
368281 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
368346 AAGATGATAAGTCCTTCAGG
196 AAGATGATAAGTCATTCGGG
* *
368366 CCATCCATAAGACCTTCGGGTAGGACGTTTTCACATGAATTTG-GAAATGAAAAAAATGATGTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAG-AATG-AAAAAATGATGTTT
* *
368430 TAAGAAGATGAAAATTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTT
64 TAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTT
*
368495 CGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
368560 GCAAGATGATAAGTCATTCGGG
194 GCAAGATGATAAGTCATTCGGG
368582 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
* * *
368647 AGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCATGATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
* * *
368712 GGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCCTT-GGGTCATCTGTAAGCATTCAGAG
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAT-CCTTCGGGTCATCTGTAAGCCTTTAGAG
368776 CAAGATGATAAGTCATTCGGG
195 CAAGATGATAAGTCATTCGGG
* * *
368797 TCATCCATAAAACCTTCGGGTAAGATATTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
* *
368862 AGAAGATGGAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
* * * * * * * * *
368927 GGTCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTTATTTATGAGTCTCTCGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
368992 AAGATGATAAATCCTTCGGG
196 AAGATGATAAGTCATTCGGG
* * *
369012 TCATCCATAAGACCTTCGGGCAGGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTT
369043 GCACCAAGAT
Statistics
Matches: 627, Mismatches: 44, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
214 49 0.08
215 369 0.59
216 208 0.33
217 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (215 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCATTCGGG
Found at i:369173 original size:56 final size:56
Alignment explanation
Indices: 369090--369202 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 56
369080 TTCTCAGAAG
* * * *
369090 AATAGGGAGCAAACTCGTTTTCAGAAGATT-TCTTGAGT-TCTATACTCCCTGAAAGA
1 AATAGGGAGCAAACACATTTGCAGAAGATTAT-TCGAGTCT-TATACTCCCTGAAAGA
*
369146 AATAGGGAGCAAACACATTTGCGGAAGATTATTCGAGTCTTATACTCCCTGAAAGA
1 AATAGGGAGCAAACACATTTGCAGAAGATTATTCGAGTCTTATACTCCCTGAAAGA
369202 A
1 A
369203 TAGAGAACAG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 48 0.96
57 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (56 bp):
AATAGGGAGCAAACACATTTGCAGAAGATTATTCGAGTCTTATACTCCCTGAAAGA
Found at i:369238 original size:55 final size:55
Alignment explanation
Indices: 369124--369254 Score: 147
Period size: 55 Copynumber: 2.3 Consensus size: 55
369114 AAGATTTCTT
* * *
369124 GAGTTCTATACTCCCTGAAAGAAATAGGGAGCAAACACATTTGCGGAAGATTATTC
1 GAGTT-TATACTCCCTGAAAGAAATAGAGAACAAACACATTTGCGGAAGATTATGC
* * * * *
369180 GAGTCTTATACTCCCTGAAAG-AATAGAGAACAGAGACGTTTGTGGAAGATTGTGC
1 GAGT-TTATACTCCCTGAAAGAAATAGAGAACAAACACATTTGCGGAAGATTATGC
*
369235 GAGTTTCATACACCCTGAAA
1 GAGTTT-ATACTCCCTGAAA
369255 ATAGGGAGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
54 2 0.03
55 42 0.66
56 19 0.30
57 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (55 bp):
GAGTTTATACTCCCTGAAAGAAATAGAGAACAAACACATTTGCGGAAGATTATGC
Found at i:371483 original size:30 final size:29
Alignment explanation
Indices: 371448--371507 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
371438 ATTATAAGAA
371448 TAAAATATATTTTATTTTTATCTTAAATTT
1 TAAAATATATTTTATTTTTATCTT-AATTT
371478 TAAAATATATTTTATTTTTATCTTAATTT
1 TAAAATATATTTTATTTTTATCTTAATTT
371507 T
1 T
371508 GATTTAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TAAAATATATTTTATTTTTATCTTAATTT
Found at i:371531 original size:43 final size:42
Alignment explanation
Indices: 371478--371570 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 42
371468 TCTTAAATTT
*
371478 TAAAATATATTTTATTTTTATCTTAATTTTGATTTAACTTAAA
1 TAAAATATATTTTATTTTTATCTTAATTTTAATTTAACTT-AA
371521 TAAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAA
1 TAAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAA
371563 -AAAATATA
1 TAAAATATA
371571 ATATATTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 8 0.16
42 2 0.04
43 39 0.80
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (42 bp):
TAAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAA
Found at i:371673 original size:18 final size:18
Alignment explanation
Indices: 371632--371676 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
371622 AAAATTAAGA
*
371632 TAAAAATAAAAAATATTT
1 TAAAAATTAAAAATATTT
*
371650 T-TAAATTAAAAATATTT
1 TAAAAATTAAAAATATTT
371667 TAAAAATTAA
1 TAAAAATTAA
371677 GATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATTAAAAATATTT
Found at i:371731 original size:47 final size:46
Alignment explanation
Indices: 371603--371735 Score: 136
Period size: 41 Copynumber: 3.0 Consensus size: 46
371593 ATATTTATTT
* *
371603 TTTAATCTAATAATATTTTAAAATTAAGATAAAAATAAAAAATAT-T
1 TTTAATCTAATAATATTTTAAAATTAATAT-AAAATAAAAAATATAC
* *
371649 TTTAAAT-TAAAAATATTTT-AAA--AAT-TAAGAT-AAAAATATAC
1 TTT-AATCTAATAATATTTTAAAATTAATATAAAATAAAAAATATAC
* *
371690 TTTATTCTTATAATATTTTAAAATTAATATAGAAATAAAAAATATA
1 TTTAATCTAATAATATTTTAAAATTAATATA-AAATAAAAAATATA
371736 TTTTTAATGT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
40 10 0.14
41 17 0.24
42 4 0.06
43 2 0.03
44 3 0.04
45 5 0.07
46 17 0.24
47 12 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (46 bp):
TTTAATCTAATAATATTTTAAAATTAATATAAAATAAAAAATATAC
Found at i:379253 original size:20 final size:20
Alignment explanation
Indices: 379219--379256 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
379209 AGTTGCTTAG
379219 GGTTTAAATTGAATAAATTT
1 GGTTTAAATTGAATAAATTT
379239 GGTTTGAAATT-AATAAAT
1 GGTTT-AAATTGAATAAAT
379257 GTGAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (20 bp):
GGTTTAAATTGAATAAATTT
Found at i:383192 original size:13 final size:11
Alignment explanation
Indices: 383162--383201 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
383152 CCTTATTAGT
383162 TAAATAATATA
1 TAAATAATATA
383173 TAAATAATATA
1 TAAATAATATA
383184 TACATATAATAT-
1 TA-A-ATAATATA
383196 TAAATA
1 TAAATA
383202 GTTAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.11
11 14 0.52
12 3 0.11
13 7 0.26
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATAATATA
Found at i:387431 original size:19 final size:18
Alignment explanation
Indices: 387409--387450 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
387399 AACTACTGAT
387409 TCAAATTGACTCAAATAAC
1 TCAAA-TGACTCAAATAAC
* *
387428 TCAAATGATTCGAATAAC
1 TCAAATGACTCAAATAAC
387446 TCAAA
1 TCAAA
387451 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (18 bp):
TCAAATGACTCAAATAAC
Found at i:394692 original size:20 final size:20
Alignment explanation
Indices: 394664--394702 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
394654 AAACATAATT
*
394664 AAATTCTAGAAATACAAAAC
1 AAATCCTAGAAATACAAAAC
*
394684 AAATCCTAGATATACAAAA
1 AAATCCTAGAAATACAAAA
394703 TAAAAGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATCCTAGAAATACAAAAC
Found at i:397734 original size:24 final size:25
Alignment explanation
Indices: 397702--397748 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
397692 CTATTCTTTC
397702 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
397726 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
397749 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:400331 original size:22 final size:22
Alignment explanation
Indices: 400306--400362 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
400296 TTTTTTCTCT
400306 TTTTTTTTCTTTTTCGAAC-ATC
1 TTTTTTTTCTTTTTCGAACTA-C
400328 TTTTTTCTT-TTTTTCGAACTAC
1 TTTTTT-TTCTTTTTCGAACTAC
400350 TATTTTTTTCTTT
1 T-TTTTTTTCTTT
400363 CTCTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.12, C:0.16, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTTTTTCTTTTTCGAACTAC
Found at i:403323 original size:6 final size:6
Alignment explanation
Indices: 403301--403371 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
403291 TGCTTGATCG
* * *
403301 AATAAA AA-AAT AA-AAA AATAAA AATAAA AAT-AA CAT-AA AACAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
* * * *
403345 AACAAA AACAAA AACAAA AACAAA AAT
1 AATAAA AATAAA AATAAA AATAAA AAT
403372 GTAACGGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
5 15 0.26
6 42 0.74
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (6 bp):
AATAAA
Found at i:403331 original size:12 final size:12
Alignment explanation
Indices: 403301--403371 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
403291 TGCTTGATCG
*
403301 AATAAAAA-AAT
1 AATAAAAACAAA
*
403312 AA-AAAAATAAA
1 AATAAAAACAAA
*
403323 AATAAAAA-TAA
1 AATAAAAACAAA
*
403334 CAT-AAAACAAA
1 AATAAAAACAAA
*
403345 AACAAAAACAAA
1 AATAAAAACAAA
*
403357 AACAAAAACAAA
1 AATAAAAACAAA
403369 AAT
1 AAT
403372 GTAACGGGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.18
11 13 0.27
12 27 0.55
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (12 bp):
AATAAAAACAAA
Found at i:403360 original size:18 final size:19
Alignment explanation
Indices: 403306--403370 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 19
403296 GATCGAATAA
* *
403306 AAAAATAAAAAAATAAAA-
1 AAAAACAAAAACATAAAAC
* *
403324 ATAAA-AATAACATAAAAC
1 AAAAACAAAAACATAAAAC
403342 AAAAACAAAAACA-AAAAC
1 AAAAACAAAAACATAAAAC
403360 AAAAACAAAAA
1 AAAAACAAAAA
403371 TGTAACGGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 10 0.25
18 24 0.60
19 6 0.15
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAACAAAAACATAAAAC
Found at i:417008 original size:22 final size:22
Alignment explanation
Indices: 416981--417047 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
416971 CACGCTGAAT
* *
416981 GCTGAACGGTTCAGTGTTCAGC
1 GCTGAACGGTTCAGCGTTCAAC
*
417003 GTTGAACGGTTCAGCGTTCAAC
1 GCTGAACGGTTCAGCGTTCAAC
* * *
417025 GCTGAATGGTTCAACATTCAAC
1 GCTGAACGGTTCAGCGTTCAAC
417047 G
1 G
417048 TTCAACGCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
GCTGAACGGTTCAGCGTTCAAC
Found at i:417016 original size:15 final size:15
Alignment explanation
Indices: 416996--417025 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
416986 ACGGTTCAGT
*
416996 GTTCAGCGTTGAACG
1 GTTCAGCGTTCAACG
417011 GTTCAGCGTTCAACG
1 GTTCAGCGTTCAACG
417026 CTGAATGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (15 bp):
GTTCAGCGTTCAACG
Found at i:417036 original size:15 final size:15
Alignment explanation
Indices: 417018--417065 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
417008 ACGGTTCAGC
417018 GTTCAACGCTGAATG
1 GTTCAACGCTGAATG
** * *
417033 GTTCAACATTCAA-C
1 GTTCAACGCTGAATG
417047 GTTCAACGCTGAATG
1 GTTCAACGCTGAATG
417062 GTTC
1 GTTC
417066 CATTCAACAG
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (15 bp):
GTTCAACGCTGAATG
Found at i:417192 original size:2 final size:2
Alignment explanation
Indices: 417187--417270 Score: 102
Period size: 2 Copynumber: 42.5 Consensus size: 2
417177 CAAGAAAAAA
*
417187 AT AT AT GT AT A- AT AT A- AT GAT AT CAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT
* *
417229 AT AT AT AG AT AT AT AT AT AT AA AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
417270 A
1 A
417271 AACTTAAATG
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.04
2 64 0.90
3 4 0.06
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:420558 original size:21 final size:21
Alignment explanation
Indices: 420534--420594 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
420524 CCAACTTTGA
420534 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
* *
420555 AAAT-G-TTTC----CTT-GA
1 AAATGGTTTTCAAAGTTTGGT
420569 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
420590 AAATG
1 AAATG
420595 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.14
19 4 0.14
20 3 0.10
21 10 0.34
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:420615 original size:36 final size:35
Alignment explanation
Indices: 420528--420643 Score: 182
Period size: 35 Copynumber: 3.3 Consensus size: 35
420518 TGGCAACCAA
420528 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
420563 CCTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
420598 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
420633 -GTTGAAAATGG
1 CTTTGAAAATGG
420644 GAATGGGTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
33 6 0.08
34 3 0.04
35 42 0.56
36 24 0.32
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:421447 original size:9 final size:9
Alignment explanation
Indices: 421433--421461 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
421423 TCTCTCCAGT
421433 ATGTTCGGG
1 ATGTTCGGG
421442 ATGTTCGGG
1 ATGTTCGGG
421451 ATGTTCGGG
1 ATGTTCGGG
421460 AT
1 AT
421462 CTGGTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.14, C:0.10, G:0.41, T:0.34
Consensus pattern (9 bp):
ATGTTCGGG
Found at i:424913 original size:21 final size:21
Alignment explanation
Indices: 424889--424949 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
424879 CCAACTTTGA
424889 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
424910 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
424924 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
424945 AAATG
1 AAATG
424950 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:424922 original size:35 final size:35
Alignment explanation
Indices: 424883--424999 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 35
424873 TGGCAACCAA
424883 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
424918 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
424953 CTTTGAAAAAT-GTTTGGT-AAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTT--TCAAAGTTTGGTAAATGTTT
*
424989 -GTTGAAAATGG
1 CTTTGAAAATGG
425000 GAATGAGTAA
Statistics
Matches: 76, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
34 5 0.07
35 48 0.63
36 22 0.29
37 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:428485 original size:20 final size:19
Alignment explanation
Indices: 428457--428509 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
428447 TTTTGAGTGC
*
428457 GTAGAATCGATACTCTAGCT
1 GTAGTATCGATACTCTAG-T
428477 GTAGTATCGATACTCTAGT
1 GTAGTATCGATACTCTAGT
*
428496 GTAAGTTTCGATAC
1 GT-AGTATCGATAC
428510 CCATGGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (19 bp):
GTAGTATCGATACTCTAGT
Found at i:428594 original size:19 final size:20
Alignment explanation
Indices: 428548--428606 Score: 86
Period size: 19 Copynumber: 3.0 Consensus size: 20
428538 TTCTGTTGCG
428548 GAAAGTATCGATACTC-TGA
1 GAAAGTATCGATACTCTTGA
428567 GGTAAAGTATCGATACTCTTGA
1 -G-AAAGTATCGATACTCTTGA
428589 -AAAGTATCGATACTCTTG
1 GAAAGTATCGATACTCTTG
428607 GCTTGAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 18 0.49
20 1 0.03
21 15 0.41
22 3 0.08
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (20 bp):
GAAAGTATCGATACTCTTGA
Found at i:432721 original size:2 final size:2
Alignment explanation
Indices: 432716--432745 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
432706 TATATATTCA
432716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432746 GAGTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435065 original size:2 final size:2
Alignment explanation
Indices: 435058--435082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
435048 GATGATGTTC
435058 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
435083 TTCTAATCAA
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:437383 original size:31 final size:31
Alignment explanation
Indices: 437345--437407 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
437335 CCCGAAGGAC
*
437345 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
437376 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
437407 C
1 C
437408 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:438456 original size:18 final size:18
Alignment explanation
Indices: 438433--438473 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
438423 ACCGGTCATA
* * *
438433 ACCCGACCTGGCCCGTTT
1 ACCCGACCCGACCCGTTG
438451 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
438469 ACCCG
1 ACCCG
438474 TTGACCGGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.49, G:0.22, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Done.