Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 134 of 226
Found at i:44758255 original size:26 final size:26
Alignment explanation
Indices: 44758218--44758267 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
44758208 TAAAAGAAAA
*
44758218 CATTCAACATTTCAGTTTAATTAGAG
1 CATTCAACATTTCAGTCTAATTAGAG
*
44758244 CATTCAATATTTCAGTCTAATTAG
1 CATTCAACATTTCAGTCTAATTAG
44758268 CATTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (26 bp):
CATTCAACATTTCAGTCTAATTAGAG
Found at i:44764680 original size:26 final size:26
Alignment explanation
Indices: 44764646--44764697 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
44764636 AATAAAAGAA
*
44764646 AACATTCAACATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
*
44764672 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
44764698 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Found at i:44770536 original size:26 final size:26
Alignment explanation
Indices: 44770502--44770553 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
44770492 AATAAAAGAA
*
44770502 AACATTCAATATTTCAGTATAATTAG
1 AACATTCAATATTTCAATATAATTAG
*
44770528 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATATAATTAG
44770554 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAATATAATTAG
Found at i:44772646 original size:26 final size:26
Alignment explanation
Indices: 44772617--44772666 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
44772607 TAAAAGAAAG
*
44772617 CATTCAATATTTCAGTTTAATTAGAA
1 CATTCAATATTTCAGTCTAATTAGAA
44772643 CATTCAATATTTCAGTCTAATTAG
1 CATTCAATATTTCAGTCTAATTAG
44772667 CATTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (26 bp):
CATTCAATATTTCAGTCTAATTAGAA
Found at i:44774800 original size:24 final size:25
Alignment explanation
Indices: 44774772--44774818 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
44774762 TCCGACCCAG
*
44774772 TTTTAGTGGAATATG-AATGGAAGC
1 TTTTAGTGGAATAAGTAATGGAAGC
*
44774796 TTTTAGTGGGATAAGTAATGGAA
1 TTTTAGTGGAATAAGTAATGGAA
44774819 CTTGGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (25 bp):
TTTTAGTGGAATAAGTAATGGAAGC
Found at i:44776224 original size:26 final size:26
Alignment explanation
Indices: 44776190--44776241 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44776180 AATAAAAGAA
*
44776190 AACATTCTATATTTCAGTTTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
44776216 AACATTCTATATTTCAGTCTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
44776242 CACTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (26 bp):
AACATTCTATATTTCAGTCTAATTAG
Found at i:44778346 original size:26 final size:26
Alignment explanation
Indices: 44778312--44778363 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44778302 AATAAAAGAA
*
44778312 AACATTCTATATTTCAGTTTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
44778338 AACATTCTATATTTCAGTCTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
44778364 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (26 bp):
AACATTCTATATTTCAGTCTAATTAG
Found at i:44780560 original size:26 final size:26
Alignment explanation
Indices: 44780531--44780580 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
44780521 AATAAAAGAA
44780531 AACATTCAATATTTCAGTTTAATTTG
1 AACATTCAATATTTCAGTTTAATTTG
44780557 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAGTTTAATT
44780581 AGCATTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTTG
Found at i:44782679 original size:26 final size:26
Alignment explanation
Indices: 44782650--44782699 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
44782640 AATAAAAGAA
44782650 AACATTCAATATTTCAGTTTAATTTG
1 AACATTCAATATTTCAGTTTAATTTG
44782676 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAGTTTAATT
44782700 AGCATTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTTG
Found at i:44784800 original size:26 final size:26
Alignment explanation
Indices: 44784771--44784822 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44784761 AATAAAAGAA
*
44784771 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44784797 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44784823 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:44785761 original size:26 final size:26
Alignment explanation
Indices: 44785732--44785783 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44785722 AATAAAAGAA
*
44785732 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44785758 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44785784 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:44788908 original size:26 final size:26
Alignment explanation
Indices: 44788879--44788928 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
44788869 AATAAAAGAA
*
44788879 AACATTCAATATTTTAGTTTAATTTG
1 AACATTCAATATTTCAGTTTAATTTG
44788905 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAGTTTAATT
44788929 AGCATTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTTG
Found at i:44791118 original size:26 final size:26
Alignment explanation
Indices: 44791089--44791140 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44791079 AATAAAAGAA
*
44791089 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
44791115 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
44791141 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:44796519 original size:26 final size:26
Alignment explanation
Indices: 44796490--44796541 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44796480 AATAAAAGAA
*
44796490 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44796516 AACATTCAATATTTCAGTTGAATTAG
1 AACATTCAATATTTCAGTTGAATTAG
44796542 CATTGATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTGAATTAG
Found at i:44797501 original size:26 final size:26
Alignment explanation
Indices: 44797452--44797501 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44797442 AATAAAAGAA
* *
44797452 AACATTCAATATTTCAGTTTAATTTG
1 AACATTCAATATTTCAATTCAATTTG
*
44797478 AACATTCAGTATTTCAATTCAATT
1 AACATTCAATATTTCAATTCAATT
44797502 AGCATTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (26 bp):
AACATTCAATATTTCAATTCAATTTG
Found at i:44799527 original size:26 final size:26
Alignment explanation
Indices: 44799498--44799549 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44799488 AATAAAAGAA
*
44799498 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
44799524 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
44799550 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:44805466 original size:19 final size:19
Alignment explanation
Indices: 44805442--44805478 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44805432 TATTTTTTTG
*
44805442 TTATAACTTTATAAAATAC
1 TTATAAATTTATAAAATAC
*
44805461 TTATAAATTTTTAAAATA
1 TTATAAATTTATAAAATA
44805479 TATATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATTTATAAAATAC
Found at i:44806326 original size:20 final size:21
Alignment explanation
Indices: 44806290--44806333 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
44806280 TTCCCGTTAT
*
44806290 CTAATAAAAATCTAAAATT-C
1 CTAATAAAAATCCAAAATTGC
44806310 CTAATAATAAA-CCAAAATTGC
1 CTAATAA-AAATCCAAAATTGC
44806331 CTA
1 CTA
44806334 TTTGATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.27
Consensus pattern (21 bp):
CTAATAAAAATCCAAAATTGC
Found at i:44807050 original size:38 final size:38
Alignment explanation
Indices: 44806971--44807051 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
44806961 GTTACAAACG
* *
44806971 TTATCTGTTTTTTACATGTTTATCTCACAAATTTTCTT
1 TTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCGT
* *
44807009 TTATCTGTTTTTTACATGTTTATCTCACTAAGTTTGGT
1 TTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCGT
44807047 TTATC
1 TTATC
44807052 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.57
Consensus pattern (38 bp):
TTATCTGTTTTTTACATGTTTATCTCACAAAGTTTCGT
Found at i:44816316 original size:4 final size:4
Alignment explanation
Indices: 44816307--44816350 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
44816297 TATGTTTTGT
* * * *
44816307 TTTA TTTA TTTA TTTA TGTA TTCA TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
44816351 CTCTTTTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:44819427 original size:3 final size:3
Alignment explanation
Indices: 44819421--44819464 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
44819411 AATATTCCAA
44819421 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44819465 AAAAAGAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:44822165 original size:22 final size:22
Alignment explanation
Indices: 44822142--44822185 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44822132 TTGTTTTTTA
*
44822142 TTTAAAAGAAATTCTAAAAATAT
1 TTTAAAA-AAATTATAAAAATAT
*
44822165 TTTTAAAAAATTATAAAAATA
1 TTTAAAAAAATTATAAAAATA
44822186 CATGAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTAAAAAAATTATAAAAATAT
Found at i:44831018 original size:18 final size:18
Alignment explanation
Indices: 44830969--44831025 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
44830959 ATCCTCTCCT
*
44830969 TCATCTTCACCCTCACCC
1 TCATCTTCACCATCACCC
* * *
44830987 TCAGCCTCTCCATCACCC
1 TCATCTTCACCATCACCC
*
44831005 TCATCTTCAGCATCACCC
1 TCATCTTCACCATCACCC
44831023 TCA
1 TCA
44831026 CTCTCATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.51, G:0.04, T:0.26
Consensus pattern (18 bp):
TCATCTTCACCATCACCC
Found at i:44831026 original size:24 final size:24
Alignment explanation
Indices: 44830975--44831032 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
44830965 TCCTTCATCT
* * *
44830975 TCACCCTCACCCTCAGCCTCTCCA
1 TCACCCTCATCCTCAGCATCACCA
* *
44830999 TCACCCTCATCTTCAGCATCACCC
1 TCACCCTCATCCTCAGCATCACCA
*
44831023 TCACTCTCAT
1 TCACCCTCAT
44831033 TTTGACCATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.52, G:0.03, T:0.26
Consensus pattern (24 bp):
TCACCCTCATCCTCAGCATCACCA
Found at i:44836381 original size:6 final size:7
Alignment explanation
Indices: 44836366--44836390 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44836356 TTTCTCTCTC
44836366 TTTTATT
1 TTTTATT
44836373 TTTTATT
1 TTTTATT
44836380 TTTTATT
1 TTTTATT
44836387 TTTT
1 TTTT
44836391 GCATTTCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:44837201 original size:2 final size:2
Alignment explanation
Indices: 44837194--44837221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44837184 GTATGTGAAC
44837194 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
44837222 GTTAGAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44837381 original size:108 final size:108
Alignment explanation
Indices: 44837201--44837417 Score: 364
Period size: 108 Copynumber: 2.0 Consensus size: 108
44837191 AACATATATA
* *
44837201 TATATATATATATATATATATGTTAGAAACATTGGATATCCTATTAATGGTCTCGGATAGAGTCG
1 TATATATATATATATATATATGTTAGAAACATTGGATATCCTATTAAGGGTCTCGAATAGAGTCG
* *
44837266 GGTATAGATGGCATGTCATAGGATTAGTGTATGAGATTTTTAC
66 GGCATAGATGGCATGTCATAGGATTAGTGTACGAGATTTTTAC
*
44837309 TATATATATATATATATATATGTTAGAAACATTGGATA-CCTTATTAAGGGTCTCGAATAGAGTT
1 TATATATATATATATATATATGTTAGAAACATTGGATATCC-TATTAAGGGTCTCGAATAGAGTC
*
44837373 GGGCATAGATGGCATTTCATAGGATTAGTGTACGAGATTTTTAC
65 GGGCATAGATGGCATGTCATAGGATTAGTGTACGAGATTTTTAC
44837417 T
1 T
44837418 TCAGTTTATA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 2 0.02
108 100 0.98
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (108 bp):
TATATATATATATATATATATGTTAGAAACATTGGATATCCTATTAAGGGTCTCGAATAGAGTCG
GGCATAGATGGCATGTCATAGGATTAGTGTACGAGATTTTTAC
Found at i:44838188 original size:113 final size:113
Alignment explanation
Indices: 44837990--44838218 Score: 458
Period size: 113 Copynumber: 2.0 Consensus size: 113
44837980 TTTGGTATTT
44837990 TGTTTATATGTGATTAATGCTTTAAATCATGTTAGCACCACTGAGTCCTATTTCTCAGTGTACGA
1 TGTTTATATGTGATTAATGCTTTAAATCATGTTAGCACCACTGAGTCCTATTTCTCAGTGTACGA
44838055 TTTTGCTTATTTCCATGTGTAGGTATCGTTAGTCTCGAAGACTCGGGG
66 TTTTGCTTATTTCCATGTGTAGGTATCGTTAGTCTCGAAGACTCGGGG
44838103 TGTTTATATGTGATTAATGCTTTAAATCATGTTAGCACCACTGAGTCCTATTTCTCAGTGTACGA
1 TGTTTATATGTGATTAATGCTTTAAATCATGTTAGCACCACTGAGTCCTATTTCTCAGTGTACGA
44838168 TTTTGCTTATTTCCATGTGTAGGTATCGTTAGTCTCGAAGACTCGGGG
66 TTTTGCTTATTTCCATGTGTAGGTATCGTTAGTCTCGAAGACTCGGGG
44838216 TGT
1 TGT
44838219 GCGATGTTGG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 116 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (113 bp):
TGTTTATATGTGATTAATGCTTTAAATCATGTTAGCACCACTGAGTCCTATTTCTCAGTGTACGA
TTTTGCTTATTTCCATGTGTAGGTATCGTTAGTCTCGAAGACTCGGGG
Found at i:44842610 original size:40 final size:39
Alignment explanation
Indices: 44842556--44842690 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
44842546 ACTAGTTTGG
*
44842556 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGA
* * * * * *
44842596 CAACTAGTGTCTCATCCGCTAAACCGAAGT-A-AATTGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
* * *
44842633 CACCCAATGCCTCATCGAATTAATCCGAAGTAATAAATTCA
1 CACCCAGTGCCTCATCGGA-TAATCCGAAGTAAT-AATTGA
*
44842674 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
44842691 ACTCAAAGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 16 0.22
38 12 0.16
39 2 0.03
40 23 0.32
41 20 0.27
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
Found at i:44855214 original size:8 final size:8
Alignment explanation
Indices: 44855201--44855225 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44855191 TAGAAGCCAC
44855201 AATACTTA
1 AATACTTA
44855209 AATACTTA
1 AATACTTA
44855217 AATACTTA
1 AATACTTA
44855225 A
1 A
44855226 CAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
AATACTTA
Found at i:44868569 original size:23 final size:22
Alignment explanation
Indices: 44868543--44868598 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
44868533 ATTTTTTTTA
44868543 CATTTTTACATGTGTTTTTCA-TG
1 CATTTTTACAT-TG-TTTTCATTG
**
44868566 CATTCATA-ATTGTTTTCATTG
1 CATTTTTACATTGTTTTCATTG
44868587 CATTTTCTACAT
1 CATTTT-TACAT
44868599 ATCTATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 4 0.15
23 8 0.31
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (22 bp):
CATTTTTACATTGTTTTCATTG
Found at i:44881165 original size:15 final size:14
Alignment explanation
Indices: 44881134--44881184 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
44881124 GTTCTTGCTG
44881134 TTTTTTGTTTTTAC
1 TTTTTTGTTTTTAC
44881148 TTTTTTGCTATTTT-C
1 TTTTTTG-T-TTTTAC
*
44881163 TTTGTTTTTTTTTAC
1 TTT-TTTGTTTTTAC
*
44881178 TATTTTG
1 TTTTTTG
44881185 CTACAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 14 0.47
15 9 0.30
16 7 0.23
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (14 bp):
TTTTTTGTTTTTAC
Found at i:44881193 original size:11 final size:11
Alignment explanation
Indices: 44881175--44881217 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
44881165 TGTTTTTTTT
44881175 TACTATTTTGC
1 TACTATTTTGC
* *
44881186 TACAATTTTAC
1 TACTATTTTGC
*
44881197 TACTATGTTGC
1 TACTATTTTGC
44881208 TACTATTTTG
1 TACTATTTTG
44881218 TTGTTATTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.51
Consensus pattern (11 bp):
TACTATTTTGC
Found at i:44881194 original size:22 final size:22
Alignment explanation
Indices: 44881175--44881216 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44881165 TGTTTTTTTT
*
44881175 TACTATTTTGCTACAATTTTAC
1 TACTATGTTGCTACAATTTTAC
*
44881197 TACTATGTTGCTACTATTTT
1 TACTATGTTGCTACAATTTT
44881217 GTTGTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (22 bp):
TACTATGTTGCTACAATTTTAC
Found at i:44887162 original size:26 final size:26
Alignment explanation
Indices: 44887016--44887165 Score: 84
Period size: 26 Copynumber: 6.0 Consensus size: 26
44887006 GTATAACAGA
* *
44887016 AAGCTCA-TAAGAGCCATAT-TCAGG
1 AAGCTCACGAAGAGCCATATATCGGG
* * *
44887040 AAGCTC-CGAATAGTCATATATTGGG
1 AAGCTCACGAAGAGCCATATATCGGG
* * *
44887065 AAGTTCAAG-CGAGCC--ATATCGGG
1 AAGCTCACGAAGAGCCATATATCGGG
* * *
44887088 AAGCT-TCGGAGAGCCAT-TAATCAGG
1 AAGCTCACGAAGAGCCATAT-ATCGGG
* * *
44887113 AAGCTCACAAAGAACC-TTTAATCGGG
1 AAGCTCACGAAGAGCCATAT-ATCGGG
*
44887139 AAGATCACGAAGAGCCATATATCGGG
1 AAGCTCACGAAGAGCCATATATCGGG
44887165 A
1 A
44887166 CGCTAATAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
22 1 0.01
23 16 0.18
24 16 0.18
25 22 0.24
26 34 0.37
27 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (26 bp):
AAGCTCACGAAGAGCCATATATCGGG
Found at i:44891977 original size:14 final size:14
Alignment explanation
Indices: 44891958--44891985 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44891948 CTTGGCTTCC
44891958 ATTTACCTCTTGTA
1 ATTTACCTCTTGTA
44891972 ATTTACCTCTTGTA
1 ATTTACCTCTTGTA
44891986 GCGGGGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTACCTCTTGTA
Found at i:44894587 original size:25 final size:24
Alignment explanation
Indices: 44894557--44894651 Score: 68
Period size: 25 Copynumber: 3.9 Consensus size: 24
44894547 CTCTCTCTCG
44894557 AGCCATATAACAGGAAGCTCATGTT
1 AGCCATATAACAGGAAGCTCAT-TT
* * *
44894582 AGCCATGTAACGGGAAGCTTATTCGT
1 AGCCATATAACAGGAAGCTCATT--T
** **
44894608 -GCTGTATAACAGGAAGCTCATAAG
1 AGCCATATAACAGGAAGCTCAT-TT
*
44894632 AGCCATAT-TCAGGAAGCTCA
1 AGCCATATAACAGGAAGCTCA
44894652 CGAAGAGCCA
Statistics
Matches: 53, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
24 12 0.23
25 40 0.75
26 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (24 bp):
AGCCATATAACAGGAAGCTCATTT
Found at i:44894647 original size:24 final size:25
Alignment explanation
Indices: 44894617--44894664 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
44894607 TGCTGTATAA
*
44894617 CAGGAAGCTCA-TAAGAGCCATATT
1 CAGGAAGCTCACGAAGAGCCATATT
44894641 CAGGAAGCTCACGAAGAGCCATAT
1 CAGGAAGCTCACGAAGAGCCATAT
44894665 ATCGGGACGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (25 bp):
CAGGAAGCTCACGAAGAGCCATATT
Found at i:44895124 original size:16 final size:16
Alignment explanation
Indices: 44895103--44895133 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44895093 ATTTAACTCA
44895103 ATTTAATACAATTCAT
1 ATTTAATACAATTCAT
*
44895119 ATTTAATTCAATTCA
1 ATTTAATACAATTCA
44895134 ATTCACATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAATACAATTCAT
Found at i:44895678 original size:13 final size:13
Alignment explanation
Indices: 44895662--44895689 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44895652 TTTTATTTTA
44895662 TTATTTTTCATCT
1 TTATTTTTCATCT
44895675 TTATTTTTCATCT
1 TTATTTTTCATCT
44895688 TT
1 TT
44895690 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTCATCT
Found at i:44896251 original size:59 final size:59
Alignment explanation
Indices: 44896162--44896279 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
44896152 CGAACATACG
* * *
44896162 CAAACAAACAAATCTGCTAGTGGCGGGGAAATGATCTAAGTCACGTTCCTGCAAGAAAA
1 CAAACAAACAAATCTGCTAGTGGCGAGGAAATGATCTAAGTCACATTCCTACAAGAAAA
* * *
44896221 CAAACAAACAAATGTGTTAGTGGTGAGGAAATGATCTAAGTCACATTCCTACAAGAAAA
1 CAAACAAACAAATCTGCTAGTGGCGAGGAAATGATCTAAGTCACATTCCTACAAGAAAA
44896280 ATTTAGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (59 bp):
CAAACAAACAAATCTGCTAGTGGCGAGGAAATGATCTAAGTCACATTCCTACAAGAAAA
Found at i:44907184 original size:18 final size:18
Alignment explanation
Indices: 44907161--44907195 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44907151 AATTTTGGAA
*
44907161 TGGAGAGATGAGAGAAAG
1 TGGAGAGAAGAGAGAAAG
44907179 TGGAGAGAAGAGAGAAA
1 TGGAGAGAAGAGAGAAA
44907196 ATATGTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.43, T:0.09
Consensus pattern (18 bp):
TGGAGAGAAGAGAGAAAG
Found at i:44907845 original size:18 final size:18
Alignment explanation
Indices: 44907822--44907884 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
44907812 TAAGTGCACT
44907822 TTAATTATTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
* ** **
44907840 TTAATTATTTAAGTGCACT
1 TTAATTATTT-TGTAAAAA
*
44907859 TTAATTTTTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
44907877 TTAATTAT
1 TTAATTAT
44907885 CTTTTCGACA
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (18 bp):
TTAATTATTTTGTAAAAA
Found at i:44907858 original size:37 final size:37
Alignment explanation
Indices: 44907810--44907884 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
44907800 ATGTTCATAT
44907810 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
1 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
*
44907847 TTTAAGTGCACTTTAATTTTTTTGTAAAAATTAATTA
1 TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
44907884 T
1 T
44907885 CTTTTCGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (37 bp):
TTTAAGTGCACTTTAATTATTTTGTAAAAATTAATTA
Found at i:44919185 original size:6 final size:6
Alignment explanation
Indices: 44919174--44919227 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
44919164 TGGTGGAGGG
44919174 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
44919222 ATGTAT
1 ATGTAT
44919228 GTGTGTTGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:44927474 original size:58 final size:59
Alignment explanation
Indices: 44927334--44927499 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 59
44927324 AAGTTCCTAA
* * ** ***
44927334 TTTATTAAATGATACTATGA-AAAAATAATTTGTATTATCTTATTCAAAAGAACTTCTAT
1 TTTATTAAATGACACAAT-ATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
* * *
44927393 TTTATTAAATGACACAATATAAAAATAATTTGTACAAAAATATTCAAAA-CACTTTTGT
1 TTTATTAAATGACACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
* * *
44927451 TTTATTAAATGA-AGCAATATAAAAATAGTTTGTACAAATATATTAAAAA
1 TTTATTAAATGACA-CAATATAAAAATAATTTGTACAAAAATATTCAAAA
44927500 AATCAATGCA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
57 1 0.01
58 51 0.55
59 40 0.43
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (59 bp):
TTTATTAAATGACACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
Found at i:44929451 original size:20 final size:21
Alignment explanation
Indices: 44929423--44929461 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
44929413 ATTAATTAAA
*
44929423 ATTACATAA-ATGAAAAAAAT
1 ATTAAATAATATGAAAAAAAT
*
44929443 ATTAAATAATATTAAAAAA
1 ATTAAATAATATGAAAAAA
44929462 TTGAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
ATTAAATAATATGAAAAAAAT
Found at i:44929467 original size:30 final size:30
Alignment explanation
Indices: 44929396--44929467 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
44929386 ACTGTTATAA
*
44929396 AAAAAATT-ATAAAAAATATTAATTAAAATT
1 AAAAAATTGA-AAAAAATATTAAATAAAATT
* *
44929426 ACATAAA-TGAAAAAAATATTAAATAATATT
1 A-AAAAATTGAAAAAAATATTAAATAAAATT
44929456 AAAAAATTGAAA
1 AAAAAATTGAAA
44929468 TTAACCGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 26 0.74
31 5 0.14
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAAATTGAAAAAAATATTAAATAAAATT
Found at i:44929754 original size:32 final size:32
Alignment explanation
Indices: 44929717--44929791 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
44929707 ATTTTGTTTC
44929717 ATGACCGTTGGCCCCAACAGTCAAATTTTTAA
1 ATGACCGTTGGCCCCAACAGTCAAATTTTTAA
* *
44929749 ATGACCTTTGGCCCGAACAGTCAAATTTTTAA
1 ATGACCGTTGGCCCCAACAGTCAAATTTTTAA
44929781 ATGACCGTTGG
1 ATGACCGTTGG
44929792 AGGTGACTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (32 bp):
ATGACCGTTGGCCCCAACAGTCAAATTTTTAA
Found at i:44932584 original size:16 final size:16
Alignment explanation
Indices: 44932563--44932594 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44932553 GTTTTGTTGC
*
44932563 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
44932579 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
44932595 CTTTCAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:44937591 original size:12 final size:12
Alignment explanation
Indices: 44937576--44937622 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
44937566 AAACCGAGCC
*
44937576 ATAAATGTTTTT
1 ATAAATATTTTT
**
44937588 ATAAATATTTGCC
1 ATAAATATTT-TT
44937601 ATAAATATTTTT
1 ATAAATATTTTT
44937613 ATAAATATTT
1 ATAAATATTT
44937623 ATGGAGTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:44937602 original size:25 final size:25
Alignment explanation
Indices: 44937573--44937622 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
44937563 TTTAAACCGA
*
44937573 GCCATAAATGTTTTTATAAATATTT
1 GCCATAAATATTTTTATAAATATTT
44937598 GCCATAAATATTTTTATAAATATTT
1 GCCATAAATATTTTTATAAATATTT
44937623 ATGGAGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (25 bp):
GCCATAAATATTTTTATAAATATTT
Found at i:44940507 original size:23 final size:23
Alignment explanation
Indices: 44940477--44940721 Score: 325
Period size: 23 Copynumber: 10.8 Consensus size: 23
44940467 GCTATGCCGA
44940477 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
44940500 TCAAGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
44940523 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* *
44940546 TCAGGCACTTTATATGTCGTATA
1 TCAGGCACTTTATGTGTCGTATT
*
44940569 TCAGGAACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
44940592 TCAGGCACCTCGTGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATT
*
44940615 TCAGGCACTTTATGTGTTGTATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
44940638 TCAGGCACCTCGTGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATT
44940661 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
44940684 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATT
44940705 TCAGGCAC-TTATGTGTC
1 TCAGGCACTTTATGTGTC
44940722 ATATACTGAT
Statistics
Matches: 191, Mismatches: 31, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
20 7 0.04
21 8 0.04
23 176 0.92
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:44940544 original size:46 final size:46
Alignment explanation
Indices: 44940476--44940721 Score: 372
Period size: 46 Copynumber: 5.4 Consensus size: 46
44940466 GGCTATGCCG
* * **
44940476 ATCAGGCACTTTATGTGTCGTATTTCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
* * ** *
44940522 TTCAGGCACTTTATGTGTCGTATTTCAGGCACTTTATATGTCGTAT
1 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
*
44940568 ATCAGGAACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
*
44940614 ATCAGGCACTTTATGTGTTGTATTTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
44940660 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
44940704 ATCAGGCAC-TTATGTGTC
1 ATCAGGCACTTTATGTGTC
44940722 ATATACTGAT
Statistics
Matches: 188, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
43 9 0.05
44 10 0.05
46 169 0.90
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (46 bp):
ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTAT
Found at i:44941548 original size:47 final size:48
Alignment explanation
Indices: 44941448--44941568 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 48
44941438 ATTGACGGAA
* * * * *
44941448 AAGACCATGGTTGGACCATGGCAAC-ATGTGATATGTGATTTCCGTAT
1 AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACCGTAT
* * * *
44941495 ATGACCATAGTTGGACTATGGCATCGGTGTGATATGTG-CTACTGTGT
1 AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACCGTAT
*
44941542 AAGACCATAGTTGGACTATGACATCGA
1 AAGACCATAGTTGGACTATGGCATCGA
44941569 GAAAAAAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 50 0.82
48 11 0.18
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (48 bp):
AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACCGTAT
Found at i:44958055 original size:48 final size:48
Alignment explanation
Indices: 44957984--44958078 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
44957974 AAAAAACAAA
44957984 CTTAAATTATTCAAGGCGTTACAACTCTACCCCCTAAAAGAAATTTCG
1 CTTAAATTATTCAAGGCGTTACAACTCTACCCCCTAAAAGAAATTTCG
44958032 CTTAAATTATTCAAGGCGTTACAACTCTACCCCCTAAAAGAAATTTC
1 CTTAAATTATTCAAGGCGTTACAACTCTACCCCCTAAAAGAAATTTC
44958079 AGCCTCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.29
Consensus pattern (48 bp):
CTTAAATTATTCAAGGCGTTACAACTCTACCCCCTAAAAGAAATTTCG
Found at i:44969517 original size:24 final size:24
Alignment explanation
Indices: 44969485--44969545 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
44969475 GTAAATTTTG
*
44969485 TAAAATATATGTAAAATAAATAAT
1 TAAATTATATGTAAAATAAATAAT
* *
44969509 TAAATTATAT-AAAAATCAATAAT
1 TAAATTATATGTAAAATAAATAAT
*
44969532 TAAATAAT-TGTAAA
1 TAAATTATATGTAAA
44969546 TTTTGCAGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.03
23 21 0.68
24 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (24 bp):
TAAATTATATGTAAAATAAATAAT
Found at i:44969835 original size:23 final size:22
Alignment explanation
Indices: 44969809--44969871 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
44969799 TGACTTGAAA
44969809 TTTTATATAATAAAA-TATATATG
1 TTTTATATAATAAAAGTA-A-ATG
* *
44969832 TTTTATTTATAGCTAAAAGTAAATT
1 TTTTA--TATA-ATAAAAGTAAATG
44969857 TTTTATATAATAAAA
1 TTTTATATAATAAAA
44969872 AATTGCAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 5 0.15
23 9 0.27
25 11 0.33
26 6 0.18
27 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTTATATAATAAAAGTAAATG
Found at i:44969916 original size:23 final size:23
Alignment explanation
Indices: 44969890--44969934 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
44969880 GAAATGTTAA
*
44969890 TTTAA-AAGTTTTTTATTTTTATT
1 TTTAAGAA-TTTTTTATATTTATT
44969913 TTTAAGAATTTTTTATATTTAT
1 TTTAAGAATTTTTTATATTTAT
44969935 ACGTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTAAGAATTTTTTATATTTATT
Found at i:44976238 original size:35 final size:35
Alignment explanation
Indices: 44976199--44976279 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
44976189 AATCCTTCCA
* *
44976199 AAACACACCATTGCTCATAAGAGCTAGTCCAACCG
1 AAACACACCAATGCTCAAAAGAGCTAGTCCAACCG
*
44976234 AAACACACCAATGCTCAAAAGAGCTAGTCCCACCG
1 AAACACACCAATGCTCAAAAGAGCTAGTCCAACCG
44976269 AAACACACCAA
1 AAACACACCAA
44976280 ACAAAAAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.12
Consensus pattern (35 bp):
AAACACACCAATGCTCAAAAGAGCTAGTCCAACCG
Found at i:44980160 original size:16 final size:17
Alignment explanation
Indices: 44980129--44980161 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44980119 TTCTAAAAAA
44980129 ATTTATGATAAAATATT
1 ATTTATGATAAAATATT
*
44980146 ATTTAT-ATGAAATATT
1 ATTTATGATAAAATATT
44980162 TGGTTGGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTTATGATAAAATATT
Found at i:44985306 original size:20 final size:20
Alignment explanation
Indices: 44985281--44985358 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
44985271 ATGGATACAT
* *
44985281 AACAGGGGCACTGAAGTGTA
1 AACAGGGACACCGAAGTGTA
* **
44985301 AACAGGGACACCGTAGTGCG
1 AACAGGGACACCGAAGTGTA
* * *
44985321 AATAGAGACACAGAAGTGTA
1 AACAGGGACACCGAAGTGTA
* *
44985341 TACAGGGGCACCGAAGTG
1 AACAGGGACACCGAAGTG
44985359 CAAATCTCGT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.33, T:0.13
Consensus pattern (20 bp):
AACAGGGACACCGAAGTGTA
Found at i:44988995 original size:22 final size:22
Alignment explanation
Indices: 44988978--44989031 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
44988968 TGGCACGTCA
* *
44988978 GTGCTTTCTGTTTAGCACATAT
1 GTGCTCTCTGTATAGCACATAT
*
44989000 GTGCTCTCTGTATAGCAC-TTT
1 GTGCTCTCTGTATAGCACATAT
*
44989021 ATGCTCTCTGT
1 GTGCTCTCTGT
44989032 TCATTAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (22 bp):
GTGCTCTCTGTATAGCACATAT
Found at i:44990835 original size:14 final size:15
Alignment explanation
Indices: 44990808--44990836 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44990798 AATATAGTAA
44990808 AATATTTAAAAAAAT
1 AATATTTAAAAAAAT
44990823 AATATTTAAAAAAA
1 AATATTTAAAAAAA
44990837 GAGATCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATTTAAAAAAAT
Found at i:44991544 original size:29 final size:29
Alignment explanation
Indices: 44991481--44991552 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
44991471 TATAAAGGCT
* * *
44991481 TATTCTTGTAAATTTTTCAAAAATTAGTC
1 TATTTTTGTAAATTTTTCAAAAATAACTC
44991510 TATTTTTGTAATATTTTT-AAAAATAACT-
1 TATTTTTGTAA-ATTTTTCAAAAATAACTC
* *
44991538 TTTTTTTTTAAATTT
1 TATTTTTGTAAATTT
44991553 AGTTTGAGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 4 0.11
28 9 0.24
29 18 0.49
30 6 0.16
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (29 bp):
TATTTTTGTAAATTTTTCAAAAATAACTC
Found at i:44998560 original size:32 final size:31
Alignment explanation
Indices: 44998467--44998597 Score: 107
Period size: 32 Copynumber: 4.3 Consensus size: 31
44998457 TTAATATTCT
* *
44998467 ATTTGGTACCTGAACTTGAC-TTTTTTTCTA
1 ATTTGGTACTTGAACTTGACATTTTTTCCTA
44998497 ATTTGGTACTT--A--T-ACATTTTTTTGTCC-A
1 ATTTGGTACTTGAACTTGACA--TTTTT-TCCTA
44998525 ATTTGGTACTTGAACTTGACATTTTTTCCCTA
1 ATTTGGTACTTGAACTTGACATTTTTT-CCTA
* * **
44998557 ATTTGATA-TCTGAAGTTGACATTTTTTTTTA
1 ATTTGGTACT-TGAACTTGACATTTTTTCCTA
44998588 ATTTGGTACT
1 ATTTGGTACT
44998598 CAATCTTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 24
0.72 0.06 0.21
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
28 18 0.22
29 2 0.02
30 12 0.15
31 17 0.21
32 26 0.32
33 3 0.04
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (31 bp):
ATTTGGTACTTGAACTTGACATTTTTTCCTA
Found at i:44998621 original size:29 final size:31
Alignment explanation
Indices: 44998586--44998656 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
44998576 CATTTTTTTT
44998586 TAATTTGGTA-CTCAATCT-T-TTTTTGGGTC
1 TAATTTGGTACCT-AATCTCTATTTTTGGGTC
**
44998615 TAATTTGGTACCTAATCTCTATTTTTTTGTC
1 TAATTTGGTACCTAATCTCTATTTTTGGGTC
*
44998646 TGATTTGGTAC
1 TAATTTGGTAC
44998657 ATGAATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.42
30 3 0.08
31 18 0.50
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
TAATTTGGTACCTAATCTCTATTTTTGGGTC
Found at i:45002834 original size:21 final size:21
Alignment explanation
Indices: 45002809--45002850 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45002799 TTTTCCAAAT
* *
45002809 ATATGTATTGGATTGAATTGA
1 ATATGAATTGGATTAAATTGA
*
45002830 ATATGAATTGTATTAAATTGA
1 ATATGAATTGGATTAAATTGA
45002851 GTTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATATGAATTGGATTAAATTGA
Found at i:45005978 original size:17 final size:19
Alignment explanation
Indices: 45005946--45005980 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
45005936 AGCATAAGTC
45005946 TAGATTTCATGTCTTATAG
1 TAGATTTCATGTCTTATAG
45005965 TAGATTT-A-GTCTTATA
1 TAGATTTCATGTCTTATA
45005981 CCGACCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (19 bp):
TAGATTTCATGTCTTATAG
Found at i:45007215 original size:30 final size:30
Alignment explanation
Indices: 45007181--45007243 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
45007171 ACTTAACAAG
*
45007181 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
*
45007211 CAAATGCCTTTAAAATAATAACAAAATGAA
1 CAAATGCCTCTAAAATAATAACAAAATGAA
45007241 CAA
1 CAA
45007244 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATGAA
Found at i:45008249 original size:238 final size:239
Alignment explanation
Indices: 45007817--45008290 Score: 598
Period size: 238 Copynumber: 2.0 Consensus size: 239
45007807 AAGTCACTTA
* * *
45007817 ATGTAACACCCCTAACCCATATCTGTCGCCGGAACAGGGTTATGGAGCACTACCAAAATTTACAA
1 ATGTAACACCCCTAACCCATATCTGTCGCCAGAACAGAGTTACGGAGCACTACCAAAATTTACAA
* *
45007882 ATCAAGTAAATAGACATTTCATATCTCTTAACATTCATACCAGAATTCTAACATAATGTCCCTTA
66 ATCAAGTAAACAGACATTTCATATCTCTTAACATTCATACCAGAAATCTAACATAATGTCCCTTA
* * * ****
45007947 AATAAGCCCTCGAGGCCCAAAACATATATTAGAAATAAGTCGGGACTAAAGTGGGTAATTAGAGA
131 AATAAGCCCTCGAGGCCCAAAACATACATTAGAAACAAGTCAGGACTAAACCAAGTAATTAGAGA
* **
45008012 ATTTTTTGTAAAATCTCAAAACTTTTCCAAGGTGCAGGGGACAC
196 ATTTTTTGCAAAATCTCAAAACTTTTCCAAACTGCAGGGGACAC
* * * * ** *
45008056 ATGTAACACCCCTAACCCGTATCTGTTGTCAGAACAGAGTTACGGAGCATTACTGAAATTTATAG
1 ATGTAACACCCCTAACCCATATCTGTCGCCAGAACAGAGTTACGGAGCACTACCAAAATTTACA-
** *
45008121 AA-C-A-TATAACAGACATTTCATATCAT-TTAGTATTCATATCAGAAATC-AATCATAATGTCC
65 AATCAAGTA-AACAGACATTTCATATC-TCTTAACATTCATACCAGAAATCTAA-CATAATGTCC
* * *
45008181 CTTATATGAGCCCTCGAGGCCCAAAACATACATTAGAAACAAGTCAGGACTAAACCAAGTACTTA
127 CTTAAATAAGCCCTCGAGGCCCAAAACATACATTAGAAACAAGTCAGGACTAAACCAAGTAATTA
* * *
45008246 GAGAATTTTTTGCAAAATTTTAAAATTTTTCCAAACTGCAGGGGA
192 GAGAATTTTTTGCAAAATCTCAAAACTTTTCCAAACTGCAGGGGA
45008291 TACACGCCCG
Statistics
Matches: 200, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
237 4 0.02
238 138 0.69
239 56 0.28
240 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (239 bp):
ATGTAACACCCCTAACCCATATCTGTCGCCAGAACAGAGTTACGGAGCACTACCAAAATTTACAA
ATCAAGTAAACAGACATTTCATATCTCTTAACATTCATACCAGAAATCTAACATAATGTCCCTTA
AATAAGCCCTCGAGGCCCAAAACATACATTAGAAACAAGTCAGGACTAAACCAAGTAATTAGAGA
ATTTTTTGCAAAATCTCAAAACTTTTCCAAACTGCAGGGGACAC
Found at i:45008657 original size:13 final size:13
Alignment explanation
Indices: 45008620--45008658 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
45008610 GTGCTAGGAC
* *
45008620 ACACACGGCTGAG
1 ACACACGCCTGTG
*
45008633 ACACACACCTGTG
1 ACACACGCCTGTG
45008646 ACACACGCCTGTG
1 ACACACGCCTGTG
45008659 TGGACGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.23, T:0.13
Consensus pattern (13 bp):
ACACACGCCTGTG
Found at i:45008938 original size:2 final size:2
Alignment explanation
Indices: 45008931--45008959 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45008921 TAAATCTACT
45008931 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 T
45008960 CAAAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45009642 original size:25 final size:25
Alignment explanation
Indices: 45009581--45009725 Score: 111
Period size: 25 Copynumber: 5.8 Consensus size: 25
45009571 ATGCTCATAA
* *
45009581 GAGCACATA-AACGGGAAGCTCTCTCT
1 GAGC-CATATAACGGGAAGCTC-ATGT
45009607 CGAGCCATATAACGGGAAGCTCATGT
1 -GAGCCATATAACGGGAAGCTCATGT
**
45009633 GAGCCATATAACAAGAAGCTCAT-T
1 GAGCCATATAACGGGAAGCTCATGT
** **
45009657 CGAGCTGTATAACGGGAAGCTCATAA
1 -GAGCCATATAACGGGAAGCTCATGT
* * *
45009683 GAGCCATAT-A-GGGAAGTTCAAGC
1 GAGCCATATAACGGGAAGCTCATGT
*
45009706 GAGCCAT-TATCGGGAAGCTC
1 GAGCCATATAACGGGAAGCTC
45009726 TGGAGAACCA
Statistics
Matches: 96, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
22 1 0.01
23 16 0.17
24 10 0.10
25 47 0.49
26 6 0.06
27 16 0.17
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:45009950 original size:24 final size:25
Alignment explanation
Indices: 45009904--45009951 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
45009894 AAAACTGGAA
* *
45009904 GCTCGTGAGAGCCAAATATTGGGAT
1 GCTCATGAGAGCCAAATAATGGGAT
*
45009929 GCTCATGAGAG-CTAATAATGGGA
1 GCTCATGAGAGCCAAATAATGGGA
45009952 AACTCTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (25 bp):
GCTCATGAGAGCCAAATAATGGGAT
Found at i:45010836 original size:18 final size:17
Alignment explanation
Indices: 45010809--45010843 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45010799 AAATGATAAT
45010809 ATTTTTATATTTAATTA
1 ATTTTTATATTTAATTA
*
45010826 ATTTTTCATATTTTATTA
1 ATTTTT-ATATTTAATTA
45010844 TTTCATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATATTTAATTA
Found at i:45018847 original size:26 final size:26
Alignment explanation
Indices: 45018810--45018892 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
45018800 AGGTTCATGC
45018810 GAGCCAA-T-ATCGGGAAGCTCCAGA
1 GAGCCAATTAATCGGGAAGCTCCAGA
*
45018834 GAGCCAATTAATCGAGAAGCT-CATGAAA
1 GAGCCAATTAATCGGGAAGCTCCA-G--A
* *
45018862 GAGCC-TTTAATCGGGAAGCTCCGGA
1 GAGCCAATTAATCGGGAAGCTCCAGA
45018887 GAGCCA
1 GAGCCA
45018893 TATTTCAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 7 0.15
25 9 0.19
26 11 0.23
27 14 0.29
28 7 0.15
ACGTcount: A:0.34, C:0.23, G:0.28, T:0.16
Consensus pattern (26 bp):
GAGCCAATTAATCGGGAAGCTCCAGA
Found at i:45027085 original size:39 final size:41
Alignment explanation
Indices: 45027001--45027090 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
45026991 TAAAAAATAT
** * *
45027001 TTATATTAAAAAACACTACCTTAAATATAATAAATGTTTTC
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
45027042 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
45027081 TTATATTAAA
1 TTATATTAAA
45027091 TATAATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 28 0.62
40 1 0.02
41 16 0.36
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:45027227 original size:22 final size:23
Alignment explanation
Indices: 45027192--45027236 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
45027182 ATTTAATATA
*
45027192 AATATATATATAAT-TATTATTT
1 AATATATATATAATATAATATTT
45027214 AATATAT-TATTAATATAATATTT
1 AATATATATA-TAATATAATATTT
45027237 TTTATAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 11 0.55
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATATATATAATATAATATTT
Found at i:45033645 original size:12 final size:12
Alignment explanation
Indices: 45033628--45033658 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
45033618 ACGGAATGTG
*
45033628 ATATATGTGTAT
1 ATATATATGTAT
45033640 ATATATATGTAT
1 ATATATATGTAT
45033652 ATATATA
1 ATATATA
45033659 AAATGCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:45033647 original size:14 final size:14
Alignment explanation
Indices: 45033628--45033658 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45033618 ACGGAATGTG
*
45033628 ATATATGTGTATAT
1 ATATATGTATATAT
45033642 ATATATGTATATAT
1 ATATATGTATATAT
45033656 ATA
1 ATA
45033659 AAATGCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:45043857 original size:19 final size:19
Alignment explanation
Indices: 45043833--45043875 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
45043823 ATTATTTACA
45043833 TATTTAGGTTAAATATTTT
1 TATTTAGGTTAAATATTTT
45043852 TATTTAGGTTAAATATTTT
1 TATTTAGGTTAAATATTTT
45043871 TATTT
1 TATTT
45043876 TAATAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (19 bp):
TATTTAGGTTAAATATTTT
Found at i:45044104 original size:15 final size:16
Alignment explanation
Indices: 45044072--45044105 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45044062 GCCTTGATTC
*
45044072 TTAAATACTAAAAGAA
1 TTAAATACTAAAAAAA
45044088 TTAAATAC-AAAAAAA
1 TTAAATACTAAAAAAA
45044103 TTA
1 TTA
45044106 TTTAAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
TTAAATACTAAAAAAA
Found at i:45044236 original size:20 final size:20
Alignment explanation
Indices: 45044211--45044250 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
45044201 TTCTAACATG
* *
45044211 AAATTTATTTATTAAATAAT
1 AAATTTATATATAAAATAAT
45044231 AAATTTATATATAAAATAAT
1 AAATTTATATATAAAATAAT
45044251 TTAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTATATATAAAATAAT
Found at i:45049371 original size:24 final size:23
Alignment explanation
Indices: 45049321--45049376 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
45049311 TTCACATACG
45049321 TACATACACTAACAAGAAAACAAT
1 TACATA-ACTAACAAGAAAACAAT
*
45049345 TACATAA-TAACAAGAAATTACATT
1 TACATAACTAACAAGAAA--ACAAT
45049369 TACATAAC
1 TACATAAC
45049377 AAAACACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.36
23 1 0.04
24 17 0.61
ACGTcount: A:0.55, C:0.18, G:0.04, T:0.23
Consensus pattern (23 bp):
TACATAACTAACAAGAAAACAAT
Found at i:45052502 original size:13 final size:13
Alignment explanation
Indices: 45052484--45052523 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
45052474 ATAAACTTTA
45052484 TTTTCAAGTTATG
1 TTTTCAAGTTATG
*
45052497 TTTTCAAGTCATG
1 TTTTCAAGTTATG
45052510 TTTTCAAGTTATG
1 TTTTCAAGTTATG
45052523 T
1 T
45052524 ATTATACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (13 bp):
TTTTCAAGTTATG
Found at i:45056017 original size:23 final size:23
Alignment explanation
Indices: 45055967--45056015 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
45055957 ATGCAAAGAT
* *
45055967 TAAA-TCCTAATTACTAAAGAAA
1 TAAATTCCTAATGACTAAAAAAA
45055989 TAAATTCCTAATGACCTAAAAAAA
1 TAAATTCCTAATGA-CTAAAAAAA
45056013 TAA
1 TAA
45056016 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (23 bp):
TAAATTCCTAATGACTAAAAAAA
Found at i:45078611 original size:20 final size:20
Alignment explanation
Indices: 45078586--45078625 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
45078576 TTTTGAAGAA
45078586 AATTTTAATTTTTAGTGAAT
1 AATTTTAATTTTTAGTGAAT
45078606 AATTTTAATTTTTAGTGAAT
1 AATTTTAATTTTTAGTGAAT
45078626 TTATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
AATTTTAATTTTTAGTGAAT
Found at i:45078636 original size:21 final size:20
Alignment explanation
Indices: 45078592--45078637 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
45078582 AGAAAATTTT
* *
45078592 AATTTTTAGTGAATAATTTT
1 AATTTTTAGTGAATAATATA
*
45078612 AATTTTTAGTGAATTTATATA
1 AATTTTTAGTGAA-TAATATA
45078633 AATTT
1 AATTT
45078638 CAAATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (20 bp):
AATTTTTAGTGAATAATATA
Found at i:45079013 original size:29 final size:30
Alignment explanation
Indices: 45078939--45079010 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
45078929 GACTAAATTA
* *
45078939 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCATGTATATAATTGAACC
* *
45078969 ACAATTAGAGTTTCATGTATATAATT-ACACT
1 A-AATTAAAGTTTCATGTATATAATTGA-ACC
45079000 AAATTAAAGTT
1 AAATTAAAGTT
45079011 CATATAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATATAATTGAACC
Found at i:45079029 original size:27 final size:25
Alignment explanation
Indices: 45078987--45079042 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
45078977 AGTTTCATGT
* *
45078987 ATATAATTACACTAAATTAAAGTTC
1 ATATAATTACACTAAATCAAAATTC
*
45079012 ATATAATTGAACATTAAATCAAAATTC
1 ATATAATT--ACACTAAATCAAAATTC
45079039 ATAT
1 ATAT
45079043 GTAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 8 0.31
27 18 0.69
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATAATTACACTAAATCAAAATTC
Found at i:45079910 original size:11 final size:11
Alignment explanation
Indices: 45079894--45079918 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45079884 TACTTTTTTA
45079894 ATTAAATATAT
1 ATTAAATATAT
45079905 ATTAAATATAT
1 ATTAAATATAT
45079916 ATT
1 ATT
45079919 TTTTTAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAAATATAT
Found at i:45080087 original size:11 final size:11
Alignment explanation
Indices: 45080068--45080099 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
45080058 TTTTATCTGG
*
45080068 ATCTGGCCCGA
1 ATCTAGCCCGA
45080079 ATCTAGCCCGA
1 ATCTAGCCCGA
45080090 ATCTAGCCCG
1 ATCTAGCCCG
45080100 GCCCATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.19
Consensus pattern (11 bp):
ATCTAGCCCGA
Found at i:45080592 original size:3 final size:3
Alignment explanation
Indices: 45080584--45080609 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45080574 TCATAACCTT
45080584 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
45080610 TTACTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:45083925 original size:18 final size:19
Alignment explanation
Indices: 45083887--45083943 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
45083877 TTTTAGAATA
*
45083887 TTATAAAATAATTATTAAAAG
1 TTATAAAA-AA-TAGTAAAAG
*
45083908 TTGTAAAAAATA-TAAAAG
1 TTATAAAAAATAGTAAAAG
*
45083926 TTATTAAAAATAGTAAAA
1 TTATAAAAAATAGTAAAA
45083944 AAATTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.50
19 7 0.22
20 2 0.06
21 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
TTATAAAAAATAGTAAAAG
Found at i:45084013 original size:9 final size:9
Alignment explanation
Indices: 45084001--45084055 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
45083991 CTAAAAATAA
*
45084001 TATATAAAT
1 TATAAAAAT
45084010 TATAAAATAT
1 TATAAAA-AT
*
45084020 TA-AAAAAC
1 TATAAAAAT
45084028 TATAAAAAT
1 TATAAAAAT
45084037 TATAAAAAAT
1 TAT-AAAAAT
*
45084047 TATTAAAAT
1 TATAAAAAT
45084056 AGTCTATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.08
9 23 0.59
10 13 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
TATAAAAAT
Found at i:45084035 original size:19 final size:20
Alignment explanation
Indices: 45083992--45084056 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 20
45083982 TAAGAAATCC
* *
45083992 TAAAAATA-ATATATAAATTA
1 TAAAAATATATA-AAAAACTA
45084012 T-AAAATAT-TAAAAAACTA
1 TAAAAATATATAAAAAACTA
*
45084030 TAAAAAT-TATAAAAAATTA
1 TAAAAATATATAAAAAACTA
*
45084049 TTAAAATA
1 TAAAAATA
45084057 GTCTATTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.22
19 28 0.76
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAATATATAAAAAACTA
Found at i:45084036 original size:27 final size:28
Alignment explanation
Indices: 45083992--45084048 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
45083982 TAAGAAATCC
* *
45083992 TAAAAATAATATATAAATTATAAAATAT
1 TAAAAATAATATAAAAATTATAAAAAAT
*
45084020 TAAAAA-ACTATAAAAATTATAAAAAAT
1 TAAAAATAATATAAAAATTATAAAAAAT
45084047 TA
1 TA
45084049 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAAAATAATATAAAAATTATAAAAAAT
Found at i:45088465 original size:31 final size:30
Alignment explanation
Indices: 45088332--45088725 Score: 167
Period size: 31 Copynumber: 12.8 Consensus size: 30
45088322 TACATAGTTA
** * *
45088332 CTGAATTGATTCATATATGGTTGTACATTG
1 CTGAATTGATTTGTATATGATTATACATTG
* * * *
45088362 CTGGAATTAATTTGTACATGGTTATATATTG
1 CT-GAATTGATTTGTATATGATTATACATTG
* * * * *
45088393 AC-GAAATTGAATTGTTTATGAATATAGGA-AG
1 -CTG-AATTGATTTGTATATGATTATA-CATTG
* *
45088424 CCGAGTTTGATTTGTATATGATTATACATTG
1 CTGA-ATTGATTTGTATATGATTATACATTG
* * * *
45088455 CTGAACTTGATTCGTGTATGGTTATGCATTG
1 CTGAA-TTGATTTGTATATGATTATACATTG
* *
45088486 CCGAATTG-TTTGGTATATGAATATA-AGTTG
1 CTGAATTGATTT-GTATATGATTATACA-TTG
* * * *
45088516 CTTAATTGATTCGTATATGGTTGTACATTG
1 CTGAATTGATTTGTATATGATTATACATTG
* * * * *
45088546 TTGGAATTAATTTGTACATGGTTATATATTG
1 CT-GAATTGATTTGTATATGATTATACATTG
* * * * * *
45088577 -TCAAAGTTGAATTGTTTATGAATATAGGA-AG
1 CT-GAA-TTGATTTGTATATGATTATA-CATTG
*
45088608 CCGAATTTGATTTGTATATGATTATACATTG
1 CTGAA-TTGATTTGTATATGATTATACATTG
* * *
45088639 CCGAACTTGATTTGTGTATGGTTATACATTG
1 CTGAA-TTGATTTGTATATGATTATACATTG
*
45088670 AC-GAATTG-TTTGGTATATTGA-TATTCATTG
1 -CTGAATTGATTT-GTATA-TGATTATACATTG
* * *
45088700 CTGAATTGGATTCGTTTATGAATATA
1 CTGAATT-GATTTGTATATGATTATA
45088726 TATATATATT
Statistics
Matches: 268, Mismatches: 72, Indels: 47
0.69 0.19 0.12
Matches are distributed among these distances:
29 7 0.03
30 68 0.25
31 187 0.70
32 6 0.02
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (30 bp):
CTGAATTGATTTGTATATGATTATACATTG
Found at i:45088647 original size:184 final size:184
Alignment explanation
Indices: 45088335--45088687 Score: 618
Period size: 184 Copynumber: 1.9 Consensus size: 184
45088325 ATAGTTACTG
45088335 AATTGATTCATATATGGTTGTACATTGCTGGAATTAATTTGTACATGGTTATATATTGACGAAAT
1 AATTGATTCATATATGGTTGTACATTGCTGGAATTAATTTGTACATGGTTATATATTGACGAAAT
* *
45088400 TGAATTGTTTATGAATATAGGAAGCCGAGTTTGATTTGTATATGATTATACATTGCTGAACTTGA
66 TGAATTGTTTATGAATATAGGAAGCCGAATTTGATTTGTATATGATTATACATTGCCGAACTTGA
* *
45088465 TTCGTGTATGGTTATGCATTGCCGAATTGTTTGGTATATGAATATAAGTTGCTT
131 TTCGTGTATGGTTATACATTGACGAATTGTTTGGTATATGAATATAAGTTGCTT
* * *
45088519 AATTGATTCGTATATGGTTGTACATTGTTGGAATTAATTTGTACATGGTTATATATTGTC-AAAG
1 AATTGATTCATATATGGTTGTACATTGCTGGAATTAATTTGTACATGGTTATATATTGACGAAA-
45088583 TTGAATTGTTTATGAATATAGGAAGCCGAATTTGATTTGTATATGATTATACATTGCCGAACTTG
65 TTGAATTGTTTATGAATATAGGAAGCCGAATTTGATTTGTATATGATTATACATTGCCGAACTTG
*
45088648 ATTTGTGTATGGTTATACATTGACGAATTGTTTGGTATAT
130 ATTCGTGTATGGTTATACATTGACGAATTGTTTGGTATAT
45088688 TGATATTCAT
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 3 0.02
184 157 0.98
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (184 bp):
AATTGATTCATATATGGTTGTACATTGCTGGAATTAATTTGTACATGGTTATATATTGACGAAAT
TGAATTGTTTATGAATATAGGAAGCCGAATTTGATTTGTATATGATTATACATTGCCGAACTTGA
TTCGTGTATGGTTATACATTGACGAATTGTTTGGTATATGAATATAAGTTGCTT
Found at i:45101631 original size:41 final size:41
Alignment explanation
Indices: 45101579--45101698 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
45101569 GAAAACGCCG
* *
45101579 CAAAAGATTAGAGCTATAGTGGCATTTTTTCATAAACACTGTA
1 CAAACGATTAGAGCTATAGTGGCATTTTTTCATAAACAC--CA
* *
45101622 -AAATG-TTAGAGCTATAGTGACATTTTTTCATAAACACCA
1 CAAACGATTAGAGCTATAGTGGCATTTTTTCATAAACACCA
* *
45101661 CAAACGATTAGAGCTATAGCGGCGTTTTTATCATAAAC
1 CAAACGATTAGAGCTATAGTGGCATTTTT-TCATAAAC
45101699 GTTGCAAAAG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 4 0.06
41 50 0.75
42 12 0.18
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
CAAACGATTAGAGCTATAGTGGCATTTTTTCATAAACACCA
Found at i:45102078 original size:31 final size:31
Alignment explanation
Indices: 45102040--45102104 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45102030 TTTTTCCCTA
*
45102040 TCTGCTGCACTGCCGTCGCCATCAAAAGTCC
1 TCTGCTGCACTGCCGTCGCCATCAAAAGCCC
* *
45102071 TCTGCTGCACTGCCGTCGCCGTCGAAAGCCC
1 TCTGCTGCACTGCCGTCGCCATCAAAAGCCC
45102102 TCT
1 TCT
45102105 ACTACATCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.15, C:0.40, G:0.22, T:0.23
Consensus pattern (31 bp):
TCTGCTGCACTGCCGTCGCCATCAAAAGCCC
Found at i:45102117 original size:31 final size:31
Alignment explanation
Indices: 45102047--45102119 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
45102037 CTATCTGCTG
* * *
45102047 CACTGCCGTCGCCATCAAAAGTCCTCTGCTG
1 CACTGCCGTCGCCATCAAAAGCCCTCTACTA
* *
45102078 CACTGCCGTCGCCGTCGAAAGCCCTCTACTA
1 CACTGCCGTCGCCATCAAAAGCCCTCTACTA
45102109 CA-TCGCCGTCG
1 CACT-GCCGTCG
45102120 AAAGTCCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.18, C:0.41, G:0.21, T:0.21
Consensus pattern (31 bp):
CACTGCCGTCGCCATCAAAAGCCCTCTACTA
Found at i:45102142 original size:25 final size:25
Alignment explanation
Indices: 45102089--45102150 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
45102079 ACTGCCGTCG
* *
45102089 CCGTCGAAAGCCCTCTACTACATCG
1 CCGTCGAAAGTCCTCTACTACATCA
** *
45102114 CCGTCGAAAGTCCTCTGTTGCATCA
1 CCGTCGAAAGTCCTCTACTACATCA
*
45102139 CCGTCGACAGTC
1 CCGTCGAAAGTC
45102151 TGCTGCAACG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (25 bp):
CCGTCGAAAGTCCTCTACTACATCA
Found at i:45102896 original size:12 final size:12
Alignment explanation
Indices: 45102879--45102912 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
45102869 TGTGATCATG
45102879 TTATAAAGGAAT
1 TTATAAAGGAAT
45102891 TTATAAAGGAAT
1 TTATAAAGGAAT
45102903 TTATAAAGGA
1 TTATAAAGGA
45102913 TTGTGGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (12 bp):
TTATAAAGGAAT
Found at i:45103200 original size:21 final size:21
Alignment explanation
Indices: 45103176--45103220 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
45103166 ACGAAAACAC
*
45103176 TATAAGTAAACCATGTTATTA
1 TATAAGTAAACCAGGTTATTA
45103197 TATAAGTAAACCAGGTTATTA
1 TATAAGTAAACCAGGTTATTA
45103218 TAT
1 TAT
45103221 CTTTGTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
TATAAGTAAACCAGGTTATTA
Found at i:45104580 original size:66 final size:65
Alignment explanation
Indices: 45104478--45104615 Score: 170
Period size: 66 Copynumber: 2.1 Consensus size: 65
45104468 ACAAATTGCT
** * *
45104478 CAACTTAAAGCGGAGGAAGCATTGAGAGAAGCAGAGGCTCAA-AGAAAATATGATGAACTCCAGC
1 CAACTTAAAGCGGAGGAAGCAGCGAGAGAAGCAGAGG--CAACAAAAAATATGACGAACTCCAGC
45104542 TA
64 TA
* * * *
45104544 CAACTTAAAGCGGAGGCAGTAGCGAGGGAAGTAGAGGCAAGCAAAAAATATGACGAACTCCAGCT
1 CAACTTAAAGCGGAGGAAGCAGCGAGAGAAGCAGAGGCAA-CAAAAAATATGACGAACTCCAGCT
45104609 A
65 A
45104610 CAACTT
1 CAACTT
45104616 CAGAATATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 3 0.05
66 59 0.95
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.14
Consensus pattern (65 bp):
CAACTTAAAGCGGAGGAAGCAGCGAGAGAAGCAGAGGCAACAAAAAATATGACGAACTCCAGCTA
Found at i:45104708 original size:27 final size:25
Alignment explanation
Indices: 45104674--45104725 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
45104664 ACTTTTGTTT
45104674 ATTTTCTGACAGAAAATTTTAATTATA
1 ATTTTCTGAC--AAAATTTTAATTATA
*
45104701 ATTTTCTGTCAAAATTTTAATTATA
1 ATTTTCTGACAAAATTTTAATTATA
45104726 TGACAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.62
27 9 0.38
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (25 bp):
ATTTTCTGACAAAATTTTAATTATA
Found at i:45104832 original size:27 final size:27
Alignment explanation
Indices: 45104802--45104859 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
45104792 GAGAAATTAT
45104802 TTAAA-AAATATAATTTTTAAAAT-GATA
1 TTAAATAAAT-TAATTTTTAAAATAGA-A
*
45104829 TTAAATAAATTATTTTTTAAAATAGAA
1 TTAAATAAATTAATTTTTAAAATAGAA
45104856 TTAA
1 TTAA
45104860 TGACGTGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
TTAAATAAATTAATTTTTAAAATAGAA
Found at i:45113611 original size:29 final size:29
Alignment explanation
Indices: 45113569--45113627 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
45113559 ACAATTGACC
*
45113569 ATTGTCTAATACCACCATTTAAATCGCAT
1 ATTGTCTAATACCACCATTTAAACCGCAT
45113598 ATTGTCTAATACCACCATTTAAACCGCAT
1 ATTGTCTAATACCACCATTTAAACCGCAT
45113627 A
1 A
45113628 CATGCTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
ATTGTCTAATACCACCATTTAAACCGCAT
Found at i:45114767 original size:118 final size:118
Alignment explanation
Indices: 45114559--45114798 Score: 462
Period size: 118 Copynumber: 2.0 Consensus size: 118
45114549 ATTTATAGAT
*
45114559 GTTTATCCATATATGAGTTTGTGTACCTAATGAACCATAATAGTGAAACCTTTGATAAATTTGAA
1 GTTTACCCATATATGAGTTTGTGTACCTAATGAACCATAATAGTGAAACCTTTGATAAATTTGAA
45114624 GTGTTTCGGGTGGAAGTGGAGAAACAACTAGGTTTACCCATAGAGGCATTTAG
66 GTGTTTCGGGTGGAAGTGGAGAAACAACTAGGTTTACCCATAGAGGCATTTAG
45114677 GTTTACCCATATATGAGTTTGTGTACCTAATGAACCATAATAGTGAAACCTTTGATAAATTTGAA
1 GTTTACCCATATATGAGTTTGTGTACCTAATGAACCATAATAGTGAAACCTTTGATAAATTTGAA
*
45114742 GTGTTTCGGGTGGAAGTGGAGAAACAACTAGGTTTACCCATAGAGGCATTTTG
66 GTGTTTCGGGTGGAAGTGGAGAAACAACTAGGTTTACCCATAGAGGCATTTAG
45114795 GTTT
1 GTTT
45114799 GATTGAGGTG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (118 bp):
GTTTACCCATATATGAGTTTGTGTACCTAATGAACCATAATAGTGAAACCTTTGATAAATTTGAA
GTGTTTCGGGTGGAAGTGGAGAAACAACTAGGTTTACCCATAGAGGCATTTAG
Found at i:45117432 original size:54 final size:54
Alignment explanation
Indices: 45117339--45117500 Score: 139
Period size: 54 Copynumber: 3.0 Consensus size: 54
45117329 AATCGAATAA
* * * * *
45117339 AGGGACACACTGCCATGTC-CTAGCCCGTGT-CTCAAATCGTGTAACTCACTGAGT
1 AGGGACACACGGCCGTGTCGC-AGGCCGTGTGC-CAGATCGTGTAACTCACTGACT
* ** * *
45117393 AGGGTCACGTGGCCGTGTCGCAGGCCGTGTGCCAGATCGTATAACTCTCTGACT
1 AGGGACACACGGCCGTGTCGCAGGCCGTGTGCCAGATCGTGTAACTCACTGACT
* * * * ** *
45117447 TGTGACACACGGCCGTGTTGCAGGCCGTGTGCTAGGCCGTGTAACACACTGACT
1 AGGGACACACGGCCGTGTCGCAGGCCGTGTGCCAGATCGTGTAACTCACTGACT
45117501 TGGTATACCA
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
54 82 0.98
55 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (54 bp):
AGGGACACACGGCCGTGTCGCAGGCCGTGTGCCAGATCGTGTAACTCACTGACT
Found at i:45117474 original size:12 final size:13
Alignment explanation
Indices: 45117457--45117488 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
45117447 TGTGACACAC
45117457 GGCCGTGTTGC-A
1 GGCCGTGTTGCTA
45117469 GGCCGTG-TGCTA
1 GGCCGTGTTGCTA
45117481 GGCCGTGT
1 GGCCGTGT
45117489 AACACACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 15 0.83
ACGTcount: A:0.06, C:0.25, G:0.44, T:0.25
Consensus pattern (13 bp):
GGCCGTGTTGCTA
Found at i:45124801 original size:21 final size:21
Alignment explanation
Indices: 45124776--45124835 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
45124766 ATATATATAT
45124776 GTTCTATAAGCTGAATTTTAC
1 GTTCTATAAGCTGAATTTTAC
*
45124797 GTTCTATAAGCTGAATTTTAT
1 GTTCTATAAGCTGAATTTTAC
*
45124818 GTTCTATAAGCTAAATTT
1 GTTCTATAAGCTGAATTT
45124836 GATTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (21 bp):
GTTCTATAAGCTGAATTTTAC
Found at i:45125158 original size:2 final size:2
Alignment explanation
Indices: 45125151--45125187 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
45125141 ATTGAATGAA
*
45125151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45125188 ANNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:45127967 original size:45 final size:45
Alignment explanation
Indices: 45127886--45128067 Score: 226
Period size: 45 Copynumber: 4.1 Consensus size: 45
45127876 AACAGAGACA
* * * *
45127886 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAATGATACT
1 CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACC
* * * * *
45127929 CGGTGAAATTAGCACATAGAAACCACCTTCATAATCAAT-AGTACC
1 CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGA-TACC
**
45127974 TAGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACC
1 CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACC
*
45128019 CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACC
45128064 CGGT
1 CGGT
45128068 ACACGTAGTA
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 5 0.04
44 12 0.10
45 100 0.85
46 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (45 bp):
CGGTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACC
Found at i:45137723 original size:2 final size:2
Alignment explanation
Indices: 45137716--45137774 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
45137706 NNNNNNNNNN
45137716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45137758 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
45137775 CTTATAGTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45138212 original size:16 final size:15
Alignment explanation
Indices: 45138183--45138211 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45138173 GGGTATAGTA
45138183 AAATATTTTAAAAAT
1 AAATATTTTAAAAAT
45138198 AAATATTTTAAAAA
1 AAATATTTTAAAAA
45138212 AAGAAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTTTAAAAAT
Found at i:45150663 original size:20 final size:20
Alignment explanation
Indices: 45150638--45150683 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
45150628 AGAACAAGCT
45150638 GCTTTTGGCTGAAATTTTTA
1 GCTTTTGGCTGAAATTTTTA
45150658 GCTTTTGGCTGAAATTTTTA
1 GCTTTTGGCTGAAATTTTTA
45150678 GCTTTT
1 GCTTTT
45150684 CAGAAGTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
GCTTTTGGCTGAAATTTTTA
Found at i:45151215 original size:13 final size:13
Alignment explanation
Indices: 45151195--45151298 Score: 120
Period size: 13 Copynumber: 8.0 Consensus size: 13
45151185 TTAAACCAAC
*
45151195 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
*
45151208 CTTCTT-AAAAGTA
1 CTT-TTCAAAAGCA
* *
45151221 CTTTTCCACAGCA
1 CTTTTCAAAAGCA
45151234 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
*
45151247 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
* *
45151260 CTTTTCCACAGCA
1 CTTTTCAAAAGCA
45151273 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
*
45151286 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
45151299 ATGAAGAACT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
12 2 0.03
13 72 0.95
14 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Done.