Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
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: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1095313 original size:159 final size:159
Alignment explanation
Indices: 1095071--1095357 Score: 400
Period size: 159 Copynumber: 1.8 Consensus size: 159
1095061 CTAGCCCCAT
* * *
1095071 TTTTATTTTCAAAAATATTAAATTTACAATTAGGGATATTCTAACCCTATTATTTCTGAGGGGAT
1 TTTTATTTTCAAAAATATTAAATTTACAATTAGGGATACTATAACCCTATTATTTCTGAGGGAAT
* *
1095136 ACTCCAACCCCACTTTTATTTCCAAAAATAT-CAAATTTTTCATCGTAGGGATACTCTAACCCTC
66 ACTCCAACCCCACTTTTATTTCCAAAAATATAAAAATTTTTCATCGTAGGGATACTCCAACCCTC
1095200 TTATTTTCAAGGGGATACTCCAACTCCTC
131 TTATTTTCAAGGGGATACTCCAACTCCTC
** * *
1095229 TTTTATTTTC-AAAATATTAAATTTTTTATCTTGGGGATACTATAATCCC-ATTATTTCTGAGGG
1 TTTTATTTTCAAAAATATTAAA-TTTACA-ATTAGGGATACTATAA-CCCTATTATTTCTGAGGG
* * * * *
1095292 AATACTCCAAGCCCATTTTTATTTTCAAAAATATAAAAATTTTTCCTTGTAGGGATACTCCAACC
63 AATACTCCAACCCCACTTTTATTTCCAAAAATATAAAAATTTTTCATCGTAGGGATACTCCAACC
1095357 C
128 C
1095358 CACTTTTATT
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
157 11 0.10
158 14 0.13
159 56 0.50
160 30 0.27
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (159 bp):
TTTTATTTTCAAAAATATTAAATTTACAATTAGGGATACTATAACCCTATTATTTCTGAGGGAAT
ACTCCAACCCCACTTTTATTTCCAAAAATATAAAAATTTTTCATCGTAGGGATACTCCAACCCTC
TTATTTTCAAGGGGATACTCCAACTCCTC
Found at i:1095364 original size:132 final size:131
Alignment explanation
Indices: 1095211--1095467 Score: 363
Period size: 132 Copynumber: 2.0 Consensus size: 131
1095201 TATTTTCAAG
* * * * * *
1095211 GGGATACTCCAACTCCTCTTTTATTTTCAAAATATTAAATTTTTTATCTTGGGGATACTAT-AAT
1 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCATGGGGATACT-TCAAC
* * * *
1095275 CCCATTATTTCTGAGGGAATACTCCAAGCCCATTTTTATTTTCAAAAATATAAAAATTTTTCCTT
65 CCCATTATTTCTAAGGGAATACTCCAACCCCACTTTTATTTCCAAAAATAT-AAAATTTTTCCTT
1095340 GTA
129 GTA
1095343 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCATGGGGATACTTCAACC
1 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCATGGGGATACTTCAACC
* * * *
1095408 CCATTTTTTCTAAGGGGATACTCTAACCCCACTTTTATTTCCAAAAATATCAAATTTTTC
66 CCATTATTTCTAAGGGAATACTCCAACCCCACTTTTATTTCCAAAAATATAAAATTTTTC
1095468 ATCACGAAGA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
131 10 0.09
132 100 0.91
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (131 bp):
GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCATGGGGATACTTCAACC
CCATTATTTCTAAGGGAATACTCCAACCCCACTTTTATTTCCAAAAATATAAAATTTTTCCTTGT
A
Found at i:1095407 original size:51 final size:53
Alignment explanation
Indices: 1095288--1095415 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 53
1095278 ATTATTTCTG
* * **
1095288 AGGGAATACTCCAAGCCCATTTTTATTTTCAAAAATATAAAAATTTTTCCTTGT
1 AGGG-ATACTCCAACCCCATTTTTATTTTCAAAAATATAAAAATTTTTCATCAT
* * *
1095342 AGGGATACTCCAACCCCACTTTTA-TTTCCAAAATAT-TAAATTTTTCATCAT
1 AGGGATACTCCAACCCCATTTTTATTTTCAAAAATATAAAAATTTTTCATCAT
* *
1095393 GGGGATACTTCAACCCCATTTTT
1 AGGGATACTCCAACCCCATTTTT
1095416 TCTAAGGGGA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 31 0.48
52 11 0.17
53 18 0.28
54 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (53 bp):
AGGGATACTCCAACCCCATTTTTATTTTCAAAAATATAAAAATTTTTCATCAT
Found at i:1095568 original size:77 final size:78
Alignment explanation
Indices: 1095343--1095593 Score: 294
Period size: 77 Copynumber: 3.2 Consensus size: 78
1095333 TTTCCTTGTA
*
1095343 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCATGGGGATACT-TCAAC
1 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATC-TCGGGATACTCT-AAC
*
1095407 CCCATT-TTTTCTAAG
64 CCCGTTATTTTC-AAG
* * * * * *
1095422 GGGATACTCTAACCCCACTTTTATTTCCAAAAATATCAAATTTTTCATCACGAAGATACTCCAAT
1 GGGATACTCCAACCCCACTTTTATTTCC-AAAATATTAAATTTTTCATCTCG-GGATACTCTAAC
1095487 CCCGTTATTTTCAAG
64 CCCGTTATTTTCAAG
* * * *
1095502 GGGATACTCTAACCTCGC-TTT-TTTCCAAAATATTAAATTTTTTATCTCAGGGATACTCTAACC
1 GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTC-GGGATACTCTAACC
*
1095565 CCGTTATTTTCAAA
65 CCGTTATTTTCAAG
*
1095579 AGGATACTCCAACCC
1 GGGATACTCCAACCC
1095594 TATTTCTTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
77 54 0.37
78 6 0.04
79 31 0.21
80 51 0.35
81 5 0.03
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (78 bp):
GGGATACTCCAACCCCACTTTTATTTCCAAAATATTAAATTTTTCATCTCGGGATACTCTAACCC
CGTTATTTTCAAG
Found at i:1096538 original size:20 final size:20
Alignment explanation
Indices: 1096513--1096551 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1096503 CGACAGCAAC
1096513 AAGTGAATGTATCGATGCAT
1 AAGTGAATGTATCGATGCAT
1096533 AAGTGAATGTATCGATGCA
1 AAGTGAATGTATCGATGCA
1096552 GAACCATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGTGAATGTATCGATGCAT
Found at i:1096669 original size:48 final size:46
Alignment explanation
Indices: 1096586--1096722 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 46
1096576 ATTCTGGAAA
* * * *
1096586 GAAAATGTATCAATGCAGTTTTTATTTTATTGATACATTCTGGGTTTG
1 GAAAATGTATCGATACA-TTTTTATTGTATCGATACATT-TGGGTTTG
*
1096634 GAAAATGTATCGATACATTTTTCATTGTATCGATACAATTTGGGTTTT
1 GAAAATGTATCGATACATTTTT-ATTGTATCGATAC-ATTTGGGTTTG
* * *
1096682 AACCTAAATGTATCGATACAATCTTTAATGTATCGATACAT
1 GA---AAATGTATCGATAC-ATTTTTATTGTATCGATACAT
1096723 CTAGTTAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
47 5 0.07
48 34 0.45
49 3 0.04
50 2 0.03
51 26 0.35
52 5 0.07
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (46 bp):
GAAAATGTATCGATACATTTTTATTGTATCGATACATTTGGGTTTG
Found at i:1104948 original size:26 final size:24
Alignment explanation
Indices: 1104918--1104987 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 24
1104908 TAGATAATGC
1104918 TTTTGTTATTTTTTAAAGCTTAACAAG
1 TTTTGTTATTTTTTAAAGCTT---AAG
*
1104945 -TTTGTTACTTTTGTTTAAAGCTTTAG
1 TTTTGTTA--TTT-TTTAAAGCTTAAG
1104971 TTTTGTTATTTTTTAAA
1 TTTTGTTATTTTTTAAA
1104988 ACTTCTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
24 6 0.16
25 3 0.08
26 9 0.24
27 7 0.18
28 3 0.08
29 10 0.26
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (24 bp):
TTTTGTTATTTTTTAAAGCTTAAG
Found at i:1106531 original size:20 final size:20
Alignment explanation
Indices: 1106484--1106531 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1106474 AAGGTTAAGT
* *
1106484 AAAAAAGAAAGAAAGAAGAT
1 AAAAAAGAAAGAAAGAAAAA
* *
1106504 GAAGAAGAAAGAAAGAAAAA
1 AAAAAAGAAAGAAAGAAAAA
1106524 AAAAAAGA
1 AAAAAAGA
1106532 GAAAAATTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAAGAAAGAAAAA
Found at i:1113323 original size:10 final size:10
Alignment explanation
Indices: 1113308--1113338 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1113298 ACCCAATCCT
1113308 AAAAAAAAAC
1 AAAAAAAAAC
1113318 AAAAAAAAACC
1 AAAAAAAAA-C
1113329 AAAAAAAAAC
1 AAAAAAAAAC
1113339 CTTTTCACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1113338 original size:11 final size:11
Alignment explanation
Indices: 1113308--1113339 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1113298 ACCCAATCCT
1113308 AAAAAAAAA-C
1 AAAAAAAAACC
1113318 AAAAAAAAACC
1 AAAAAAAAACC
1113329 AAAAAAAAACC
1 AAAAAAAAACC
1113340 TTTTCACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:1114451 original size:27 final size:27
Alignment explanation
Indices: 1114379--1114842 Score: 748
Period size: 27 Copynumber: 17.0 Consensus size: 27
1114369 GTGGCATTTT
*
1114379 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114406 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1114434 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114461 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1114488 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1114515 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1114542 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1114570 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
1114597 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1114625 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1114652 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114679 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114706 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1114734 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114761 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1114788 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1114815 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1114842 C
1 C
1114843 ATTTCAAAGC
Statistics
Matches: 404, Mismatches: 29, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
27 305 0.75
28 99 0.25
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1114580 original size:109 final size:108
Alignment explanation
Indices: 1114379--1114842 Score: 748
Period size: 109 Copynumber: 4.3 Consensus size: 108
1114369 GTGGCATTTT
* *
1114379 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1114444 CACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1114488 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1114553 ATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
** *
1114597 CTTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1114662 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1114706 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1114771 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1114815 CTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCC
1114843 ATTTCAAAGC
Statistics
Matches: 328, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
108 66 0.20
109 194 0.59
110 68 0.21
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.28
Consensus pattern (108 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1114880 original size:32 final size:32
Alignment explanation
Indices: 1114825--1115202 Score: 623
Period size: 32 Copynumber: 11.8 Consensus size: 32
1114815 CTTTTAAATC
* *
1114825 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1114856 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1114888 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1114920 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1114952 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1114984 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1115016 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1115048 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1115080 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1115112 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1115144 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1115176 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1115203 TCACCATTTT
Statistics
Matches: 326, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
31 12 0.04
32 314 0.96
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1121012 original size:3 final size:3
Alignment explanation
Indices: 1121004--1121041 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1120994 CTAGTTGGTT
1121004 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1121042 GTGAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1121834 original size:3 final size:3
Alignment explanation
Indices: 1121828--1121858 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1121818 AATTCAAAAG
1121828 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1121859 GTTGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1121863 original size:3 final size:3
Alignment explanation
Indices: 1121857--1121911 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
1121847 ATTATTATTA
* * * * *
1121857 TTG TTG TTG TTG TTG TTA TTA TTG TTG TTG TTG TCG TTG TTG TTA CTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1121905 TTG TTG T
1 TTG TTG T
1121912 ATTTGAGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.05, C:0.04, G:0.27, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:1121875 original size:21 final size:21
Alignment explanation
Indices: 1121851--1121890 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1121841 ATTATTATTA
1121851 TTATTATTGTTGTTGTTGTTG
1 TTATTATTGTTGTTGTTGTTG
1121872 TTATTATTGTTGTTGTTGT
1 TTATTATTGTTGTTGTTGT
1121891 CGTTGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.68
Consensus pattern (21 bp):
TTATTATTGTTGTTGTTGTTG
Found at i:1121875 original size:24 final size:24
Alignment explanation
Indices: 1121848--1121911 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
1121838 ATTATTATTA
* *
1121848 TTATTATTATTGTTGTTGTTGTTG
1 TTATTATTGTTGTTGTTGTCGTTG
1121872 TTATTATTGTTGTTGTTGTCGTTG
1 TTATTATTGTTGTTGTTGTCGTTG
* *
1121896 TTGTTACTGTTGTTGT
1 TTATTATTGTTGTTGT
1121912 ATTTGAGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.09, C:0.03, G:0.23, T:0.64
Consensus pattern (24 bp):
TTATTATTGTTGTTGTTGTCGTTG
Found at i:1123290 original size:17 final size:17
Alignment explanation
Indices: 1123268--1123357 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
1123258 AAATAGATTG
1123268 GATTATTTTTTAATTTA
1 GATTATTTTTTAATTTA
*
1123285 GATTA--TTGTAAGTTTA
1 GATTATTTTTTAA-TTTA
* * *
1123301 GATT-TTATTTGAGTTTT
1 GATTATT-TTTTAATTTA
1123318 GATTA--TTTTAGATTTA
1 GATTATTTTTTA-ATTTA
* *
1123334 -AATATTTTTTAGTTTA
1 GATTATTTTTTAATTTA
1123350 GATTATTT
1 GATTATTT
1123358 CAAGTTTGGA
Statistics
Matches: 53, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
15 12 0.23
16 15 0.28
17 23 0.43
18 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (17 bp):
GATTATTTTTTAATTTA
Found at i:1123363 original size:16 final size:16
Alignment explanation
Indices: 1123344--1123393 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1123334 AATATTTTTT
*
1123344 AGTTTAGATTATTTCA
1 AGTTTAGATAATTTCA
*
1123360 AGTTTGGATAATTTCA
1 AGTTTAGATAATTTCA
* **
1123376 AGCTCGGATAATTTCA
1 AGTTTAGATAATTTCA
1123392 AG
1 AG
1123394 CTCGACTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (16 bp):
AGTTTAGATAATTTCA
Found at i:1123394 original size:16 final size:16
Alignment explanation
Indices: 1123354--1123397 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1123344 AGTTTAGATT
* *
1123354 ATTTCAAGTTTGGATA
1 ATTTCAAGCTCGGATA
1123370 ATTTCAAGCTCGGATA
1 ATTTCAAGCTCGGATA
1123386 ATTTCAAGCTCG
1 ATTTCAAGCTCG
1123398 ACTATCTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (16 bp):
ATTTCAAGCTCGGATA
Found at i:1124042 original size:25 final size:22
Alignment explanation
Indices: 1124014--1124062 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1124004 TTGTTATTAG
1124014 ATTTGTTAAAAATCTTTGTATTATA
1 ATTT-TTAAAAA--TTTGTATTATA
**
1124039 ATTTTTTTAAATTTGTATTATA
1 ATTTTTAAAAATTTGTATTATA
1124061 AT
1 AT
1124063 CTGATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 13 0.59
24 5 0.23
25 4 0.18
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTTAAAAATTTGTATTATA
Found at i:1124374 original size:20 final size:19
Alignment explanation
Indices: 1124349--1124386 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1124339 ATAATATTAT
1124349 ATATATTTATTCTTTATATA
1 ATATATTTATT-TTTATATA
1124369 ATATATTTATTTTTATAT
1 ATATATTTATTTTTATAT
1124387 GATAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATTTATTTTTATATA
Found at i:1127602 original size:3 final size:3
Alignment explanation
Indices: 1127594--1127619 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1127584 TGTCCAGCCC
1127594 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1127620 AACACGATGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1128017 original size:20 final size:20
Alignment explanation
Indices: 1127994--1128051 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1127984 TATAAAAATA
1127994 TTAATATTAAAATAAATTTT
1 TTAATATTAAAATAAATTTT
**
1128014 TTAATATTTTAAT--ATTTT
1 TTAATATTAAAATAAATTTT
*
1128032 TTAAATAATAAAATAAATTT
1 TT-AATATTAAAATAAATTT
1128052 GAGTTAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.23
19 8 0.27
20 11 0.37
21 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATATTAAAATAAATTTT
Found at i:1128285 original size:16 final size:17
Alignment explanation
Indices: 1128246--1128285 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1128236 AAAATAAAAC
*
1128246 TTTATATTTAAATTTTA
1 TTTAAATTTAAATTTTA
1128263 TTT-AATTTAAATTTT-
1 TTTAAATTTAAATTTTA
1128278 TTTAAATT
1 TTTAAATT
1128286 ACTGATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 15 0.71
17 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAAATTTAAATTTTA
Found at i:1129806 original size:19 final size:19
Alignment explanation
Indices: 1129782--1129819 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1129772 TGTTAGTGGT
1129782 AAAATTATTTTCTTGGACA
1 AAAATTATTTTCTTGGACA
1129801 AAAATTATTTTCTTGGACA
1 AAAATTATTTTCTTGGACA
1129820 CCACTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAATTATTTTCTTGGACA
Found at i:1134454 original size:13 final size:13
Alignment explanation
Indices: 1134436--1134461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1134426 CTATTTATGA
1134436 TGTATCGATACAC
1 TGTATCGATACAC
1134449 TGTATCGATACAC
1 TGTATCGATACAC
1134462 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1134572 original size:32 final size:32
Alignment explanation
Indices: 1134516--1134595 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
1134506 CATGAATAGT
*
1134516 GATACGTGAACAGTG-TGAATAGTGATGTATC
1 GATACATGAACAGTGATGAATAGTGATGTATC
1134547 GATACATGAACAGTGATGAATAGTGATGTATC
1 GATACATGAACAGTGATGAATAGTGATGTATC
*
1134579 GATACTTGAA-AGTGATG
1 GATACATGAACAGTGATG
1134596 TATCGATACA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 21 0.46
32 25 0.54
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.29
Consensus pattern (32 bp):
GATACATGAACAGTGATGAATAGTGATGTATC
Found at i:1134592 original size:21 final size:22
Alignment explanation
Indices: 1134562--1134617 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
1134552 ATGAACAGTG
*
1134562 ATGAATAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
*
1134584 TTGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1134605 ATGAACAGTGATG
1 ATGAACAGTGATG
1134618 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1134624 original size:10 final size:10
Alignment explanation
Indices: 1134605--1134635 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1134595 GTATCGATAC
1134605 ATGAACAGTG
1 ATGAACAGTG
*
1134615 ATGAATAGTG
1 ATGAACAGTG
1134625 ATGAACAGTG
1 ATGAACAGTG
1134635 A
1 A
1134636 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1134775 original size:20 final size:20
Alignment explanation
Indices: 1134712--1134782 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1134702 GCCAATGACC
**
1134712 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTAATG
* *
1134732 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
1134752 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1134772 TGTATCGATAC
1 TGTATCGATAC
1134783 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1135835 original size:19 final size:19
Alignment explanation
Indices: 1135811--1135857 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
1135801 TTGAATTATG
1135811 TATTTTAGT-ATAATAGTTA
1 TATTTTA-TAATAATAGTTA
1135830 TATTTTATAATAATAGTTA
1 TATTTTATAATAATAGTTA
1135849 TAGTTTTAT
1 TA-TTTTAT
1135858 TTTGCTAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.73
20 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (19 bp):
TATTTTATAATAATAGTTA
Found at i:1136658 original size:26 final size:29
Alignment explanation
Indices: 1136624--1136676 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1136614 TTATTATATT
1136624 AATA-TTTTTAT-AT-ATAATTAAATTTA
1 AATATTTTTTATAATAATAATTAAATTTA
1136650 AATATTTTTTATAATAATAATTAAATT
1 AATATTTTTTATAATAATAATTAAATT
1136677 AATAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 7 0.29
28 2 0.08
29 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AATATTTTTTATAATAATAATTAAATTTA
Found at i:1137738 original size:25 final size:26
Alignment explanation
Indices: 1137696--1137790 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 26
1137686 TCTAATTAAA
1137696 TTTATTATTAAATATTAAA-ATATTT
1 TTTATTATTAAATATTAAATATATTT
*
1137721 TTTATT-TTAATATTTTAAATATATTT
1 TTTATTATTAA-ATATTAAATATATTT
*
1137747 TTAATCGTATTTAAATA--AAATA-ATTT
1 TTTAT--TA-TTAAATATTAAATATATTT
*
1137773 TTTCATAATTGAAATATT
1 TTT-ATTATT-AAATATT
1137791 TTTACAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
24 6 0.11
25 19 0.35
26 16 0.29
27 7 0.13
28 1 0.02
29 2 0.04
30 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTATTAAATATTAAATATATTT
Found at i:1138473 original size:35 final size:38
Alignment explanation
Indices: 1138407--1138483 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
1138397 ATATGATTTG
* *
1138407 ATTTAAATTAATTTTTAATAATTTATAAATA-TTAT-T
1 ATTTAAATTAATTTATAATAATATATAAATATTTATAT
1138443 ATTTAAATTTAA-TTATAA-AATATATAAATATTTATAT
1 ATTTAAA-TTAATTTATAATAATATATAAATATTTATAT
1138480 ATTT
1 ATTT
1138484 TTTTAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
35 11 0.31
36 16 0.44
37 9 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
ATTTAAATTAATTTATAATAATATATAAATATTTATAT
Found at i:1138589 original size:23 final size:22
Alignment explanation
Indices: 1138531--1138589 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
1138521 TTAATAAATC
*
1138531 AAATTAAATTAAAAATATATTT
1 AAATTAAATTTAAAATATATTT
* *
1138553 AAATAAAAAATTAAAATA-ATTTT
1 AAAT-TAAATTTAAAATATA-TTT
1138576 AAATTATAATTTAA
1 AAATTA-AATTTAA
1138590 TTTTAATCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAAATTTAAAATATATTT
Found at i:1140905 original size:6 final size:6
Alignment explanation
Indices: 1140894--1140924 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1140884 GGGAGAAGGG
1140894 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
1140925 GAAAAGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:1145433 original size:5 final size:5
Alignment explanation
Indices: 1145423--1145467 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
1145413 TAATACTATT
* * *
1145423 TATAA TATAA TATAA TATAA TGTAA TGTAA TATAA TATAT TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1145468 AATACTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:1147906 original size:33 final size:33
Alignment explanation
Indices: 1147866--1147936 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1147856 AATTTAATTT
*
1147866 ATTTTATGAGTTTTGCATTTTTTTCATATAATA
1 ATTTTATGAGTTTTGCATTTTCTTCATATAATA
*
1147899 ATTTTATGAGTTTTGCGTTTTCTTCATATAATA
1 ATTTTATGAGTTTTGCATTTTCTTCATATAATA
1147932 ATTTT
1 ATTTT
1147937 TTCGTGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.58
Consensus pattern (33 bp):
ATTTTATGAGTTTTGCATTTTCTTCATATAATA
Found at i:1149687 original size:29 final size:29
Alignment explanation
Indices: 1149654--1149723 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
1149644 GGTTAATGTG
1149654 TAATTTTGAAAAGTTTAA-AGGTCAA-AGTA
1 TAATTTTGAAAAGTTTAAGA-GTCAATA-TA
*
1149683 TAATTTTGAGAAGTTTAAGAGTCAATATA
1 TAATTTTGAAAAGTTTAAGAGTCAATATA
1149712 TAATTTT-AAAAG
1 TAATTTTGAAAAG
1149724 CCTAGGAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.11
29 31 0.84
30 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (29 bp):
TAATTTTGAAAAGTTTAAGAGTCAATATA
Found at i:1150177 original size:153 final size:152
Alignment explanation
Indices: 1149822--1150272 Score: 471
Period size: 153 Copynumber: 3.0 Consensus size: 152
1149812 TGTCATATTT
* * ** * * * * *
1149822 TTTAAGGTTACCGAGATACTTTCATGTTGAATGTATACTCAAAGGCATTTTGGTAATTTTTCTAA
1 TTTAAGATTACCAAGATACTTTCGCGTCGAAAGTATACTCAAGGGCATTTTAGTAATTTTTCTAG
** * * * * * * **
1149887 AACTGAGTCTTAGGTAGTCGTCACCTGGTCATTTTTATGCCAAAAGTTTAAATTTAGGGCAAATT
66 AACCAATTCTTAGGTA---GTCACCTGGTCATTTTTATGCCAAAGGTCTACATTTATGGTAGGTT
* * *
1149952 TATGCTTTTATGAT-TTTCTGTGTCC
128 CACGCTTTTATGATCTTT-TGTGTCA
* *
1149977 TTTAAGATTACCAAGATAC-TTGGACGTCAAAAGTATACTCAAGGGCATTTTAGTAATTTTTCTA
1 TTTAAGATTACCAAGATACTTTCG-CGTCGAAAGTATACTCAAGGGCATTTTAGTAATTTTTCTA
* * *
1150041 GAACCAATTCTTAGGTAGTCACATGTTCGTTTTTATGCCAAAGGTCTACATTTATGGTAGGTTCA
65 GAACCAATTCTTAGGTAGTCACCTGGTCATTTTTATGCCAAAGGTCTACATTTATGGTAGGTTCA
* *
1150106 CGCTATTATGATCCTTTTGTGTTA
130 CGCTTTTATGAT-CTTTTGTGTCA
* * * * * *
1150130 TTTAGGGTTGCCAAGATACTTTCGCGTCGAAGGTATACTCAAGGGCATTTTAATAATTTTTTTAG
1 TTTAAGATTACCAAGATACTTTCGCGTCGAAAGTATACTCAAGGGCATTTTAGTAATTTTTCTAG
* *
1150195 AACCAATTCCTA-G--GTCACCTGGTCTTTTTTATGCCAAAGGTCTACATTTATGGTAGGTTCAC
66 AACCAATTCTTAGGTAGTCACCTGGTCATTTTTATGCCAAAGGTCTACATTTATGGTAGGTTCAC
*
1150257 TCTTTTATGATCTTTT
131 GCTTTTATGATCTTTT
1150273 CATGTCTTTA
Statistics
Matches: 249, Mismatches: 43, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
149 5 0.02
150 55 0.22
152 48 0.19
153 69 0.28
154 8 0.03
155 64 0.26
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (152 bp):
TTTAAGATTACCAAGATACTTTCGCGTCGAAAGTATACTCAAGGGCATTTTAGTAATTTTTCTAG
AACCAATTCTTAGGTAGTCACCTGGTCATTTTTATGCCAAAGGTCTACATTTATGGTAGGTTCAC
GCTTTTATGATCTTTTGTGTCA
Found at i:1152539 original size:19 final size:19
Alignment explanation
Indices: 1152514--1152572 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
1152504 TTGTAGTGAT
*
1152514 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGA
*
1152533 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
*
1152552 ACAAATGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
1152572 A
1 A
1152573 ACTAGCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:1152562 original size:20 final size:19
Alignment explanation
Indices: 1152518--1152572 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1152508 AGTGATACAT
** *
1152518 TGTATCGATACATGTTCAT
1 TGTATCGATACATGAACAA
1152537 TGTATCGATACATGAACAAA
1 TGTATCGATACATGAAC-AA
1152557 TGTATCGATACATGAA
1 TGTATCGATACATGAA
1152573 ACTAGCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGAACAA
Found at i:1152638 original size:13 final size:13
Alignment explanation
Indices: 1152620--1152644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1152610 CATGGCACAT
1152620 TGTATCGATACAA
1 TGTATCGATACAA
1152633 TGTATCGATACA
1 TGTATCGATACA
1152645 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1154079 original size:97 final size:97
Alignment explanation
Indices: 1153914--1154135 Score: 277
Period size: 97 Copynumber: 2.3 Consensus size: 97
1153904 TTAAATTTTT
* * *
1153914 GTTTGAAAAATAGGGTTAGAGTATCCCCTCAGAAGAATGGGGTTGGAGTATCCCCCACAATGATA
1 GTTT-AAAAATGGGGTTGGAGTATCCCCTCAGAAGAATGGGGTTGGAGTATCCCCCACAATGACA
** *
1153979 ATTT-GGTCG-AAATAAGACTTTAAATTTTGATGA
65 ATTTAACT-GAAAATAAGA-TTTAAATTTTGATAA
* * * * **
1154012 GTTTAAAAATGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAA
1 GTTTAAAAATGGGGTTGGAGTATCCCCTCAGAAGAATGGGGTTGGAGTATCCCCCACAATGACAA
*
1154077 TTTAACTGAAAATAAGATTTTAATTTTGATAA
66 TTTAACTGAAAATAAGATTTAAATTTTGATAA
*
1154109 GGTTAAAAATGGGGTTGGAGTATCCCC
1 GTTTAAAAATGGGGTTGGAGTATCCCC
1154136 GTCAATGATA
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
97 95 0.88
98 13 0.12
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (97 bp):
GTTTAAAAATGGGGTTGGAGTATCCCCTCAGAAGAATGGGGTTGGAGTATCCCCCACAATGACAA
TTTAACTGAAAATAAGATTTAAATTTTGATAA
Found at i:1154129 original size:70 final size:69
Alignment explanation
Indices: 1154046--1154201 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 69
1154036 CCCTCGGAGG
* * * *
1154046 AATGGGGTTGGAGTGTCCCCGAT-GATGACAATTTA-ACTGAAAATAAGATTTTAATTTTGATAA
1 AATGGGGTTGGAGTATCCCCG-TCAATGACAATTTAGA-T-AAAATAAGATTTAAATCTTGATAA
1154109 GGTTAAA
63 GGTTAAA
* * *
1154116 AATGGGGTTGGAGTATCCCCGTCAATGATAATTTAGATAAAATAATATTTAAATCTTGATAAGTT
1 AATGGGGTTGGAGTATCCCCGTCAATGACAATTTAGATAAAATAAGATTTAAATCTTGATAAGGT
1154181 TAAA
66 TAAA
* *
1154185 AATGAGGTTAGAGTATC
1 AATGGGGTTGGAGTATC
1154202 TCTTCAGAGG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
69 43 0.57
70 31 0.41
71 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (69 bp):
AATGGGGTTGGAGTATCCCCGTCAATGACAATTTAGATAAAATAAGATTTAAATCTTGATAAGGT
TAAA
Found at i:1154225 original size:166 final size:167
Alignment explanation
Indices: 1153949--1154299 Score: 517
Period size: 166 Copynumber: 2.1 Consensus size: 167
1153939 CCCTCAGAAG
* * * *
1153949 AATGGGGTTGGAGTATCCCCCACAATGATAATTTGGTCGAAATAAGACTTTAAATTTTGATGAGT
1 AATGGGGTTGGAGTATCCCCCACAATGATAATTTGATCAAAATAAGACTTTAAATCTTGATAAGT
* * * *
1154014 TTAAAAATGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATT
66 TTAAAAATGAGGTTAGAGTATCCCCTCAGAGGAATGGGATTGGAGTGTCCCCGATGATGACAATT
**
1154079 TAACTGAAAATAAGATTTTAATTTTGATAAGGTTAAA
131 TAACCAAAAATAAGATTTTAATTTTGATAAGGTTAAA
** *
1154116 AATGGGGTTGGAGTATCCCCGTCAATGATAATTTAGAT-AAAATAATA-TTTAAATCTTGATAAG
1 AATGGGGTTGGAGTATCCCCCACAATGATAATTT-GATCAAAATAAGACTTTAAATCTTGATAAG
* *
1154179 TTTAAAAATGAGGTTAGAGTATCTCTTCAGAGGAATGGGATTGGAGTGTCCCCGATGATGACAAT
65 TTTAAAAATGAGGTTAGAGTATCCCCTCAGAGGAATGGGATTGGAGTGTCCCCGATGATGACAAT
*
1154244 TTAACCAAAAATAAGATTTTAATTTTGATAAGTTTAAA
130 TTAACCAAAAATAAGATTTTAATTTTGATAAGGTTAAA
**
1154282 AACAGGGTTGGAGTATCC
1 AATGGGGTTGGAGTATCC
1154300 TTTCAGAGGA
Statistics
Matches: 165, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
166 124 0.75
167 39 0.24
168 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (167 bp):
AATGGGGTTGGAGTATCCCCCACAATGATAATTTGATCAAAATAAGACTTTAAATCTTGATAAGT
TTAAAAATGAGGTTAGAGTATCCCCTCAGAGGAATGGGATTGGAGTGTCCCCGATGATGACAATT
TAACCAAAAATAAGATTTTAATTTTGATAAGGTTAAA
Found at i:1154328 original size:97 final size:97
Alignment explanation
Indices: 1154116--1154331 Score: 237
Period size: 97 Copynumber: 2.2 Consensus size: 97
1154106 TAAGGTTAAA
* * * * *
1154116 AATGGGGTTGGAGTATCCCCG-TCAATGATAATTTAGA--TAAAATAATATTTAAATCTTGATAA
1 AATGGGATTGGAGTATCCCCGAT-GATGACAATTTA-ACCAAAAATAAGATTTAAATCTTGATAA
*
1154178 GTTTAAAAATGAGGTTAGAGTATCTCTTCAGAGG
64 GTTTAAAAAAGAGGTTAGAGTATCTCTTCAGAGG
* * *
1154212 AATGGGATTGGAGTGTCCCCGATGATGACAATTTAACCAAAAATAAGATTTTAATTTTGATAAGT
1 AATGGGATTGGAGTATCCCCGATGATGACAATTTAACCAAAAATAAGATTTAAATCTTGATAAGT
*
1154277 TTAAAAACAG-GGTTGGAGTATC-CTTTCAGAGG
66 TTAAAAA-AGAGGTTAGAGTATCTC-TTCAGAGG
* *
1154309 AATATGG-TTGGTGTATCCCCGAT
1 AAT-GGGATTGGAGTATCCCCGAT
1154332 AAACCAAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
95 1 0.01
96 30 0.30
97 67 0.66
98 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (97 bp):
AATGGGATTGGAGTATCCCCGATGATGACAATTTAACCAAAAATAAGATTTAAATCTTGATAAGT
TTAAAAAAGAGGTTAGAGTATCTCTTCAGAGG
Found at i:1156571 original size:15 final size:15
Alignment explanation
Indices: 1156553--1156581 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1156543 GAATATTATT
1156553 ATTTTTAATTTTTTA
1 ATTTTTAATTTTTTA
1156568 ATTTTTAATTTTTT
1 ATTTTTAATTTTTT
1156582 TTATTATTCT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTAATTTTTTA
Found at i:1157320 original size:21 final size:21
Alignment explanation
Indices: 1157296--1157363 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1157286 AAAGATGATA
1157296 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* * *
1157317 AA-G-GCCAGTGATGTTGGACTTA
1 AAGGTGCCAAT-ATGCT-GA-TTC
*
1157339 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1157360 AAGG
1 AAGG
1157364 CCAGCGACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 10 0.29
22 6 0.17
23 4 0.11
24 5 0.14
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1157339 original size:61 final size:61
Alignment explanation
Indices: 1157217--1157341 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 61
1157207 AAAGATGATG
** *
1157217 AAGATGAGAAAAGTGATAAAGATGCCAATATGCTGATTCAAGGCTTGCGATATTGGGCTTA
1 AAGATGAGAAAAGTGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
* * *
1157278 AAGATGAG-AAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATGTTGGACTTA
1 AAGATGAGAAAAG-TGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1157339 AAG
1 AAG
1157342 GTGCCAATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 4 0.07
61 53 0.93
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (61 bp):
AAGATGAGAAAAGTGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
Found at i:1157355 original size:43 final size:43
Alignment explanation
Indices: 1157294--1157384 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
1157284 AGAAAGATGA
* **
1157294 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATGTTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
*
1157337 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
1157380 TAAAG
1 TAAAG
1157385 ATGACAAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
Found at i:1157620 original size:49 final size:49
Alignment explanation
Indices: 1157296--1157930 Score: 557
Period size: 49 Copynumber: 12.8 Consensus size: 49
1157286 AAAGATGATA
* * **
1157296 AAGGTGCCAATATGCTGATTCAAGGCCAGTGATGTTGGACTT----A--
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
1157339 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * * * *
1157388 ACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGGTGCG
1 ---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G
* * * * * *
1157442 AAGAATGTCAATGTGTTGATTCATGGCCAGCGACATTAGACTTGAAGATGAG
1 AAG-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G
* * * * **
1157494 AAGAATG-AAATGTGCTGATTCAAGGCCAACGACATTGGGCTTAGGGATG
1 AAG-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
** * * * * * *
1157543 TTAAAAATACTAATATGCTGATTTAAGGCCAGCGATATCGGACTTAAAGATG
1 ---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
1157595 AAGGTTCCAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * * *
1157644 GAGGTGCCAATATGCTAATTCAAGGCTAGCGACATTGTACTTAAATGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GATG
* * * *
1157694 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGATT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
1157743 AAGGTGCCAATGTGTTGATTCAAGGCCATCGACATTGGATTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
1157792 GAGGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGACTTAAATG-TGG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GAT-G
* * * * *
1157842 TAAAAGTGCCAATATGTTGATTCAAGGCCAGCAATATTGGACTTAAAGATG
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
1157893 AAGGTGCCAATGTGCTAATTCAAGGTCAGTGACATTGG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
1157931 GCCTAAAAGG
Statistics
Matches: 475, Mismatches: 95, Indels: 38
0.78 0.16 0.06
Matches are distributed among these distances:
43 38 0.08
47 1 0.00
49 192 0.40
50 47 0.10
51 39 0.08
52 157 0.33
54 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
Found at i:1157747 original size:148 final size:149
Alignment explanation
Indices: 1157296--1157917 Score: 663
Period size: 148 Copynumber: 4.2 Consensus size: 149
1157286 AAAGATGATA
* ** **
1157296 AAGGTGCCAATATGCTGATTCAAGGCCAGTGATGTTGGACTT--A-A---AGGTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGAGGTGCCAATGTGCT
* * *
1157355 GATTCAAGGCCAGCGACATTGGACTTAAA-GATGACAAAGGCGCCAATATGCTGATTCAAGGCTA
66 AATTCAAGGCCAGCGACATTGGACTTAAATGATGA-AAA-GTGCCAATATGCTGATTCAAGGCCA
* *
1157419 GCGATATTGGGCTTAAAGGTGCG
129 GCGATATTGGACTTAAAGAT--G
* * * * * * * * *
1157442 AAGAATGTCAATGTGTTGATTCATGGCCAGCGACATTAGACTTGAAGATGAGAAGAATG-AAATG
1 AAG-GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG-G-AG-GTGCCAATG
* * * * * * * * *
1157506 TGCTGATTCAAGGCCAACGACATTGGGCTTAGGGATG-TTAAAAATACTAATATGCTGATTTAAG
62 TGCTAATTCAAGGCCAGCGACATTGGACTTA--AATGATGAAAAGTGCCAATATGCTGATTCAAG
*
1157570 GCCAGCGATATCGGACTTAAAGATG
125 GCCAGCGATATTGGACTTAAAGATG
* * *
1157595 AAGGTTCCAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGGAGGTGCCAATATGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGAGGTGCCAATGTGCT
* * * *
1157660 AATTCAAGGCTAGCGACATTGTACTTAAATGATG-AAGGTGCCAATATGCTAATTCAAGGCCAGC
66 AATTCAAGGCCAGCGACATTGGACTTAAATGATGAAAAGTGCCAATATGCTGATTCAAGGCCAGC
*
1157724 GATATTGGACTTAAAGATT
131 GATATTGGACTTAAAGATG
* * *
1157743 AAGGTGCCAATGTGTTGATTCAAGGCCATCGACATTGGATTTAAAGATGGAGGTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGAGGTGCCAATGTGCT
* *
1157808 AATTCAAGGCTAGCGACATTGGACTTAAATG-TGGTAAAAGTGCCAATATGTTGATTCAAGGCCA
66 AATTCAAGGCCAGCGACATTGGACTTAAATGAT-G-AAAAGTGCCAATATGCTGATTCAAGGCCA
*
1157872 GCAATATTGGACTTAAAGATG
129 GCGATATTGGACTTAAAGATG
*
1157893 AAGGTGCCAATGTGCTAATTCAAGG
1 AAGGTGCCAATGTGCTGATTCAAGG
1157918 TCAGTGACAT
Statistics
Matches: 393, Mismatches: 65, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
146 3 0.01
147 31 0.08
148 134 0.34
149 4 0.01
150 99 0.25
151 1 0.00
152 37 0.09
153 4 0.01
155 71 0.18
156 5 0.01
157 3 0.01
158 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (149 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGAGGTGCCAATGTGCT
AATTCAAGGCCAGCGACATTGGACTTAAATGATGAAAAGTGCCAATATGCTGATTCAAGGCCAGC
GATATTGGACTTAAAGATG
Found at i:1158113 original size:94 final size:94
Alignment explanation
Indices: 1157951--1158127 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 94
1157941 AGATGCCACC
*
1157951 AACTTGTGTGGGCTTTTGAAAGGGTTGCCACCAGCTTGAGTGGCCTTTGAGAAGGGTTGCCACCA
1 AACTTGTGTGGGCTTTTGAAAGGGTTGCCACCAGCTTGAGTGGCCTTTAAGAAGGGTTGCCACCA
* *
1158016 GCTTGTGTGGGTTTTGAGGGGTTGCCAAT
66 GCTTGTGTAGGCTTTGAGGGGTTGCCAAT
* * * *
1158045 AACTTGTGTGGGC-TTTGAAAAGGGTTGCCATC-GACTTGTGTGGGCTTTAAGAAGGGTTGTCAC
1 AACTTGTGTGGGCTTTTG-AAAGGGTTGCCACCAG-CTTGAGTGGCCTTTAAGAAGGGTTGCCAC
*
1158108 TAGCTTGTGTAGGCTTTGAG
64 CAGCTTGTGTAGGCTTTGAG
1158128 AAGGTTTCTC
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 5 0.07
94 68 0.93
ACGTcount: A:0.18, C:0.15, G:0.34, T:0.32
Consensus pattern (94 bp):
AACTTGTGTGGGCTTTTGAAAGGGTTGCCACCAGCTTGAGTGGCCTTTAAGAAGGGTTGCCACCA
GCTTGTGTAGGCTTTGAGGGGTTGCCAAT
Found at i:1158130 original size:32 final size:32
Alignment explanation
Indices: 1157944--1158131 Score: 204
Period size: 32 Copynumber: 5.9 Consensus size: 32
1157934 TAAAAGGAGA
* *
1157944 TGCCACCAACTTGTGTGGGCTTTTGA-AAGGGT
1 TGCCACTAGCTTGTGTGGGC-TTTGAGAAGGGT
* * *
1157976 TGCCACCAGCTTGAGTGGCCTTTGAGAAGGGT
1 TGCCACTAGCTTGTGTGGGCTTTGAGAAGGGT
* *
1158008 TGCCACCAGCTTGTGTGGGTTTTGAG--GGGT
1 TGCCACTAGCTTGTGTGGGCTTTGAGAAGGGT
* * *
1158038 TGCCAATAACTTGTGTGGGCTTTGAAAAGGGT
1 TGCCACTAGCTTGTGTGGGCTTTGAGAAGGGT
* *
1158070 TGCCA-TCGACTTGTGTGGGCTTTAAGAAGGGT
1 TGCCACTAG-CTTGTGTGGGCTTTGAGAAGGGT
* *
1158102 TGTCACTAGCTTGTGTAGGCTTTGAGAAGG
1 TGCCACTAGCTTGTGTGGGCTTTGAGAAGG
1158132 TTTCTCCACT
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.19
31 6 0.05
32 99 0.75
33 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (32 bp):
TGCCACTAGCTTGTGTGGGCTTTGAGAAGGGT
Found at i:1158286 original size:32 final size:32
Alignment explanation
Indices: 1158250--1158354 Score: 138
Period size: 32 Copynumber: 3.3 Consensus size: 32
1158240 ATTAGCTTGA
* *
1158250 GTGGGCTTTAAAAACGGTTGCCACTAACTTAT
1 GTGGGCTTTAAAAAGGGTTGCCACCAACTTAT
* *
1158282 GTGGGCTTTAAAAAGGGTTGCCACCGACTTGT
1 GTGGGCTTTAAAAAGGGTTGCCACCAACTTAT
* ** *
1158314 GTGGGCTTTAAGAAGGGTTGCCACCGGCTTGT
1 GTGGGCTTTAAAAAGGGTTGCCACCAACTTAT
1158346 GTGGGCTTT
1 GTGGGCTTT
1158355 GAAGAGGTGC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
GTGGGCTTTAAAAAGGGTTGCCACCAACTTAT
Found at i:1174840 original size:69 final size:70
Alignment explanation
Indices: 1174679--1174840 Score: 211
Period size: 70 Copynumber: 2.3 Consensus size: 70
1174669 ATCCTCTCAG
* * *
1174679 AAAAATGGGGTTGGAGTATCCCCGACAATGATAATTTGGTTGAAATAAGACTTTAAATTTCAATG
1 AAAAATGGGGTTGGAGTATCCCCGACAATGATAATTTAGATAAAATAAGACTTTAAATTTCAATG
1174744 AGTTT
66 AGTTT
* * * * *
1174749 AAAAATGGGGTTGGATTGTCCCCGTCAATGATAATTTAGATAAAATAATA-TTTAAATCTT-GAT
1 AAAAATGGGGTTGGAGTATCCCCGACAATGATAATTTAGATAAAATAAGACTTTAAAT-TTCAAT
*
1174812 TAGTTT
65 GAGTTT
*
1174818 AAAAACGGGGTTGGAGTATCCCC
1 AAAAATGGGGTTGGAGTATCCCC
1174841 TCAGAGGAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
69 34 0.43
70 45 0.57
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (70 bp):
AAAAATGGGGTTGGAGTATCCCCGACAATGATAATTTAGATAAAATAAGACTTTAAATTTCAATG
AGTTT
Found at i:1175004 original size:165 final size:165
Alignment explanation
Indices: 1174744--1175100 Score: 538
Period size: 165 Copynumber: 2.2 Consensus size: 165
1174734 AATTTCAATG
* * * *
1174744 AGTTTAAAAATGGGGTTGGATTGTCCCCGTCAATGATAATTTAGATAAAATAATATTTAAATCTT
1 AGTTTAAAAATGGGGTTGGAGTATCCCAGTCAATGATAATTTAGACAAAATAATATTTAAATCTT
* * *
1174809 GATTAGTTTAAAAACGGGGTTGGAGTATCCCCTCAGAGGAATGGGGTTGGGGTGTCCCT-ATTGA
66 GATGAGTTTAAAAACAGGGTTGGAGTATCCCCTCAGAGGAATGGGGTTGGAGTGTCCCTCA-TGA
* *
1174873 TGACAATTTAATCGAAAATAAAATTTTAATTTTGATA
130 TGACAACTTAACCG-AAATAAAATTTTAATTTTGATA
* * *
1174910 AGTTTAAAAACGAGGTTGGAGTATCTCAGTCAATGATAA-TTAGACAAAATAATATTTAAATCTT
1 AGTTTAAAAATGGGGTTGGAGTATCCCAGTCAATGATAATTTAGACAAAATAATATTTAAATCTT
* *
1174974 GATGAGTTTAAAAACAGGGTTGGAGTATCCCTTCGGAGGAATGGGGTTGGAGTGTCCCTCATGAT
66 GATGAGTTTAAAAACAGGGTTGGAGTATCCCCTCAGAGGAATGGGGTTGGAGTGTCCCTCATGAT
*
1175039 GACAACTTAACCGAAATAAGATTTTAATTTTGATA
131 GACAACTTAACCGAAATAAAATTTTAATTTTGATA
*
1175074 ATTTTAAAAATGGGGTTGGAGTATCCC
1 AGTTTAAAAATGGGGTTGGAGTATCCC
1175101 CTAAGAGGAA
Statistics
Matches: 171, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
164 44 0.26
165 93 0.54
166 34 0.20
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (165 bp):
AGTTTAAAAATGGGGTTGGAGTATCCCAGTCAATGATAATTTAGACAAAATAATATTTAAATCTT
GATGAGTTTAAAAACAGGGTTGGAGTATCCCCTCAGAGGAATGGGGTTGGAGTGTCCCTCATGAT
GACAACTTAACCGAAATAAAATTTTAATTTTGATA
Found at i:1177385 original size:6 final size:7
Alignment explanation
Indices: 1177368--1177392 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1177358 TTTTATTGAT
1177368 TTTTTTA
1 TTTTTTA
1177375 TTTTTTA
1 TTTTTTA
1177382 TTTTTTA
1 TTTTTTA
1177389 TTTT
1 TTTT
1177393 AATTTTGTAT
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):
TTTTTTA
Found at i:1177392 original size:19 final size:20
Alignment explanation
Indices: 1177348--1177398 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1177338 CTGAATATTA
**
1177348 TTATTTTAAATTTTATTGAT
1 TTATTTTATTTTTTATTGAT
*
1177368 TT-TTTTATTTTTTATT-TT
1 TTATTTTATTTTTTATTGAT
1177386 TTATTTTAATTTT
1 TTATTTT-ATTTT
1177399 GTATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 16 0.62
20 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTTTATTTTTTATTGAT
Found at i:1179284 original size:13 final size:13
Alignment explanation
Indices: 1179266--1179290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179256 CAATTTATTA
1179266 TGTATCGATACAT
1 TGTATCGATACAT
1179279 TGTATCGATACA
1 TGTATCGATACA
1179291 ATGCGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1179388 original size:19 final size:20
Alignment explanation
Indices: 1179340--1179392 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1179330 CTGTCAGTTT
**
1179340 CATATATCGATACAATTGTC
1 CATATATCGATACAATTGAA
*
1179360 CATGTATCGATACAA-TGAA
1 CATATATCGATACAATTGAA
*
1179379 TATATATCGATACA
1 CATATATCGATACA
1179393 TTATATCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (20 bp):
CATATATCGATACAATTGAA
Found at i:1179399 original size:13 final size:13
Alignment explanation
Indices: 1179381--1179405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179371 ACAATGAATA
1179381 TATATCGATACAT
1 TATATCGATACAT
1179394 TATATCGATACA
1 TATATCGATACA
1179406 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:1179405 original size:32 final size:33
Alignment explanation
Indices: 1179364--1179425 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1179354 ATTGTCCATG
*
1179364 TATCGATACAATGAAT-ATATATCGATACATTA
1 TATCGATACAAAGAATAATATATCGATACATTA
* *
1179396 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAGAATAATATATCGATACA
1179426 ACTGGGTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (33 bp):
TATCGATACAAAGAATAATATATCGATACATTA
Found at i:1186395 original size:3 final size:3
Alignment explanation
Indices: 1186387--1186431 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1186377 TCATCCGAGC
* *
1186387 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT TAT CAT CTT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1186432 TGTCTTTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:1190888 original size:13 final size:13
Alignment explanation
Indices: 1190870--1190895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1190860 TACACCAAGT
1190870 ATGTATCGATACA
1 ATGTATCGATACA
1190883 ATGTATCGATACA
1 ATGTATCGATACA
1190896 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1190914 original size:34 final size:32
Alignment explanation
Indices: 1190852--1190916 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1190842 TAGCCAAACT
**
1190852 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1190884 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1190917 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1197070 original size:13 final size:13
Alignment explanation
Indices: 1197052--1197089 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1197042 GGAAATTCAA
1197052 TGTATCGATACAT
1 TGTATCGATACAT
1197065 TGTATCGATACAT
1 TGTATCGATACAT
1197078 TGTATCGATACA
1 TGTATCGATACA
1197090 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1197235 original size:21 final size:20
Alignment explanation
Indices: 1197211--1197257 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1197201 AAATCTTTTG
*
1197211 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACTTTATTTTTCA--T
*
1197232 CAAATTACTTTATTTTTCAT
1 CAAAATACTTTATTTTTCAT
1197252 CAAAAT
1 CAAAAT
1197258 CAGCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (20 bp):
CAAAATACTTTATTTTTCAT
Found at i:1197574 original size:21 final size:20
Alignment explanation
Indices: 1197532--1197574 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1197522 GCAGCACCCA
* *
1197532 CCAGGTCGCGACCGGCATTC
1 CCAGGTCGCAACCGGCAGTC
1197552 CCAGGTCGCAACCGGGCAGTC
1 CCAGGTCGCAACC-GGCAGTC
1197573 CC
1 CC
1197575 CACACTAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.16, C:0.42, G:0.30, T:0.12
Consensus pattern (20 bp):
CCAGGTCGCAACCGGCAGTC
Found at i:1199680 original size:13 final size:13
Alignment explanation
Indices: 1199662--1199687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1199652 TACACCAAGT
1199662 ATGTATCGATACA
1 ATGTATCGATACA
1199675 ATGTATCGATACA
1 ATGTATCGATACA
1199688 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1199706 original size:34 final size:34
Alignment explanation
Indices: 1199644--1199739 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
1199634 TAGCCAAACT
**
1199644 TGTATCGATACACC-AAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAAATTGTATCGATACAA
1199676 TGTATCGATACACCAAAAAATTGTATCGATACAA
1 TGTATCGATACACCAAAAAATTGTATCGATACAA
1199710 TGTATCGATACACCAAAAAATTGTATCGAT
1 TGTATCGATACACCAAAAAATTGTATCGAT
1199740 TCATTGGCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 14 0.23
33 3 0.05
34 43 0.72
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAATTGTATCGATACAA
Found at i:1199715 original size:13 final size:13
Alignment explanation
Indices: 1199697--1199721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1199687 ACCAAAAAAT
1199697 TGTATCGATACAA
1 TGTATCGATACAA
1199710 TGTATCGATACA
1 TGTATCGATACA
1199722 CCAAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1200929 original size:130 final size:130
Alignment explanation
Indices: 1200696--1200969 Score: 334
Period size: 130 Copynumber: 2.1 Consensus size: 130
1200686 TCATCACGGA
* * * * *
1200696 GATACTCCAATCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAATCCC
1 GATACTCCAACCCCAATTTTATTTCTAAAACACCAATATTTCACAATCAGGGATACTCCAATCCC
* * * * ** * *
1200761 CTTATTTTTGAGGGGATAATCTAACTCCGGTTTTATTTCTAAAATATTGA-TTTCTCAAAATCGG
66 CTTATTTTCGAGGGGATAATCCAACCCCAGCCTTATTTCTAAAACATCGATTTTC-CAAAATCGG
1200825 G
130 G
* * *
1200826 GATACTTCAACCCCAATTTTATTTCTAAAACACCAATATTTCACAATCGGGGATACTCCAATCCT
1 GATACTCCAACCCCAATTTTATTTCTAAAACACCAATATTTCACAATCAGGGATACTCCAATCCC
* * * * *
1200891 GTTATTTTCGTGGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTCCACAATCGGG
66 CTTATTTTCGAGGGGATAATCCAACCCCAGCCTTATTTCTAAAACATCGATTTTCCAAAATCGGG
*
1200956 GATGCTCCAACCCC
1 GATACTCCAACCCC
1200970 GTTATTTTCG
Statistics
Matches: 120, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 116 0.97
131 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (130 bp):
GATACTCCAACCCCAATTTTATTTCTAAAACACCAATATTTCACAATCAGGGATACTCCAATCCC
CTTATTTTCGAGGGGATAATCCAACCCCAGCCTTATTTCTAAAACATCGATTTTCCAAAATCGGG
Found at i:1201054 original size:79 final size:80
Alignment explanation
Indices: 1200823--1201047 Score: 264
Period size: 79 Copynumber: 2.9 Consensus size: 80
1200813 TCTCAAAATC
* * *
1200823 GGGGATACTTCAACCCCA-ATTTTATTTCTAAAACACCAATATTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAGATTTTATTTCTAAAACACTAATTTTTCACAATCGGGGATACTCCAA
* *
1200887 TCCTGTTATTTTCGT
66 CCCTGTTATTTTCGA
** * * * *
1200902 GGGGATACTCCAACCCCAG-CCTTATTTCTAAAGCA-TCGATTTTCCACAATCGGGGATGCTCCA
1 GGGGATACTCCAACCCCAGATTTTATTTCTAAAACACT-AATTTTTCACAATCGGGGATACTCCA
*
1200965 ACCCCGTTATTTTCGA
65 ACCCTGTTATTTTCGA
* *
1200981 GGGGATACTCCAA-CCCAGATTTTATTT-TCAAAACACTAATTTTTTATAATCGGGGATACTCC-
1 GGGGATACTCCAACCCCAGATTTTATTTCT-AAAACACTAATTTTTCACAATCGGGGATACTCCA
1201043 ACCCT
65 ACCCT
1201048 TATTATTATC
Statistics
Matches: 120, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
78 10 0.08
79 109 0.91
80 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (80 bp):
GGGGATACTCCAACCCCAGATTTTATTTCTAAAACACTAATTTTTCACAATCGGGGATACTCCAA
CCCTGTTATTTTCGA
Found at i:1205712 original size:43 final size:43
Alignment explanation
Indices: 1205651--1206164 Score: 524
Period size: 43 Copynumber: 11.1 Consensus size: 43
1205641 TAAAGGTGGA
* * *
1205651 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205694 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* * * *
1205743 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1205786 AGAGGTGCCAATGTGCTGATTCAAGGCCAGCTTCATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205829 AAAGGTGAGGTGCCAATGTGCTGATTCAATGCCAAGCTACATTGGACTT
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCC-AGCTACATTGGACTT
*
1205878 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* * *
1205933 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1205976 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1206019 AAAGGTGAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
1206067 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1206116 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1206159 AGAAGG
1 A-AAGG
1206165 GTTTCCACCG
Statistics
Matches: 403, Mismatches: 34, Indels: 67
0.80 0.07 0.13
Matches are distributed among these distances:
43 157 0.39
44 9 0.02
48 66 0.16
49 139 0.34
50 25 0.06
51 1 0.00
52 3 0.01
53 1 0.00
54 1 0.00
55 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1205719 original size:21 final size:21
Alignment explanation
Indices: 1205652--1205719 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1205642 AAAGGTGGAA
1205652 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
1205673 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
1205695 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1205716 AAGG
1 AAGG
1205720 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 14 0.39
22 10 0.28
23 2 0.06
24 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1205765 original size:49 final size:49
Alignment explanation
Indices: 1205546--1206159 Score: 679
Period size: 49 Copynumber: 12.9 Consensus size: 49
1205536 AAGATGAGAA
* * *
1205546 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1205596 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
1205648 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1205694 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1205743 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTT--AG--
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1205788 --AGGTGCCAATGTGCTGATTCAAGGCCAGCTTCATTGGACTTAAAGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1205835 -GAGGTGCCAATGTGCTGATTCAATGCCAAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCC-AGCTACATTGGACTTAAAGAT
* * *
1205884 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
1205933 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1205976 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1206025 -GAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
1206072 AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T
1 A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
1206116 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1206160 GAAGGGTTTC
Statistics
Matches: 492, Mismatches: 45, Indels: 56
0.83 0.08 0.09
Matches are distributed among these distances:
43 150 0.30
44 4 0.01
45 2 0.00
46 1 0.00
47 2 0.00
48 70 0.14
49 153 0.31
50 24 0.05
51 1 0.00
52 80 0.16
53 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:1205792 original size:92 final size:92
Alignment explanation
Indices: 1205601--1206161 Score: 670
Period size: 92 Copynumber: 6.0 Consensus size: 92
1205591 AAGATGGAAA
* *
1205601 AGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGGAAAAGGTGCCAATATG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT---AAAGGTGCCAATATG
* * *
1205666 CTGATTCAAGGCCAGCGATATTGGACTTAA
63 CTGATTCAAGGCCAGCTACATTGGACTTAG
* *
1205696 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGTTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCTG
* *
1205761 ATTCAAGGCCAGCTATATTGGGCTTAG
66 ATTCAAGGCCAGCTACATTGGACTTAG
* * * *
1205788 AGGTGCCAATGTGCTGATTCAAGGCCAGCTTCATTGGACTTAAAGGT-GAGGTGCCAATGTGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCTG
*
1205852 ATTCAATGCCAAGCTACATTGGACTTAAAGATG
66 ATTCAAGGCC-AGCTACATTGGACTT----A-G
* * *
1205885 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCT
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCT
* * *
1205950 AATTCAAGGCCAGCTATATTGGACTTAA
65 GATTCAAGGCCAGCTACATTGGACTTAG
* * * * *
1205978 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCTAATGTGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCTG
1206042 ATTCAAGGCCAGCTACATTGGACTTAAAGAAG
66 ATTCAAGGCCAGCTACATTGGACTT-----AG
* * *
1206074 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCAATGTGCT
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCT
1206133 GATTCAAGGCCAGCTACATTGGACTTAG
65 GATTCAAGGCCAGCTACATTGGACTTAG
1206161 A
1 A
1206162 AGGGTTTCCA
Statistics
Matches: 413, Mismatches: 38, Indels: 39
0.84 0.08 0.08
Matches are distributed among these distances:
86 1 0.00
87 2 0.00
91 61 0.15
92 184 0.45
94 1 0.00
95 44 0.11
96 3 0.01
97 36 0.09
98 58 0.14
99 23 0.06
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTAAAGGTGCCAATATGCTG
ATTCAAGGCCAGCTACATTGGACTTAG
Found at i:1206237 original size:28 final size:27
Alignment explanation
Indices: 1206197--1206257 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1206187 TTTGAGAAGA
* *
1206197 AAAAGGTTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACAGAATTGTGGAC-TT
* *
1206225 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAATTGTGGACTT
1206252 AAAAGG
1 AAAAGG
1206258 AACAAGGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAATTGTGGACTT
Found at i:1206299 original size:34 final size:34
Alignment explanation
Indices: 1206225--1206421 Score: 297
Period size: 34 Copynumber: 5.8 Consensus size: 34
1206215 TGTGGGCTTT
* * *
1206225 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
1206258 AACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1206292 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
1206326 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*** * *
1206360 ATGGAGGTGCCACGAAGTTGCGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1206394 AAAAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT
1206422 GCAGAAAAGG
Statistics
Matches: 146, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 22 0.15
34 124 0.85
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:1206385 original size:102 final size:95
Alignment explanation
Indices: 1206183--1206421 Score: 300
Period size: 102 Copynumber: 2.4 Consensus size: 95
1206173 CGACTTGTGT
* * * *
1206183 GGGCTTTGAGAAGAAAAAGGTTGCCACAGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGG
1 GGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGG
* *
1206248 ACTTAAAAGGAACAAGGTGCCACGGAGTTGT
65 ACTTAAAAGGAACAAGGTGCCACGAAGTTGC
1206279 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAG-----GGTGCCACGGAGT
* ***
1206344 TGTGGGCTTTGAAAA-GATGGAGGTGCCACGAAGTTGC
60 TGTGGAC-TT-AAAAGGAACAAGGTGCCACGAAGTTGC
1206381 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1206422 GCAGAAAAGG
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
95 19 0.15
96 23 0.18
101 19 0.15
102 60 0.48
103 4 0.03
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22
Consensus pattern (95 bp):
GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGA
CTTAAAAGGAACAAGGTGCCACGAAGTTGC
Found at i:1206422 original size:68 final size:66
Alignment explanation
Indices: 1206180--1206422 Score: 307
Period size: 68 Copynumber: 3.7 Consensus size: 66
1206170 CACCGACTTG
* * * *
1206180 TGTGGGCTTTGAGAAGAAAAAGGTTGCCACAGAATTGTGGGCTTT--AAA-AG-GGTGCCACGGA
1 TGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTGAAAAGAGAGGTGCCACGGA
1206241 GT
65 GT
* * * * *
1206243 TGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGG
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG--AGAGGTGCCACGG
1206307 AGT
64 AGT
*
1206310 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGATGGAGGTGCCACGA
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA--GAGGTGCCACGG
1206375 AGT
64 AGT
*
1206378 TGCGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG
1206423 CAGAAAAGGA
Statistics
Matches: 156, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
61 19 0.12
62 11 0.07
63 9 0.06
66 2 0.01
67 19 0.12
68 96 0.62
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (66 bp):
TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAGAGGTGCCACGGAG
T
Found at i:1206535 original size:31 final size:31
Alignment explanation
Indices: 1206395--1206553 Score: 178
Period size: 32 Copynumber: 5.1 Consensus size: 31
1206385 TTTAAAAAGA
* * *
1206395 AAAAGG-TGCCACGGAGTTGTGGGCTTTGCAG
1 AAAAGGATGCCACTGAGTCGTGGACTTTG-AG
*
1206426 AAAAGGATGCCACTAAGTCGTGGACTTTGAG
1 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
** * *
1206457 ACAAAATATGCCACTAAGTCATGGACTTTGAAG
1 A-AAAGGATGCCACTGAGTCGTGGACTTTG-AG
1206490 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
* *
1206521 AAGA-GATTGCCACTGAGTCGTGGACTTTAAG
1 AAAAGGA-TGCCACTGAGTCGTGGACTTTGAG
1206552 AA
1 AA
1206554 GGTATTTGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.02
31 39 0.35
32 67 0.60
33 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.23
Consensus pattern (31 bp):
AAAAGGATGCCACTGAGTCGTGGACTTTGAG
Found at i:1207834 original size:1 final size:1
Alignment explanation
Indices: 1207828--1207888 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
1207818 GCCTTTGCAC
* * * * * * *
1207828 TTTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTCTTTTTTGTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1207889 GGAAAAGAAC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:1207843 original size:10 final size:10
Alignment explanation
Indices: 1207828--1207872 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
1207818 GCCTTTGCAC
1207828 TTTTTTTTTG
1 TTTTTTTTTG
1207838 TTTTTTTTTG
1 TTTTTTTTTG
*
1207848 TTTTTTTGT-
1 TTTTTTTTTG
*
1207857 TTTTTTTTTC
1 TTTTTTTTTG
1207867 TTTTTT
1 TTTTTT
1207873 GTTTTCTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 8 0.25
10 24 0.75
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1207851 original size:18 final size:17
Alignment explanation
Indices: 1207828--1207888 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 17
1207818 GCCTTTGCAC
1207828 TTTTTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTT
1207845 TTGTTTTTTTGTTTTTTT
1 TT-TTTTTTTGTTTTTTT
1207863 TTTCTTTTTTGTTTTCTTT
1 TTT-TTTTTTGTTTT-TTT
*
1207882 CTTTTTT
1 TTTTTTT
1207889 GGAAAAGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 3 0.08
18 32 0.80
19 5 0.12
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTGTTTTTTT
Found at i:1207859 original size:26 final size:27
Alignment explanation
Indices: 1207829--1207888 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1207819 CCTTTGCACT
* *
1207829 TTTTTTTTGTTTTTTTTTGTTTT-TTTG
1 TTTTTTTT-TTCTTTTTTGTTTTCTTTC
1207856 TTTTTTTTTTCTTTTTTGTTTTCTTTC
1 TTTTTTTTTTCTTTTTTGTTTTCTTTC
1207883 TTTTTT
1 TTTTTT
1207889 GGAAAAGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (27 bp):
TTTTTTTTTTCTTTTTTGTTTTCTTTC
Found at i:1208132 original size:299 final size:301
Alignment explanation
Indices: 1207587--1208156 Score: 927
Period size: 299 Copynumber: 1.9 Consensus size: 301
1207577 TTTTTTTGTA
* * * *
1207587 TTTGGAAAAGAACAATTTTTCGAAGAGTAGGTTCTCCAGTTCACCCGGCAATGTTCGATCGAAAT
1 TTTGGAAAAGAACAATTCTCCGAAGAGTAGGTTCTCCAGTTCACCCGACAATGTCCGATCGAAAT
* *
1207652 GGACTTTTGAAGGACCGTAATATAGGCTAAGGTTCTTGGTTCAGAAAGAAAGGATAAAAAGGCCC
66 GGACTTTTGAAGGACCGTAACATAGGCCAAGGTTCTTGGTTCAGAAAGAAAGGATAAAAAGGCCC
1207717 AAAAATATGTCATTTTAAGGGTAATAGGATCAAGGATCATTTTTGTTCATATAGGCATTCATGTC
131 AAAAATATGTCATTTTAAGGGTAATAGGATCAAGGATCATTTTTGTTCATATAGGCATTCATGTC
* * *
1207782 CTTGTTTTTTGACTTTGGTGCTCCCTTTTTGATTTTGCCTTTGCACTTTTTTTT-TGTTTTTT-T
196 CTTGTTTTTCGACTTTGGTGCTCCCTTTTTGATTTTGACTTTGCACTTTTTTTTCTGTTTTTTGC
1207845 TTGTTTTTTTGTTTTTTTTTTCTTTTTTGTTTTCTTTCTTT
261 TTGTTTTTTTGTTTTTTTTTTCTTTTTTGTTTTCTTTCTTT
*
1207886 TTTGGAAAAGAACAATTCTCCGAAGAGTAGGTTTTCCAGTTCACCCGACAATGTCCGATC-AAAG
1 TTTGGAAAAGAACAATTCTCCGAAGAGTAGGTTCTCCAGTTCACCCGACAATGTCCGATCGAAA-
*
1207950 TGGACTTTTGAAGGACCGTAACGTAGGCCAAGGTTCTTGGTTCAGAAAGAAAGGATAAAAAGGCC
65 TGGACTTTTGAAGGACCGTAACATAGGCCAAGGTTCTTGGTTCAGAAAGAAAGGATAAAAAGGCC
*
1208015 C-AAAATATGTCATTTTAAGGGTAATAGGATCAAGGATCA-TTTTGTTCATAT-GAGTATTCATG
130 CAAAAATATGTCATTTTAAGGGTAATAGGATCAAGGATCATTTTTGTTCATATAG-GCATTCATG
* *
1208077 TCCTTGTTTTTCGACCTTTGTTGTTCCCTTTTTGATTTTGACTTTGCACCTTTTTTTTCGTGTTT
194 TCCTTGTTTTTCGA-CTTTGGTGCTCCCTTTTTGATTTTGACTTTGCA-CTTTTTTTTC-TGTTT
1208142 TTTGCTTGTTTTTTT
256 TTTGCTTGTTTTTTT
1208157 TTCATCATTT
Statistics
Matches: 250, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
296 1 0.00
297 33 0.13
298 71 0.28
299 127 0.51
301 8 0.03
302 10 0.04
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (301 bp):
TTTGGAAAAGAACAATTCTCCGAAGAGTAGGTTCTCCAGTTCACCCGACAATGTCCGATCGAAAT
GGACTTTTGAAGGACCGTAACATAGGCCAAGGTTCTTGGTTCAGAAAGAAAGGATAAAAAGGCCC
AAAAATATGTCATTTTAAGGGTAATAGGATCAAGGATCATTTTTGTTCATATAGGCATTCATGTC
CTTGTTTTTCGACTTTGGTGCTCCCTTTTTGATTTTGACTTTGCACTTTTTTTTCTGTTTTTTGC
TTGTTTTTTTGTTTTTTTTTTCTTTTTTGTTTTCTTTCTTT
Found at i:1209964 original size:60 final size:61
Alignment explanation
Indices: 1209780--1210258 Score: 495
Period size: 61 Copynumber: 8.0 Consensus size: 61
1209770 GAGCAAGACG
* * **
1209780 CCTTTCAAAGCCCACACCAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
1209840 -C----AAAGCCCACACAAGCTAGTGGCACCTT-CAGT-CTCAAAGAGTAGGATGACTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1209894 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTGTCCTCAAAGAGAAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
1209954 CCTTTTAAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGCA-AACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1210015 CCTTTTAAAGCCCA-TCAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-TTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTT-T
* * * * *
1210075 CCTTTTAAAGACCAAACAAATTGGTGGCACCTTCCAGTCCTTAAAGAGCAGGATG-C-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
*
1210134 CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* ** ** * **
1210197 -CTTTTCAAAGCCCACACGAA-TTGATGGCAATTTTTAGTCCTTAAAGAATAGGACGCCTTTT
1 CCTTTT-AAAGCCCACAC-AAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
1210258 C
1 C
1210259 TTTCTCTCCT
Statistics
Matches: 351, Mismatches: 49, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
53 15 0.04
54 7 0.02
55 23 0.07
59 52 0.15
60 82 0.23
61 153 0.44
62 16 0.05
63 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1210083 original size:181 final size:179
Alignment explanation
Indices: 1209780--1210213 Score: 539
Period size: 181 Copynumber: 2.4 Consensus size: 179
1209770 GAGCAAGACG
*
1209780 CCTTTCAAAGCCCACACCAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTTC--
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTT
*
1209841 --AAAGCCCACACAAGCTAGTGGCACCTTCAGTCTCAAAGAGTAGGATGACTTTTCCTTTTAAAG
66 TTAAAGCCCACACAAGCTAGTGGCACCTTCAGTCTCAAAGAGCAGGATGACTTTTCCTTTTAAAG
* * * *
1209904 CCCACACAAGTTGGTGGCACCTT-CTGTCCTCAAAGAGAAGGACGCCTTTT
131 ACCAAACAAATTGGTGGCACCTTCCAGTCCTCAAAGAGAAGGACG-C-TTT
* * * * *
1209954 CCTTTTAAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGCA-AACACCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-CT
* * * *
1210018 TTTAAAGCCCA-TCAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-TTTTCTCCTTTT
65 TTTAAAGCCCACACAAGCTAGTGGCACCTT-CAGT-CTCAAAGAGCAGGATGACTTT-TCCTTTT
* * *
1210081 AAAGACCAAACAAATTGGTGGCACCTTCCAGTCCTTAAAGAGCAGGATGCTTT
127 AAAGACCAAACAAATTGGTGGCACCTTCCAGTCCTCAAAGAGAAGGACGCTTT
*
1210134 CTCTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
1 C-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
1210198 TTTTCAAAGCCCACAC
64 TTTT-AAAGCCCACAC
1210214 GAATTGATGG
Statistics
Matches: 219, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
174 30 0.14
175 23 0.11
176 1 0.00
179 15 0.07
180 19 0.09
181 74 0.34
182 56 0.26
183 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (179 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTT
TTAAAGCCCACACAAGCTAGTGGCACCTTCAGTCTCAAAGAGCAGGATGACTTTTCCTTTTAAAG
ACCAAACAAATTGGTGGCACCTTCCAGTCCTCAAAGAGAAGGACGCTTT
Found at i:1210219 original size:122 final size:120
Alignment explanation
Indices: 1209780--1210213 Score: 480
Period size: 121 Copynumber: 3.6 Consensus size: 120
1209770 GAGCAAGACG
* **
1209780 CCTTTCAAAGCCCACACCAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC----C-TTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTTCTTTT
* * *
1209840 CAAAGCCCACACAAGCTAGTGGCACCTT-CAGT-CTCAAAGAGTAGGATGACTTTT
66 CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTT
* * *
1209894 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTGTCCTCAAAGAGAAGGACGCCTTTTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-CTTTT-CTT
* * * * **
1209958 TT-AAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGCA-AACACCTTTT
64 TTCAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGA-TGCTTTT
* * *
1210015 CCTTTTAAAGCCCA-TCAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-TTTTCTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTTCT--T
* * * * *
1210078 TTTAAAGACCAAACAAATTGGTGGCACCTTCCAGTCCTTAAAGAGCAGGATGC-TTT
64 TTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTT
1210134 CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCT
1 C-CTTT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-CTTTTCT
1210199 TTTCAAAGCCCACAC
63 TTTCAAAGCCCACAC
1210214 GAATTGATGG
Statistics
Matches: 264, Mismatches: 35, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
113 19 0.07
114 30 0.11
118 2 0.01
119 30 0.11
120 47 0.18
121 70 0.27
122 60 0.23
124 6 0.02
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (120 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTTCTTTT
CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTT
Found at i:1210391 original size:41 final size:41
Alignment explanation
Indices: 1210265--1210583 Score: 252
Period size: 41 Copynumber: 7.5 Consensus size: 41
1210255 TTTCTTTCTC
*
1210265 TCCTTTGTCCTTAAAGAGCAGGACACATTTCATTTCCTTCTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCC-T-TTT
* ** ** *
1210308 TCCCTTTTGTCTTCAAAGAGCAGGATGC-TTTTTTTTCTTTTT
1 T-CC-TTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTT
* *
1210350 TCCTTTGTCCTCAAAGAGCGGGACACACTTCATTTCCTTTTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCC--TTTT
* *
1210393 TCCCTTCTAGTTCTCAAAGAGTAGGACACACTTT-ATTCTCCTTTT
1 T-CCTT-T-GTCCTCAAAGAGCAGGACACA-TTTCATT-TCCTTTT
* *
1210438 TCCTTTGTCCTCAGAA-AGCAAGACACATTTAATTTCCTTTT
1 TCCTTTGTCCTCA-AAGAGCAGGACACATTTCATTTCCTTTT
* * ** *
1210479 TCCTTTGTCTTCAAAGGGCAGGATGCATTTTATTTCCTTTTT
1 TCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCC-TTTT
* * * *
1210521 TCCTTAGTCCCCAAGGAGCAAGAC-CTATTTCATTCTCC-TTT
1 TCCTTTGTCCTCAAAGAGCAGGACAC-ATTTCATT-TCCTTTT
**
1210562 TCCTTAATCCTCAAAGAGCAGG
1 TCCTTTGTCCTCAAAGAGCAGG
1210584 GCACCCTCTT
Statistics
Matches: 220, Mismatches: 40, Indels: 34
0.75 0.14 0.12
Matches are distributed among these distances:
40 21 0.10
41 68 0.31
42 50 0.23
43 13 0.06
44 17 0.08
45 25 0.11
46 21 0.10
47 5 0.02
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (41 bp):
TCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTT
Found at i:1210394 original size:85 final size:85
Alignment explanation
Indices: 1210254--1210562 Score: 299
Period size: 85 Copynumber: 3.6 Consensus size: 85
1210244 ATAGGACGCC
* * *
1210254 TTTTCTTTCTCTCCTTTGTCCTTAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTTTGTC
1 TTTTCTTT-TTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTC
1210319 TTCAAAGAGCAGGATGCTTTT
65 TTCAAAGAGCAGGATGCTTTT
* * *
1210340 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCGGGACACACTTCATTTCCTTTTTTTCCCTTCTAGT-
1 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTT-TTGTC
* ** *
1210404 TCTCAAAGAGTAGGACACACTTTA
65 T-TCAAAGAGCAGG--ATGCTTTT
* * * *
1210428 TTCTCCTTTTTCCTTTGTCCTCAGAA-AGCAAGACACATTTAATTTCC--TTTTT-CC-TTTGTC
1 TTTTCTTTTTTCCTTTGTCCTCA-AAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTC
*
1210488 TTCAAAGGGCAGGATGCATTTT
65 TTCAAAGAGCAGGATGC-TTTT
* * * * *
1210510 ATTTCCTTTTTTCCTTAGTCCCCAAGGAGCAAGAC-CTATTTCATTCTCCTTTT
1 -TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACAC-ATTTCATT-TCCTTTT
1210563 CCTTAATCCT
Statistics
Matches: 181, Mismatches: 29, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
81 2 0.01
82 5 0.03
83 46 0.25
84 5 0.03
85 49 0.27
86 29 0.16
88 43 0.24
89 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.43
Consensus pattern (85 bp):
TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTCT
TCAAAGAGCAGGATGCTTTT
Found at i:1210541 original size:83 final size:85
Alignment explanation
Indices: 1210265--1210562 Score: 297
Period size: 83 Copynumber: 3.5 Consensus size: 85
1210255 TTTCTTTCTC
* * *
1210265 TCCTTTGTCCTTAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTTTGTCTTCAAAGAGCA
1 TCCTTTGTCCTCAAGGAGCAAGACACATTTCATTTCCTT-TTTTCCC-TTTGTCTTCAAAGAGCA
*
1210330 GGATGC-TTTT-TTTTCTTTTT
64 GGATGCATTTTATTTCCTTTTT
* ** *
1210350 TCCTTTGTCCTCAAAGAGCGGGACACACTTCATTTCCTTTTTTTCCCTTCTAGT-TCTCAAAGAG
1 TCCTTTGTCCTCAAGGAGCAAGACACATTTCATTTCC-TTTTTTCCCTT-T-GTCT-TCAAAGAG
* ** *
1210414 TAGGACACACTTTATTCTCC-TTTT
62 CAGGATGCATTTTATT-TCCTTTTT
* * *
1210438 TCCTTTGTCCTC-AGAAAGCAAGACACATTTAATTTCC-TTTTT-CCTTTGTCTTCAAAGGGCAG
1 TCCTTTGTCCTCAAG-GAGCAAGACACATTTCATTTCCTTTTTTCCCTTTGTCTTCAAAGAGCAG
1210500 GATGCATTTTATTTCCTTTTT
65 GATGCATTTTATTTCCTTTTT
* *
1210521 TCCTTAGTCCCCAAGGAGCAAGAC-CTATTTCATTCTCCTTTT
1 TCCTTTGTCCTCAAGGAGCAAGACAC-ATTTCATT-TCCTTTT
1210563 CCTTAATCCT
Statistics
Matches: 176, Mismatches: 23, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
82 4 0.02
83 50 0.28
84 9 0.05
85 50 0.28
86 22 0.12
87 4 0.02
88 35 0.20
89 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (85 bp):
TCCTTTGTCCTCAAGGAGCAAGACACATTTCATTTCCTTTTTTCCCTTTGTCTTCAAAGAGCAGG
ATGCATTTTATTTCCTTTTT
Found at i:1211170 original size:20 final size:20
Alignment explanation
Indices: 1211145--1211249 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1211135 TTTTCACAAT
1211145 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1211165 TTGTATCGATACATTCTAGGTTTTACCTA
1 TTGTATCGATACA-T-T--G--TT--C-A
* * * *
1211194 GATGTATGGATATATTATTCA
1 -TTGTATCGATACATTGTTCA
*
1211215 TTGTATCGCTACATTGTTCA
1 TTGTATCGATACATTGTTCA
1211235 TTGTATCGATACATT
1 TTGTATCGATACATT
1211250 ATATCGATAC
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
20 42 0.65
21 2 0.03
22 2 0.03
24 3 0.05
26 2 0.03
28 2 0.03
29 2 0.03
30 10 0.15
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1211249 original size:13 final size:13
Alignment explanation
Indices: 1211233--1211262 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1211223 CTACATTGTT
*
1211233 CATTGTATCGATA
1 CATTATATCGATA
1211246 CATTATATCGATA
1 CATTATATCGATA
1211259 CATT
1 CATT
1211263 CTAGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:1213767 original size:51 final size:51
Alignment explanation
Indices: 1213681--1213793 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
1213671 TCGAGGGGAT
* * * **
1213681 ACTCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCAAAATCA-AGGAC
1 ACTCCAACCCCAACTTTATTTCTAAAACACCAATTTCTCAAAATCAGA-GAC
* * * * *
1213732 ACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGAGAT
1 ACTCCAACCCCAACTTTATTTCTAAAACACCAATTTCTCAAAATCAGAGAC
1213783 ACTCCAACCCC
1 ACTCCAACCCC
1213794 GTTATTTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.30
Consensus pattern (51 bp):
ACTCCAACCCCAACTTTATTTCTAAAACACCAATTTCTCAAAATCAGAGAC
Found at i:1213863 original size:79 final size:79
Alignment explanation
Indices: 1213732--1213954 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 79
1213722 AATCAAGGAC
**
1213732 ACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTT
1 ACTCCAACCCCAACCTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTT
*
1213797 ATTTTGGCA-GGGAT
66 ATTTTCG-AGGGGAT
* ** * * * * *
1213811 ACTCCAACCCCAGCCTTATTTCTAAAGTATCGATTTTTCACAATCGGGGATACTCCAATCTCGTT
1 ACTCCAACCCCAACCTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTT
1213876 ATTTTCGAGGGGAT
66 ATTTTCGAGGGGAT
* * * ** * * *
1213890 ACTCTAACCTCGATTTTATTT-TCAAAACACTAA-TTTTCTATAATC-GAGGATACTCCATCCCC
1 ACTCCAACCCCAACCTTATTTCT-AAAACACCAATTTTTC-ACAATCGGA-GATACTCCAACCCC
1213952 GTT
63 GTT
1213955 GTTATCCCCA
Statistics
Matches: 113, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
78 8 0.07
79 105 0.93
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (79 bp):
ACTCCAACCCCAACCTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTT
ATTTTCGAGGGGAT
Found at i:1213866 original size:130 final size:130
Alignment explanation
Indices: 1213595--1213868 Score: 322
Period size: 130 Copynumber: 2.1 Consensus size: 130
1213585 TTTTTCATCA
* ** * * *
1213595 CAGGGATACTCCAACTCCGGTTTTATTTCCAAAACATCAATTTTTTATAATCGATGATACTCCAA
1 CAGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACAATCGATGATACTCCAA
* * *
1213660 TCCCCTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCAAAAT
66 TCCCCTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCTAAAATATCAATTTCTCAAAAT
* * *
1213725 CAAGGACACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGA-GATACTCCA
1 CAGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACAATC-GATGATACTCCA
* * * *
1213789 A-CCCCGTTATTTTGGCA-GGGATACTCCAACCCC-AGCCTTATTTCTAAAGTATCGATTTTTCA
65 ATCCCC-TTATTTTCG-AGGGGATACTCCAACCCCGA-CCTTATTTCTAAAATATCAATTTCTCA
*
1213851 CAAT
127 AAAT
*
1213855 CGGGGATACTCCAA
1 CAGGGATACTCCAA
1213869 TCTCGTTATT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
129 5 0.04
130 112 0.93
131 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (130 bp):
CAGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCACAATCGATGATACTCCAA
TCCCCTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCTAAAATATCAATTTCTCAAAAT
Found at i:1215060 original size:13 final size:13
Alignment explanation
Indices: 1215042--1215066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215032 ACAATGAATA
1215042 TGTATCGATACAT
1 TGTATCGATACAT
1215055 TGTATCGATACA
1 TGTATCGATACA
1215067 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1220599 original size:20 final size:21
Alignment explanation
Indices: 1220576--1220627 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1220566 TTTCAGGCAC
1220576 GTATCGATACATTCACT-TAT
1 GTATCGATACATTCACTATAT
* *
1220596 GTATCGACACATTCACTATTT
1 GTATCGATACATTCACTATAT
*
1220617 GTATCGTTACA
1 GTATCGATACA
1220628 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATCGATACATTCACTATAT
Found at i:1224714 original size:14 final size:13
Alignment explanation
Indices: 1224695--1224726 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1224685 ATTATCAAAT
1224695 AAATTTTTTAATTA
1 AAATTTTTTAA-TA
1224709 AAATTTTTTAATA
1 AAATTTTTTAATA
1224722 AAATT
1 AAATT
1224727 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AAATTTTTTAATA
Found at i:1225413 original size:21 final size:20
Alignment explanation
Indices: 1225378--1225423 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1225368 AAATTGAATC
1225378 ATATAAAAAATTTTAAAAAT
1 ATATAAAAAATTTTAAAAAT
* *
1225398 ATATAAAACTATTTTAAATAT
1 ATATAAAA-AATTTTAAAAAT
1225419 ATATA
1 ATATA
1225424 TATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAAAAAATTTTAAAAAT
Found at i:1227332 original size:2 final size:2
Alignment explanation
Indices: 1227320--1227372 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1227310 CCTAGTAGAA
*
1227320 AT AT GT AT AT AT 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 AT AT AT AT AT AT
1227362 AT AT AT AT AT A
1 AT AT AT AT AT A
1227373 AACTTACAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1232016 original size:3 final size:3
Alignment explanation
Indices: 1232008--1232032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1231998 ACCATTTAGC
1232008 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1232033 CCGATGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1232255 original size:16 final size:16
Alignment explanation
Indices: 1232236--1232280 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1232226 AATAATTAAA
1232236 TTAATTAAATTT-TCAT
1 TTAATTAAATTTAT-AT
*
1232252 TTAATTTAATTTATAT
1 TTAATTAAATTTATAT
*
1232268 TAAATTAAATTTA
1 TTAATTAAATTTA
1232281 AATATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTAAATTTATAT
Found at i:1232321 original size:37 final size:36
Alignment explanation
Indices: 1232219--1232342 Score: 100
Period size: 38 Copynumber: 3.4 Consensus size: 36
1232209 TATTAAATAA
*
1232219 TAATTTTAA-TAATTAAAT-TAA-TTAAAT-TTTCATT
1 TAATTTTAATTAATTTAATATAATTTAAATATTT--TT
*
1232253 TAA-TTTAATTTATATTAA-ATTAAATTTAAATATTTTT
1 TAATTTTAATTAAT-TTAATA-T-AATTTAAATATTTTT
1232290 TAATTTTAATTAATTTAATATAATTTAAAATATATTTT
1 TAATTTTAATTAATTTAATATAATTT-AAATAT-TTTT
*
1232328 T-ATTTAAATTTAATT
1 TAATTTTAA-TTAATT
1232343 ATAAAACTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
33 5 0.07
34 6 0.08
35 3 0.04
36 6 0.08
37 24 0.32
38 27 0.36
39 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.56
Consensus pattern (36 bp):
TAATTTTAATTAATTTAATATAATTTAAATATTTTT
Found at i:1232354 original size:42 final size:39
Alignment explanation
Indices: 1232244--1232354 Score: 90
Period size: 36 Copynumber: 2.8 Consensus size: 39
1232234 AATTAATTAA
*
1232244 ATTTTCATTTAATTTAATTTATATTAAAT-TAAATTTAAATAT
1 ATTTTTATTTAATTTAA-TTATA--AAATAT-AATTTAAATAT
1232286 -TTTTTAATTTTAA-TTAATT-T--AATATAATTTAAAATAT
1 ATTTTT-A-TTTAATTTAATTATAAAATATAATTT-AAATAT
1232323 ATTTTTATTTAAATTTAATTATAAAACTATAA
1 ATTTTTATTT-AATTTAATTATAAAA-TATAA
1232355 AAATCAAATC
Statistics
Matches: 57, Mismatches: 1, Indels: 22
0.71 0.01 0.28
Matches are distributed among these distances:
36 11 0.19
37 10 0.18
38 11 0.19
39 1 0.02
40 1 0.02
41 8 0.14
42 10 0.18
43 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (39 bp):
ATTTTTATTTAATTTAATTATAAAATATAATTTAAATAT
Found at i:1232454 original size:2 final size:2
Alignment explanation
Indices: 1232447--1232482 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1232437 TAAAACACAA
1232447 AT AT AT 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 AT AT AT
1232483 TCAGCTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1233139 original size:34 final size:31
Alignment explanation
Indices: 1233093--1233163 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 31
1233083 AATTAATTCA
*
1233093 TATTAATTTTATAATAA-TAAAATTTATATATT
1 TATTAATTTTATAAAAAGTAAAA--TATATATT
1233125 TATTAGATTATTATAAAAAGGTAAAATATATATT
1 TATTA-ATT-TTATAAAAA-GTAAAATATATATT
1233159 TATTA
1 TATTA
1233164 TATAATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
32 5 0.15
33 3 0.09
34 21 0.62
36 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (31 bp):
TATTAATTTTATAAAAAGTAAAATATATATT
Found at i:1233295 original size:25 final size:25
Alignment explanation
Indices: 1233260--1233349 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
1233250 TATTTTTTTA
1233260 TTTATAATAATATTAAAATATAAAT
1 TTTATAATAATATTAAAATATAAAT
* *
1233285 TTTATATTAATATT----TATATAT
1 TTTATAATAATATTAAAATATAAAT
* *
1233306 TTTATTATTAA-ATTTAAATA-AAAT
1 TTTA-TAATAATATTAAAATATAAAT
1233330 TTT-TAATAATTATTAAAATA
1 TTTATAATAA-TATTAAAATA
1233350 ATAATTTAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
21 13 0.25
22 11 0.21
24 14 0.26
25 15 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTATAATAATATTAAAATATAAAT
Found at i:1233307 original size:21 final size:21
Alignment explanation
Indices: 1233270--1233321 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1233260 TTTATAATAA
*
1233270 TATTAAA-ATATAAATTTTA-
1 TATTAAATTTATAAATTTTAT
*
1233289 TATTAATATTTATATATTTTAT
1 TATTAA-ATTTATAAATTTTAT
1233311 TATTAAATTTA
1 TATTAAATTTA
1233322 AATAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.21
20 1 0.04
21 15 0.54
22 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAAATTTATAAATTTTAT
Found at i:1236004 original size:2 final size:2
Alignment explanation
Indices: 1235997--1236033 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1235987 CCTACCATGA
1235997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1236034 AAAATTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1236884 original size:4 final size:4
Alignment explanation
Indices: 1236875--1236901 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1236865 AAACAAAAAC
1236875 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1236902 ATGAACTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1241117 original size:2 final size:2
Alignment explanation
Indices: 1241110--1241138 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1241100 TAACAGTGGG
1241110 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1241139 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1241149 original size:8 final size:8
Alignment explanation
Indices: 1241136--1241165 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1241126 ACACACACAC
1241136 ACATATAT
1 ACATATAT
*
1241144 ATATATAT
1 ACATATAT
1241152 ACATATAT
1 ACATATAT
1241160 ACATAT
1 ACATAT
1241166 GTAAACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
ACATATAT
Found at i:1246720 original size:17 final size:17
Alignment explanation
Indices: 1246670--1246728 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1246660 TTAATTAATT
*
1246670 AATATATTATTTATAATA
1 AATATATT-TTTATATTA
* * *
1246688 ATAAACATTATTATATTA
1 A-ATATATTTTTATATTA
1246706 AATATATTTTTATATTA
1 AATATATTTTTATATTA
1246723 AATATA
1 AATATA
1246729 ATATTAGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 19 0.58
18 9 0.27
19 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATATTTTTATATTA
Done.