Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 116 of 206
Found at i:34552002 original size:17 final size:17
Alignment explanation
Indices: 34551975--34552078 Score: 88
Period size: 16 Copynumber: 6.2 Consensus size: 17
34551965 ACGAAAATAT
34551975 TTTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
* *
34551991 TTTTAGAGACACGAAAA
1 TTTTAGAAACACGAGAA
* *
34552008 TTCTTAAAAACACGAAAA
1 TT-TTAGAAACACGAGAA
* * *
34552026 TTTTTGAAAACACAACAA
1 TTTTAG-AAACACGAGAA
*
34552044 TTTT-GAAACATGAGAA
1 TTTTAGAAACACGAGAA
*
34552060 ATTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
34552076 TTT
1 TTT
34552079 GTTTTGAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
16 28 0.40
17 14 0.20
18 28 0.40
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
TTTTAGAAACACGAGAA
Found at i:34552022 original size:18 final size:18
Alignment explanation
Indices: 34551962--34552047 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
34551952 TATTTTTGCG
*
34551962 AACACGAAAATATTTTTAA
1 AACACGAAAAT-TTTTAAA
* *
34551981 AACACGAGAA-TTTTAGA
1 AACACGAAAATTTTTAAA
* *
34551998 GACACGAAAATTCTTAAA
1 AACACGAAAATTTTTAAA
*
34552016 AACACGAAAATTTTTGAA
1 AACACGAAAATTTTTAAA
34552034 AACAC-AACAATTTT
1 AACACGAA-AATTTT
34552048 GAAACATGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.27
18 31 0.56
19 9 0.16
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (18 bp):
AACACGAAAATTTTTAAA
Found at i:34552305 original size:20 final size:21
Alignment explanation
Indices: 34552277--34552316 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34552267 ATCGGGATTC
*
34552277 TATTAAAACGCGAG-AATTTT
1 TATTAAAACACGAGTAATTTT
*
34552297 TATTTAAACACGAGTAATTT
1 TATTAAAACACGAGTAATTT
34552317 CGAACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TATTAAAACACGAGTAATTTT
Found at i:34552634 original size:19 final size:20
Alignment explanation
Indices: 34552610--34552651 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
34552600 TTGTGGGCCC
34552610 TTTTCTT-T-TTTCCCTTTTT
1 TTTTCTTCTCTTT-CCTTTTT
34552629 TTTTCTTCTCTTTCCTTTTT
1 TTTTCTTCTCTTTCCTTTTT
34552649 TTT
1 TTT
34552652 CTGCTGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTCTTTCCTTTTT
Found at i:34552641 original size:15 final size:14
Alignment explanation
Indices: 34552607--34552649 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34552597 AAGTTGTGGG
34552607 CCCTTTTCTTTTTT
1 CCCTTTTCTTTTTT
*
34552621 CCCTTTTTTTTTCTT
1 CCCTTTTCTTTT-TT
* *
34552636 CTCTTTCCTTTTTT
1 CCCTTTTCTTTTTT
34552650 TTCTGCTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
CCCTTTTCTTTTTT
Found at i:34552981 original size:9 final size:10
Alignment explanation
Indices: 34552967--34553058 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 10
34552957 CGACTGTTAA
34552967 TTTATTT-TT
1 TTTATTTCTT
34552976 TTTATTTC-T
1 TTTATTTCTT
* *
34552985 TTTCTTTCCT
1 TTTATTTCTT
*
34552995 TTT-TTTCTC
1 TTTATTTCTT
34553004 TTT-TTTCTT
1 TTTATTTCTT
34553013 TCTT-TTTCTT
1 T-TTATTTCTT
* *
34553023 CTTTCTTTTTT
1 -TTTATTTCTT
*
34553034 CTTTCTTTCTT
1 -TTTATTTCTT
*
34553045 TCTTCTTTCTT
1 T-TTATTTCTT
34553056 TTT
1 TTT
34553059 TCTTCCTTCT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
9 28 0.39
10 17 0.24
11 26 0.37
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTCTT
Found at i:34552998 original size:11 final size:11
Alignment explanation
Indices: 34552984--34553062 Score: 83
Period size: 11 Copynumber: 7.0 Consensus size: 11
34552974 TTTTTATTTC
34552984 TTTTCTTTCCTT
1 TTTTCTTT-CTT
*
34552996 TTTT-TCTCTT
1 TTTTCTTTCTT
34553006 TTTTCTTTCTTT
1 TTTTCTTTC-TT
34553018 TTCTTCTTTCTT
1 TT-TTCTTTCTT
34553030 TTTTCTTTCTT
1 TTTTCTTTCTT
34553041 TCTTTC-TTCTT
1 T-TTTCTTTCTT
34553052 TCTTT-TTTCTT
1 T-TTTCTTTCTT
34553063 CCTTCTCCGT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
10 7 0.12
11 30 0.50
12 16 0.27
13 7 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:34553000 original size:22 final size:21
Alignment explanation
Indices: 34552972--34553059 Score: 96
Period size: 22 Copynumber: 4.3 Consensus size: 21
34552962 GTTAATTTAT
*
34552972 TTTTTTTATTTCTTTTCTTTCC
1 TTTTTTTCTTTCTTTTCTTT-C
34552994 TTTTTTTCTCTT-TTTTCTTTC
1 TTTTTTTCT-TTCTTTTCTTTC
34553015 TTTTTCTTCTTTC-TTT-TTTC
1 TTTTT-TTCTTTCTTTTCTTTC
*
34553035 TTTCTTTCTTTC--TTCTTTC
1 TTTTTTTCTTTCTTTTCTTTC
34553054 TTTTTT
1 TTTTTT
34553060 CTTCCTTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.03
19 16 0.27
20 8 0.14
21 11 0.19
22 20 0.34
23 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTTCTTTTCTTTC
Found at i:34553014 original size:26 final size:24
Alignment explanation
Indices: 34552971--34553062 Score: 98
Period size: 26 Copynumber: 3.7 Consensus size: 24
34552961 TGTTAATTTA
*
34552971 TTTTTT-TTATTTCTTTTCTTTCCTT
1 TTTTTTCTTTTTTC-TTTCTTT-CTT
34552996 TTTTTCTCTTTTTTCTTTCTTT-TT
1 TTTTT-TCTTTTTTCTTTCTTTCTT
*
34553020 CTTCTTTCTTTTTTCTTTCTTTCTT
1 -TTTTTTCTTTTTTCTTTCTTTCTT
34553045 TCTTCTTTCTTTTTTCTT
1 T-TT-TTTCTTTTTTCTT
34553063 CCTTCTCCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
24 19 0.33
25 12 0.21
26 21 0.36
27 6 0.10
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTTCTTTCTTTCTT
Found at i:34553038 original size:4 final size:4
Alignment explanation
Indices: 34552980--34553062 Score: 82
Period size: 4 Copynumber: 20.5 Consensus size: 4
34552970 ATTTTTTTTA
* * *
34552980 TTTC TTTTC TTTCC TTTT TTTC TCTTT TTTC TTTC TTTT TCTTC TTTC
1 TTTC -TTTC TTT-C TTTC TTTC T-TTC TTTC TTTC TTTC T-TTC TTTC
34553028 TTT- TTTC TTTC TTTC TTTC -TTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
34553063 CCTTCTCCGT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
3 9 0.14
4 43 0.65
5 14 0.21
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:34553053 original size:7 final size:7
Alignment explanation
Indices: 34552998--34553068 Score: 71
Period size: 7 Copynumber: 10.7 Consensus size: 7
34552988 CTTTCCTTTT
34552998 TTTC-TC
1 TTTCTTC
*
34553004 TTTTTTC
1 TTTCTTC
34553011 TTTCTT-
1 TTTCTTC
34553017 TTTCTTC
1 TTTCTTC
34553024 TTTC-T-
1 TTTCTTC
34553029 TTT-TTC
1 TTTCTTC
34553035 TTTCTTTC
1 TTTC-TTC
34553043 TTTCTTC
1 TTTCTTC
*
34553050 TTTCTTT
1 TTTCTTC
34553057 TTTCTTC
1 TTTCTTC
*
34553064 CTTCT
1 TTTCT
34553069 CCGTTCAGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 4 0.07
6 13 0.24
7 30 0.56
8 7 0.13
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTC
Found at i:34553192 original size:22 final size:24
Alignment explanation
Indices: 34553167--34553222 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
34553157 CCCCCTTTTC
34553167 CTTTTTCTTTTTCT-TCTTTGC-T-
1 CTTTTTCTTTTTCTCT-TTTGCTTG
*
34553189 CTTTCTCTTTTTCTCTTTTGCTTG
1 CTTTTTCTTTTTCTCTTTTGCTTG
34553213 CTTTTTCTTT
1 CTTTTTCTTT
34553223 GTTTTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.62
23 2 0.07
24 9 0.31
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.71
Consensus pattern (24 bp):
CTTTTTCTTTTTCTCTTTTGCTTG
Found at i:34553607 original size:30 final size:30
Alignment explanation
Indices: 34553574--34553701 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 30
34553564 GGGCCAAGCA
* * *
34553574 TAATTTTGAGAAAATTTAGGGGTCAAAATA
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
* * * *
34553604 TAATTTCAAG-AAGTTGATGGGCCAAAATG
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
* * *
34553633 TAATTTTAAGAAAGTTTAGGGGTGAAAATG
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
*
34553663 TAATTTTTTAA-AAAAGTTGAGGGGTTAAAATG
1 TAA--TTTTAAGAAAA-TTGAGGGGTCAAAATG
34553695 TAATTTT
1 TAATTTT
34553702 TGTTTTTGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.29
30 30 0.38
31 3 0.04
32 23 0.29
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
TAATTTTAAGAAAATTGAGGGGTCAAAATG
Found at i:34553636 original size:29 final size:30
Alignment explanation
Indices: 34553582--34553700 Score: 96
Period size: 32 Copynumber: 3.9 Consensus size: 30
34553572 CATAATTTTG
* * * *
34553582 AGAAAATTTAGGGGTCAAAATATAATTTCA
1 AGAAAGTTGAGGGGCCAAAATGTAATTTCA
* *
34553612 AG-AAGTTGATGGGCCAAAATGTAATTTTA
1 AGAAAGTTGAGGGGCCAAAATGTAATTTCA
* ** *
34553641 AGAAAGTTTAGGGGTGAAAATGTAATTTTTTA
1 AGAAAGTTGAGGGGCCAAAATGTAA--TTTCA
* **
34553673 AAAAAGTTGAGGGGTTAAAATGTAATTT
1 AGAAAGTTGAGGGGCCAAAATGTAATTT
34553701 TTGTTTTTGT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 23 0.32
30 23 0.32
32 27 0.37
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
AGAAAGTTGAGGGGCCAAAATGTAATTTCA
Found at i:34553679 original size:32 final size:32
Alignment explanation
Indices: 34553627--34553702 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
34553617 TTGATGGGCC
* *
34553627 AAAATGTAA--TTTTAAGAAAGTTTAGGGGTG
1 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
*
34553657 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTT
1 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
34553689 AAAATGTAATTTTT
1 AAAATGTAATTTTT
34553703 GTTTTTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.22
32 32 0.78
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (32 bp):
AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
Found at i:34555127 original size:18 final size:18
Alignment explanation
Indices: 34555100--34555136 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34555090 CTGGTGCATT
*
34555100 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
34555118 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
34555136 T
1 T
34555137 TCTTTTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:34555595 original size:24 final size:25
Alignment explanation
Indices: 34555568--34555614 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
34555558 TATTTTGATA
34555568 TTATTTGATGTAAT-AAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
34555592 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
34555615 ATTTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:34555697 original size:23 final size:24
Alignment explanation
Indices: 34555666--34556260 Score: 459
Period size: 23 Copynumber: 26.8 Consensus size: 24
34555656 ATTAATACCC
*
34555666 TTAACTTAAAAACCCTAACATAAT
1 TTAACTTAAAAACCCTAACCTAAT
* *
34555690 TTAA-TTAAAAACCTTAAACC---C
1 TTAACTTAAAAACCCT-AACCTAAT
* *
34555711 CTAACTTAAAAATCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34555734 TTAAATTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
* *
34555757 TTAAATTAAAAACCCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
34555778 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34555801 TTAAATTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
* ** *
34555824 TTAAATTAAAAATTCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
34555845 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34555868 TTAACTTAAAAACCCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
34555889 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
* *
34555912 TTAACTTAAAAACTCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
34555933 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
* *
34555956 TTAAATTAAAAACCTTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34555979 TTAAATTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
34556002 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34556025 TTAAATTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34556048 TTAAATT-AAAACCCTAATCC----
1 TTAACTTAAAAACCCTAA-CCTAAT
*
34556068 TTAACTTAAAAACCCTAACCAAAT
1 TTAACTTAAAAACCCTAACCTAAT
* *
34556092 TTTA-TTAAAAACTCTAAACCCT-A-
1 TTAACTTAAAAACCCT-AA-CCTAAT
* **
34556115 --AACTTAAAAACCTTAACC--CG
1 TTAACTTAAAAACCCTAACCTAAT
*
34556135 TT-ACTTAAAAACCCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
* *
34556155 TTAACTTAAAAACACTAAACC---C
1 TTAACTTAAAAACCCT-AACCTAAT
* *
34556177 TTAACTTAAAAACACTAAACC---C
1 TTAACTTAAAAACCCT-AACCTAAT
*
34556199 TTAACTTAAAAACCCTAACC---C
1 TTAACTTAAAAACCCTAACCTAAT
34556220 TTAACTTAAAAACCCTAACCTAA-
1 TTAACTTAAAAACCCTAACCTAAT
*
34556243 TTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
34556261 ACGAAATTAA
Statistics
Matches: 497, Mismatches: 36, Indels: 77
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.02
21 148 0.30
22 70 0.14
23 252 0.51
24 13 0.03
25 2 0.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (24 bp):
TTAACTTAAAAACCCTAACCTAAT
Found at i:34555796 original size:44 final size:43
Alignment explanation
Indices: 34555666--34556260 Score: 585
Period size: 44 Copynumber: 13.4 Consensus size: 43
34555656 ATTAATACCC
* * *
34555666 TTAACTTAAAAACCCTAACATAATTTAA-TTAAAAACCTTAAACCC
1 TTAACTTAAAAACCCTAAC-CAA-TTAACTTAAAAACCCT-AACCA
* * *
34555711 CTAACTTAAAAATCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACC--A
* *
34555757 TTAAATTAAAAACCCTAACC-CTTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCAATTAACTTAAAAACCCTAACC--A
* * ** *
34555801 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAATTCTAACCC
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACCA
*
34555845 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCC
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACCA
* *
34555889 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAACCC
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACCA
* *
34555933 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACCTAA
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACC--A
*
34555979 TTAAATTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAACC--A
* *
34556025 TTAAATTAAAAACCCTAACCTAATTAAATT-AAAACCCTAATCC-
1 TTAACTTAAAAACCCTAACC-AATTAACTTAAAAACCCTAA-CCA
* * *
34556068 TTAACTTAAAAACCCTAACCAAATTTTA-TTAAAAACTCTAAACCC
1 TTAACTTAAAAACCCTAACC-AA-TTAACTTAAAAACCCT-AACCA
* * ** *
34556113 TAAACTTAAAAACCTTAACCCGTT-ACTTAAAAACCCTAACCC
1 TTAACTTAAAAACCCTAACCAATTAACTTAAAAACCCTAACCA
* * * *
34556155 TTAACTTAAAAACACTAAACC-CTTAACTTAAAAACACTAAACCC
1 TTAACTTAAAAACCCT-AACCAATTAACTTAAAAACCCT-AACCA
*
34556199 TTAACTTAAAAACCCTAACC-CTTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCAATTAACTTAAAAACCCTAACC--A
*
34556243 TTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
34556261 ACGAAATTAA
Statistics
Matches: 485, Mismatches: 46, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
42 25 0.05
43 71 0.15
44 222 0.46
45 59 0.12
46 108 0.22
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (43 bp):
TTAACTTAAAAACCCTAACCAATTAACTTAAAAACCCTAACCA
Found at i:34555804 original size:67 final size:66
Alignment explanation
Indices: 34555666--34556260 Score: 629
Period size: 67 Copynumber: 8.9 Consensus size: 66
34555656 ATTAATACCC
* * * * *
34555666 TTAACTTAAAAACCCTAACATAATTTAATTAAAAACCTTAAACCCCTAACTTAAAAATCCTAACC
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACC
34555731 TAA
65 -AA
*
34555734 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACC-
34555799 AA
65 AA
* **
34555801 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAATTCTAACCCTTAACTTAAAAACCCTAACCT
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACC-
34555866 AA
65 AA
* * * *
34555868 TTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAAC
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAC
*
34555931 C-C
64 CAA
* * *
34555933 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACCTAATTAAATTAAAAACCCTAAC
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAC
34555998 CTAA
64 C-AA
* *
34556002 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT-AAAACCCTAAT
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA-
34556066 CC--
63 CCAA
* ** * * *
34556068 TTAACTTAAAAACCCTAACCAAATTTTATTAAAAACTCTAAACCCTAAACTTAAAAACCTTAACC
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACC
**
34556133 CG
65 AA
* * * *
34556135 TT-ACTTAAAAACCCTAACC--CTTAACTTAAAAACACTAAACCCTTAACTTAAAAACACTAAAC
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCT-AAC
*
34556197 C-C
64 CAA
* * * *
34556199 TTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA
34556261 ACGAAATTAA
Statistics
Matches: 468, Mismatches: 44, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
64 37 0.08
65 83 0.18
66 75 0.16
67 174 0.37
68 45 0.10
69 54 0.12
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (66 bp):
TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCA
A
Found at i:34556121 original size:22 final size:22
Alignment explanation
Indices: 34556096--34556262 Score: 209
Period size: 21 Copynumber: 7.7 Consensus size: 22
34556086 CCAAATTTTA
* *
34556096 TTAAAAACTCTAAACCCTAAAC
1 TTAAAAACCCTAAACCCTTAAC
*
34556118 TTAAAAA-CCTTAACCCGTT-AC
1 TTAAAAACCCTAAACCC-TTAAC
34556139 TTAAAAACCCT-AACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAC
*
34556160 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAC
*
34556182 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAC
34556204 TTAAAAACCCT-AACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAC
* *
34556225 TTAAAAACCCT-AACCTAATTAAA
1 TTAAAAACCCTAAACC--CTTAAC
34556248 TTAAAAACCCTAAAC
1 TTAAAAACCCTAAAC
34556263 GAAATTAATA
Statistics
Matches: 131, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.02
21 58 0.44
22 53 0.40
23 15 0.11
24 3 0.02
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (22 bp):
TTAAAAACCCTAAACCCTTAAC
Found at i:34556408 original size:116 final size:116
Alignment explanation
Indices: 34556265--34556508 Score: 418
Period size: 116 Copynumber: 2.1 Consensus size: 116
34556255 CCCTAAACGA
* * **
34556265 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATG-TTTTGACTGGTACTAACAAT
*
34556330 TAATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
65 TAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
*
34556381 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTGACTGGTATTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTGACTGGTACTAACAATT
34556446 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
34556497 AATTAATAATTT
1 AATTAATAATTT
34556509 CACAAACTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
115 41 0.34
116 80 0.66
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:34559742 original size:125 final size:125
Alignment explanation
Indices: 34559520--34559894 Score: 599
Period size: 125 Copynumber: 3.0 Consensus size: 125
34559510 AACATGCTAT
* *
34559520 TGTAGCAAAAGCGCATTCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTCCTAG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
34559585 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
* ** * * *
34559645 TGTAGCAAAAGCACATCCACGAGGGCGTAATTTTCACAAATTCTTCTCAAATGGTATCCTGCTAA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
34559710 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTCCATGACCTAC
* *
34559771 TGTAGCAAAAGCGCGTCCACTAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
* ** *
34559835 AAGCGATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCTA
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGACCTA
34559895 AAAATCCTAA
Statistics
Matches: 228, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
124 2 0.01
125 173 0.76
126 53 0.23
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (125 bp):
TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
Found at i:34562018 original size:29 final size:27
Alignment explanation
Indices: 34561971--34562041 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 27
34561961 AAAAATTATA
*
34561971 AAAAATAAAAAAATATTAAACTTTAAT
1 AAAAATAAAAAAATATTAAAATTTAAT
*
34561998 AAAAATATAAAAAATATTTAAAATTTAGT
1 AAAAATA-AAAAAATA-TTAAAATTTAAT
34562027 AAAAATTAGAAAAAA
1 AAAAA-TA-AAAAAA
34562042 AAATTGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.18
28 8 0.21
29 15 0.39
30 8 0.21
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATAAAAAAATATTAAAATTTAAT
Found at i:34562079 original size:19 final size:19
Alignment explanation
Indices: 34562064--34562101 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
34562054 TTGTAAAATT
34562064 TTATGAAAAT-CATAAAAAA
1 TTAT-AAAATGCATAAAAAA
34562083 TTATAAAATGCATAAAAAA
1 TTATAAAATGCATAAAAAA
34562102 AGGTCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
TTATAAAATGCATAAAAAA
Found at i:34562358 original size:10 final size:10
Alignment explanation
Indices: 34562344--34562401 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
34562334 AATTTATAAA
34562344 ATTTTATATAT
1 ATTTT-TATAT
* *
34562355 TTTTTTCTAT
1 ATTTTTATAT
*
34562365 ATTTCTATAT
1 ATTTTTATAT
34562375 A-TTTTATA-
1 ATTTTTATAT
34562383 ATTTTTA-AT
1 ATTTTTATAT
34562392 GATTTTTATA
1 -ATTTTTATA
34562402 ATCTTTTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 2 0.05
9 11 0.30
10 19 0.51
11 5 0.14
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:34570073 original size:22 final size:23
Alignment explanation
Indices: 34570038--34570084 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
34570028 ACATATACAT
**
34570038 TGATTCTATGATGTAA-AAAAAA
1 TGATTCTACAATGTAAGAAAAAA
*
34570060 TGATTCTACAATGTAAGAAAGAA
1 TGATTCTACAATGTAAGAAAAAA
34570083 TG
1 TG
34570085 GAGTGATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (23 bp):
TGATTCTACAATGTAAGAAAAAA
Found at i:34579054 original size:105 final size:106
Alignment explanation
Indices: 34578901--34579092 Score: 246
Period size: 105 Copynumber: 1.8 Consensus size: 106
34578891 ACTCAAAAAT
* * *
34578901 AGCAGCTAATTTTAAATATTAATAGAAATTCAGCTTCTACAATCAAAAACAAAATAATC-AATGA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGCTTCTAAAATAAAAAACAAAAT-ATCTAATGA
* * *
34578965 AAATTAACGATCCTTATACCAATAATATTGCAATCACTAGAC
65 AAATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
* * * * *
34579007 AGCAGCTAATTTTAGA-CTTATTAGAAACTCAGCATT-TAAAATAAAAAACCAACTATCTAATGA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGC-TTCTAAAATAAAAAACAAAATATCTAATGA
34579070 AAATTAACAATCCTCACACCAAT
65 AAATTAACAATCCTCACACCAAT
34579093 TAAAATTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
104 3 0.04
105 53 0.73
106 17 0.23
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (106 bp):
AGCAGCTAATTTTAAATATTAATAGAAACTCAGCTTCTAAAATAAAAAACAAAATATCTAATGAA
AATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
Found at i:34580384 original size:236 final size:235
Alignment explanation
Indices: 34579957--34580397 Score: 686
Period size: 236 Copynumber: 1.9 Consensus size: 235
34579947 GAGGGCTGAA
* *
34579957 TTCAAACAGAAATCAATGATAGACTGGATACAAAGGGCAACTTAACACAAAATTGGTTCATATGA
1 TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
* * * * *
34580022 TGGTCAAACGCAAGCACTGTAGGGCCACTATAAGGATATTAACTGATTTGGTGGGGAATAAATTG
66 TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
* *
34580087 GAAACTTCGCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAGTTGTTGCCTACTGCAGA
131 GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCAGA
*
34580152 TGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
196 CGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
*
34580192 TTCAAACAGAAATCAATAATAGACTGGATACAAATGGGCAACTCAACACAAAATTGTTTCATATG
1 TTCAAACAGAAATCAATAATAGACTGGATACAAA-GGGCAACTCAACACAAAATTGGTTCATATG
* * * *
34580257 ATGGTCAAAAGCAAGCACTTTAGGGACACTATAA-CATTTTTATCTGATTTGGAGGTAAATAAAT
65 ATGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCA-TATTAACTGATTTGGAGGGAAATAAAT
** * *
34580321 TGGAAACTTCCCAGCAGATTTTAAGGGAAGTCACAATGTTCTTCAAGTAATTGTTGGCTACTGCA
129 TGGAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCA
34580386 GACGGCCAGATT
194 GACGGCCAGATT
34580398 ACAGGATGCA
Statistics
Matches: 185, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
235 34 0.18
236 151 0.82
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (235 bp):
TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCAGA
CGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
Found at i:34583380 original size:107 final size:108
Alignment explanation
Indices: 34583205--34583407 Score: 304
Period size: 107 Copynumber: 1.9 Consensus size: 108
34583195 ACCAATAACA
*
34583205 TTAAATACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
*
34583270 TCCTCA-GACCAAT-GATATTCCAATCAGTAAACAGCAGCTAATT
66 TCCT-AGGACCAATAAAT-TTCCAATCAGTAAACAGCAGCTAATT
* * * *
34583313 TTAAACACTACTAGAAACTTAGCATTTACAATAAA-AAAACTAAATAATCCATTAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
*
34583377 TCCTAGGACCAATAAATTTCCATTCAGTAAA
66 TCCTAGGACCAATAAATTTCCAATCAGTAAA
34583408 TTTATAAACC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 1 0.01
107 50 0.58
108 35 0.41
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.26
Consensus pattern (108 bp):
TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
TCCTAGGACCAATAAATTTCCAATCAGTAAACAGCAGCTAATT
Found at i:34585355 original size:27 final size:27
Alignment explanation
Indices: 34585325--34585379 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
34585315 AGTAGCAGAA
*
34585325 CAAACATTATATGCAATCTCTCAGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
*
34585352 CAAACATTATATGCAATCGCTCGGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
34585379 C
1 C
34585380 TCTTATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (27 bp):
CAAACATTATATGCAATCGCTCAGTTT
Found at i:34608506 original size:16 final size:16
Alignment explanation
Indices: 34608486--34608524 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34608476 TGGAATATGA
34608486 CTGTAATAGAATAAAG
1 CTGTAATAGAATAAAG
* * *
34608502 TTGTAATGGAATGAAG
1 CTGTAATAGAATAAAG
34608518 CTGTAAT
1 CTGTAAT
34608525 TAGTAATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAAAG
Found at i:34608595 original size:44 final size:46
Alignment explanation
Indices: 34608506--34608598 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
34608496 ATAAAGTTGT
* *
34608506 AATGGAATGAAGCTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
*
34608552 AATGGAATAAAACTGTAA-TA-TCATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATTAGTAATTCATT-TGTTTGGTTGAATGG
34608596 AAT
1 AAT
34608599 AAATGTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 23 0.53
45 2 0.05
46 16 0.37
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (46 bp):
AATGGAATAAAACTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
Found at i:34608726 original size:16 final size:16
Alignment explanation
Indices: 34608702--34608743 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
34608692 AAAAAATAAA
*
34608702 TAATTTAATTA-TACTT
1 TAATATAATTATTA-TT
34608718 TAATATAATTATTATT
1 TAATATAATTATTATT
*
34608734 AAATATAATT
1 TAATATAATT
34608744 TAACAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATAATTATTATT
Found at i:34608733 original size:56 final size:60
Alignment explanation
Indices: 34608668--34608834 Score: 191
Period size: 56 Copynumber: 2.8 Consensus size: 60
34608658 TTTTACGTAG
* *
34608668 AATTATTATTAAATATAATTTAATAAAAAAT-A-A-ATAATTTAATTATACT-TTAATAT
1 AATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAACACTCTTAATAT
* *
34608724 AATTATTATTAAATATAATTTAACAAAGATAATAATATATAATTTAATAACATTCTTAATAT
1 AATTATTATTAAATATAATTTAATAAA-A-AATAATATATAATTTAATAACACTCTTAATAT
*
34608786 AATTATTATCAAAATATGAA-TTAATAAAAATCATAATATATAATATTAA
1 AATTATTAT-TAAATAT-AATTTAATAAAAA--ATAATATATAAT-TTAA
34608835 AAAATAATAT
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
56 26 0.28
57 1 0.01
58 3 0.03
59 1 0.01
60 1 0.01
61 14 0.15
62 17 0.18
63 25 0.27
64 6 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (60 bp):
AATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAACACTCTTAATAT
Found at i:34611827 original size:17 final size:18
Alignment explanation
Indices: 34611801--34611835 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34611791 AGGCCAATCT
*
34611801 GGGCGTGTGGG-CCACAC
1 GGGCGCGTGGGCCCACAC
34611818 GGGCGCGTGGGCCCACAC
1 GGGCGCGTGGGCCCACAC
34611836 AGGCATGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.34, G:0.46, T:0.09
Consensus pattern (18 bp):
GGGCGCGTGGGCCCACAC
Found at i:34612086 original size:13 final size:13
Alignment explanation
Indices: 34612054--34612089 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
34612044 AAGCATGTTA
34612054 TATT-TATATCTG
1 TATTCTATATCTG
34612066 TA-TCTATATCTG
1 TATTCTATATCTG
34612078 TATTCTATATCT
1 TATTCTATATCT
34612090 ATTTTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 12 0.55
13 9 0.41
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (13 bp):
TATTCTATATCTG
Found at i:34612302 original size:13 final size:13
Alignment explanation
Indices: 34612286--34612323 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
34612276 GGGGGTAGGA
34612286 ATCTGTATATCTG
1 ATCTGTATATCTG
*
34612299 ATCTGCATATCTG
1 ATCTGTATATCTG
34612312 ATCTGTATATCT
1 ATCTGTATATCT
34612324 ATAACTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (13 bp):
ATCTGTATATCTG
Found at i:34616230 original size:26 final size:26
Alignment explanation
Indices: 34616151--34616231 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
34616141 ATGGGGAAGT
* *
34616151 ATACTA-TATTGGCAGCTTTGCCATA-T
1 ATACTATTACTGGCAGCTTTG-C-TACG
* *** *
34616177 ATACTGTTACTGGCAGCTTCATTGCG
1 ATACTATTACTGGCAGCTTTGCTACG
34616203 ATACTATTACTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTACG
34616229 ATA
1 ATA
34616232 TTGGTGTGTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
25 1 0.02
26 29 0.71
27 11 0.27
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTACG
Found at i:34618161 original size:13 final size:13
Alignment explanation
Indices: 34618143--34618170 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34618133 GTTCTTCTAA
34618143 AAGGCCTAAAAAG
1 AAGGCCTAAAAAG
34618156 AAGGCCTAAAAAG
1 AAGGCCTAAAAAG
34618169 AA
1 AA
34618171 TGTCATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.21, T:0.07
Consensus pattern (13 bp):
AAGGCCTAAAAAG
Found at i:34619418 original size:26 final size:26
Alignment explanation
Indices: 34619382--34619431 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
34619372 AAGTATACTG
34619382 TACTGGCAGCTTTGCTGCAATATTAA
1 TACTGGCAGCTTTGCTGCAATATTAA
*
34619408 TACTGGCAGCTTTGCTGCGATATT
1 TACTGGCAGCTTTGCTGCAATATT
34619432 GGTATGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCAATATTAA
Found at i:34619568 original size:33 final size:33
Alignment explanation
Indices: 34619526--34619590 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
34619516 TGCATTATTG
34619526 CACTGTACTGATACTGTATT-GGGCTAAGGCCCA
1 CACTGTACTGATACTG-ATTAGGGCTAAGGCCCA
* *
34619559 CACTGTACTGTTACTGATTAGGGCTCAGGCCC
1 CACTGTACTGATACTGATTAGGGCTAAGGCCC
34619591 GGACTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (33 bp):
CACTGTACTGATACTGATTAGGGCTAAGGCCCA
Found at i:34623833 original size:31 final size:31
Alignment explanation
Indices: 34623798--34623896 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 31
34623788 TTCATGTATC
34623798 ATTATATTAAATTATTTAAATATTATTCGTT
1 ATTATATTAAATTATTTAAATATTATTCGTT
* **
34623829 ATTATATTAAATTATTTAAATCTTATTTATT
1 ATTATATTAAATTATTTAAATATTATTCGTT
* *
34623860 ATTATATTTAATT-TTTAAAATAGTTTATGCGTT
1 ATTATATTAAATTATTT-AAATA--TTATTCGTT
34623893 ATTA
1 ATTA
34623897 ATTTTACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
30 3 0.05
31 44 0.77
33 10 0.18
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTCGTT
Found at i:34625004 original size:43 final size:43
Alignment explanation
Indices: 34624943--34625028 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
34624933 TATTATATTT
34624943 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
*
34624986 CTATTACCATAATTTAAATGACCTAAATTGATAAGTGCTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
34625029 GAAACATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (43 bp):
CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
Found at i:34626329 original size:20 final size:20
Alignment explanation
Indices: 34626295--34626343 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34626285 TTTATATCTA
*
34626295 TTAATTTAGCCATTTTTATTT
1 TTAATTTAG-TATTTTTATTT
* *
34626316 TTATTTTAGTATTTTTGTTT
1 TTAATTTAGTATTTTTATTT
34626336 TTAATTTA
1 TTAATTTA
34626344 ATTTTTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (20 bp):
TTAATTTAGTATTTTTATTT
Found at i:34628422 original size:28 final size:29
Alignment explanation
Indices: 34628382--34628436 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
34628372 GTATGATCAA
* *
34628382 GAAATGAGTAGATCAGTTG-TTAATCGTGG
1 GAAATGAGAAGATC-GTTGAGTAATCGTGG
34628411 GAAA-GAGAAGATCGTTGAGTAATCGT
1 GAAATGAGAAGATCGTTGAGTAATCGT
34628437 CTTCGATCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 15 0.65
29 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.31, T:0.27
Consensus pattern (29 bp):
GAAATGAGAAGATCGTTGAGTAATCGTGG
Found at i:34638487 original size:12 final size:12
Alignment explanation
Indices: 34638470--34638517 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
34638460 ACCGTGTGTC
34638470 ACACATGGTCCA
1 ACACATGGTCCA
**
34638482 ACACATGGTCTGTT
1 ACACATGGTC--CA
34638496 ACACATGGTCCA
1 ACACATGGTCCA
34638508 ACACATGGTC
1 ACACATGGTC
34638518 TGTCACACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (12 bp):
ACACATGGTCCA
Found at i:34638506 original size:26 final size:26
Alignment explanation
Indices: 34638466--34638525 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
34638456 CCAGACCGTG
34638466 TGTCACACATGGTCCAACACATGGTC
1 TGTCACACATGGTCCAACACATGGTC
*
34638492 TGTTACACATGGTCCAACACATGGTC
1 TGTCACACATGGTCCAACACATGGTC
34638518 TGTCACAC
1 TGTCACAC
34638526 GGCCTACCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (26 bp):
TGTCACACATGGTCCAACACATGGTC
Found at i:34646209 original size:6 final size:5
Alignment explanation
Indices: 34646182--34646229 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
34646172 ATGGTAACCA
* * *
34646182 AAAAT AAAAT AAAAT AAAAT AAAGAT AATAT AAACT AAAAC AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AA
34646230 TACAATTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:34649544 original size:20 final size:20
Alignment explanation
Indices: 34649519--34649566 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
34649509 GAGCATTTGA
34649519 GAGCAAAATGAGCGAAAAAC
1 GAGCAAAATGAGCGAAAAAC
* *
34649539 GAGCAAAATGAGCGCAAAAT
1 GAGCAAAATGAGCGAAAAAC
34649559 GAGCAAAA
1 GAGCAAAA
34649567 ACCAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.25, T:0.06
Consensus pattern (20 bp):
GAGCAAAATGAGCGAAAAAC
Found at i:34649546 original size:9 final size:9
Alignment explanation
Indices: 34649519--34649566 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 9
34649509 GAGCATTTGA
34649519 GAGCAAAAT
1 GAGCAAAAT
*
34649528 GAGCGAAAAAC
1 GAGC--AAAAT
34649539 GAGCAAAAT
1 GAGCAAAAT
34649548 GAGCGCAAAAT
1 GA--GCAAAAT
34649559 GAGCAAAA
1 GAGCAAAA
34649567 ACCAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 16 0.48
11 17 0.52
ACGTcount: A:0.54, C:0.15, G:0.25, T:0.06
Consensus pattern (9 bp):
GAGCAAAAT
Found at i:34649696 original size:17 final size:17
Alignment explanation
Indices: 34649674--34649711 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
34649664 GCTTGACCAT
*
34649674 ACGGTCGTGTGAGCCAC
1 ACGGTCATGTGAGCCAC
34649691 ACGGTCATGTGAGCCAC
1 ACGGTCATGTGAGCCAC
34649708 ACGG
1 ACGG
34649712 GCTACCACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (17 bp):
ACGGTCATGTGAGCCAC
Found at i:34651465 original size:22 final size:20
Alignment explanation
Indices: 34651414--34651458 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
34651404 TTTAGTAAAG
34651414 AACTTAAAGTTCTATGAAAA
1 AACTTAAAGTTCTATGAAAA
*
34651434 AACTTAAAGTTTTATGAAAA
1 AACTTAAAGTTCTATGAAAA
34651454 AACTT
1 AACTT
34651459 GAGAAGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
AACTTAAAGTTCTATGAAAA
Found at i:34653321 original size:2 final size:2
Alignment explanation
Indices: 34653314--34653341 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34653304 TGTAAGGTAA
34653314 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
34653342 GGACAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34656364 original size:16 final size:16
Alignment explanation
Indices: 34656343--34656416 Score: 94
Period size: 16 Copynumber: 4.2 Consensus size: 16
34656333 TTTGGTTCGC
34656343 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
34656359 TGTATTGGATTGGGATTAGAGG
1 TG---T--ATT-GGATTAGAGG
34656381 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
34656397 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
34656413 TGTA
1 TGTA
34656417 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
16 32 0.62
17 3 0.06
19 2 0.04
21 3 0.06
22 12 0.23
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:34656375 original size:22 final size:22
Alignment explanation
Indices: 34656349--34656391 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
34656339 TCGCTGTATT
34656349 GGATTAGAGGTGTATTGGATTG
1 GGATTAGAGGTGTATTGGATTG
34656371 GGATTAGAGGTGTATTGGATT
1 GGATTAGAGGTGTATTGGATT
34656392 AGAGGTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (22 bp):
GGATTAGAGGTGTATTGGATTG
Found at i:34656481 original size:44 final size:45
Alignment explanation
Indices: 34656397--34656487 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
34656387 GGATTAGAGG
* * *
34656397 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
34656442 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
34656486 TG
1 TG
34656488 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:34656978 original size:121 final size:121
Alignment explanation
Indices: 34656635--34657218 Score: 1080
Period size: 121 Copynumber: 4.8 Consensus size: 121
34656625 ATCATATTTA
34656635 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
34656700 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
34656756 AACATAATTTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTA
1 AACATAA-TTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTA
34656821 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
34656878 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
34656943 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
34656999 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
34657064 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * *
34657120 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAT-TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTA
34657185 ATATTC-TTATATTAATTTACTCAAATCATAATAT
65 ATATTCTTTATATTAATTTACTCAAATCATAATAT
34657219 TCTTAATAAT
Statistics
Matches: 453, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
121 275 0.61
122 178 0.39
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (121 bp):
AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:34657139 original size:243 final size:243
Alignment explanation
Indices: 34656635--34657218 Score: 1082
Period size: 243 Copynumber: 2.4 Consensus size: 243
34656625 ATCATATTTA
34656635 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
34656700 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
*
34656765 TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAATATTCTTT
131 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
34656830 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
196 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
34656878 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
34656943 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAA-T
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
34657007 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
131 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
*
34657072 ATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * *
34657120 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAT-TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTA
34657185 ATATTC-TTATATTAATTTACTCAAATCATAATAT
65 ATATTCTTTATATTAATTTACTCAAATCATAATAT
34657219 TCTTAATAAT
Statistics
Matches: 332, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
242 147 0.44
243 185 0.56
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (243 bp):
AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:34657192 original size:16 final size:16
Alignment explanation
Indices: 34657171--34657239 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
34657161 ATTTAATAAA
34657171 ATTCTTAATAATTAAT
1 ATTCTTAATAATTAAT
34657187 ATTCTT-AT-ATTAAT
1 ATTCTTAATAATTAAT
* *
34657201 -TTACTCAAATCA-TAAT
1 ATT-CT-TAATAATTAAT
34657217 ATTCTTAATAATTAAT
1 ATTCTTAATAATTAAT
34657233 ATTCTTA
1 ATTCTTA
34657240 TATTAACTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.05
14 8 0.18
15 6 0.14
16 25 0.57
17 3 0.07
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTCTTAATAATTAAT
Found at i:34672340 original size:17 final size:17
Alignment explanation
Indices: 34672318--34672352 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34672308 GCGTTTTTAG
*
34672318 GAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAAC
34672335 GAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAAC
34672352 G
1 G
34672353 CGTCCTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.06, G:0.29, T:0.06
Consensus pattern (17 bp):
GAGAGAAAAATGAAAAC
Found at i:34672347 original size:58 final size:58
Alignment explanation
Indices: 34672277--34672393 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
34672267 GTTGTTTTTG
* * *
34672277 GAGAGAGAAATGAAAACGCATCATGTAGGACGCGTTTTTAGGAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
* * *
34672335 GAGAGAAAAATGAAAACGCGTCCTGAAGGACGTGTTTTTAGGAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
34672393 G
1 G
34672394 CGTCCTGCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (58 bp):
GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
Found at i:34676007 original size:15 final size:17
Alignment explanation
Indices: 34675989--34676021 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34675979 AAAATAGAAT
34675989 TTTA-AAAAAATT-ATA
1 TTTATAAAAAATTGATA
34676004 TTTATAAAAAATTGATA
1 TTTATAAAAAATTGATA
34676021 T
1 T
34676022 AAATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTATAAAAAATTGATA
Found at i:34685112 original size:36 final size:38
Alignment explanation
Indices: 34685071--34685145 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
34685061 TGAATCAAAG
34685071 TTAATTGGTTCATGTAA-C-AAAAAAAAAAAGAATTAA
1 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
*
34685107 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
34685145 T
1 T
34685146 GGTTTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 17 0.47
37 1 0.03
38 18 0.50
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (38 bp):
TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
Found at i:34687368 original size:8 final size:8
Alignment explanation
Indices: 34687357--34687402 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
34687347 ATTTTAAATT
34687357 TTTTTATA
1 TTTTTATA
34687365 TTTTTATA
1 TTTTTATA
34687373 TTTTTGA-A
1 TTTTT-ATA
34687381 -TTTTATA
1 TTTTTATA
*
34687388 TTTATATA
1 TTTTTATA
34687396 TATTTTA
1 T-TTTTA
34687403 AAATATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
6 1 0.03
7 5 0.16
8 21 0.66
9 5 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:34696075 original size:17 final size:17
Alignment explanation
Indices: 34696042--34696075 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34696032 TTGTGTTTTG
*
34696042 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
34696059 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
34696076 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:34696646 original size:2 final size:2
Alignment explanation
Indices: 34696639--34696669 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34696629 ATGATATGAA
34696639 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 A
34696670 AGAGGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34696998 original size:41 final size:41
Alignment explanation
Indices: 34696914--34697016 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
34696904 GGCTATGTGC
* * * *
34696914 CTAGCAGGCTTGATGCCGGTAAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
34696955 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
34696996 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
34697017 TACTGAATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:34700090 original size:96 final size:96
Alignment explanation
Indices: 34699926--34700123 Score: 371
Period size: 96 Copynumber: 2.1 Consensus size: 96
34699916 TACATTCCAT
* *
34699926 GTGTAGACTTCACAGATGTGTTTTCTCCAGTTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
1 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
34699991 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
66 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
34700022 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
1 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
34700087 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
66 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
34700118 GT-TAGA
1 GTGTAGA
34700124 TGTAAGAACA
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
95 4 0.04
96 96 0.96
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (96 bp):
GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
TTGTTGCCACGTATGATTTGGAGCTTGAGCA
Found at i:34701885 original size:18 final size:18
Alignment explanation
Indices: 34701864--34701924 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
34701854 AAAATAAATA
*
34701864 AAATGAAAAAAAAGATAG
1 AAATGAAAAAAAAGAAAG
** *
34701882 AAATGACGAAGAAGAAAG
1 AAATGAAAAAAAAGAAAG
* *
34701900 AAATAAAAAAATAAAAAAG
1 AAATGAAAAAA-AAGAAAG
34701919 -AATGAA
1 AAATGAA
34701925 CTATCGTTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.10
Consensus pattern (18 bp):
AAATGAAAAAAAAGAAAG
Found at i:34708181 original size:24 final size:25
Alignment explanation
Indices: 34708130--34708187 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
34708120 TGGCTTTCAC
* * *
34708130 GAGCTTCCCGTTATATGGTTCTTGT
1 GAGCTTCCCGTTATATAGCTCTTAT
*
34708155 GAGCTTTCCGTTA-ATAGCTCTTAT
1 GAGCTTCCCGTTATATAGCTCTTAT
*
34708179 GAGCATCCC
1 GAGCTTCCC
34708188 AATTTGGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTAT
Found at i:34708278 original size:25 final size:26
Alignment explanation
Indices: 34708250--34708307 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
34708240 CCCGATATAT
34708250 GGCTCTTC-GGAGCTTCCCAATTAAA
1 GGCTCTTCAGGAGCTTCCCAATTAAA
* * *
34708275 GGCTCTTTCATGAGCTTCCTAATTAAT
1 GGCTC-TTCAGGAGCTTCCCAATTAAA
34708302 GGCTCT
1 GGCTCT
34708308 CTAGAGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 4 0.14
27 19 0.68
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
GGCTCTTCAGGAGCTTCCCAATTAAA
Found at i:34713265 original size:19 final size:19
Alignment explanation
Indices: 34713241--34713277 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
34713231 ATTTTGATGT
34713241 TGTGGTATG-ATAGTTTAAA
1 TGTGGTATGTAT-GTTTAAA
34713260 TGTGGTATGTATGTTTAA
1 TGTGGTATGTATGTTTAA
34713278 TTCCATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (19 bp):
TGTGGTATGTATGTTTAAA
Found at i:34717544 original size:20 final size:19
Alignment explanation
Indices: 34717520--34717566 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
34717510 AAAGGAGAGT
**
34717520 GAAAAAAATGAGAAAA-GAA
1 GAAAAAAAAAAGAAAATG-A
34717539 GAAAAAGAAAAAGAAAATGA
1 GAAAAA-AAAAAGAAAATGA
34717559 GAAAAAAA
1 GAAAAAAA
34717567 GTTTGAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAATGA
Found at i:34725032 original size:3 final size:3
Alignment explanation
Indices: 34725024--34725052 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34725014 GAAAAAGGAA
34725024 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
34725053 AGAGATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34725721 original size:13 final size:12
Alignment explanation
Indices: 34725703--34725761 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
34725693 TGGGAAAGAA
34725703 AAAGATATGAGAG
1 AAAGATA-GAGAG
34725716 AAAGATAGAG-G
1 AAAGATAGAGAG
* *
34725727 AACGAGAGAGA-
1 AAAGATAGAGAG
*
34725738 AAGAGATATGGGAG
1 AA-AGATA-GAGAG
34725752 AAAGATAGAG
1 AAAGATAGAG
34725762 GGTTAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 11 0.31
12 8 0.22
13 15 0.42
14 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.36, T:0.10
Consensus pattern (12 bp):
AAAGATAGAGAG
Found at i:34725761 original size:19 final size:19
Alignment explanation
Indices: 34725705--34725761 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
34725695 GGAAAGAAAA
34725705 AGATATGAGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
* *
34725724 AGGA-ACGAGAG--AGAAAG
1 A-GATATGAGAGAAAGATAG
*
34725741 AGATATGGGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
34725760 AG
1 AG
34725762 GGTTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.07
17 11 0.38
19 14 0.48
20 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.37, T:0.11
Consensus pattern (19 bp):
AGATATGAGAGAAAGATAG
Found at i:34726674 original size:35 final size:35
Alignment explanation
Indices: 34726628--34726698 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
34726618 AAAAAATTCA
*
34726628 AGCCAATATTTTAATAATAATAAAGTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
* * *
34726663 AGCCAATATTTTAATAAGATTACATTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
34726698 A
1 A
34726699 ACTAATGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (35 bp):
AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
Found at i:34728672 original size:34 final size:34
Alignment explanation
Indices: 34728634--34728711 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
34728624 GCAATATGAC
** * *
34728634 ATGCTTATAACAGA-TCAATGTGGTAGCAATTTAT
1 ATGCTTATAACA-ATTCAATACGGTAGCAAATAAT
* *
34728668 ATGCTAATAACAATTCGATACGGTAGCAAATAAT
1 ATGCTTATAACAATTCAATACGGTAGCAAATAAT
34728702 ATGCTTATAA
1 ATGCTTATAA
34728712 TGGACCAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 1 0.03
34 35 0.97
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (34 bp):
ATGCTTATAACAATTCAATACGGTAGCAAATAAT
Found at i:34743576 original size:45 final size:47
Alignment explanation
Indices: 34743487--34743579 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
34743477 TATAAAAAAA
*
34743487 TATTTATATTTATGTAAAAATACCAGATTTAAATGAAAAATTAAATAAT
1 TATTTATATTTATGTAAAAACACCAGATTT--ATGAAAAATTAAATAAT
*
34743536 TATTTGTATTTATGT-AAAACACCAGA-TT-TGAAACAATTAAATAA
1 TATTTATATTTATGTAAAAACACCAGATTTATGAAA-AATTAAATAA
34743580 ACAAGGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 5 0.12
45 10 0.24
47 2 0.05
48 10 0.24
49 14 0.34
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (47 bp):
TATTTATATTTATGTAAAAACACCAGATTTATGAAAAATTAAATAAT
Found at i:34747185 original size:12 final size:12
Alignment explanation
Indices: 34747168--34747192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34747158 ACATTACATT
34747168 AAATTATAAAAA
1 AAATTATAAAAA
34747180 AAATTATAAAAA
1 AAATTATAAAAA
34747192 A
1 A
34747193 TTATATAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATTATAAAAA
Found at i:34747279 original size:14 final size:14
Alignment explanation
Indices: 34747260--34747287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34747250 TTTAATTTAC
34747260 ATTAAAAAATAAAA
1 ATTAAAAAATAAAA
34747274 ATTAAAAAATAAAA
1 ATTAAAAAATAAAA
34747288 GAATACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
ATTAAAAAATAAAA
Found at i:34752424 original size:40 final size:40
Alignment explanation
Indices: 34752352--34752427 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
34752342 ATTGTTCATG
*
34752352 CCACGTCAGCAAATCGCGTCCTAGGGGGCGCGATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
* *
34752392 CCACGTCAGCAAATCGCG-CTTACGTGGACGCGATTT
1 CCACGTCAGCAAATCGCGTCCTA-GGGGACGCGATTT
34752428 CCTGGCGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
Found at i:34754274 original size:17 final size:17
Alignment explanation
Indices: 34754230--34754277 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
34754220 TTAGAGAGTT
*
34754230 TTTTAAATAATTATAAA
1 TTTTAAATAATTTTAAA
** **
34754247 AATTATTTAATTTTAAA
1 TTTTAAATAATTTTAAA
34754264 TTTTAAATAATTTT
1 TTTTAAATAATTTT
34754278 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAATAATTTTAAA
Found at i:34756014 original size:40 final size:40
Alignment explanation
Indices: 34755961--34756071 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
34755951 GTTTGGATAA
* *
34755961 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTACA-T
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTT-CAGG
* *
34756001 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGATTTCAGG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGG
* **
34756041 GAAGTGCCGCTAAAAA-TGAGCATTAGCGGCG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCG
34756072 TTTGTTGGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 16 0.26
40 45 0.74
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGG
Found at i:34756095 original size:39 final size:39
Alignment explanation
Indices: 34755960--34756096 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 39
34755950 CGTTTGGATA
* **
34755960 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCG-CTTTAC
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCGGCGTTTTTGG
* **
34755999 ATAAAACGCCGCTAAAGATCGAGCATTAGCGGCGATTTCAGG
1 A-AAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTTTTGG
* **
34756041 -GAAGTGCCGCTAAAAATGAGCATTAGCGGCGTTTGTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTT-TTGG
*
34756080 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
34756097 CTAAGCCCAA
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
38 3 0.04
39 18 0.24
40 54 0.71
42 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTGG
Found at i:34756198 original size:41 final size:41
Alignment explanation
Indices: 34756153--34756406 Score: 291
Period size: 41 Copynumber: 6.2 Consensus size: 41
34756143 GCTTCTTGAA
*
34756153 AAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* *
34756194 AAGCGCCACTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* *
34756235 AAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTGAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* * * * * *
34756276 AAGCGCCACTAATGTTCGGGGTTTTAGCGGCGTTTTTTAAA-
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCG-TTTTTAAAG
* *
34756317 AAGCGCCGC-AACTGCTCAGAGCTTTAGCACCGTTTTTAAGG
1 AAGCGCCGCTAA-TGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* * * * *
34756358 AAGTGCCACTAATGCTC-GGGATTTAGCGGCGTTTTTGAAA-
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTT-AAAG
34756398 AAGCGCCGC
1 AAGCGCCGC
34756407 AAAAACATTT
Statistics
Matches: 180, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.17
41 140 0.78
42 9 0.05
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
Found at i:34756269 original size:82 final size:80
Alignment explanation
Indices: 34756134--34756406 Score: 350
Period size: 82 Copynumber: 3.3 Consensus size: 80
34756124 CTTTCGGGGC
* * *
34756134 TTTAGCGGCGCTTCTTGAAAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
1 TTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
* * *
34756199 CCACTAGTGCTCAGAGC
65 CCACTAATGCTC-GGGA
* * *
34756216 TTTAGCAGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTGAAGAAGCG
1 TTTAGCGGCGTTTTTAAA-AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
* *
34756281 CCACTAATGTTCGGGGT
65 CCACTAATGCTC-GGGA
* * *
34756298 TTTAGCGGCGTTTTTTAAAAAGCGCCGC-AACTGCTCAGAGCTTTAGCACCGTTTTTAAGGAAGT
1 TTTAGCGGCG-TTTTTAAAAAGCGCCGCTAA-TGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGC
34756362 GCCACTAATGCTCGGGA
64 GCCACTAATGCTCGGGA
34756379 TTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 TTTAGCGGCGTTTTT-AAAAAGCGCCGC
34756407 AAAAACATTT
Statistics
Matches: 168, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
80 5 0.03
81 33 0.20
82 122 0.73
83 8 0.05
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (80 bp):
TTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCGC
CACTAATGCTCGGGA
Found at i:34756351 original size:123 final size:121
Alignment explanation
Indices: 34756132--34756404 Score: 341
Period size: 123 Copynumber: 2.2 Consensus size: 121
34756122 ACCTTTCGGG
* * *
34756132 GCTTTAGCGGCGCTTCTTGAAAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAG
1 GCTTTAGCGGCG-TTTTTGAAAAGCGCCACTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAG
* * * *
34756197 CGCCACTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
65 CGCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTC-GA
* * * * *
34756255 GCTTTAGCGGCGTTTTTGAAGAAGCGCCACTAATGTTCGGGGTTTTAGCGGCGTTTTTTAAA-AA
1 GCTTTAGCGGCGTTTTTGAA-AAGCGCCACTAATGCTCAGAGCTTTAGCAGCG-TTTTTAAAGAA
* * * *
34756319 GCGCCGCAACTGCTCAGAGCTTTAGCACCGTTTTTAAGGAAGTGCCACTAATGCTCGG
64 GCGCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTCGA
*
34756377 GATTTAGCGGCGTTTTTGAAAAAGCGCC
1 GCTTTAGCGGCGTTTTTG-AAAAGCGCC
34756405 GCAAAAACAT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
122 32 0.25
123 90 0.69
124 8 0.06
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (121 bp):
GCTTTAGCGGCGTTTTTGAAAAGCGCCACTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGC
GCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTCGA
Found at i:34756897 original size:21 final size:21
Alignment explanation
Indices: 34756853--34756897 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34756843 AATTTAAGGT
* * *
34756853 TTATGGGTTAGGGGCTAGGGG
1 TTATGGGTTAGAGGCTAAGAG
*
34756874 TTATGGGTTAGAGGTTAAGAG
1 TTATGGGTTAGAGGCTAAGAG
34756895 TTA
1 TTA
34756898 GGGATTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.42, T:0.33
Consensus pattern (21 bp):
TTATGGGTTAGAGGCTAAGAG
Found at i:34756996 original size:14 final size:14
Alignment explanation
Indices: 34756973--34757048 Score: 84
Period size: 14 Copynumber: 5.5 Consensus size: 14
34756963 ATATATTAAA
* *
34756973 TAAGGTTTAGGAGT
1 TAAGGGTTAGGGGT
34756987 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
*
34757001 TGAA--GTTAGTGGT
1 T-AAGGGTTAGGGGT
*
34757014 TAGGGGTTAGGGGT
1 TAAGGGTTAGGGGT
*
34757028 TTAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
34757042 TAAGGGT
1 TAAGGGT
34757049 CGAGTTAGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 1 0.02
13 9 0.18
14 39 0.76
15 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (14 bp):
TAAGGGTTAGGGGT
Found at i:34757000 original size:7 final size:7
Alignment explanation
Indices: 34756979--34757048 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
34756969 TAAATAAGGT
*
34756979 TTAGGAG
1 TTAGGGG
*
34756986 TTAAGGG
1 TTAGGGG
34756993 TTAGGGG
1 TTAGGGG
**
34757000 TT-GAAG
1 TTAGGGG
*
34757006 TTAGTGG
1 TTAGGGG
34757013 TTAGGGG
1 TTAGGGG
34757020 TTAGGGG
1 TTAGGGG
34757027 TTTA-GGG
1 -TTAGGGG
34757034 TTAGGGG
1 TTAGGGG
*
34757041 TTAAGGG
1 TTAGGGG
34757048 T
1 T
34757049 CGAGTTAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 7 0.14
7 41 0.80
8 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:34757144 original size:18 final size:18
Alignment explanation
Indices: 34757111--34757145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34757101 TAAATAAGGT
*
34757111 TTAGGGGTTAGTGGTTAA
1 TTAGGGGTTAGGGGTTAA
*
34757129 TTAGGGGTTTGGGGTTA
1 TTAGGGGTTAGGGGTTA
34757146 GAGATTAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (18 bp):
TTAGGGGTTAGGGGTTAA
Found at i:34757166 original size:21 final size:20
Alignment explanation
Indices: 34757128--34757184 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
34757118 TTAGTGGTTA
* *
34757128 ATTAGGGGTTTGGGGTTAGAG
1 ATTA-GGGTTTAGAGTTAGAG
*
34757149 ATTAGAGGTTTAGAGTTAGTG
1 ATTAG-GGTTTAGAGTTAGAG
34757170 ATTTAGGGTTTAGAG
1 A-TTAGGGTTTAGAG
34757185 ATTTGGGGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.37
Consensus pattern (20 bp):
ATTAGGGTTTAGAGTTAGAG
Found at i:34757178 original size:130 final size:128
Alignment explanation
Indices: 34756942--34757178 Score: 271
Period size: 130 Copynumber: 1.8 Consensus size: 128
34756932 AGGGTTTAGA
*
34756942 TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTAGGGGTTGAAGT
1 TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTA--GATTGAAGT
* * * * * *
34757007 TAGTGGTTAGGGGTTAGGGGTTTAGGGTTAGGGGTTAAGGGTCGAGTTAGAGTATAGTATTTTAT
64 TAGGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGTCGAGTTAGAGTATAGTATTTTAT
* * * **
34757072 TTAATTAGTGTTTTTTAATTTATATATATTAAATAAGGTTTAGGGGTT-AGTGGTTA-ATTAGGG
1 TTAATTAGAGTGTTTTAA-TT-TATATATTAAATAAGGTTTAGGAGTTAAG-GGTTAGATT-GAA
* * *
34757135 GTTTGGGGTTAGAGATTAGAGGTTTAGAGTTAGTGATTTAGGGT
62 GTTAGGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGT
34757179 TTAGAGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
129 2 0.02
130 52 0.59
131 4 0.05
132 30 0.34
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.41
Consensus pattern (128 bp):
TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTAGATTGAAGTTA
GGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGTCGAGTTAGAGTATAGTATTTTAT
Found at i:34758839 original size:4 final size:4
Alignment explanation
Indices: 34758830--34758868 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
34758820 TAATAATGAG
34758830 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
34758869 CTAAGTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:34761387 original size:7 final size:7
Alignment explanation
Indices: 34761375--34761416 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
34761365 ATGTGAATTT
34761375 GATATTA
1 GATATTA
34761382 GATATTA
1 GATATTA
*
34761389 GATATTT
1 GATATTA
*
34761396 GGTATT-
1 GATATTA
34761402 GATATTA
1 GATATTA
34761409 GATATTA
1 GATATTA
34761416 G
1 G
34761417 GCTGTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:34761407 original size:20 final size:21
Alignment explanation
Indices: 34761371--34761414 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
34761361 TTTGATGTGA
34761371 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
34761392 ATTTGGTATT-GATATTAGAT
1 ATTTGATATTAGATATTAGAT
34761412 ATT
1 ATT
34761415 AGGCTGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:34761584 original size:13 final size:13
Alignment explanation
Indices: 34761566--34761593 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34761556 GCATTTTCAG
34761566 AGTTGTTAAATTT
1 AGTTGTTAAATTT
34761579 AGTTGTTAAATTT
1 AGTTGTTAAATTT
34761592 AG
1 AG
34761594 GCTACTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (13 bp):
AGTTGTTAAATTT
Found at i:34761771 original size:7 final size:7
Alignment explanation
Indices: 34761759--34761800 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
34761749 ATGTGAATTT
34761759 GATATTA
1 GATATTA
34761766 GATATTA
1 GATATTA
*
34761773 GATATTT
1 GATATTA
*
34761780 GGTATTA
1 GATATTA
34761787 -ATATTA
1 GATATTA
34761793 GATATTA
1 GATATTA
34761800 G
1 G
34761801 GGTTTAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:34761792 original size:20 final size:21
Alignment explanation
Indices: 34761755--34761798 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
34761745 TTTGATGTGA
34761755 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
34761776 ATTTGGTATTA-ATATTAGAT
1 ATTTGATATTAGATATTAGAT
34761796 ATT
1 ATT
34761799 AGGGTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:34762100 original size:25 final size:25
Alignment explanation
Indices: 34762061--34762479 Score: 306
Period size: 25 Copynumber: 16.9 Consensus size: 25
34762051 AACTTATTAA
* *
34762061 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
34762086 TCCATAACTTCCATAATACAAAATT
1 TACATAACTTACATAATACATAACT
* * *
34762111 TATATAACTTATATAAGAC--AACT
1 TACATAACTTACATAATACATAACT
* *
34762134 TACATAATTTACTTAATACATAACT
1 TACATAACTTACATAATACATAACT
*** *
34762159 TACATGTTTTACATAATATATAACT
1 TACATAACTTACATAATACATAACT
* *
34762184 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * *
34762209 TCCATAACTTTCATAATACACAACT
1 TACATAACTTACATAATACATAACT
* *
34762234 TACACAACTTAAATAACTTACATAAC-
1 TACATAACTTACATAA--TACATAACT
*
34762260 T-CACAACTTACATAACTTACATAACT
1 TACATAACTTACATAA--TACATAACT
* *
34762286 TACATAACTCACA-ACTTACAT-A--
1 TACATAACTTACATA-ATACATAACT
* * *
34762308 T-CTTAA-TTACATTATACACAACT
1 TACATAACTTACATAATACATAACT
* ** *
34762331 TACATAGCTTACATTCTACACAACT
1 TACATAACTTACATAATACATAACT
*
34762356 TACATAACATACATAACTTACATAA--
1 TACATAACTTACATAA--TACATAACT
*
34762381 TACATAACTTA-ATTTAATACACAACT
1 TACATAACTTACA--TAATACATAACT
*
34762407 TACATAGCTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
*
34762432 TACATAACTTATATAATACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
34762457 TATATGATTTACTTAATACATAA
1 TACATAACTTACATAATACATAA
34762480 ATATATATCA
Statistics
Matches: 309, Mismatches: 65, Indels: 40
0.75 0.16 0.10
Matches are distributed among these distances:
20 8 0.03
21 5 0.02
22 1 0.00
23 18 0.06
24 11 0.04
25 227 0.73
26 16 0.05
27 23 0.07
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.33
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:34762190 original size:9 final size:9
Alignment explanation
Indices: 34762061--34762458 Score: 221
Period size: 9 Copynumber: 47.2 Consensus size: 9
34762051 AACTTATTAA
*
34762061 TACATAACC
1 TACATAACT
34762070 TACATAA--
1 TACATAACT
*
34762077 GACATAACT
1 TACATAACT
*
34762086 TCCATAACT
1 TACATAACT
*
34762095 TCCATAA--
1 TACATAACT
* *
34762102 TACAAAATT
1 TACATAACT
*
34762111 TATATAACT
1 TACATAACT
*
34762120 TATATAA--
1 TACATAACT
*
34762127 GAC--AACT
1 TACATAACT
*
34762134 TACATAATT
1 TACATAACT
*
34762143 TACTTAA--
1 TACATAACT
34762150 TACATAACT
1 TACATAACT
***
34762159 TACATGTTT
1 TACATAACT
34762168 TACATAA--
1 TACATAACT
*
34762175 TATATAACT
1 TACATAACT
*
34762184 TACATAACC
1 TACATAACT
34762193 TACATAA--
1 TACATAACT
*
34762200 GACATAACT
1 TACATAACT
*
34762209 TCCATAACT
1 TACATAACT
*
34762218 TTCATAA--
1 TACATAACT
*
34762225 TACACAACT
1 TACATAACT
*
34762234 TACACAACT
1 TACATAACT
*
34762243 TAAATAACT
1 TACATAACT
34762252 TACATAAC-
1 TACATAACT
*
34762260 T-CACAACT
1 TACATAACT
34762268 TACATAACT
1 TACATAACT
34762277 TACATAACT
1 TACATAACT
34762286 TACATAAC-
1 TACATAACT
*
34762294 T-CACAACT
1 TACATAACT
*
34762302 TACATATCT
1 TACATAACT
*
34762311 TA-ATTACATT
1 TACA-TA-ACT
*
34762321 ATACACAACT
1 -TACATAACT
*
34762331 TACATAGCT
1 TACATAACT
*
34762340 TACAT-TC-
1 TACATAACT
*
34762347 TACACAACT
1 TACATAACT
*
34762356 TACATAACA
1 TACATAACT
34762365 TACATAACT
1 TACATAACT
34762374 TACATAA--
1 TACATAACT
34762381 TACATAACT
1 TACATAACT
34762390 TA-ATTTAA--
1 TACA--TAACT
*
34762398 TACACAACT
1 TACATAACT
*
34762407 TACATAGCT
1 TACATAACT
34762416 TACATAA--
1 TACATAACT
34762423 TACATAACT
1 TACATAACT
34762432 TACATAACT
1 TACATAACT
*
34762441 TATATAA--
1 TACATAACT
34762448 TACATAACT
1 TACATAACT
34762457 TA
1 TA
34762459 TATGATTTAC
Statistics
Matches: 298, Mismatches: 54, Indels: 74
0.70 0.13 0.17
Matches are distributed among these distances:
5 2 0.01
7 73 0.24
8 10 0.03
9 203 0.68
10 6 0.02
11 3 0.01
12 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:34762216 original size:34 final size:32
Alignment explanation
Indices: 34762178--34762456 Score: 118
Period size: 34 Copynumber: 8.5 Consensus size: 32
34762168 TACATAATAT
* *
34762178 ATAACTTACATAACCTACATAAGACATAACTTCC
1 ATAACTTACATAA-CTACA-AATACATAACTTAC
* * *
34762212 ATAACTTTCATAA-TACACAACTTACACAACTTAA
1 ATAACTTACATAACTACA-AA--TACATAACTTAC
*
34762246 ATAACTTACATAACTCACAACTTACATAACTTAC
1 ATAACTTACATAACT-ACAA-ATACATAACTTAC
* *
34762280 ATAACTTACATAACTCACAACTTACATATCTTA-
1 ATAACTTACATAACT-ACAA-ATACATAACTTAC
* * *
34762313 ATTACATT--AT-AC-ACAACTTACATAGCTTAC
1 ATAAC-TTACATAACTACAA-ATACATAACTTAC
* *
34762343 AT-TC-TACACAACTTACATAACATACATAACTTAC
1 ATAACTTACATAAC-TAC--AA-ATACATAACTTAC
*
34762377 ATAA--TACATAACTTA-ATTTAATACACAACTTAC
1 ATAACTTACATAAC-TACA---AATACATAACTTAC
* *
34762410 ATAGCTTACATAA-TACATAACTTACATAACTTAT
1 ATAACTTACATAACTACA-AA--TACATAACTTAC
34762444 ATAA--TACATAACT
1 ATAACTTACATAACT
34762457 TATATGATTT
Statistics
Matches: 197, Mismatches: 24, Indels: 49
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.01
29 18 0.09
30 4 0.02
31 3 0.02
32 20 0.10
33 22 0.11
34 117 0.59
35 9 0.05
36 3 0.02
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (32 bp):
ATAACTTACATAACTACAAATACATAACTTAC
Found at i:34762461 original size:16 final size:16
Alignment explanation
Indices: 34762043--34762458 Score: 142
Period size: 16 Copynumber: 24.9 Consensus size: 16
34762033 TTTAAATTTT
*
34762043 TAATACATAACTTA-T
1 TAATACATAACTTACA
*
34762058 TAATACATAACCTACA
1 TAATACATAACTTACA
* *
34762074 TAAGACATAACTTCCA
1 TAATACATAACTTACA
*
34762090 TAACTTCCATAA--TACA
1 TAA--TACATAACTTACA
* * *
34762106 AAATTTATATAACTTATA
1 TAA--TACATAACTTACA
*
34762124 TAAGAC--AACTTACA
1 TAATACATAACTTACA
*
34762138 TAATTTACTTAA--TACA
1 TAA--TACATAACTTACA
***
34762154 TAACTTACATGTTTTACA
1 TAA--TACATAACTTACA
*
34762172 TAATATATAACTTACA
1 TAATACATAACTTACA
*
34762188 TAACCTACATAA--GACA
1 TAA--TACATAACTTACA
* *
34762204 TAACTTCCATAACTTTCA
1 TAA--TACATAACTTACA
*
34762222 TAATACACAACTTACA
1 TAATACATAACTTACA
* *
34762238 CAACTTAAATAACTTACA
1 TAA--TACATAACTTACA
*
34762256 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
34762272 TAACTTACATAACTTACA
1 TAA--TACATAACTTACA
*
34762290 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
* *
34762306 TATCTTA-ATTACATTATACA
1 TA--ATACA-TA-ACT-TACA
* *
34762326 CAACTTACATAGCTTACA
1 TAA--TACATAACTTACA
** *
34762344 TTCTACACAACTTACA
1 TAATACATAACTTACA
34762360 TAACATACATAACTTACA
1 T-A-ATACATAACTTACA
34762378 TAATACATAACTTA-A
1 TAATACATAACTTACA
*
34762393 TTTAATACACAACTTACA
1 --TAATACATAACTTACA
*
34762411 TAGCTTACATAA--TACA
1 TA--ATACATAACTTACA
*
34762427 TAACTTACATAACTTATA
1 TAA--TACATAACTTACA
34762445 TAATACATAACTTA
1 TAATACATAACTTA
34762459 TATGATTTAC
Statistics
Matches: 296, Mismatches: 66, Indels: 77
0.67 0.15 0.18
Matches are distributed among these distances:
14 10 0.03
15 14 0.05
16 153 0.52
17 19 0.06
18 87 0.29
19 3 0.01
20 9 0.03
21 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (16 bp):
TAATACATAACTTACA
Found at i:34764300 original size:43 final size:43
Alignment explanation
Indices: 34764253--34764361 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
34764243 AGTTTATAGA
* * * **
34764253 AAAAGTGCCGCTAAAAGTCATGTTCTTTAGTGGCGTTTGGGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
* *
34764296 AAAAGCGCCGCTAAAAGTTATGATCTATAGCAGCGTTTGTGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
* *
34764339 AAAAGCGCCACTAAAGGTCATGA
1 AAAAGCGCCGCTAAAAGTCATGA
34764362 CCTTTAGAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
Found at i:34766214 original size:35 final size:35
Alignment explanation
Indices: 34766168--34766263 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
34766158 TACTCTCTGT
*
34766168 TTGGTGTGTTTCGGAGGGATTAGCTCTTTTAAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
** * *
34766203 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
* * *
34766238 ATGGTGTGTTTTGGAGGGATTGGCTC
1 TTGGTGTGTTTCGGAGGGATTAGCTC
34766264 GTGTGAGCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.40
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
Found at i:34782527 original size:44 final size:44
Alignment explanation
Indices: 34782459--34782982 Score: 665
Period size: 44 Copynumber: 11.9 Consensus size: 44
34782449 TAAGCCACAA
* * * * *
34782459 GTCCTATCTCCCTGACCAGTAGCGGAATAGGTTGAAAATTGTAT
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * * * * *
34782503 GTCCTATTTCCCAGGCCAGCAGCGGAATAGGTGGAAGATTGCAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* *
34782547 GTCCTATCTCCCTCACCAGCAGTGGAATAGGTTGAAGATTGTAG
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782591 GTCCTATGC-CCCTGACTAGCAGTGGAATAGGTTGAAGATTACAA
1 GTCCTAT-CTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782635 GTCCTATCTCCCTGACCAACAGTGGAATAGGTTCAAGATTGTAG
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782679 GTCGTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGA-TGACAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG-CAG
* *
34782723 GTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTACAG
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782767 GTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGGTTGTAG
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * * *
34782811 GTCCTATGTCCCTGACCAGCAGTGGAATAGTTTGAAGATTACAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782855 GTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGGTTGTAG
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* * *
34782899 GTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAGATTACAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
* *
34782943 GTCCTATCTCCCTGACCAACAGTGGAATAGGTGGAAGATT
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
34782983 AGTCTCTATA
Statistics
Matches: 412, Mismatches: 64, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
43 3 0.01
44 407 0.99
45 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (44 bp):
GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAG
Found at i:34784456 original size:12 final size:12
Alignment explanation
Indices: 34784439--34784465 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34784429 TACTGGAATG
34784439 TTTATATAATTA
1 TTTATATAATTA
34784451 TTTATATAATTA
1 TTTATATAATTA
34784463 TTT
1 TTT
34784466 TCTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATATAATTA
Found at i:34787532 original size:20 final size:20
Alignment explanation
Indices: 34787493--34787532 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34787483 ACATAAATTG
*
34787493 GTTTTTCTATAAAAATTCAA
1 GTTTTTCTATAAAAACTCAA
34787513 GTTTTTCGTAT-AAAACTCAA
1 GTTTTTC-TATAAAAACTCAA
34787533 CTAATTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (20 bp):
GTTTTTCTATAAAAACTCAA
Found at i:34793437 original size:13 final size:13
Alignment explanation
Indices: 34793419--34793444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34793409 GCGTGTGGGC
34793419 CCACACGGGCATG
1 CCACACGGGCATG
34793432 CCACACGGGCATG
1 CCACACGGGCATG
34793445 TGGGTTTTGG
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:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (13 bp):
CCACACGGGCATG
Found at i:34796674 original size:25 final size:25
Alignment explanation
Indices: 34796615--34796702 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
34796605 GTATATGTAT
*
34796615 GCTCAGACGAGCT--ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
* * *
34796639 GCACCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * *
34796664 GCTCATACGAGCTGAGTATCGATAA
1 GCTCATACGAGCTGAATAACGGTAA
*
34796689 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
34796703 GAACCAGCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
24 9 0.18
25 40 0.78
26 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:34801781 original size:7 final size:7
Alignment explanation
Indices: 34801758--34801796 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
34801748 GTGTAGATAA
34801758 TAAAATT
1 TAAAATT
34801765 TAAATTATT
1 TAAA--ATT
34801774 TAAAATT
1 TAAAATT
*
34801781 TAAACTT
1 TAAAATT
34801788 TAAAATT
1 TAAAATT
34801795 TA
1 TA
34801797 GTTAATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (7 bp):
TAAAATT
Found at i:34801839 original size:27 final size:27
Alignment explanation
Indices: 34801807--34801899 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 27
34801797 GTTAATCAAT
34801807 GATAAT-TTTGAACTAATTTAAAATTTA
1 GATAATATTT-AACTAATTTAAAATTTA
*
34801834 GATAATAAGTTTAA--AATTTAAATTTTA
1 GATAAT-A-TTTAACTAATTTAAAATTTA
34801861 GATAATAAATTTTAAGCTAATTTAAAATTTA
1 GATAAT--A-TTTAA-CTAATTTAAAATTTA
34801892 -A-AATATTT
1 GATAATATTT
34801900 CAATTTTATT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
26 3 0.05
27 25 0.45
28 7 0.12
29 5 0.09
30 4 0.07
31 12 0.21
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
GATAATATTTAACTAATTTAAAATTTA
Found at i:34804028 original size:47 final size:46
Alignment explanation
Indices: 34803960--34804052 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 46
34803950 TCCTCTATGT
* *
34803960 CCCTAAATTTTTGGTAACCTTTTATATGTTAGTACTATCACTAAAG
1 CCCTAAACTTTCGGTAACCTTTTATATGTTAGTACTATCACTAAAG
34804006 CCCTAAACTTTCGGCTAACCTTTTATATGTTAGTACTATCACTAAAG
1 CCCTAAACTTTCGG-TAACCTTTTATATGTTAGTACTATCACTAAAG
34804053 ACGATTGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 12 0.27
47 32 0.73
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (46 bp):
CCCTAAACTTTCGGTAACCTTTTATATGTTAGTACTATCACTAAAG
Found at i:34810622 original size:22 final size:22
Alignment explanation
Indices: 34810594--34810639 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34810584 GACGGATTCC
34810594 AATATTATATACTAGTCTTTCA
1 AATATTATATACTAGTCTTTCA
34810616 AATATTATATACTAGTCTTTCA
1 AATATTATATACTAGTCTTTCA
34810638 AA
1 AA
34810640 GATAGTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (22 bp):
AATATTATATACTAGTCTTTCA
Found at i:34811507 original size:18 final size:18
Alignment explanation
Indices: 34811484--34811525 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
34811474 CTCATAAATA
34811484 TGAAATAATGAAATATAC-
1 TGAAATAATGAAATA-ACT
34811502 TGAAATAATGAAATAACT
1 TGAAATAATGAAATAACT
34811520 TGAAAT
1 TGAAAT
34811526 TCAATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (18 bp):
TGAAATAATGAAATAACT
Found at i:34811525 original size:10 final size:8
Alignment explanation
Indices: 34811479--34811517 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
34811469 AACAACTCAT
34811479 AAAT-ATG
1 AAATAATG
34811486 AAATAATG
1 AAATAATG
34811494 AAATATACTG
1 AAATA-A-TG
34811504 AAATAATG
1 AAATAATG
34811512 AAATAA
1 AAATAA
34811518 CTTGAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.14
8 16 0.55
9 2 0.07
10 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (8 bp):
AAATAATG
Found at i:34814297 original size:17 final size:17
Alignment explanation
Indices: 34814275--34814311 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34814265 AATCAATATT
*
34814275 CACTAAGATGATTGTAC
1 CACTAAGACGATTGTAC
*
34814292 CACTAAGGCGATTGTAC
1 CACTAAGACGATTGTAC
34814309 CAC
1 CAC
34814312 ATCTGTCTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (17 bp):
CACTAAGACGATTGTAC
Found at i:34814868 original size:35 final size:35
Alignment explanation
Indices: 34814838--34814936 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 35
34814828 AATTATTGAT
*
34814838 ATTCTGATTCGCATGTTAAGCATGCTATTATTCTG
1 ATTCTGATTCGCATGTTAAGCATGCCATTATTCTG
* *
34814873 ATTATGATTTGCATGTTAAGCATGCCATTATTCTG
1 ATTCTGATTCGCATGTTAAGCATGCCATTATTCTG
* * * *
34814908 ATTCTGATTCTCAAGTTAAACATGTCATT
1 ATTCTGATTCGCATGTTAAGCATGCCATT
34814937 GTGTTAAGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (35 bp):
ATTCTGATTCGCATGTTAAGCATGCCATTATTCTG
Done.