Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 76 of 214
Found at i:21486692 original size:12 final size:12
Alignment explanation
Indices: 21486677--21486702 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21486667 TTTTTTTCAC
21486677 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21486689 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21486701 TT
1 TT
21486703 CGATTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:21488057 original size:20 final size:20
Alignment explanation
Indices: 21488023--21488082 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
21488013 ACCAATAAAT
21488023 AAATGAGCT-GAATTGTAGCT-
1 AAATGAGCTCG-ATTG-AGCTG
*
21488043 AATTGAGCTCGATTGAGCTG
1 AAATGAGCTCGATTGAGCTG
* *
21488063 AAATGAGCTCAATTAAGCTG
1 AAATGAGCTCGATTGAGCTG
21488083 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 29 0.85
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCGATTGAGCTG
Found at i:21488069 original size:10 final size:10
Alignment explanation
Indices: 21488026--21488082 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
21488016 AATAAATAAA
21488026 TGAGCTGAAT
1 TGAGCTGAAT
21488036 TGTAGCT-AAT
1 TG-AGCTGAAT
21488046 TGAGCTCG-AT
1 TGAGCT-GAAT
*
21488056 TGAGCTGAAA
1 TGAGCTGAAT
*
21488066 TGAGCTCAAT
1 TGAGCTGAAT
*
21488076 TAAGCTG
1 TGAGCTG
21488083 GTCGGAGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 5 0.13
10 29 0.76
11 4 0.11
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:21490019 original size:32 final size:32
Alignment explanation
Indices: 21489982--21490043 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
21489972 GATTACTCAC
21489982 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTT
*
21490014 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21490044 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 16 0.59
33 10 0.37
34 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.55
Consensus pattern (32 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTT
Found at i:21490070 original size:21 final size:21
Alignment explanation
Indices: 21490041--21490096 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21490031 CAAGCTCTCT
*
21490041 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21490062 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21490083 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21490097 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21490089 original size:14 final size:14
Alignment explanation
Indices: 21490040--21490096 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21490030 TCAAGCTCTC
21490040 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21490053 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21490067 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21490081 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21490095 TT
1 TT
21490097 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21490147 original size:11 final size:11
Alignment explanation
Indices: 21490128--21490162 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21490118 TCTTTTGCAA
*
21490128 TTTCTTTTTCT
1 TTTCGTTTTCT
21490139 TTTCGTTTTCT
1 TTTCGTTTTCT
*
21490150 TTTTGTTTTCT
1 TTTCGTTTTCT
21490161 TT
1 TT
21490163 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:21491191 original size:10 final size:10
Alignment explanation
Indices: 21491178--21491239 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 10
21491168 GACTTTTCAC
21491178 TTTTTTTTCT
1 TTTTTTTTCT
21491188 TTTTTTTTGCT
1 TTTTTTTT-CT
21491199 CATTTTTTTTCT
1 --TTTTTTTTCT
21491211 TCTTTTTTT-T
1 T-TTTTTTTCT
21491221 TCTTTTTTTCAT
1 T-TTTTTTTC-T
21491233 TTTTTTT
1 TTTTTTT
21491240 GAATTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
10 19 0.41
11 15 0.33
12 4 0.09
13 8 0.17
ACGTcount: A:0.03, C:0.11, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:21491204 original size:13 final size:12
Alignment explanation
Indices: 21491177--21491229 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 12
21491167 AGACTTTTCA
21491177 CTTTTTTTTCTT
1 CTTTTTTTTCTT
*
21491189 -TTTTTTTGC-T
1 CTTTTTTTTCTT
21491199 CATTTTTTTTCTT
1 C-TTTTTTTTCTT
21491212 C-TTTTTTT-TT
1 CTTTTTTTTCTT
21491222 CTTTTTTT
1 CTTTTTTT
21491230 CATTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.11
11 21 0.60
12 8 0.23
13 2 0.06
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:21491239 original size:13 final size:12
Alignment explanation
Indices: 21491178--21491229 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
21491168 GACTTTTCAC
21491178 TTTTTTTTC-TT
1 TTTTTTTTCTTT
* **
21491189 TTTTTTTGCTCA
1 TTTTTTTTCTTT
21491201 TTTTTTTTCTTCT
1 TTTTTTTTCTT-T
21491214 TTTTTTTTCTTT
1 TTTTTTTTCTTT
21491226 TTTT
1 TTTT
21491230 CATTTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 8 0.24
12 14 0.42
13 11 0.33
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.85
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:21491248 original size:13 final size:12
Alignment explanation
Indices: 21491232--21491264 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
21491222 CTTTTTTTCA
21491232 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21491244 TTTTTTTTGAAT
1 TTTTTTTTGAAT
21491256 TTCTTTTTT
1 TT-TTTTTT
21491265 TTAATCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:21492585 original size:18 final size:19
Alignment explanation
Indices: 21492562--21492601 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
21492552 TCACATAAAT
21492562 ATGAGCT-GAATTGAGCT-A
1 ATGAGCTCG-ATTGAGCTGA
21492580 ATGAGCTCGATTGAGCTGA
1 ATGAGCTCGATTGAGCTGA
21492599 ATG
1 ATG
21492602 GCTATTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (19 bp):
ATGAGCTCGATTGAGCTGA
Found at i:21494635 original size:38 final size:37
Alignment explanation
Indices: 21494593--21494725 Score: 94
Period size: 38 Copynumber: 3.5 Consensus size: 37
21494583 TTTCAAGCTC
*
21494593 TCTTTCAATTTCTTTTTTCGCTTTTTCTTTTTCAATTT
1 TCTTTCAATTTCTTTTTTCACTTTTTCTTTTTC-ATTT
* ** *
21494631 TCTTTCTTCATTTCTTTTCTCTCAC-TTTTCGATTTCTTTT
1 TCTTTC--AATTTCTTTT-T-TCACTTTTTCTTTTTCATTT
* *
21494671 TCTTTGCAA-TTC-TTTTTCTTCTTCGTTTCTTTTT-GTTT
1 TCTTT-CAATTTCTTTTTTC-ACTT--TTTCTTTTTCATTT
21494709 TCTTTCAATTTCTTTTT
1 TCTTTCAATTTCTTTTT
21494726 CAATCTCTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
35 2 0.03
36 2 0.03
37 7 0.09
38 20 0.27
39 12 0.16
40 17 0.23
41 11 0.15
42 3 0.04
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.68
Consensus pattern (37 bp):
TCTTTCAATTTCTTTTTTCACTTTTTCTTTTTCATTT
Found at i:21495747 original size:14 final size:14
Alignment explanation
Indices: 21495730--21495779 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
21495720 TAACTTGATT
21495730 TTTTTTTTGCTCAC
1 TTTTTTTTGCTCAC
*
21495744 TTTTTTTT-CTTTCTC
1 TTTTTTTTGC--TCAC
21495759 TTTTTTTTGCTCGA-
1 TTTTTTTTGCTC-AC
21495773 TTTTTTT
1 TTTTTTT
21495780 CACTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.03
14 17 0.57
15 11 0.37
16 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:21495797 original size:10 final size:11
Alignment explanation
Indices: 21495773--21495807 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21495763 TTTTGCTCGA
* *
21495773 TTTTTTTCACT
1 TTTTTTTGAAT
21495784 TTTTTTTGAAT
1 TTTTTTTGAAT
21495795 TTTTTTTGAAT
1 TTTTTTTGAAT
21495806 TT
1 TT
21495808 CGATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:21497199 original size:20 final size:21
Alignment explanation
Indices: 21497159--21497214 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21497149 ACCAATAAAA
21497159 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21497179 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21497199 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21497215 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21499276 original size:33 final size:33
Alignment explanation
Indices: 21499238--21499300 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21499228 GATTACTCAC
21499238 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21499271 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21499301 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21499313 original size:13 final size:13
Alignment explanation
Indices: 21499297--21499351 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
21499287 TCAAGCTCTC
21499297 TTTCAATTTCTTT
1 TTTCAATTTCTTT
**
21499310 TTTCGCTTT-TTCT
1 TTTCAATTTCTT-T
21499323 TTTCAATTTTCTTT
1 TTTCAA-TTTCTTT
21499337 TCTTC-ATTTCTTT
1 T-TTCAATTTCTTT
21499350 TT
1 TT
21499352 CTCTCACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.09
13 20 0.59
14 6 0.18
15 5 0.15
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCAATTTCTTT
Found at i:21499405 original size:18 final size:17
Alignment explanation
Indices: 21499358--21499416 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
21499348 TTTTCTCTCA
21499358 CTTTTCGATTTCTTTTT
1 CTTTTCGATTTCTTTTT
*
21499375 CTTTTGCAATTTCTTTTT
1 CTTTT-CGATTTCTTTTT
*
21499393 CTTCTTCGTTTTCTTTTT
1 CTT-TTCGATTTCTTTTT
*
21499411 GTTTTC
1 CTTTTC
21499417 TTTCAATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.22
18 26 0.72
19 2 0.06
ACGTcount: A:0.05, C:0.19, G:0.07, T:0.69
Consensus pattern (17 bp):
CTTTTCGATTTCTTTTT
Found at i:21500507 original size:29 final size:28
Alignment explanation
Indices: 21500426--21500507 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
21500416 CGCAAGACTT
**
21500426 TCACTTTTTTTTTAACTTGATTTTTTTTGC
1 TCAC-TTTTTTTT-ACTTTTTTTTTTTTGC
21500456 TCACTTTTTTTT-CTTTCTCTTTTTTTTGC
1 TCACTTTTTTTTACTTT-T-TTTTTTTTGC
21500485 TCGA-TTTTTTTTCACTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTT
21500508 GAATTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
27 3 0.07
29 32 0.71
30 6 0.13
31 4 0.09
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:21500514 original size:10 final size:11
Alignment explanation
Indices: 21500488--21500524 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
21500478 TTTTTGCTCG
*
21500488 ATTTTTTTTCA
1 ATTTTTTTTGA
*
21500499 CTTTTTTTTGA
1 ATTTTTTTTGA
21500510 ATTTTTTTTGA
1 ATTTTTTTTGA
21500521 ATTT
1 ATTT
21500525 CGATTTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:21501908 original size:20 final size:21
Alignment explanation
Indices: 21501868--21501923 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21501858 ACCAATAAAA
21501868 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21501888 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21501908 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21501924 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21503995 original size:33 final size:33
Alignment explanation
Indices: 21503957--21504019 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21503947 GATTACTCAC
21503957 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21503990 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21504020 AATTCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21504051 original size:13 final size:12
Alignment explanation
Indices: 21504035--21504153 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
21504025 TTTTTTCGCT
21504035 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
21504048 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
21504062 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
21504073 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
21504087 -TTTCTTTTTC-
1 TTTTCTTTTTCA
**
21504097 TTTTGCAATTTC-
1 TTTT-CTTTTTCA
* *
21504109 TTTTCTTCTTCG
1 TTTTCTTTTTCA
*
21504121 TTTTCTTTTT-G
1 TTTTCTTTTTCA
21504132 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
21504142 ATTTCTTTTTCA
1 TTTTCTTTTTCA
21504154 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 23
0.70 0.10 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 14 0.17
12 42 0.51
13 8 0.10
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:21504056 original size:26 final size:27
Alignment explanation
Indices: 21504016--21504072 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
21504006 TCAAGCTCTC
*
21504016 TTTCAATTCTTTTTTC-GCTTTTTCTT
1 TTTCAATTCTTTTTTCTGCATTTTCTT
*
21504042 TTTCAATT-TTCTTTTCTTCATTTTCTT
1 TTTCAATTCTT-TTTTCTGCATTTTCTT
21504069 TTTC
1 TTTC
21504073 TCTCACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 13 0.48
27 12 0.44
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTCAATTCTTTTTTCTGCATTTTCTT
Found at i:21504064 original size:14 final size:14
Alignment explanation
Indices: 21504035--21504071 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
21504025 TTTTTTCGCT
21504035 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
21504048 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
21504062 TTTTCTTTTT
1 TTTTCTTTTT
21504072 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:21504100 original size:17 final size:17
Alignment explanation
Indices: 21504080--21504136 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
21504070 TTCTCTCACT
21504080 TTTTCGATTTCTTTTTC
1 TTTTCGATTTCTTTTTC
*
21504097 TTTTGCAATTTC-TTTTC
1 TTTT-CGATTTCTTTTTC
* *
21504114 TTCTTCGTTTTCTTTTTG
1 TT-TTCGATTTCTTTTTC
21504132 TTTTC
1 TTTTC
21504137 TTTCAATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.05, C:0.18, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTCGATTTCTTTTTC
Found at i:21504146 original size:56 final size:55
Alignment explanation
Indices: 21504033--21504152 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 55
21504023 TCTTTTTTCG
* *
21504033 CTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTT
1 CTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCT--CTTTTTCAATTT
* * *
21504090 CTTTTTCTTTTGCAATTTCTTTTCTTCTTCGTTTTCTTTTTGT-T-TTCTTTCAATTT
1 CTTTTTCTTTTGCAATTT-TCTT-TTCTTCATTTTCTTTTTCTCTCTT-TTTCAATTT
21504146 CTTTTTC
1 CTTTTTC
21504153 AATCTCTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
55 2 0.04
56 15 0.27
57 17 0.31
58 4 0.07
59 17 0.31
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.69
Consensus pattern (55 bp):
CTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCTTTTTCAATTT
Found at i:21504152 original size:6 final size:6
Alignment explanation
Indices: 21504033--21504139 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
21504023 TCTTTTTTCG
* * * **
21504033 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
21504084 CGATTT CTTTTT CTTTTG CAATTT C-TTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
21504131 -GTTTT CTTT
1 CTTTTT CTTT
21504140 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 8 0.11
6 51 0.72
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:21505189 original size:15 final size:15
Alignment explanation
Indices: 21505171--21505223 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21505161 TTTAACTTGA
21505171 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
* *
21505186 TTTTTTTTCT-TTCTC
1 TTTTTTTT-TGCTCAC
21505201 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
21505216 TTTTTTTT
1 TTTTTTTT
21505224 CACTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:21505241 original size:10 final size:11
Alignment explanation
Indices: 21505215--21505251 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
21505205 TTTTTGCTCG
*
21505215 ATTTTTTTTCA
1 ATTTTTTTTGA
*
21505226 CTTTTTTTTGA
1 ATTTTTTTTGA
21505237 ATTTTTTTTGA
1 ATTTTTTTTGA
21505248 ATTT
1 ATTT
21505252 CGATTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:21506644 original size:20 final size:21
Alignment explanation
Indices: 21506604--21506659 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21506594 ACCAATAAAA
21506604 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21506624 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21506644 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21506660 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21508721 original size:33 final size:33
Alignment explanation
Indices: 21508683--21508745 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21508673 GATTACTCAC
21508683 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
21508716 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
21508746 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:21508772 original size:21 final size:21
Alignment explanation
Indices: 21508743--21508798 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
21508733 CAAGCTCTCT
*
21508743 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
21508764 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
21508785 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
21508799 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:21508791 original size:14 final size:14
Alignment explanation
Indices: 21508742--21508798 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
21508732 TCAAGCTCTC
21508742 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
21508755 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
21508769 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
21508783 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
21508797 TT
1 TT
21508799 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:21508825 original size:17 final size:17
Alignment explanation
Indices: 21508805--21508856 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
21508795 TTTTCTCTCA
21508805 CTTTTTCGATTTCTTTT
1 CTTTTTCGATTTCTTTT
* *
21508822 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTC-TTTT
* *
21508840 CTTCTTCGTTTTCTTTT
1 CTTTTTCGATTTCTTTT
21508857 TGTTTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (17 bp):
CTTTTTCGATTTCTTTT
Found at i:21508863 original size:11 final size:11
Alignment explanation
Indices: 21508807--21508866 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
21508797 TTCTCTCACT
*
21508807 TTTTCGATTTC
1 TTTTCGTTTTC
21508818 TTTTC-TTTTGC
1 TTTTCGTTTT-C
* *
21508829 AATTTCTTTTTC
1 -TTTTCGTTTTC
21508841 TTCTTCGTTTTC
1 TT-TTCGTTTTC
*
21508853 TTTTTGTTTTC
1 TTTTCGTTTTC
21508864 TTT
1 TTT
21508867 CAATTTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 3 0.08
11 18 0.45
12 15 0.38
13 4 0.10
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTCGTTTTC
Found at i:21508879 original size:6 final size:6
Alignment explanation
Indices: 21508760--21508866 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
21508750 TCTTTTTTCG
* * * **
21508760 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
21508811 CGATTT C-TTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
21508858 -GTTTT CTTT
1 CTTTTT CTTT
21508867 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 8 0.11
6 51 0.72
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:21509916 original size:15 final size:15
Alignment explanation
Indices: 21509898--21509950 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21509888 TTTAACTTGA
21509898 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
* *
21509913 TTTTTTTTCT-TTCTC
1 TTTTTTTT-TGCTCAC
21509928 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
21509943 TTTTTTTT
1 TTTTTTTT
21509951 CACTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:21509968 original size:10 final size:11
Alignment explanation
Indices: 21509942--21509978 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
21509932 TTTTTGCTCG
*
21509942 ATTTTTTTTCA
1 ATTTTTTTTGA
*
21509953 CTTTTTTTTGA
1 ATTTTTTTTGA
21509964 ATTTTTTTTGA
1 ATTTTTTTTGA
21509975 ATTT
1 ATTT
21509979 CGATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:21511373 original size:20 final size:21
Alignment explanation
Indices: 21511333--21511388 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
21511323 ACCAATAAAA
21511333 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCGAATTGTAGC
21511353 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCTCGAATTGTAGC
21511373 TGAAATGAGCTC-AATT
1 T-AAATGAGCTCGAATT
21511389 AAGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 18 0.56
21 13 0.41
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TAAATGAGCTCGAATTGTAGC
Found at i:21511733 original size:54 final size:54
Alignment explanation
Indices: 21511649--21511781 Score: 146
Period size: 54 Copynumber: 2.4 Consensus size: 54
21511639 ACATCACTCA
* * *
21511649 TTTCTTTTGT-ACTCTCGTTTCTTTCTTCAATCTCACTCTCT-TTTTCAGTTTTCT
1 TTTCTTTT-TCACACTCGTTTCTTTCTTCAATCTCAATCT-TATTTTCAATTTTCT
*
21511703 TTTCTTTTTCACACTCGTTTTTATTC-TCAATCTCAATCTTATTTTCAATTTTCT
1 TTTCTTTTTCACACTCGTTTCT-TTCTTCAATCTCAATCTTATTTTCAATTTTCT
* * *
21511757 TTTCTATCTCACACTCATCTTCTTT
1 TTTCTTTTTCACACTCGT-TTCTTT
21511782 TTCTTTCATT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
53 2 0.03
54 59 0.88
55 6 0.09
ACGTcount: A:0.14, C:0.26, G:0.03, T:0.57
Consensus pattern (54 bp):
TTTCTTTTTCACACTCGTTTCTTTCTTCAATCTCAATCTTATTTTCAATTTTCT
Found at i:21511796 original size:15 final size:16
Alignment explanation
Indices: 21511771--21511802 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21511761 TATCTCACAC
21511771 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21511787 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21511802 T
1 T
21511803 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:21512412 original size:41 final size:41
Alignment explanation
Indices: 21512350--21512435 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
21512340 TTTAATTAGG
*
21512350 TGTTTTAAATATGCCTGGACGAATTTAACGCTGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAACGCTGCCACTACA
* * *
21512391 TGTTATAAATATGCCTGGACGAATTTAATGCTGCTATTACA
1 TGTTATAAATATGCCTGGACGAATTTAACGCTGCCACTACA
21512432 TGTT
1 TGTT
21512436 TGGCCGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACGAATTTAACGCTGCCACTACA
Found at i:21515401 original size:22 final size:23
Alignment explanation
Indices: 21515364--21515409 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
21515354 AGTAGTTTCT
21515364 TCAAAAAAAATTTTGAAAAAAAAA
1 TCAAAAAAAA-TTTGAAAAAAAAA
21515388 TCAAAAAAAA-TTGAAAAAAAAA
1 TCAAAAAAAATTTGAAAAAAAAA
21515410 CTATTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.55
24 10 0.45
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (23 bp):
TCAAAAAAAATTTGAAAAAAAAA
Found at i:21515471 original size:15 final size:15
Alignment explanation
Indices: 21515451--21515505 Score: 92
Period size: 15 Copynumber: 3.6 Consensus size: 15
21515441 GATATCAAGT
21515451 TGAAAAAAAATTTCG
1 TGAAAAAAAATTTCG
*
21515466 TGAAAAAAAAATTCG
1 TGAAAAAAAATTTCG
21515481 TGAAAAAAAAATTTCG
1 TG-AAAAAAAATTTCG
21515497 TGAAAAAAA
1 TGAAAAAAA
21515506 GAAGAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 23 0.62
16 14 0.38
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (15 bp):
TGAAAAAAAATTTCG
Found at i:21515474 original size:16 final size:16
Alignment explanation
Indices: 21515453--21515505 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
21515443 TATCAAGTTG
21515453 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
21515469 AAAAAAAA-TTCGTGA
1 AAAAAAAATTTCGTGA
21515484 AAAAAAAATTTCGTGA
1 AAAAAAAATTTCGTGA
21515500 AAAAAA
1 AAAAAA
21515506 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.42
16 21 0.58
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAAAAAATTTCGTGA
Found at i:21516212 original size:52 final size:52
Alignment explanation
Indices: 21516132--21516242 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
21516122 CAAAATGTAC
*
21516132 GTTATTAAATTGGTCTTAAATCTGGTCAAACTTAATTATGCATGATATTTTA
1 GTTATTAAATTGGTCTTAAATCTAGTCAAACTTAATTATGCATGATATTTTA
21516184 GTTATTAAATTGGTCTTAAATCTAGTCAAACTTAATTATGCATGATATTTTA
1 GTTATTAAATTGGTCTTAAATCTAGTCAAACTTAATTATGCATGATATTTTA
21516236 GTTATTA
1 GTTATTA
21516243 TGACATGTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (52 bp):
GTTATTAAATTGGTCTTAAATCTAGTCAAACTTAATTATGCATGATATTTTA
Found at i:21517258 original size:22 final size:21
Alignment explanation
Indices: 21517227--21517277 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
21517217 ACCTCTTTGA
21517227 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
21517250 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
21517271 TCCATAC
1 ACCATAC
21517278 TATTTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:21517277 original size:21 final size:21
Alignment explanation
Indices: 21517232--21517294 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
21517222 TTTGAACCAT
* *
21517232 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
21517254 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* * *
21517275 TACTATTTTGAACCAATTCC
1 TACCATTTCGTACCAATTCC
21517295 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:21520678 original size:20 final size:20
Alignment explanation
Indices: 21520655--21520708 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21520645 AGTTTTTCCC
*
21520655 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21520675 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21520695 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21520709 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21520690 original size:30 final size:30
Alignment explanation
Indices: 21520655--21520728 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21520645 AGTTTTTCCC
21520655 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21520685 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21520715 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21520729 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21520718 original size:20 final size:20
Alignment explanation
Indices: 21520655--21520719 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21520645 AGTTTTTCCC
* * * *
21520655 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21520675 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21520694 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21520715 AGCTC
1 AGCTC
21520720 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21523365 original size:15 final size:16
Alignment explanation
Indices: 21523345--21523376 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21523335 AGAAAATGAA
21523345 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
21523360 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
21523376 A
1 A
21523377 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:21523491 original size:17 final size:18
Alignment explanation
Indices: 21523459--21523492 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21523449 AAAAGAGAGT
*
21523459 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21523477 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21523493 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:21524780 original size:20 final size:20
Alignment explanation
Indices: 21524757--21524810 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21524747 AGTTTTTCCC
*
21524757 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21524777 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21524797 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21524811 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21524792 original size:30 final size:30
Alignment explanation
Indices: 21524757--21524830 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21524747 AGTTTTTCCC
21524757 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21524787 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21524817 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21524831 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21524820 original size:20 final size:20
Alignment explanation
Indices: 21524757--21524821 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21524747 AGTTTTTCCC
* * * *
21524757 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21524777 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21524796 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21524817 AGCTC
1 AGCTC
21524822 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21526836 original size:15 final size:15
Alignment explanation
Indices: 21526788--21526840 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
21526778 TCTATTGATT
21526788 GAGAAAA-AAAAAGA
1 GAGAAAAGAAAAAGA
*
21526802 GA-AAAACAAAAAGA
1 GAGAAAAGAAAAAGA
*
21526816 GTGAAAAGAAAAAGA
1 GAGAAAAGAAAAAGA
*
21526831 AAGAAAAGAA
1 GAGAAAAGAA
21526841 TGAGGAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 4 0.12
14 10 0.30
15 19 0.58
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (15 bp):
GAGAAAAGAAAAAGA
Found at i:21536700 original size:29 final size:28
Alignment explanation
Indices: 21536666--21536731 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
21536656 CAATCACTCT
21536666 TTTTTTTTCAATT-TCAATTTTTTTCTTC
1 TTTTTTTTCAATTCT-AATTTTTTTCTTC
* *
21536694 TTCTTTTTTTAATTCTGATTTTTTTCTTC
1 TT-TTTTTTCAATTCTAATTTTTTTCTTC
21536723 TTTTTTTTC
1 TTTTTTTTC
21536732 TTCAATACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
29 24 0.73
30 1 0.03
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTTTTTCAATTCTAATTTTTTTCTTC
Found at i:21536791 original size:11 final size:11
Alignment explanation
Indices: 21536775--21536803 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
21536765 GAATACAAAC
21536775 TTTTTTTTGAA
1 TTTTTTTTGAA
21536786 TTTTTTTTGAA
1 TTTTTTTTGAA
21536797 TTTTTTT
1 TTTTTTT
21536804 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21540397 original size:22 final size:22
Alignment explanation
Indices: 21540367--21540410 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21540357 TTTGGTATTT
21540367 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
21540389 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
21540411 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21540584 original size:13 final size:13
Alignment explanation
Indices: 21540566--21540591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21540556 CACACTCGAG
21540566 TTTAAGGAGTGAT
1 TTTAAGGAGTGAT
21540579 TTTAAGGAGTGAT
1 TTTAAGGAGTGAT
21540592 AAGTTCGGAA
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:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
TTTAAGGAGTGAT
Found at i:21548417 original size:26 final size:27
Alignment explanation
Indices: 21548370--21548420 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
21548360 ATACTTAATT
* * *
21548370 TAGACTCAATTTAAATTTTCTAAACAA
1 TAGACACAATTTAAAGTGTCTAAACAA
21548397 TAGACACAA-TTAAAGTGTCTAAAC
1 TAGACACAATTTAAAGTGTCTAAAC
21548421 TAAGCCCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (27 bp):
TAGACACAATTTAAAGTGTCTAAACAA
Found at i:21552935 original size:11 final size:13
Alignment explanation
Indices: 21552919--21552950 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
21552909 TAGCTTCGAA
21552919 AAAAAAAAG-TT-
1 AAAAAAAAGTTTC
21552930 AAAAAAAAGTTTC
1 AAAAAAAAGTTTC
21552943 AAAAAAAA
1 AAAAAAAA
21552951 AATCCGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAAAAGTTTC
Found at i:21552975 original size:40 final size:40
Alignment explanation
Indices: 21552915--21552992 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
21552905 ATCGTAGCTT
* * *
21552915 CGAAAAAAAAAAGTTAAAAAAAAGTTTCAAAAAAAAAATC
1 CGAAAAAAAAAAGTAAAAAAAAAATTGCAAAAAAAAAATC
21552955 CGAAAAAAAAAAG-AAGAAAAAAAATTGCAAAAAAAAAA
1 CGAAAAAAAAAAGTAA-AAAAAAAATTGCAAAAAAAAAA
21552993 AATTGCATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.10
Consensus pattern (40 bp):
CGAAAAAAAAAAGTAAAAAAAAAATTGCAAAAAAAAAATC
Found at i:21552988 original size:14 final size:13
Alignment explanation
Indices: 21552942--21552992 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
21552932 AAAAAAGTTT
*
21552942 CAAAAAAAAAATC
1 CAAAAAAAAAATG
21552955 CGAAAAAAAAAA-G
1 C-AAAAAAAAAATG
21552968 -AAGAAAAAAAATTG
1 CAA-AAAAAAAA-TG
21552982 CAAAAAAAAAA
1 CAAAAAAAAAA
21552993 AATTGCATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
11 2 0.06
12 8 0.25
13 1 0.03
14 19 0.59
15 2 0.06
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (13 bp):
CAAAAAAAAAATG
Found at i:21553744 original size:15 final size:15
Alignment explanation
Indices: 21553712--21553745 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21553702 GTTCAACGAA
*
21553712 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
21553727 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
21553742 GAGG
1 GAGG
21553746 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:21557738 original size:52 final size:50
Alignment explanation
Indices: 21557640--21557740 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 50
21557630 TCGTATCATC
*
21557640 CATGCTAGTTAAGTATGCATCATAAATAATGACATGCATTATGTAACTCT
1 CATGCTAGTTAAGTATGCATCATAAATAATGACATGCATTAAGTAACTCT
* * * *
21557690 CATGTTAGTTTAAGTCTGCATCATTAAATTAA-GTCTTGCATTAAGTAACTC
1 CATGCTAG-TTAAGTATGCATCA-TAAA-TAATGACATGCATTAAGTAACTC
21557741 ATTTGTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
50 7 0.16
51 13 0.30
52 20 0.47
53 3 0.07
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (50 bp):
CATGCTAGTTAAGTATGCATCATAAATAATGACATGCATTAAGTAACTCT
Found at i:21560458 original size:21 final size:23
Alignment explanation
Indices: 21560413--21560459 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21560403 TCACCTGCAA
* *
21560413 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21560436 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21560457 TAA
1 TAA
21560460 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21564478 original size:18 final size:18
Alignment explanation
Indices: 21564457--21564495 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21564447 GATTGAGAGT
* *
21564457 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
21564475 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
21564493 GAA
1 GAA
21564496 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:21570673 original size:46 final size:46
Alignment explanation
Indices: 21570620--21570713 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
21570610 CAAAGAAAAG
* *
21570620 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAAACTTGGTATATGATGA
21570666 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
21570712 AC
1 AC
21570714 ACCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
Found at i:21573438 original size:19 final size:18
Alignment explanation
Indices: 21573402--21573441 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21573392 TTTCCACTCG
*
21573402 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
21573420 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
21573439 TTT
1 TTT
21573442 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:21574521 original size:15 final size:15
Alignment explanation
Indices: 21574501--21574555 Score: 101
Period size: 15 Copynumber: 3.6 Consensus size: 15
21574491 TAGATTCTTC
21574501 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
21574516 TTTTTTTTTTCACGAA
1 -TTTTTTTTTCACGAA
21574532 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
21574547 TTTTTTTTT
1 TTTTTTTTT
21574556 TCAACTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
15 24 0.62
16 15 0.38
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:21574522 original size:16 final size:16
Alignment explanation
Indices: 21574501--21574558 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
21574491 TAGATTCTTC
21574501 TTTTTTTTTCACGAAT
1 TTTTTTTTTCACGAAT
21574517 TTTTTTTTTCACGAA-
1 TTTTTTTTTCACGAAT
21574532 TTTTTTTTTCACGAAT
1 TTTTTTTTTCACGAAT
21574548 TTTTTTTTTCA
1 TTTTTTTTTCA
21574559 ACTTGATATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.37
16 26 0.63
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTTTTTCACGAAT
Found at i:21574615 original size:12 final size:12
Alignment explanation
Indices: 21574598--21574640 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
21574588 GGAAGCCAAA
21574598 TTTTTTTGAATT
1 TTTTTTTGAATT
21574610 TTTTTTTGAATT
1 TTTTTTTGAATT
* *
21574622 TCTTTTTCGAGTT
1 T-TTTTTTGAATT
21574635 TTTTTT
1 TTTTTT
21574641 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:21574616 original size:13 final size:13
Alignment explanation
Indices: 21574598--21574640 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
21574588 GGAAGCCAAA
21574598 TTTTTTTGAA-TT
1 TTTTTTTGAATTT
21574610 TTTTTTTGAATTT
1 TTTTTTTGAATTT
* * *
21574623 CTTTTTCGAGTTT
1 TTTTTTTGAATTT
21574636 TTTTT
1 TTTTT
21574641 CGAGAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:21575011 original size:46 final size:46
Alignment explanation
Indices: 21574958--21575051 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
21574948 CAAAGAAAAG
* *
21574958 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAAACTTGGTATATGATGA
21575004 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
21575050 AC
1 AC
21575052 ACCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
Found at i:21576609 original size:15 final size:16
Alignment explanation
Indices: 21576552--21576607 Score: 87
Period size: 16 Copynumber: 3.4 Consensus size: 16
21576542 CTTCTTCTTC
21576552 TTTTTTTT-ACGAAAATT
1 TTTTTTTTCACG--AATT
21576569 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
21576585 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
21576601 TTTTTTT
1 TTTTTTT
21576608 CAACTTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 27 0.71
17 8 0.21
18 3 0.08
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:21576666 original size:13 final size:13
Alignment explanation
Indices: 21576646--21576681 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
21576636 AATGGAAACC
21576646 AATTTTTTTTTC-
1 AATTTTTTTTTCA
21576658 AATTTTTTTTTCGA
1 AATTTTTTTTTC-A
21576672 AATTTTTTTT
1 AATTTTTTTT
21576682 GAAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
14 10 0.45
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:21577715 original size:21 final size:23
Alignment explanation
Indices: 21577670--21577716 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21577660 TCACCTGCAA
* *
21577670 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21577693 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21577714 TAA
1 TAA
21577717 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21584879 original size:4 final size:4
Alignment explanation
Indices: 21584870--21584897 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21584860 AAGTTTTATT
21584870 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21584898 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:21588035 original size:4 final size:4
Alignment explanation
Indices: 21588026--21588053 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21588016 AAGTTTTATT
21588026 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21588054 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:21589990 original size:22 final size:22
Alignment explanation
Indices: 21589939--21590004 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
21589929 GGTATTTGGG
** *
21589939 AATTGGTTTGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
21589960 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
21589982 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
21590005 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21592565 original size:14 final size:14
Alignment explanation
Indices: 21592546--21592575 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21592536 TATATGTGTG
21592546 TTTTATTATTGGAA
1 TTTTATTATTGGAA
21592560 TTTTATTATTGGAA
1 TTTTATTATTGGAA
21592574 TT
1 TT
21592576 GAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTTATTATTGGAA
Found at i:21596271 original size:6 final size:6
Alignment explanation
Indices: 21596262--21596311 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
21596252 AACAGCATGT
** *
21596262 GAAAAA GAAAAA GAAAAA GAAAGT GAAAAA GAAATA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
21596310 GA
1 GA
21596312 GTGCGAGCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:21596271 original size:24 final size:24
Alignment explanation
Indices: 21596260--21596307 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21596250 GAAACAGCAT
*
21596260 GTGAAAAAGAAAAAGAAAAAGAAA
1 GTGAAAAAGAAATAGAAAAAGAAA
21596284 GTGAAAAAGAAATAGAAAAAGAAA
1 GTGAAAAAGAAATAGAAAAAGAAA
21596308 AAGAGTGCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (24 bp):
GTGAAAAAGAAATAGAAAAAGAAA
Found at i:21596344 original size:17 final size:16
Alignment explanation
Indices: 21596323--21596362 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
21596313 TGCGAGCGAG
21596323 AAAATGAAA-AAGAAAA
1 AAAATGAAACAA-AAAA
21596339 AGAAATGAAACAAAAAA
1 A-AAATGAAACAAAAAA
21596356 AAAATGA
1 AAAATGA
21596363 GTGTGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 13 0.59
18 2 0.09
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAATGAAACAAAAAA
Found at i:21598081 original size:22 final size:22
Alignment explanation
Indices: 21598051--21598094 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21598041 TTTGGTATTT
21598051 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
21598073 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
21598095 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:21601277 original size:21 final size:23
Alignment explanation
Indices: 21601232--21601278 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21601222 TCACCTGCAA
* *
21601232 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21601255 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21601276 TAA
1 TAA
21601279 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21610266 original size:19 final size:18
Alignment explanation
Indices: 21610230--21610269 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21610220 TTTCCACTCG
*
21610230 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
21610248 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
21610267 TTT
1 TTT
21610270 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:21611350 original size:13 final size:13
Alignment explanation
Indices: 21611332--21611383 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
21611322 ACTAGCTCTC
21611332 TTTTTTTT-ACAA
1 TTTTTTTTCACAA
21611344 TTTTTTTTCACAA
1 TTTTTTTTCACAA
*
21611357 TTGTTTTTTCAAAA
1 TT-TTTTTTCACAA
21611371 TTTTTTTTCACAA
1 TTTTTTTTCACAA
21611384 CTTGATATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 8 0.22
13 16 0.44
14 12 0.33
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:21611439 original size:13 final size:13
Alignment explanation
Indices: 21611421--21611467 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
21611411 TGGAAACTAG
21611421 TTTTTTTTCGAATT
1 TTTTTTTTCGAA-T
*
21611435 TTTTTTTTTGAAT
1 TTTTTTTTCGAAT
*
21611448 TTTTTTTTCGAGT
1 TTTTTTTTCGAAT
21611461 TTTTTTT
1 TTTTTTT
21611468 GAGAAACTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:21611440 original size:14 final size:14
Alignment explanation
Indices: 21611421--21611467 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
21611411 TGGAAACTAG
21611421 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
*
21611435 TTTTTTTTTGAA-T
1 TTTTTTTTCGAATT
*
21611448 TTTTTTTTCGAGTT
1 TTTTTTTTCGAATT
21611462 TTTTTT
1 TTTTTT
21611468 GAGAAACTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:21617209 original size:20 final size:19
Alignment explanation
Indices: 21617186--21617250 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21617176 AAGCTCAAAC
21617186 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21617206 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21617226 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21617246 GAGCT
1 GAGCT
21617251 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21618538 original size:17 final size:18
Alignment explanation
Indices: 21618516--21618549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21618506 ACAACACTCC
*
21618516 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
21618533 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
21618550 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:21618657 original size:15 final size:16
Alignment explanation
Indices: 21618632--21618663 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21618622 TATCTCACAC
21618632 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21618648 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
21618663 T
1 T
21618664 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:21619652 original size:12 final size:11
Alignment explanation
Indices: 21619637--21619666 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
21619627 TTCAATCAAT
21619637 TTTTTTTTTCGA
1 TTTTTTTTT-GA
21619649 TTTTTTTTTGA
1 TTTTTTTTTGA
21619660 TTTTTTT
1 TTTTTTT
21619667 GTTACTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:21619744 original size:13 final size:14
Alignment explanation
Indices: 21619726--21619759 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
21619716 TACAACTCAA
21619726 TTTTTTTTTGA-TT
1 TTTTTTTTTGACTT
21619739 TTTTTTTTTGACTT
1 TTTTTTTTTGACTT
21619753 TTTTTTT
1 TTTTTTT
21619760 ACATTACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTGACTT
Found at i:21621286 original size:20 final size:19
Alignment explanation
Indices: 21621263--21621327 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21621253 AAGCTCAAAC
21621263 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21621283 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21621303 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21621323 GAGCT
1 GAGCT
21621328 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21624405 original size:12 final size:12
Alignment explanation
Indices: 21624366--21624422 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
21624356 TTGGAGTAAC
*
21624366 AAAAAAAA-TAA
1 AAAAAAAATTGA
21624377 AAAAAAAGAGTTCGA
1 AAAAAAA-A-TT-GA
21624392 AAAAAAAATTGA
1 AAAAAAAATTGA
*
21624404 AAAAAAAATCGA
1 AAAAAAAATTGA
21624416 AAGAAAA
1 AA-AAAA
21624423 GAAAAAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 7 0.18
12 16 0.41
13 6 0.15
14 2 0.05
15 8 0.21
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:21624457 original size:18 final size:18
Alignment explanation
Indices: 21624419--21624460 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21624409 AAATCGAAAG
* **
21624419 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
21624437 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
21624455 AAAAGA
1 AAAAGA
21624461 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:21627628 original size:20 final size:20
Alignment explanation
Indices: 21627603--21627649 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21627593 AGCTCGTTTC
21627603 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
21627623 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
21627643 CAGCTCA
1 CAGCTCA
21627650 ATCTTAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:21627647 original size:10 final size:10
Alignment explanation
Indices: 21627614--21627651 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21627604 AGCTCACTCG
*
21627614 AGCTCAAGTC
1 AGCTCAATTC
21627624 AGCTC-ATTC
1 AGCTCAATTC
21627633 GAGCTCAATTC
1 -AGCTCAATTC
21627644 AGCTCAAT
1 AGCTCAAT
21627652 CTTAACCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:21629220 original size:23 final size:24
Alignment explanation
Indices: 21629174--21629240 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
21629164 ACGAAATTCA
21629174 AAAAAAAAAGAAGTGAGCAAA-AAAA-
1 AAAAAAAAA-AAGTGA--AAAGAAAAG
*
21629199 AGAAAAAAAAAGT-AAAAGAAAAG
1 AAAAAAAAAAAGTGAAAAGAAAAG
*
21629222 AACAAAAAAAAGTGAAAAG
1 AAAAAAAAAAAGTGAAAAG
21629241 TATTGTGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.08
22 4 0.11
23 12 0.33
24 9 0.25
25 8 0.22
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAGTGAAAAGAAAAG
Found at i:21629220 original size:24 final size:24
Alignment explanation
Indices: 21629173--21629240 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
21629163 AACGAAATTC
* *
21629173 AAAAAAAAAAGAAGTGAGCAA-AAA
1 AAAAAAAAAAAAAGTGA-AAAGAAA
*
21629197 AAAGAAAAAAAAAGT-AAAAGAAA
1 AAAAAAAAAAAAAGTGAAAAGAAA
* *
21629220 AGAACAAAAAAAAGTGAAAAG
1 AAAAAAAAAAAAAGTGAAAAG
21629241 TATTGTGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 2 0.06
23 16 0.44
24 18 0.50
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAAAGTGAAAAGAAA
Found at i:21631964 original size:20 final size:20
Alignment explanation
Indices: 21631939--21631985 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21631929 AGCTCGTTTC
21631939 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
21631959 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
21631979 CAGCTCA
1 CAGCTCA
21631986 ATCTTAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:21631983 original size:10 final size:10
Alignment explanation
Indices: 21631950--21631987 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21631940 AGCTCACTCG
*
21631950 AGCTCAAGTC
1 AGCTCAATTC
21631960 AGCTC-ATTC
1 AGCTCAATTC
21631969 GAGCTCAATTC
1 -AGCTCAATTC
21631980 AGCTCAAT
1 AGCTCAAT
21631988 CTTAACCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:21633340 original size:39 final size:40
Alignment explanation
Indices: 21633281--21633358 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
21633271 CGGGCATCTT
*
21633281 AAGTGAACCTGACTCCATCAACCGAGCCGGATCACATCAC
1 AAGTGAACCTGACTCAATCAACCGAGCCGGATCACATCAC
* *
21633321 AAGTGAATC-GACTCAATCAACTGAGCCGGATCACATCA
1 AAGTGAACCTGACTCAATCAACCGAGCCGGATCACATCA
21633359 TTAAGTTCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.17
Consensus pattern (40 bp):
AAGTGAACCTGACTCAATCAACCGAGCCGGATCACATCAC
Found at i:21633623 original size:45 final size:45
Alignment explanation
Indices: 21633574--21633761 Score: 304
Period size: 45 Copynumber: 4.2 Consensus size: 45
21633564 TCGGCCATGG
* * * *
21633574 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
21633619 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21633664 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * *
21633709 TGCTTCCTCAAATTATCCCATGAATTATGCATGATTTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21633754 TGCTTCCT
1 TGCTTCCT
21633762 TAATTTCATG
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:21635483 original size:80 final size:79
Alignment explanation
Indices: 21635334--21635556 Score: 232
Period size: 80 Copynumber: 2.8 Consensus size: 79
21635324 GTGAATGCTG
* * * ** * * * * *
21635334 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAGCCGGGCTAAG-TCCCGAAGGCATT
*
21635398 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* *
21635414 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGGCATTC
* **
21635479 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * * *
21635494 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGGCATT
21635557 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 35 0.29
80 81 0.68
81 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:21635537 original size:39 final size:40
Alignment explanation
Indices: 21635387--21635556 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
21635377 GGACTAAGAT
* * *
21635387 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
21635427 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
21635467 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
21635507 CCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
21635546 CCGAAGGCATT
1 CCGAAGGCATT
21635557 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 35 0.30
40 83 0.70
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:21635576 original size:79 final size:80
Alignment explanation
Indices: 21635409--21635591 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
21635399 GTGCGAGATA
* *
21635409 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
** **
21635474 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
21635489 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
*
21635553 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
21635568 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
21635592 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:21643335 original size:40 final size:40
Alignment explanation
Indices: 21643238--21643462 Score: 222
Period size: 40 Copynumber: 5.7 Consensus size: 40
21643228 GTGAATGCTG
* * ** * *
21643238 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGCGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
21643278 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
21643318 TCTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * **
21643358 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
21643398 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
21643437 TCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
21643463 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 35 0.22
40 115 0.73
41 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:21643441 original size:39 final size:40
Alignment explanation
Indices: 21643291--21643460 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
21643281 GGACTAAGAT
* * * *
21643291 CCGAAGGCCTTTGTGCGAGATACTAAATCTGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
21643331 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
21643371 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
21643411 CCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
21643450 CCGAAGGCATT
1 CCGAAGGCATT
21643461 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 35 0.30
40 82 0.70
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:21643480 original size:79 final size:80
Alignment explanation
Indices: 21643313--21643495 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
21643303 GTGCGAGATA
* * *
21643313 CTAAATCTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
** **
21643378 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
21643393 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
*
21643457 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
21643472 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
21643496 TATGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAGCCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:21650147 original size:17 final size:16
Alignment explanation
Indices: 21650125--21650169 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
21650115 TTCAATCACT
21650125 TTTTTTTTAATTTCGAA
1 TTTTTTTTAATTTC-AA
**
21650142 TTTTTTTTGAATTTCTC
1 TTTTTTTT-AATTTCAA
21650159 TTTTTTTTAAT
1 TTTTTTTTAAT
21650170 ACCGAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAATTTCAA
Found at i:21650163 original size:18 final size:17
Alignment explanation
Indices: 21650123--21650166 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
21650113 ATTTCAATCA
21650123 CTTTTTTTTTAATTTCG
1 CTTTTTTTTTAATTTCG
* * *
21650140 AATTTTTTTTGAATTTCT
1 -CTTTTTTTTTAATTTCG
21650158 CTTTTTTTT
1 CTTTTTTTT
21650167 AATACCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (17 bp):
CTTTTTTTTTAATTTCG
Found at i:21650997 original size:45 final size:45
Alignment explanation
Indices: 21650948--21651135 Score: 313
Period size: 45 Copynumber: 4.2 Consensus size: 45
21650938 TCGGCCATGG
* * * *
21650948 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
21650993 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21651038 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
21651083 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATTTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
21651128 TGCTTCCT
1 TGCTTCCT
21651136 TAATTTCATG
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:21655405 original size:11 final size:10
Alignment explanation
Indices: 21655391--21655424 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
21655381 AAAAATTTTG
21655391 AAAAACAAATC
1 AAAAA-AAATC
21655402 AAAAAAAATC
1 AAAAAAAATC
21655412 AAAGAAAAATC
1 AAA-AAAAATC
21655423 AA
1 AA
21655425 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAAAAAATC
Done.