Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002289.1 Hibiscus syriacus cultivar Beakdansim tig00004656_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 69059
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1953 original size:12 final size:12
Alignment explanation
Indices: 1932--1984 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
1922 ATTACGTATT
1932 TATT-TTATGTA
1 TATTATTATGTA
1943 TATTATTATGTA
1 TATTATTATGTA
1955 T-TTATTTTATGTA
1 TATTA--TTATGTA
*
1968 TATTATTATATA
1 TATTATTATGTA
1980 TATTA
1 TATTA
1985 CTTTATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 7 0.19
12 19 0.51
13 8 0.22
14 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
TATTATTATGTA
Found at i:1976 original size:25 final size:25
Alignment explanation
Indices: 1921--2000 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
1911 ATGTTTTATG
*
1921 TATTACGTATTTATTTTATGTATAT
1 TATTATGTATTTATTTTATGTATAT
1946 TATTATGTATTTATTTTATGTATAT
1 TATTATGTATTTATTTTATGTATAT
* *
1971 TATTATATATATTACTTTAT-TATAT
1 TATTATGTAT-TTATTTTATGTATAT
1996 ATATT
1 -TATT
2001 TATATAATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
25 38 0.76
26 12 0.24
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (25 bp):
TATTATGTATTTATTTTATGTATAT
Found at i:2004 original size:25 final size:25
Alignment explanation
Indices: 1935--2011 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
1925 ACGTATTTAT
* *
1935 TTTATGTATATTA-TTATGTATTTAT
1 TTTATGTATATTATTTATATA-TTAC
1960 TTTATGTATATTATTATATATATTAC
1 TTTATGTATATTATT-TATATATTAC
*
1986 TTTAT-TATATATATTTATATAATAC
1 TTTATGTATAT-TATTTATATATTAC
2011 T
1 T
2012 ACATATATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 28 0.61
26 13 0.28
27 5 0.11
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTATGTATATTATTTATATATTAC
Found at i:4709 original size:20 final size:21
Alignment explanation
Indices: 4684--4732 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
4674 AATTCCTTTG
4684 TTGCATTTACATTTTGCAT-T
1 TTGCATTTACATTTTGCATCT
**
4704 TTGCATTCCCATTTTGCATCT
1 TTGCATTTACATTTTGCATCT
4725 TTGCATTT
1 TTGCATTT
4733 GTATGAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (21 bp):
TTGCATTTACATTTTGCATCT
Found at i:4728 original size:28 final size:29
Alignment explanation
Indices: 4688--4759 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
4678 CCTTTGTTGC
* **
4688 ATTTACAT-TTTGCATTTTGCATTCCCAT
1 ATTTGCATCTTTGCATTTTGCATGACCAT
* *
4716 -TTTGCATCTTTGCA-TTTGTATGAGCAT
1 ATTTGCATCTTTGCATTTTGCATGACCAT
4743 ATTTGCATCTTTGCATT
1 ATTTGCATCTTTGCATT
4760 AGCATCTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.42
28 20 0.56
29 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.50
Consensus pattern (29 bp):
ATTTGCATCTTTGCATTTTGCATGACCAT
Found at i:6155 original size:10 final size:9
Alignment explanation
Indices: 6073--6210 Score: 80
Period size: 9 Copynumber: 14.1 Consensus size: 9
6063 GAAGAGATAT
6073 AGAAAAAAA
1 AGAAAAAAA
*
6082 ATAAAAAAA
1 AGAAAAAAA
6091 AGAAAGCAAAA
1 AGAAA--AAAA
*
6102 ACAAAAAAA
1 AGAAAAAAA
6111 ATGAAAGAAGAA
1 A-GAAA-AA-AA
*
6123 AAAAATAAAA
1 AGAAA-AAAA
*
6133 ATGAGTAAAAA
1 A-GA-AAAAAA
6144 AGAAAAACAA
1 AGAAAAA-AA
*
6154 AGAAAAAGA
1 AGAAAAAAA
6163 AGAAAAAGAGA
1 AGAAAAA-A-A
*
6174 A-AAAAGAA
1 AGAAAAAAA
*
6182 AGAGAAAAAC
1 AGA-AAAAAA
* *
6192 AGTAGAAAA
1 AGAAAAAAA
6201 AGAAAAAAA
1 AGAAAAAAA
6210 A
1 A
6211 TAGAAAATAG
Statistics
Matches: 98, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
8 2 0.02
9 42 0.43
10 27 0.28
11 23 0.23
12 4 0.04
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.04
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:6159 original size:9 final size:8
Alignment explanation
Indices: 6073--6209 Score: 63
Period size: 8 Copynumber: 17.1 Consensus size: 8
6063 GAAGAGATAT
6073 AGAAAAAA
1 AGAAAAAA
*
6081 A-ATAAAA
1 AGAAAAAA
*
6088 A-AAAGAA
1 AGAAAAAA
6095 AGCAAAAACA
1 AG-AAAAA-A
6105 A-AAAAAA
1 AGAAAAAA
* *
6112 TG-AAAGA
1 AGAAAAAA
6119 AGAAAAAA
1 AGAAAAAA
* *
6127 ATAAAAATG
1 AGAAAAA-A
*
6136 AGTAAAAA
1 AGAAAAAA
6144 AGAAAAACA
1 AGAAAAA-A
*
6153 A-AGAAAA
1 AGAAAAAA
6160 AGAAGAAAA
1 AGAA-AAAA
6169 AGAGAAAAA
1 AGA-AAAAA
*
6178 AG--AAAG
1 AGAAAAAA
*
6184 AGAAAAAC
1 AGAAAAAA
*
6192 AGTAGAAAA
1 AG-AAAAAA
6201 AGAAAAAA
1 AGAAAAAA
6209 A
1 A
6210 ATAGAAAATA
Statistics
Matches: 95, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
6 5 0.05
7 19 0.20
8 38 0.40
9 30 0.32
10 3 0.03
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.04
Consensus pattern (8 bp):
AGAAAAAA
Found at i:6163 original size:41 final size:40
Alignment explanation
Indices: 6098--6219 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 40
6088 AAAAGAAAGC
* *
6098 AAAAACAAAAA-AAATGAAAGAAGAAAAAAATA-AAAATGAG
1 AAAAAGAAAAACAAA-GAAA-AAGAAAAAAATAGAAAATAAG
*
6138 TAAAAAAGAAAAACAAAGAAAAAGAAGAAAAAGAGAAAA-AAG
1 --AAAAAGAAAAACAAAGAAAAAGAA-AAAAATAGAAAATAAG
* *
6180 AAAGAGAAAAACAGTAGAAAAAGAAAAAAAATAGAAAATA
1 AAAAAGAAAAACA-AAGAAAAAG-AAAAAAATAGAAAATA
6220 GACAGATCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
40 12 0.18
41 24 0.35
42 25 0.37
43 7 0.10
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (40 bp):
AAAAAGAAAAACAAAGAAAAAGAAAAAAATAGAAAATAAG
Found at i:6167 original size:19 final size:20
Alignment explanation
Indices: 6139--6215 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 20
6129 AAAAATGAGT
6139 AAAA-AAGAAAAACA-AAGA
1 AAAAGAAGAAAAACAGAAGA
*
6157 AAAAGAAGAAAAAGAGAA-A
1 AAAAGAAGAAAAACAGAAGA
* *
6176 AAAGAAAGAGAAAAACAGTAGA
1 AAA-AGA-AGAAAAACAGAAGA
* *
6198 AAAAGAAAAAAAATAGAA
1 AAAAGAAGAAAAACAGAA
6216 AATAGACAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.09
19 13 0.28
20 13 0.28
21 12 0.26
22 4 0.09
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAAGAAGAAAAACAGAAGA
Found at i:6168 original size:24 final size:23
Alignment explanation
Indices: 6056--6207 Score: 82
Period size: 23 Copynumber: 6.3 Consensus size: 23
6046 CAACACAGAG
6056 AGAAAAAGAAGAGATATAGAAAAAAA
1 AGAAAAAGAAGA-A-A-AGAAAAAAA
* *
6082 ATAAAAAAAAG-AAAGCAAAAACAA
1 AGAAAAAGAAGAAAAG-AAAAA-AA
*
6106 A-AAAAATGAA-AGAAGAAAAAAA
1 AGAAAAA-GAAGAAAAGAAAAAAA
6128 TA-AAAATGAGTAA-AAAAGAAAAACAA
1 -AGAAAA--AG-AAGAAAAGAAAAA-AA
*
6154 AGAAAAAGAAGAAAAAGAGAAAAA
1 AGAAAAAGAAG-AAAAGAAAAAAA
* * *
6178 AGAAAGAGAA-AAACAGTAGAAAA
1 AGAAAAAGAAGAAA-AGAAAAAAA
6201 AGAAAAA
1 AGAAAAA
6208 AAATAGAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
22 7 0.07
23 35 0.34
24 23 0.23
25 22 0.22
26 15 0.15
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (23 bp):
AGAAAAAGAAGAAAAGAAAAAAA
Found at i:6204 original size:17 final size:17
Alignment explanation
Indices: 6098--6217 Score: 81
Period size: 17 Copynumber: 7.2 Consensus size: 17
6088 AAAAGAAAGC
*
6098 AAAAACAAAAAAAAT-G
1 AAAAAGAAAAAAAATAG
6114 AAAGAAG-AAAAAAATA-
1 AAA-AAGAAAAAAAATAG
* **
6130 AAAATGAGTAAAAA-AG
1 AAAAAGAAAAAAAATAG
* *
6146 AAAAACAAAGAAAAAGAAG
1 AAAAAGAAA-AAAAA-TAG
*
6165 AAAAAG-AGAAAAA-AG
1 AAAAAGAAAAAAAATAG
* * *
6180 AAAGAGAAAAACAGTAG
1 AAAAAGAAAAAAAATAG
6197 AAAAAGAAAAAAAATAG
1 AAAAAGAAAAAAAATAG
6214 AAAA
1 AAAA
6218 TAGACAGATC
Statistics
Matches: 78, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
15 10 0.13
16 28 0.36
17 32 0.41
18 1 0.01
19 7 0.09
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAAAATAG
Found at i:6216 original size:11 final size:10
Alignment explanation
Indices: 6075--6217 Score: 64
Period size: 10 Copynumber: 14.3 Consensus size: 10
6065 AGAGATATAG
*
6075 AAAAAAAA-T
1 AAAAAAAAGA
6084 AAAAAAAAGA
1 AAAAAAAAGA
* *
6094 AAGCAAAAACA
1 AA-AAAAAAGA
*
6105 AAAAAAATGA
1 AAAAAAAAGA
6115 AAGAAGAAAA-A
1 AA-AA-AAAAGA
*
6126 AATAAAAATGA
1 AA-AAAAAAGA
**
6137 GTAAAAAAGA
1 AAAAAAAAGA
*
6147 AAAACAAAG-
1 AAAAAAAAGA
*
6156 AAAAAGAAG-
1 AAAAAAAAGA
*
6165 -AAAAAGAGA
1 AAAAAAAAGA
6174 AAAAAGAAAGA
1 AAAAA-AAAGA
* *
6185 GAAAAACAG-
1 AAAAAAAAGA
* *
6194 TAGAAAAAGA
1 AAAAAAAAGA
6204 AAAAAAATAGA
1 AAAAAAA-AGA
6215 AAA
1 AAA
6218 TAGACAGATC
Statistics
Matches: 97, Mismatches: 27, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
8 6 0.06
9 21 0.22
10 37 0.38
11 30 0.31
12 3 0.03
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:6895 original size:28 final size:29
Alignment explanation
Indices: 6853--6929 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
6843 GCAAGAAGCC
*
6853 AACCTGG-AACACATTGCTTCCCCAAATT
1 AACCTGGAAACACATTACTTCCCCAAATT
* **
6881 AA-CTGGAAACACATTACTTCTCTTAATT
1 AACCTGGAAACACATTACTTCCCCAAATT
6909 AACCT-GAAACACATTATCTTC
1 AACCTGGAAACACATTA-CTTC
6930 TCAAGTCAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
28 32 0.76
29 6 0.14
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (29 bp):
AACCTGGAAACACATTACTTCCCCAAATT
Found at i:8318 original size:54 final size:54
Alignment explanation
Indices: 8173--8533 Score: 395
Period size: 54 Copynumber: 6.7 Consensus size: 54
8163 GTTTTTTAGG
* * * *
8173 AACTAATTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA-ATTTTAAAGA
* * *
8228 AATTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAATTGAATTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTTAAAGA
* * * * * *
8282 AACTAAGTCCGATATTC-GAAAGTTTCTTGATTATTTTTAAACGAGCTTTTAAAAA
1 AACTAAGTCTGATTTTCAG-AAGTTTCTTGATGATTTTTAAATGA-ATTTTAAAGA
* * * * *
8337 AACTAAATCTGTTTTTCAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTTAAAGA
*
8391 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTTAAAGA
** * * * * *
8445 AGTTAAGCCCGATTTTCA-AGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
1 AACTAAGTCTGATTTTCAGA-AGTTTCTTGATGATTTTTAAATGAATTTTAAAGA
* ** *
8498 AACTAAGTCTAATTTTTGGAAGTTTCTTGATTATTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTT
8534 GATCTTTCTA
Statistics
Matches: 252, Mismatches: 48, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
53 42 0.17
54 127 0.50
55 82 0.33
56 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.42
Consensus pattern (54 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTTTAAAGA
Found at i:8318 original size:109 final size:109
Alignment explanation
Indices: 8173--8533 Score: 419
Period size: 109 Copynumber: 3.3 Consensus size: 109
8163 GTTTTTTAGG
* *
8173 AACTAATTCTGATTTTC-AGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAGGAAATTAAGTC
1 AACTAAGTCTGATTTTCGA-AAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTC
* *
8237 TGATTTTTAGAAGTTTCTTGATGATTTTTAATTGAATTTTAAAGA
65 TGATTTTTAGAAGTTTCTTGATGATTTTCAAATGAATTTTAAAGA
* * * * * * * *
8282 AACTAAGTCCGATATTCGAAAGTTTCTTGATTATTTTTAAACGAGCTTTTAAAAAAACTAAATCT
1 AACTAAGTCTGATTTTCGAAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
* *
8347 G-TTTTTCAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
66 GATTTTT-AGAAGTTTCTTGATGATTTTCAAATGAATTTTAAAGA
* * *
8391 AACTAAGTCTGATTTTC-AGAAGTTTCTTGATGATTTTTAAATGA-ATTTCAAAGAAGTTAAGCC
1 AACTAAGTCTGATTTTCGA-AAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTC
* * * *
8454 CGATTTTCA-AGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAGA
65 TGATTTTTAGA-AGTTTCTTGATGATTTTCAAATGAATTTTAAAGA
* * * *
8498 AACTAAGTCTAATTTTTGGAAGTTTCTTGATTATTT
1 AACTAAGTCTGATTTTCGAAAGTTTCTTGATGATTT
8534 GATCTTTCTA
Statistics
Matches: 211, Mismatches: 35, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
107 51 0.24
108 30 0.14
109 129 0.61
110 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.42
Consensus pattern (109 bp):
AACTAAGTCTGATTTTCGAAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCT
GATTTTTAGAAGTTTCTTGATGATTTTCAAATGAATTTTAAAGA
Found at i:8648 original size:20 final size:20
Alignment explanation
Indices: 8623--8694 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
8613 GAATGATGTG
8623 TAAGTCCTTCGAGCCATCTA
1 TAAGTCCTTCGAGCCATCTA
* * **
8643 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGAGCCATCT-A
* *
8664 TAAGTCATTCGAGCCATCCA
1 TAAGTCCTTCGAGCCATCTA
*
8684 TAAGACCTTCG
1 TAAGTCCTTCG
8695 GGTAAGATGT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (20 bp):
TAAGTCCTTCGAGCCATCTA
Found at i:8678 original size:41 final size:41
Alignment explanation
Indices: 8574--8687 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 41
8564 AAGGGTTTCT
* *
8574 TGATGAGTAAGTCCTTCGGGCCAT-TAGTAAGTCTTTTGAGAA
1 TGATGA-TAAGTCCTTCGAGCCATCTA-TAAGTCTTTCGAGAA
*
8616 TGATGTGTAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGCAA
1 TGATG-ATAAGTCCTTCGAGCCATCTATAAGTCTTTCGAG-AA
* *
8659 -GATGATAAGTCATTCGAGCCATCCATAAG
1 TGATGATAAGTCCTTCGAGCCATCTATAAG
8688 ACCTTCGGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 22 0.35
42 37 0.59
43 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGAA
Found at i:8702 original size:41 final size:41
Alignment explanation
Indices: 8623--8703 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
8613 GAATGATGTG
* * * *
8623 TAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGCAAGATGA
1 TAAGTCATTCGAGCCATCCATAAGACCTTCGAGCAAGATGA
* *
8664 TAAGTCATTCGAGCCATCCATAAGACCTTCGGGTAAGATG
1 TAAGTCATTCGAGCCATCCATAAGACCTTCGAGCAAGATG
8704 TTTTCAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
TAAGTCATTCGAGCCATCCATAAGACCTTCGAGCAAGATGA
Found at i:8765 original size:52 final size:52
Alignment explanation
Indices: 8700--8808 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
8690 CTTCGGGTAA
*
8700 GATGTTTTCAAATGAATTTTT-AGAAACTAAGCCTGATTTTAAGAGGTTTCTT
1 GATGTTTTCAAATGAATTTTTAAGAAACTAAGCCTAATTTT-AGAGGTTTCTT
* * *
8752 GATGTTTTTAAATGAATTTTTGAAAGAAGCTAAGCCTAATTTTAGGGGTTTCTT
1 GATGTTTTCAAATGAATTTTT--AAGAAACTAAGCCTAATTTTAGAGGTTTCTT
8806 GAT
1 GAT
8809 AACTGTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 20 0.40
54 13 0.26
55 17 0.34
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (52 bp):
GATGTTTTCAAATGAATTTTTAAGAAACTAAGCCTAATTTTAGAGGTTTCTT
Found at i:8818 original size:54 final size:54
Alignment explanation
Indices: 8709--8835 Score: 143
Period size: 55 Copynumber: 2.4 Consensus size: 54
8699 AGATGTTTTC
* * *** *
8709 AAATGAATTTTT--AGAAACTAAGCCTGATTTTAAGAGGTTTCTTGATGTTTTT
1 AAATGAATTTTTGAAGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGT
*
8761 AAATGAATTTTTGAAAGAAGCTAAGCCTAATTTT-AGGGGTTTCTTGATAACTGT
1 AAATGAATTTTTG-AAGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGT
8815 AAATGAATCTTTTTGAAGAAG
1 AAATGAA--TTTTTGAAGAAG
8836 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
52 12 0.19
54 22 0.35
55 23 0.37
56 6 0.10
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (54 bp):
AAATGAATTTTTGAAGAAGCTAAGCCTAATTTTAAGAGGTTTCTTGATAACTGT
Found at i:9844 original size:136 final size:132
Alignment explanation
Indices: 9541--10311 Score: 776
Period size: 136 Copynumber: 5.6 Consensus size: 132
9531 TAAACCAATC
* * **
9541 AACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
1 AACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCATAAT
** * *
9606 GAGAAGAACTCATTCAACCT-TAGCTCGATTCATCGCATATGGAGTTGAATCAGAAACACCTCAC
65 GAGAAGAACTTGTTCAACCTATA-CTTGATTCAT-G-ATAT----TTGAATCAGCAACACCTCAC
* *
9670 TCGAGGGATT
123 TTGAGGGAAT
*
9680 AACATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAA
1 AACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAGAAGTTCATAA
* * ** * * *
9745 TGAGAAGAACTTGTTCGACCTATCACTTGATTCATGGTATTTCGAATCAGTGACGCCTCGCTTAA
64 TGAGAAGAACTTGTTCAACCTAT-ACTTGATTCATGATATTT-GAATCAGCAACACCTCACTTGA
9810 GGGAAT
127 GGGAAT
* * **
9816 GATATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
1 AACATTTCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCATAAT
9881 GAGAAGAACTTGTTCAACCT-TAGCTTGATTCATCGCATATGGAGTTGAATCAGCAACACCTCAC
65 GAGAAGAACTTGTTCAACCTATA-CTTGATTCAT-G-ATAT----TTGAATCAGCAACACCTCAC
*
9945 TCGAGGG-AT
123 TTGAGGGAAT
9954 CAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATA
1 -AACATTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAGAAGTTCATA
* * * * * ** * *
10019 ATCAGAAGAGCTTATTCGACCTATCACTTGATTCACGGCAT-TTTGAATCAGTGACGCCTCACGT
63 ATGAGAAGAACTTGTTCAACCTAT-ACTTGATTCA-TG-ATATTTGAATCAGCAACACCTCACTT
10083 GAGGGAAT
125 GAGGGAAT
* * *
10091 GACATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAGAAGTTCATAA
* * * * ** * * * *
10156 TGAGAAGATCTTGTTCGACCTATTGCTCGATTCACAACACTTCGAGTCAGCAACACCTCGCTTGA
64 TGAGAAGAACTTGTTCAACCTA-TACTTGATTCATGATA-TTTGAATCAGCAACACCTCACTTGA
*
10221 GGGATT
127 GGGAAT
* * * *
10227 AACATTTCCAGTGGAGAGTTCATAATGAGAATAACCCATCCGATAAGGGAGAATAAGTTCATAAT
1 AACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCATAAT
*
10292 AAGAAGAACTTGTTCAACCT
65 GAGAAGAACTTGTTCAACCT
10312 TGGTGATTCC
Statistics
Matches: 535, Mismatches: 73, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
133 1 0.00
134 12 0.02
135 83 0.16
136 226 0.42
137 6 0.01
138 2 0.00
139 100 0.19
140 79 0.15
141 24 0.04
142 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (132 bp):
AACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTATACTTGATTCATGATATTTGAATCAGCAACACCTCACTTGAGGGA
AT
Found at i:10042 original size:275 final size:275
Alignment explanation
Indices: 9542--10311 Score: 1133
Period size: 275 Copynumber: 2.8 Consensus size: 275
9532 AAACCAATCA
*
9542 ACATTTCCA-ATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
1 ACATTT-CAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
** *
9606 GAGAAGAACTCATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGAAACACCTCACT
65 GAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACT
*
9671 CGAGGGATTAACATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGA
130 CGAGGGATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGA
* * * *
9736 AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTTGATTCATGGTATTTCGAATCAGTGACGC
195 AGTTCATAATAAGAAGAACTTATTCGACCTATCACTTGATTCACGGCATTTCGAATCAGTGACGC
* *
9801 CTCGCTTAAGGGAATG
260 CTCACGTAAGGGAATG
*
9817 ATATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATG
1 ACATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATG
*
9882 AGAAGAACTTGTTCAACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
* *
9947 GAGGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAA
131 GAGGGATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAA
* * *
10012 GTTCATAATCAGAAGAGCTTATTCGACCTATCACTTGATTCACGGCATTTTGAATCAGTGACGCC
196 GTTCATAATAAGAAGAACTTATTCGACCTATCACTTGATTCACGGCATTTCGAATCAGTGACGCC
*
10077 TCACGTGAGGGAATG
261 TCACGTAAGGGAATG
* *
10092 ACATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCCGA-TGAGGGAGAAGAAGTTCATAAT
* * * * * * *
10157 GAGAAGATCTTGTTCGACCTATTGCTCGATTCA---CA-A--CACTTCGAGTCAGCAACACCTCG
65 GAGAAGAACTTGTTCAACCT-TAGCTCGATTCATCGCATATGGAGTT-GAATCAGCAACACCTCA
* * * *
10216 CTTGAGGGATTAACATTTCCAGTGGAGAGTTCATAATGAGAATAACCCATCCGA-TAAGGGAGAA
128 CTCGAGGGATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAA
* * *
10280 TAAGTTCATAATAAGAAGAACTTGTTCAACCT
193 GAAGTTCATAATAAGAAGAACTTATTCGACCT
10312 TGGTGATTCC
Statistics
Matches: 451, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
271 39 0.09
272 64 0.14
273 1 0.00
274 4 0.01
275 294 0.65
276 39 0.09
277 10 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (275 bp):
ACATTTCAGATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
GAGGGATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAA
GTTCATAATAAGAAGAACTTATTCGACCTATCACTTGATTCACGGCATTTCGAATCAGTGACGCC
TCACGTAAGGGAATG
Found at i:11449 original size:12 final size:12
Alignment explanation
Indices: 11428--11480 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
11418 GTTACGTATT
11428 TATT-TTATGTA
1 TATTATTATGTA
11439 TATTATTATGTA
1 TATTATTATGTA
*
11451 T-TTATTTTACGTA
1 TATTA--TTATGTA
*
11464 TATTATTATATA
1 TATTATTATGTA
11476 TATTA
1 TATTA
11481 CTTTATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 7 0.20
12 18 0.51
13 7 0.20
14 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (12 bp):
TATTATTATGTA
Found at i:11452 original size:25 final size:25
Alignment explanation
Indices: 11423--11496 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
11413 TATGTGTTAC
11423 GTATTTATTTTATGTATATTATTAT
1 GTATTTATTTTATGTATATTATTAT
*
11448 GTATTTATTTTACGTATATTATTAT
1 GTATTTATTTTATGTATATTATTAT
* *
11473 ATATATTACTTTAT-TATATATATT
1 GTAT-TTATTTTATGTATAT-TATT
11497 TATATAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 32 0.74
26 11 0.26
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (25 bp):
GTATTTATTTTATGTATATTATTAT
Found at i:11492 original size:27 final size:26
Alignment explanation
Indices: 11437--11516 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
11427 TTATTTTATG
* * *
11437 TATATTATTATGTAT-TTATTTTACG
1 TATATTATTATATATATTACTTTACA
*
11462 TATATTATTATATATATTACTTTA-T
1 TATATTATTATATATATTACTTTACA
*
11487 TATATATATT-TATATAATAC--TACA
1 TATAT-TATTATATATATTACTTTACA
11511 TATATT
1 TATATT
11517 GTATTGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 3 0.06
24 5 0.11
25 28 0.60
26 11 0.23
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (26 bp):
TATATTATTATATATATTACTTTACA
Found at i:12756 original size:16 final size:16
Alignment explanation
Indices: 12735--12772 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
12725 CCTTGAAACC
*
12735 ATTATTTATTGGTTAT
1 ATTATTAATTGGTTAT
12751 ATTATTAATTGGTTAT
1 ATTATTAATTGGTTAT
12767 ATTATT
1 ATTATT
12773 GGTTCGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (16 bp):
ATTATTAATTGGTTAT
Found at i:15951 original size:22 final size:22
Alignment explanation
Indices: 15926--15968 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
15916 GGCGACATCC
15926 GTCCCCATCTCCGACGAAATCT
1 GTCCCCATCTCCGACGAAATCT
*
15948 GTCCCCATTTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
15969 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCT
Found at i:17997 original size:21 final size:21
Alignment explanation
Indices: 17973--18022 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
17963 GTTAGGGGAA
*
17973 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
17994 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
18015 TTACGTGA
1 TTACGTGA
18023 AGATAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:18513 original size:21 final size:21
Alignment explanation
Indices: 18445--18520 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
18435 GGTGTCTCTT
*
18445 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCCATC
* * *
18466 ATC-ATCGAAGAAG-CCCCTTCC
1 ATCGTTC-AAGAGGCCCCCAT-C
* *
18487 ACCGTTCAAGAGGCCCCCGTC
1 ATCGTTCAAGAGGCCCCCATC
18508 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
18521 TCCCGCCCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 6 0.14
21 29 0.69
22 7 0.17
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCCATC
Found at i:19993 original size:61 final size:62
Alignment explanation
Indices: 19893--20029 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 62
19883 TTTTACATTG
* *
19893 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAACTGATTTGTA
1 AAAGTTGATTTATTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAACTGATTTGTA
** * * *
19953 AAAGTTGATTTATTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTATTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAACTGATTTGT
20018 A
62 A
20019 AAAGTTGATTT
1 AAAGTTGATTT
20030 GTTGTTTCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 16 0.25
61 17 0.27
64 4 0.06
66 27 0.42
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.50
Consensus pattern (62 bp):
AAAGTTGATTTATTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAACTGATTTGTA
Found at i:20138 original size:20 final size:20
Alignment explanation
Indices: 20115--20157 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20105 GATTTTCGGT
20115 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
20135 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
20155 TTG
1 TTG
20158 ATCGCAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:20385 original size:39 final size:39
Alignment explanation
Indices: 20331--20417 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
20321 TCAAGTTGTA
*
20331 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
*
20370 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
20409 GATTTTGAT
1 GATTTTGAT
20418 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
Found at i:20681 original size:11 final size:11
Alignment explanation
Indices: 20665--20715 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
20655 TTATACATAC
20665 AATGTTCAAAT
1 AATGTTCAAAT
20676 AATGTTCAAAT
1 AATGTTCAAAT
* *
20687 AATGTACCCATAAC
1 AATGT--TCA-AAT
20701 AATGTTCAAAT
1 AATGTTCAAAT
20712 AATG
1 AATG
20716 CACCCACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 22 0.67
12 2 0.06
13 2 0.06
14 7 0.21
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:20709 original size:25 final size:25
Alignment explanation
Indices: 20676--20731 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
20666 ATGTTCAAAT
* *
20676 AATGTTCAAATAATGTACCCATAAC
1 AATGTTCAAATAATGCACCCACAAC
20701 AATGTTCAAATAATGCACCCACAAC
1 AATGTTCAAATAATGCACCCACAAC
20726 AATGTT
1 AATGTT
20732 TAATTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (25 bp):
AATGTTCAAATAATGCACCCACAAC
Found at i:20915 original size:20 final size:20
Alignment explanation
Indices: 20866--20915 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20856 TGGTTTGCGA
20866 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
20886 TATCGTGTTGCGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
*
20906 TTTCACGTTG
1 TTTCGCGTTG
20916 ATCGCAACAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:20946 original size:17 final size:17
Alignment explanation
Indices: 20924--20969 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
20914 TGATCGCAAC
20924 ATACAACATCAAGGTAT
1 ATACAACATCAAGGTAT
20941 ATACAACATCAAGGTAT
1 ATACAACATCAAGGTAT
20958 ATACAACATCAA
1 ATACAACATCAA
20970 ACACATTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.22
Consensus pattern (17 bp):
ATACAACATCAAGGTAT
Found at i:23575 original size:24 final size:24
Alignment explanation
Indices: 23508--23567 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
23498 CCATCACATC
23508 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
23532 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
23556 ATCAAATTTCGA
1 ATCAAAATTCGA
23568 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:24477 original size:19 final size:19
Alignment explanation
Indices: 24447--24545 Score: 162
Period size: 19 Copynumber: 5.1 Consensus size: 19
24437 TCGCGAAACT
24447 AAATTCATGTTGCGAATTTG
1 AAATTCA-GTTGCGAATTTG
24467 AAATTCAGTTGCGAATTTG
1 AAATTCAGTTGCGAATTTG
24486 AAATTCAGTTGCGAATTTG
1 AAATTCAGTTGCGAATTTG
24505 AAATTCAGTTGCGAATTTG
1 AAATTCAGTTGCGAATTTG
*
24524 AAATTTCGCGTTGCGAATTTG
1 AAA-TTC-AGTTGCGAATTTG
24545 A
1 A
24546 CTTTTGTGTT
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
19 53 0.70
20 10 0.13
21 13 0.17
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATTCAGTTGCGAATTTG
Found at i:24561 original size:20 final size:20
Alignment explanation
Indices: 24512--24599 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
24502 TTGAAATTCA
* * *
24512 GTTGCGAATTTGAAATTTCGC
1 GTTGCGAATTTG-ACTTTTGT
24533 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
24553 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
24573 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
24593 GTTGCGA
1 GTTGCGA
24600 TTTACAAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
20 43 0.78
21 12 0.22
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:24613 original size:40 final size:41
Alignment explanation
Indices: 24474--24620 Score: 157
Period size: 40 Copynumber: 3.7 Consensus size: 41
24464 TTGAAATTCA
* * *
24474 GTTGCGAATTTGA-AATTC-AGTTGCGAATTTGAAATTC--A
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTG-ACTTCTGT
*
24512 GTTGCGAATTTGA-AATTTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAA-TTCGCGTTGCGAATTTGACTTCTGT
* *
24553 GTTGTGAATTTGACTA-TCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGT
24593 GTTGCG-ATTT-ACAAATTCGCGTTGCGAA
1 GTTGCGAATTTGAC-AATTCGCGTTGCGAA
24621 ATTGGAAAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
38 17 0.18
39 11 0.12
40 52 0.56
41 12 0.13
42 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (41 bp):
GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGT
Found at i:24661 original size:21 final size:21
Alignment explanation
Indices: 24615--24661 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
24605 AAATTCGCGT
24615 TGCGAAATTGGAAAATCGCAA
1 TGCGAAATTGGAAAATCGCAA
* * *
24636 CGCGAATTTGGAAAATCGTAA
1 TGCGAAATTGGAAAATCGCAA
24657 TGCGA
1 TGCGA
24662 TTTACATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (21 bp):
TGCGAAATTGGAAAATCGCAA
Found at i:28636 original size:88 final size:88
Alignment explanation
Indices: 28508--28724 Score: 381
Period size: 88 Copynumber: 2.5 Consensus size: 88
28498 ATTGAACGAA
28508 AATATTTAGCCACTGTTTTTTTTC--CATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
1 AATATTTAGCCACTGTTTTTTTTCTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
*
28571 CAATCAAACAAGCTCATAAACTC
66 CAATCAAACAAGCCCATAAACTC
*
28594 AATATTTAGCCATTGTTTTTTTTCTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
1 AATATTTAGCCACTGTTTTTTTTCTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
28659 CAATCAAACAAGCCCATAAACTC
66 CAATCAAACAAGCCCATAAACTC
28682 AATATTTAGCCACTG--TTTTTT-TTCATCAAACTAAGTTTGCCAC
1 AATATTTAGCCACTGTTTTTTTTCTTCATCAAACTAAGTTTGCCAC
28725 AGTGTGACAG
Statistics
Matches: 126, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
85 22 0.17
86 29 0.23
88 75 0.60
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (88 bp):
AATATTTAGCCACTGTTTTTTTTCTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAA
CAATCAAACAAGCCCATAAACTC
Found at i:29197 original size:8 final size:8
Alignment explanation
Indices: 29184--29211 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
29174 AATCAAGCAC
29184 AAGGGATT
1 AAGGGATT
29192 AAGGGATT
1 AAGGGATT
29200 AAGGGATT
1 AAGGGATT
29208 AAGG
1 AAGG
29212 CCAAAGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (8 bp):
AAGGGATT
Found at i:30544 original size:7 final size:7
Alignment explanation
Indices: 30506--30560 Score: 56
Period size: 7 Copynumber: 7.1 Consensus size: 7
30496 TTTTCACCCC
30506 ATAAAATT
1 ATAAAA-T
30514 ATAAAAT
1 ATAAAAT
*
30521 AATTAATAT
1 -A-TAAAAT
30530 ATTAAAAAT
1 A-T-AAAAT
30539 ATAAAAT
1 ATAAAAT
30546 ATAAAAT
1 ATAAAAT
30553 ATAAAAT
1 ATAAAAT
30560 A
1 A
30561 ATTTGAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 21 0.50
8 11 0.26
9 10 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAAAAT
Found at i:30553 original size:25 final size:25
Alignment explanation
Indices: 30507--30558 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
30497 TTTCACCCCA
* *
30507 TAAAATTATAAAATAATTAATATAT
1 TAAAAATATAAAATAATAAATATAT
30532 TAAAAATATAAAAT-ATAAA-ATA-
1 TAAAAATATAAAATAATAAATATAT
30554 TAAAA
1 TAAAA
30559 TAATTTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 3 0.12
24 4 0.16
25 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAATATAAAATAATAAATATAT
Found at i:30838 original size:29 final size:29
Alignment explanation
Indices: 30805--30890 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
30795 AAATTACTTG
**
30805 ATAATGATATTTTTCGTGAATCAAATATA
1 ATAATGATATTTTTCACGAATCAAATATA
30834 ATAATGATATTTTTCACGAATCAAATATA
1 ATAATGATATTTTTCACGAATCAAATATA
*
30863 ATAATGATATTTTTTACGAATCAAATAT
1 ATAATGATATTTTTCACGAATCAAATAT
30891 CTCAATATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
ATAATGATATTTTTCACGAATCAAATATA
Found at i:32793 original size:35 final size:35
Alignment explanation
Indices: 32747--32822 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
32737 AAAACAGTCC
* *
32747 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
32782 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
32817 TCAATT
1 TCAATT
32823 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:33445 original size:129 final size:130
Alignment explanation
Indices: 33219--33465 Score: 415
Period size: 129 Copynumber: 1.9 Consensus size: 130
33209 TATTTATATA
* **
33219 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
33284 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
33349 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCA-TTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
33413 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
33466 GAAGACCTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 67 0.61
130 42 0.39
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:33475 original size:13 final size:13
Alignment explanation
Indices: 33457--33483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33447 ACATGTCACC
33457 ACCTAATTAGAAG
1 ACCTAATTAGAAG
33470 ACCTAATTAGAAG
1 ACCTAATTAGAAG
33483 A
1 A
33484 AAATTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCTAATTAGAAG
Found at i:33837 original size:28 final size:27
Alignment explanation
Indices: 33806--33868 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
33796 AGTTGATACA
*
33806 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
33834 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
33862 ATATTTT
1 ATATTTT
33869 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:33969 original size:16 final size:18
Alignment explanation
Indices: 33948--33981 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
33938 ATTTCTTATT
33948 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
33964 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
33982 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:34780 original size:18 final size:20
Alignment explanation
Indices: 34757--34794 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
34747 ATTGTTACTT
34757 AAAATATT-ATTTT-TTATA
1 AAAATATTAATTTTGTTATA
34775 AAAATATTAATTTTGTTATA
1 AAAATATTAATTTTGTTATA
34795 TAATTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAATATTAATTTTGTTATA
Found at i:34895 original size:20 final size:20
Alignment explanation
Indices: 34870--34949 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
34860 ATATTTTAAA
34870 TAACATTTTATCAAAAATGT
1 TAACATTTTATCAAAAATGT
34890 TAACA-TTT-T---AAA---
1 TAACATTTTATCAAAAATGT
*
34902 TAACAGTTTATCAAAAATGT
1 TAACATTTTATCAAAAATGT
34922 TAACATTTTATCAAAAATGT
1 TAACATTTTATCAAAAATGT
34942 TAACATTT
1 TAACATTT
34950 CTTATAAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
12 5 0.10
13 3 0.06
14 1 0.02
15 3 0.06
17 3 0.06
18 1 0.02
19 3 0.06
20 32 0.63
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAACATTTTATCAAAAATGT
Found at i:34899 original size:32 final size:32
Alignment explanation
Indices: 34862--34931 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
34852 AAAAAATAAT
*
34862 ATTTTAAATAACATTTTATCAAAAATGTTAAC
1 ATTTTAAATAACAGTTTATCAAAAATGTTAAC
34894 ATTTTAAATAACAGTTTATCAAAAATGTTAAC
1 ATTTTAAATAACAGTTTATCAAAAATGTTAAC
34926 ATTTTA
1 ATTTTA
34932 TCAAAAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (32 bp):
ATTTTAAATAACAGTTTATCAAAAATGTTAAC
Found at i:35485 original size:12 final size:12
Alignment explanation
Indices: 35468--35502 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35458 GCTTCTCTAT
35468 TGCTTCTTCTGC
1 TGCTTCTTCTGC
35480 TGCTTCTTCTGC
1 TGCTTCTTCTGC
* *
35492 TTCTGCTTCTG
1 TGCTTCTTCTG
35503 ACTAGGGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.51
Consensus pattern (12 bp):
TGCTTCTTCTGC
Found at i:42842 original size:110 final size:111
Alignment explanation
Indices: 42703--42923 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
42693 TGGAAATCAT
*
42703 ATATCTCTACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
* * * * * *
42768 TATTTAG-TTATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTTATTCATTTAATACATGATTATAAGATTAAGAATTAA
* *
42813 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
42878 TAATTAGTTTATTCATTTAATACATGATTATAAGATTAAGAATTAA
66 TAATTAGTTTATTCATTTAATACATGATTATAAGATTAAGAATTAA
42924 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 68 0.67
111 33 0.33
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTTATTCATTTAATACATGATTATAAGATTAAGAATTAA
Found at i:44450 original size:18 final size:18
Alignment explanation
Indices: 44427--44466 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
44417 CCAACAACCA
44427 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
44445 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
44463 CCGC
1 CCGC
44467 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:45027 original size:26 final size:24
Alignment explanation
Indices: 44955--45027 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
44945 ATATATTTGT
44955 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
44980 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
45003 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
45028 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:48022 original size:50 final size:51
Alignment explanation
Indices: 47947--48070 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 51
47937 CCCTACGTGG
* * * **
47947 CGTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCATGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
* *
47997 CGTATAGCACGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
* *
48048 CGTATAACGCGGTGCAAGGGGCG
1 CGTATAGCGCGGTGCAGGGGGCG
48071 AGCTTTACTA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 27 0.43
51 36 0.57
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.15
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
Found at i:49304 original size:23 final size:23
Alignment explanation
Indices: 49269--49318 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
49259 ATACTTTACA
*
49269 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATC
**
49292 ATATAAGTGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
49315 ATAT
1 ATAT
49319 TTTTACCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:49470 original size:467 final size:466
Alignment explanation
Indices: 48868--50640 Score: 2805
Period size: 489 Copynumber: 3.7 Consensus size: 466
48858 TTATAATATG
* *
48868 TTGAAAGTGTCTATACTTTTTTATAAAAA-AATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
48932 TTCAA-TTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
48996 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
49061 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* ** * *
49126 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
49191 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
49256 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAGTGCTACCTATTACATCATATTT
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAGTGCTACCTATTACATCATATTT
49321 TTACCTATTATA
455 TTACCTATTATA
*
49333 TTGAAAGTGTTCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
49398 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
49463 CAAAAAATTATTTTATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
49528 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
**
49593 ATTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* *
49658 CAAAAGATAACCTTAAATTAATGTTTACCACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
49723 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATAT-AA-G-----------------T--
*
49788 ACGCTACCTATTACATTATATTTTTACCTATTATA
434 --GCTACCTATTACATCATATTTTTACCTATTATA
49823 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
49888 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
49953 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
50018 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
** *
50083 TTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTTACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
50148 AAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
50213 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAG-----------------------CACTACCTATTACATTATATAAG
*
50278 CGCTACCTATTACATCATATTTTTACCTATTATA
433 TGCTACCTATTACATCATATTTTTACCTATTATA
*
50312 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * *
50376 TTAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTGCAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
50441 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
50506 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
50571 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTATTATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
50636 CAAAA
325 CAAAA
50641 TATGTACATA
Statistics
Matches: 1219, Mismatches: 39, Indels: 76
0.91 0.03 0.06
Matches are distributed among these distances:
464 12 0.01
465 53 0.04
467 345 0.28
468 2 0.00
469 1 0.00
486 1 0.00
488 29 0.02
489 653 0.54
490 100 0.08
510 1 0.00
511 2 0.00
512 20 0.02
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (466 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTT
TACCTATTATA
Found at i:49771 original size:23 final size:23
Alignment explanation
Indices: 49736--49808 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
49726 ATACTTTACA
* *
49736 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
49759 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
49782 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
49805 ATAT
1 ATAT
49809 TTTTACCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:50258 original size:23 final size:23
Alignment explanation
Indices: 50225--50297 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
50215 ATACTTTACA
50225 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
50248 ATATAAACACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
50271 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
50294 ATAT
1 ATAT
50298 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:53437 original size:183 final size:183
Alignment explanation
Indices: 53129--54068 Score: 1652
Period size: 183 Copynumber: 5.1 Consensus size: 183
53119 TACTTAAAAT
53129 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
53194 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
53259 CGACACTTTTTGACAAGGTGTCGACACAATTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
53312 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
53377 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
53442 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * *
53495 TACCGACACAATATTAAAAAGTATTGATATAGGTTGTAGACATATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
53560 TTTATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
53625 CGACACTTTGTGACAAGGTATCGACACATTTTTCTTCCAATCTGGATATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
53678 TACCGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
53743 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
53808 CGATACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
53861 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAACCCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
53926 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
*
53991 --TCGACACTTTTTGA-AATGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTGACAA-GGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
54045 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
54069 GAAAACTTTA
Statistics
Matches: 723, Mismatches: 30, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
183 648 0.90
184 71 0.10
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:55289 original size:6 final size:6
Alignment explanation
Indices: 55278--55361 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
55268 ACTTGTTTGG
* * * * *
55278 ATCATC ATCATC ATCGTC ATCATC TTCATC GTCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * * * *
55326 GTCAGC TTCATC GTCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
55362 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:55299 original size:12 final size:12
Alignment explanation
Indices: 55279--55365 Score: 102
Period size: 12 Copynumber: 7.2 Consensus size: 12
55269 CTTGTTTGGA
*
55279 TCATCATCATCA
1 TCATCATCATCG
* *
55291 TCGTCATCATCT
1 TCATCATCATCG
*
55303 TCATCGTCATCG
1 TCATCATCATCG
*
55315 TCATCTTCATCG
1 TCATCATCATCG
* *
55327 TCAGCTTCATCG
1 TCATCATCATCG
55339 TCATCATCATCG
1 TCATCATCATCG
*
55351 TCATCTTCATCG
1 TCATCATCATCG
55363 TCA
1 TCA
55366 GCTTCATCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:55370 original size:12 final size:12
Alignment explanation
Indices: 55297--55378 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
55287 ATCATCGTCA
* *
55297 TCATCTTCATCG
1 TCATCGTCATCT
55309 TCATCGTCATCT
1 TCATCGTCATCT
*
55321 TCATCGTCAGCT
1 TCATCGTCATCT
*
55333 TCATCGTCATCA
1 TCATCGTCATCT
55345 TCATCGTCATCT
1 TCATCGTCATCT
*
55357 TCATCGTCAGCT
1 TCATCGTCATCT
*
55369 TCATCTTCAT
1 TCATCGTCAT
55379 TGACCGCTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:55372 original size:18 final size:18
Alignment explanation
Indices: 55297--55378 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
55287 ATCATCGTCA
*
55297 TCATCTTCATCGTCATCG
1 TCATCTTCATCGTCAGCG
*
55315 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCG
* * *
55333 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCG
*
55351 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCG
55369 TCATCTTCAT
1 TCATCTTCAT
55379 TGACCGCTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCG
Found at i:55378 original size:6 final size:6
Alignment explanation
Indices: 55297--55365 Score: 84
Period size: 6 Copynumber: 11.5 Consensus size: 6
55287 ATCATCGTCA
* * * * *
55297 TCATCT TCATCG TCATCG TCATCT TCATCG TCAGCT TCATCG TCATCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
*
55345 TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCA
55366 GCTTCATCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (6 bp):
TCATCG
Found at i:57375 original size:200 final size:200
Alignment explanation
Indices: 56873--58038 Score: 2003
Period size: 200 Copynumber: 5.8 Consensus size: 200
56863 AACATTAAAC
* * * * *
56873 AGTGTCGATACA-TATTATATACCAATTTTCTCATAAAACCGGTATACTTGTACCGGTTAGATTA
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
56937 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACATTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
57002 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGGCACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
57067 TAAAAAA
195 T-ACAAA
* *
57074 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
57139 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGA-ATCTTTTTATATAT
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACA-CTTTTTATATAT
57203 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
57268 TACAAA
195 TACAAA
*
57274 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
57339 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * * *
57404 GATCGACACTTTATGGTTGCAGCATGTTTGCCATTCATTATGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
57469 AAAAAA
196 -ACAAA
*
57475 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
57540 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
57605 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
57670 ACAAA
196 ACAAA
*
57675 AGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
57740 AAAATTACGTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
57805 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
57870 ACAAA
196 ACAAA
* * *
57875 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGCACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
57940 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
58005 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
58039 ATTGTAAATT
Statistics
Matches: 918, Mismatches: 43, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
200 544 0.59
201 370 0.40
202 4 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:57616 original size:401 final size:401
Alignment explanation
Indices: 56873--58038 Score: 2059
Period size: 401 Copynumber: 2.9 Consensus size: 401
56863 AACATTAAAC
* * * * *
56873 AGTGTCGATACA-TATTATATACCAATTTTCTCATAAAACCGGTATACTTGTACCGGTTAGATTA
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * * *
56937 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACATTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* * * *
57002 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGGCACAAAC
130 GGATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAAC
*
57067 TAAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACTGGTATACTTGTACCGGTT
195 TAAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTT
57132 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGA-ATCTTTT
260 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACA-CTTTT
57196 TATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGA
324 TATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGA
57261 CACAAACTACAAA
389 CACAAACTACAAA
*
57274 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
57339 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
57404 GATCGACACTTTATGGTTGCAGCATGTTTGCCATTCATTATGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
57469 AAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTA
196 AAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTA
57534 GATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTA
261 GATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTA
57599 TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACA
326 TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACA
57664 CAAACTACAAA
391 CAAACTACAAA
*
57675 AGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
57740 AAAATTACGTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
57805 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
* * * * *
57870 -ACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGCACCGATTA
196 AAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTA
* *
57934 GATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTA
261 GATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTA
57999 TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
326 TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
58039 ATTGTAAATT
Statistics
Matches: 734, Mismatches: 29, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
400 162 0.22
401 567 0.77
402 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (401 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
AAAAAAAGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTA
TATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACA
CAAACTACAAA
Found at i:59940 original size:33 final size:33
Alignment explanation
Indices: 59903--59968 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
59893 CATCTTAATA
*
59903 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
59936 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
59969 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:60027 original size:21 final size:21
Alignment explanation
Indices: 60002--60066 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
59992 CCCCTTATGC
* *
60002 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
60023 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
60044 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
60065 CT
1 CT
60067 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:62304 original size:17 final size:18
Alignment explanation
Indices: 62282--62324 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
62272 ATATATCCGG
62282 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
62299 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
62319 TATCAT
1 TATCAT
62325 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:62342 original size:20 final size:19
Alignment explanation
Indices: 62287--62333 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
62277 TCCGGTATCA
62287 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
62306 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
62327 TTTTACC
1 TTTTACC
62334 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:62494 original size:21 final size:20
Alignment explanation
Indices: 62468--62515 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
62458 TCCGGTAACG
*
62468 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
62488 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
62509 TTTTACC
1 TTTTACC
62516 TGGTATATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:62560 original size:182 final size:182
Alignment explanation
Indices: 62265--62727 Score: 685
Period size: 182 Copynumber: 2.5 Consensus size: 182
62255 AAGTATAAAC
* *
62265 ACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTT
1 ACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTT
* * * *
62330 TACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTATAGGCGCTAAAA
66 TACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAAAA
*
62395 CTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTATCGAA
131 CTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGAA
*
62446 ACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTGTTACCGGTTTTATCATATTT
1 ACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTTGATACCGGTTTTATCATATTT
* * * **
62511 TTACCTGGTATATTGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTATAGGATTTAAA
65 TTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAAA
* *
62576 ACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAGTACCGAC
130 ACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGAA
* * * * ** * *
62629 ACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTTTGTCATAGTTT
1 ACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTT
* *
62694 TACTTGTTATATCGTTTTGGATCGACACATTTTT
66 TACCTGTTATATCGTTTTGGATCGATACATTTTT
62728 AATTTGGATC
Statistics
Matches: 252, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 37 0.15
182 170 0.67
183 45 0.18
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
ACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTT
TACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCTAAAA
CTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTACCGAA
Found at i:65657 original size:94 final size:94
Alignment explanation
Indices: 65549--65919 Score: 705
Period size: 94 Copynumber: 4.0 Consensus size: 94
65539 TTCCAAAAGG
*
65549 TATATATATATATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
1 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
65614 ATGAAAAATCTGAAAGAACATTCAGATTA
66 ATGAAAAATCTGAAAGAACATTCAGATTA
65643 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
1 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
65708 ATGAAAAATCTGAAAGAACATTCAGATTA
66 ATGAAAAATCTGAAAGAACATTCAGATTA
65737 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
1 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
65802 ATGAAAAATCTGAAAGAACATTCAG---A
66 ATGAAAAATCTGAAAGAACATTCAGATTA
65828 TATATATA-TTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
1 TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
65892 ATGAAAAATCTGAAAGAACATTCAGATT
66 ATGAAAAATCTGAAAGAACATTCAGATT
65920 TGGAAAGTTG
Statistics
Matches: 273, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 81 0.30
91 9 0.03
94 183 0.67
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (94 bp):
TATATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAG
ATGAAAAATCTGAAAGAACATTCAGATTA
Found at i:67623 original size:3 final size:3
Alignment explanation
Indices: 67615--67663 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
67605 TCACCCATTA
67615 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
67661 ATT
1 ATT
67664 GAGAAAGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.