Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008246.1 Hibiscus syriacus cultivar Beakdansim tig00110896_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: 500120
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:247981 original size:6 final size:6
Alignment explanation
Indices: 247959--247994 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
247949 TTGATCGAAT
*
247959 AAAATA AAAAGTG AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAA-TA AAAATA AAAATA AAAATA AAAAT
247995 TTAACGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:248421 original size:21 final size:21
Alignment explanation
Indices: 248395--248439 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
248385 CGATTTATGG
248395 CAAAGTTAGATTCATCATCAA
1 CAAAGTTAGATTCATCATCAA
248416 CAAAGTTAGATTCATCATCAA
1 CAAAGTTAGATTCATCATCAA
248437 CAA
1 CAA
248440 GTTCAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (21 bp):
CAAAGTTAGATTCATCATCAA
Found at i:250899 original size:18 final size:19
Alignment explanation
Indices: 250876--250913 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
250866 TATTTAAGTT
*
250876 ATAAAAGCAA-TTAAATAA
1 ATAAAAACAATTTAAATAA
250894 ATAAAAACAATTTAAATAA
1 ATAAAAACAATTTAAATAA
250913 A
1 A
250914 AATAAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAAAAACAATTTAAATAA
Found at i:258744 original size:19 final size:18
Alignment explanation
Indices: 258716--258753 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
258706 CACGTAAAGA
258716 TTTTAAATTTTTATATAAT
1 TTTTAAATTTTTAT-TAAT
*
258735 TTTTATATTTTTATTAAT
1 TTTTAAATTTTTATTAAT
258753 T
1 T
258754 ATCTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAAATTTTTATTAAT
Found at i:259745 original size:21 final size:21
Alignment explanation
Indices: 259715--259758 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
259705 AATTAAAAAA
* *
259715 TATTTTTAAATAAAATATTTT
1 TATTTATAAATAAAATATATT
*
259736 TATTTATAAATAAGATATATT
1 TATTTATAAATAAAATATATT
259757 TA
1 TA
259759 AATAAAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTATAAATAAAATATATT
Found at i:261368 original size:53 final size:53
Alignment explanation
Indices: 261278--261435 Score: 262
Period size: 53 Copynumber: 3.0 Consensus size: 53
261268 CGATAGAAGG
* * *
261278 CGTGCTCACGCCTTAATTGAAGACTTCTTCTGTGATAGCTCAGGATGAATAAGC
1 CGTGCTCACGCCTTAACTG-AGACTTCTTCTGCGATAGCTAAGGATGAATAAGC
* *
261332 CGTGCCCACGCCTTAACTGAGACTTCTTCTGCGATAGTTAAGGATGAATAAGC
1 CGTGCTCACGCCTTAACTGAGACTTCTTCTGCGATAGCTAAGGATGAATAAGC
261385 CGTGCTCACGCCTTAACTGAGACTTCTTCTGCGATAGCTAAGGATGAATAA
1 CGTGCTCACGCCTTAACTGAGACTTCTTCTGCGATAGCTAAGGATGAATAA
261436 CCACATTCTC
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 80 0.82
54 17 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (53 bp):
CGTGCTCACGCCTTAACTGAGACTTCTTCTGCGATAGCTAAGGATGAATAAGC
Found at i:264000 original size:20 final size:21
Alignment explanation
Indices: 263975--264067 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
263965 TTTTCCCAAT
*
263975 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
263995 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
264016 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
264036 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
264057 TCGCAATGCGA
1 TCGCAATGCGA
264068 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:264020 original size:41 final size:41
Alignment explanation
Indices: 263975--264067 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
263965 TTTTCCCAAT
263975 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
264016 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
264057 TCGCAATGCGA
1 TCGCAATGCGA
264068 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:264080 original size:41 final size:41
Alignment explanation
Indices: 263994--264128 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
263984 GAATAAGTAA
* *
263994 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
264035 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** *
264076 ATCGCAATGCGATAAT-ACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
264117 TTCGCAACGCGA
1 ATCGCAACGCGA
264129 TTGACTTTCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.05
41 76 0.93
42 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:264081 original size:20 final size:20
Alignment explanation
Indices: 264056--264168 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
264046 AATTGGGAAA
* *
264056 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
264076 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
264097 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
264117 TTCGCAACGCGAT--TGACT
1 ATCGCAACGCGATAATGACT
*
264135 TTCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
264155 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
264169 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
18 18 0.23
19 4 0.05
20 29 0.37
21 25 0.32
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:264102 original size:21 final size:22
Alignment explanation
Indices: 264012--264115 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 22
264002 GCGAATTGGG
264012 AAAATCGCAATGCGAATAA-G--
1 AAAATCGCAATGCG-ATAATGAC
* * * **
264032 TAAATCGCAACGCGA-ATTGGG
1 AAAATCGCAATGCGATAATGAC
*
264053 AAAATCGCAATGCGATACTGAC
1 AAAATCGCAATGCGATAATGAC
*
264075 --TATCGCAATGCGATAAT-AC
1 AAAATCGCAATGCGATAATGAC
* *
264094 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAATGCGATAATGAC
264116 TTTCGCAACG
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.02
19 4 0.06
20 27 0.42
21 27 0.42
22 5 0.08
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAATCGCAATGCGATAATGAC
Found at i:264135 original size:18 final size:19
Alignment explanation
Indices: 264098--264148 Score: 86
Period size: 18 Copynumber: 2.7 Consensus size: 19
264088 TAATACAAAA
264098 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATA-TGACTT
264118 TCGCAACGCGAT-TGACTT
1 TCGCAACGCGATATGACTT
264136 TCGCAACGCGATA
1 TCGCAACGCGATA
264149 ATACATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.60
20 12 0.40
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAACGCGATATGACTT
Found at i:264363 original size:22 final size:22
Alignment explanation
Indices: 264335--264378 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
264325 CACTCTCTCA
*
264335 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
264357 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
264379 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:264666 original size:20 final size:20
Alignment explanation
Indices: 264641--264689 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
264631 GCGATTCTTT
264641 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
264661 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
264681 TGTTGCGAT
1 CGTTGCGAT
264690 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:266012 original size:18 final size:18
Alignment explanation
Indices: 265991--266035 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
265981 TCTACTTCGG
*
265991 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
266009 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
266027 GAGCCATCA
1 GAGCCATCA
266036 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:266571 original size:19 final size:20
Alignment explanation
Indices: 266517--266583 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
266507 TAGTTTACTT
*
266517 TCGCAACACGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
266537 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
266557 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
266576 TCGCAACG
1 TCGCAACG
266584 ACAAAATCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:266591 original size:14 final size:14
Alignment explanation
Indices: 266572--266629 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
266562 ATGCGAAATG
266572 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
266586 AAAATCACAATGCGAA
1 AAAATCGCAA--CGAC
266602 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
266618 AAAATCGCAACG
1 AAAATCGCAACG
266630 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:266614 original size:32 final size:33
Alignment explanation
Indices: 266560--266646 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
266550 ATGGCTATCG
266560 CAATGCGAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
266593 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
266625 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
266647 TGCGATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:266723 original size:20 final size:20
Alignment explanation
Indices: 266698--266744 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
266688 CATCATTTCA
266698 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
266718 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
266738 TTGCGAT
1 TTGCGAT
266745 TTTAAGTTTC
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:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:269319 original size:24 final size:24
Alignment explanation
Indices: 269292--269338 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
269282 AGTCAGTATT
269292 CGAAATTTGATC-TTGGTCAATACC
1 CGAAATTTGA-CATTGGTCAATACC
*
269316 CGAACTTTGACATTGGTCAATAC
1 CGAAATTTGACATTGGTCAATAC
269339 ACGGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (24 bp):
CGAAATTTGACATTGGTCAATACC
Found at i:269542 original size:12 final size:12
Alignment explanation
Indices: 269525--269549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
269515 ATATAATCCT
269525 GAAGAAGAAAAA
1 GAAGAAGAAAAA
269537 GAAGAAGAAAAA
1 GAAGAAGAAAAA
269549 G
1 G
269550 TCCACGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:271883 original size:33 final size:33
Alignment explanation
Indices: 271841--271967 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
271831 GGAAATTACT
*
271841 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
271874 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
271906 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
271940 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
271968 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:271948 original size:66 final size:66
Alignment explanation
Indices: 271842--271974 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
271832 GAAATTACTA
* *
271842 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
271907 T
66 T
*
271908 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
271973 T
66 T
271974 T
1 T
271975 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:271999 original size:14 final size:14
Alignment explanation
Indices: 271982--272038 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
271972 TTTAATTTCG
271982 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
271996 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
272014 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
272029 CGTTGCGATT
1 CGTTGCGATT
272039 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:272020 original size:19 final size:19
Alignment explanation
Indices: 271996--272056 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
271986 GCGATTCTCT
271996 CGTTGCGATTTTCATTTTG
1 CGTTGCGATTTTCATTTTG
*
272015 CGTTGCGA--TTC--TCT-
1 CGTTGCGATTTTCATTTTG
*
272029 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTTG
*
272048 CATTGCGAT
1 CGTTGCGAT
272057 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 3 0.09
17 3 0.09
18 1 0.03
19 16 0.48
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTTG
Found at i:272023 original size:33 final size:33
Alignment explanation
Indices: 271967--272056 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
271957 AAATCGCAAC
* *
271967 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
272000 GCGATTTTCATTTTGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
272033 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
272057 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:272182 original size:14 final size:14
Alignment explanation
Indices: 272163--272199 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
272153 CATCAATTAA
272163 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
272177 ACAAATCATCTTTT
1 ACAAATCAACTTTT
272191 ACAAATCAA
1 ACAAATCAA
272200 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:273622 original size:21 final size:21
Alignment explanation
Indices: 273556--273622 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
273546 GTGAATCGGG
*
273556 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
273576 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
273598 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
273619 CTCT
1 CTCT
273623 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:273641 original size:42 final size:41
Alignment explanation
Indices: 273556--273678 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
273546 GTGAATCGGG
* * * *
273556 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
273598 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
273640 CTCTTCAACGATAGGAGTGGACTCTTGAGGGGTGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
273679 CGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:275720 original size:20 final size:19
Alignment explanation
Indices: 275675--275806 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
275665 TCTTTTGGTT
*
275675 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
275694 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
275714 GGAAATGACTATCGCGA--C
1 -GAAATGAAAATCGCAACGC
*
275732 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
275748 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
275767 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
275786 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
275805 GA
1 GA
275807 TTTTTGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 52 0.55
20 26 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:275838 original size:19 final size:19
Alignment explanation
Indices: 275802--275868 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
275792 AAAATCGCAA
*
275802 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
275821 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
275840 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
275860 TGCGATTTT
1 TGCGATTTT
275869 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:276471 original size:20 final size:20
Alignment explanation
Indices: 276386--276479 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
276376 CGCTATGTAA
* *
276386 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
276406 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*** * *
276426 ATCTTGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
276447 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
276467 ATCGCATTGCGAT
1 ATCGCATTGCGAT
276480 TTTTCCAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.73
21 11 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:277680 original size:17 final size:17
Alignment explanation
Indices: 277658--277691 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
277648 AATTCAAGAG
277658 CTCGATTCAAACTCGAA
1 CTCGATTCAAACTCGAA
*
277675 CTCGATTCAAGCTCGAA
1 CTCGATTCAAACTCGAA
277692 ATCAAAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAACTCGAA
Found at i:280448 original size:7 final size:7
Alignment explanation
Indices: 280433--280510 Score: 63
Period size: 7 Copynumber: 11.3 Consensus size: 7
280423 CATAATTAGA
*
280433 TTTAGGG
1 TTTATGG
280440 TTTATGG
1 TTTATGG
*
280447 TTTATAG
1 TTTATGG
280454 TTTA-GTG
1 TTTATG-G
280461 TTTATGG
1 TTTATGG
*
280468 TTTAAGG
1 TTTATGG
280475 TTTA-GTG
1 TTTATG-G
*
280482 TTTATGA
1 TTTATGG
*
280489 TTTAGGG
1 TTTATGG
280496 TTTA-GG
1 TTTATGG
*
280502 TTTAGGG
1 TTTATGG
280509 TT
1 TT
280511 CACTGCAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
6 7 0.12
7 50 0.85
8 2 0.03
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (7 bp):
TTTATGG
Found at i:280463 original size:21 final size:20
Alignment explanation
Indices: 280433--280510 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
280423 CATAATTAGA
*
280433 TTTAGGGTTTATGGTTTATAG
1 TTTAGTGTTTATGGTTTA-AG
280454 TTTAGTGTTTATGGTTTAAGG
1 TTTAGTGTTTATGGTTTAA-G
* *
280475 TTTAGTGTTTATGATTTAGGG
1 TTTAGTGTTTATGGTTTA-AG
*
280496 TTTAG-GTTTAGGGTT
1 TTTAGTGTTTATGGTT
280511 CACTGCAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.18
21 41 0.82
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (20 bp):
TTTAGTGTTTATGGTTTAAG
Found at i:280580 original size:7 final size:7
Alignment explanation
Indices: 280565--280615 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
280555 GTAAGTATAA
280565 TTTAAGG
1 TTTAAGG
*
280572 TTTAGGG
1 TTTAAGG
*
280579 TTTAGGG
1 TTTAAGG
280586 TTTAAGG
1 TTTAAGG
*
280593 TTTAGGG
1 TTTAAGG
280600 TTTAAGG
1 TTTAAGG
280607 TTTAAGG
1 TTTAAGG
280614 TT
1 TT
280616 CATTACAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
TTTAAGG
Found at i:280591 original size:21 final size:21
Alignment explanation
Indices: 280565--280615 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
280555 GTAAGTATAA
*
280565 TTTAAGGTTTAGGGTTTAGGG
1 TTTAAGGTTTAGGGTTTAAGG
280586 TTTAAGGTTTAGGGTTTAAGG
1 TTTAAGGTTTAGGGTTTAAGG
280607 TTTAAGGTT
1 TTTAAGGTT
280616 CATTACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAAGG
Found at i:285303 original size:17 final size:17
Alignment explanation
Indices: 285281--285317 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
285271 CAAAATTAAC
285281 AAAATAAATTAAATATT
1 AAAATAAATTAAATATT
285298 AAAATAAATTAAATATT
1 AAAATAAATTAAATATT
285315 AAA
1 AAA
285318 TGGTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAAATTAAATATT
Found at i:285324 original size:24 final size:22
Alignment explanation
Indices: 285288--285332 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
285278 AACAAAATAA
*
285288 ATTAAATATTAAAATAAATTAAAT
1 ATTAAATAGT-AAAT-AATTAAAT
*
285312 ATTAAATGGTAAATAATTAAA
1 ATTAAATAGTAAATAATTAAA
285333 AAAATTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
ATTAAATAGTAAATAATTAAAT
Found at i:287457 original size:27 final size:28
Alignment explanation
Indices: 287405--287458 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
287395 CTAAAATTAT
*
287405 TAATAATTACAAAAATTAATATATAAAC
1 TAATAATTACAAAAATTAATAAATAAAC
287433 TAATAA-TA-AAAAATTAAATAAATAAA
1 TAATAATTACAAAAATT-AATAAATAAA
287459 TTATTACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 11 0.46
28 6 0.25
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
TAATAATTACAAAAATTAATAAATAAAC
Found at i:294496 original size:42 final size:42
Alignment explanation
Indices: 294447--294530 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
294437 AAAAAAATCT
294447 AAAATATATAATAATTTTCAGGAACAA-TCGCTCCATCCACTC
1 AAAATATATAATAATTTTCAGGAACAACT-GCTCCATCCACTC
*
294489 AAAATATATAATAATTTTCAGGAACAACTGCTCTATCCACTC
1 AAAATATATAATAATTTTCAGGAACAACTGCTCCATCCACTC
294531 CCCTTAGTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (42 bp):
AAAATATATAATAATTTTCAGGAACAACTGCTCCATCCACTC
Found at i:295722 original size:29 final size:29
Alignment explanation
Indices: 295661--295746 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 29
295651 CCCAACCCAT
* * ****
295661 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* * *
295690 AGGTTGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
295719 AGGTCGCCATGCACGCCCGGCGACCAAG
1 AGGTCGCCATGCACGCCCGGCGACCAAG
295747 CTTTTAACCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:295924 original size:29 final size:29
Alignment explanation
Indices: 295890--296003 Score: 156
Period size: 29 Copynumber: 3.9 Consensus size: 29
295880 CAAGGAGACA
* ***
295890 AGGTCGCCGGGCGTGCATGGCGACCTCCT
1 AGGTCGCCGGGAGTGCATGGCGACCTAGG
* *
295919 TGGTCGCCCGGAGTGCATGGCGACCTAGG
1 AGGTCGCCGGGAGTGCATGGCGACCTAGG
*
295948 AGGTCGCTGGGAGTGCATGGCGACCTAGG
1 AGGTCGCCGGGAGTGCATGGCGACCTAGG
*
295977 AGGTCGCTGGGAGTGCATGGCGACCTA
1 AGGTCGCCGGGAGTGCATGGCGACCTA
296004 TGGGTTGGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (29 bp):
AGGTCGCCGGGAGTGCATGGCGACCTAGG
Found at i:299002 original size:37 final size:36
Alignment explanation
Indices: 298883--299000 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 36
298873 TGGTAACCAA
*
298883 CTTTGAAAAAATGGTTTTCAAAATTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
298920 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
298955 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
298992 -GTTGAAAAA
1 CTTTGAAAAA
299001 ATGATAATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:299418 original size:16 final size:16
Alignment explanation
Indices: 299392--299430 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
299382 TGGGGTTACT
299392 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATAGTGA
299409 ATTTCGTGAATAGTGA
1 ATTTCGTGAATAGTGA
*
299425 AATTCG
1 ATTTCG
299431 ATCGGCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATAGTGA
Found at i:299428 original size:17 final size:17
Alignment explanation
Indices: 299392--299425 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
299382 TGGGGTTACT
299392 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTGA
299409 ATTT-CGTGAATAGTGA
1 ATTTACGTGAATAGTGA
299425 A
1 A
299426 ATTCGATCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTGA
Found at i:303511 original size:21 final size:21
Alignment explanation
Indices: 303487--303547 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
303477 AACTTTGAAA
303487 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
303508 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
303522 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
303543 AAATG
1 AAATG
303548 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:303578 original size:37 final size:37
Alignment explanation
Indices: 303479--303597 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
303469 TGGTAACCAA
303479 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
303516 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
303551 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
303588 -GTTGAAAAAT
1 CTTTGAAAAAT
303598 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:309602 original size:62 final size:65
Alignment explanation
Indices: 309535--309699 Score: 219
Period size: 75 Copynumber: 2.4 Consensus size: 65
309525 TATATTTTAA
309535 TTTTTAATATATATTATAGCATATTTTTAAAATTTTG-T-A-TTATTCAAAGTGAAAATTATTAT
1 TTTTTAATATATATTATAGCATATTTTTAAAATTTTGATAATTTATTCAAAGTGAAAATTATTAT
309597 TTTTTAATATATATTATAGCATATTTTTAAAATTTTGTATTAATACAAAATTTTATTCAAAGTGA
1 TTTTTAATATATATTATAGCATATTTTTAAAATTTTG-----AT----AA-TTTATTCAAAGTGA
309662 AAATTATTAT
56 AAATTATTAT
309672 TTTTTAATATATATTATAGCATATTTTT
1 TTTTTAATATATATTATAGCATATTTTT
309700 TAAGTTATAT
Statistics
Matches: 90, Mismatches: 0, Indels: 13
0.87 0.00 0.13
Matches are distributed among these distances:
62 37 0.41
68 1 0.01
73 1 0.01
75 51 0.57
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (65 bp):
TTTTTAATATATATTATAGCATATTTTTAAAATTTTGATAATTTATTCAAAGTGAAAATTATTAT
Found at i:309773 original size:2 final size:2
Alignment explanation
Indices: 309705--309761 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
309695 TTTTTTAAGT
309705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
309747 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
309762 TAAATTTATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:312143 original size:3 final size:3
Alignment explanation
Indices: 312135--312185 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
312125 AAATGTTAGA
312135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
312183 AAT
1 AAT
312186 CATTAAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:312258 original size:26 final size:26
Alignment explanation
Indices: 312205--312252 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
312195 AATCAAAGAG
312205 AAAATAAA-AAAAAAGATTAAATTAA
1 AAAATAAATAAAAAAGATTAAATTAA
*
312230 AAAATAAATAAAAATG-TTAAATT
1 AAAATAAATAAAAAAGATTAAATT
312253 TTAAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATAAATAAAAAAGATTAAATTAA
Found at i:312318 original size:22 final size:22
Alignment explanation
Indices: 312287--312328 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
312277 TAGTAAGAAG
312287 TAAAAAAAT-ATAAAACAATGTT
1 TAAAAAAATAATAAAA-AATGTT
*
312309 TAAAATAATAATAAAAAATG
1 TAAAAAAATAATAAAAAATG
312329 AAAAAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
TAAAAAAATAATAAAAAATGTT
Found at i:313423 original size:17 final size:17
Alignment explanation
Indices: 313401--313454 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
313391 CCTAAAAACG
313401 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAT
* *
313418 AAAATAAATAAGTGAAAT
1 AAAATAAA-AAATAAAAT
*
313436 -AAATAAATAATATAAAT
1 AAAATAAAAAATA-AAAT
313453 AA
1 AA
313455 CTAACTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.07
17 19 0.66
18 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:313428 original size:4 final size:4
Alignment explanation
Indices: 313402--313467 Score: 55
Period size: 4 Copynumber: 16.0 Consensus size: 4
313392 CTAAAAACGA
*
313402 AAAT AAA- AAAT AAAAT AAAAT AAAT AAGT GAAAT AAAT AAAT AATAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AA-AT
* *
313449 AAAT AACT AACT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT
313468 TATACATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 6 0.11
4 31 0.58
5 16 0.30
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:313437 original size:13 final size:12
Alignment explanation
Indices: 313402--313467 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
313392 CTAAAAACGA
313402 AAATAAA-AAAT
1 AAATAAATAAAT
313413 AAAATAAAATAAAT
1 -AAAT-AAATAAAT
*
313427 AAGTGAAATAAAT
1 AAAT-AAATAAAT
313440 AAATAATATAAAT
1 AAATAA-ATAAAT
* *
313453 AACTAACTAAA-
1 AAATAAATAAAT
313464 AAAT
1 AAAT
313468 TATACATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 3 0.07
12 10 0.22
13 28 0.62
14 4 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:313572 original size:72 final size:71
Alignment explanation
Indices: 313468--313685 Score: 271
Period size: 72 Copynumber: 3.0 Consensus size: 71
313458 ACTAAAAAAT
* * * * * *
313468 TATACATTTTCAAAACCTC-TTTTAAAAACTATATTATATATTTTC-AAAATTATTTTCGAAACT
1 TATATATTTTCAAAA-ATCATTTTCAAAACTATATAATATATTTTCAAAAATTGTTTTCAAAACT
313531 ATAATATA
65 AT-ATATA
* * ** *
313539 TATATGTTTTCACAAATTGTTTTTCAAAACTATATAATATATTTTCAAAAATCGTTTTCAAAACT
1 TATATATTTTCA-AAAATCATTTTCAAAACTATATAATATATTTTCAAAAATTGTTTTCAAAACT
313604 ATATA-A
65 ATATATA
313610 TATATATTTTCAAAAATCATTTTCAAAACTATATAATATAGTTTTCAAAAAATTGTTTTCAAAAC
1 TATATATTTTCAAAAATCATTTTCAAAACTATATAATATA-TTTTC-AAAAATTGTTTTCAAAAC
313675 TATATATA
64 TATATATA
313683 TAT
1 TAT
313686 TCAGAAACCG
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
70 25 0.20
71 28 0.22
72 53 0.42
73 21 0.17
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.44
Consensus pattern (71 bp):
TATATATTTTCAAAAATCATTTTCAAAACTATATAATATATTTTCAAAAATTGTTTTCAAAACTA
TATATA
Found at i:313620 original size:36 final size:35
Alignment explanation
Indices: 313468--313685 Score: 239
Period size: 36 Copynumber: 6.1 Consensus size: 35
313458 ACTAAAAAAT
* * *
313468 TATACATTTTCAAAACCTC-TTTTAAAAACTATAT-
1 TATATATTTTCAAAA-ATCGTTTTCAAAACTATATA
** *
313502 TATATATTTTC-AAAATTATTTTCGAAACTATAATA
1 TATATATTTTCAAAAATCGTTTTCAAAACTAT-ATA
* *
313537 TATATATGTTTTCACAAATTGTTTTTCAAAACTATATA
1 TATATA--TTTTCAAAAATCG-TTTTCAAAACTATATA
313575 -ATATATTTTCAAAAATCGTTTTCAAAACTATATAA
1 TATATATTTTCAAAAATCGTTTTCAAAACTATAT-A
*
313610 TATATATTTTCAAAAATCATTTTCAAAACTATATA
1 TATATATTTTCAAAAATCGTTTTCAAAACTATATA
*
313645 -ATATAGTTTTCAAAAAATTGTTTTCAAAACTATATA
1 TATATA-TTTTC-AAAAATCGTTTTCAAAACTATATA
313681 TATAT
1 TATAT
313686 TCAGAAACCG
Statistics
Matches: 159, Mismatches: 13, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
32 1 0.01
33 14 0.09
34 32 0.20
35 24 0.15
36 54 0.34
37 14 0.09
38 8 0.05
39 12 0.08
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATATTTTCAAAAATCGTTTTCAAAACTATATA
Found at i:313721 original size:40 final size:38
Alignment explanation
Indices: 313677--313759 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
313667 TTCAAAACTA
* * **
313677 TATATATATTCAGAAACCGATTTTTTTTAAATGTATATAT
1 TATATATATTCAAAAACCG-TTTTCTAAAAAT-TATATAT
* *
313717 TATATGTTTTCAAAAACCGTTTTCTAAAAATTATATAT
1 TATATATATTCAAAAACCGTTTTCTAAAAATTATATAT
313755 TATAT
1 TATAT
313760 TTTTTCGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 12 0.32
39 9 0.24
40 16 0.43
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (38 bp):
TATATATATTCAAAAACCGTTTTCTAAAAATTATATAT
Found at i:313752 original size:36 final size:36
Alignment explanation
Indices: 313466--313793 Score: 172
Period size: 36 Copynumber: 9.2 Consensus size: 36
313456 TAACTAAAAA
* *
313466 ATTATACATTTTC-AAAA-CCTCTTT-TAAAAACTAT
1 ATTATATATTTTCAAAAATCGT-TTTCTAAAAACTAT
** *
313500 ATTATATATTTTC-AAAATTATTTTC--GAAACTAT
1 ATTATATATTTTCAAAAATCGTTTTCTAAAAACTAT
* * *
313533 AATATATATATGTTTTCACAAATTGTTTT-TCAAAACTAT
1 -AT-TATATA--TTTTCAAAAATCGTTTTCTAAAAACTAT
*
313572 ATAATATATTTTCAAAAATCGTTTTC--AAAACTAT
1 ATTATATATTTTCAAAAATCGTTTTCTAAAAACTAT
*
313606 ATAATATATATTTTCAAAAATCATTTTC--AAAACTAT
1 AT--TATATATTTTCAAAAATCGTTTTCTAAAAACTAT
* *
313642 ATAATATAGTTTTCAAAAAATTGTTTTC--AAAACTAT
1 ATTATATA-TTTTC-AAAAATCGTTTTCTAAAAACTAT
* * * *
313678 A-TATATA--TTCAGAAACCGATTTTTTTTAAATGTA-TAT
1 ATTATATATTTTCAAAAATCG---TTTTCTAAA--AACTAT
* * *
313715 ATTATATGTTTTCAAAAACCGTTTTCTAAAAATTATAT
1 ATTATATATTTTCAAAAATCGTTTTCTAAAAA--CTAT
* * *
313753 ATTATATTTTTTCGAAAAT-ATTTTC-AAAAACTAT
1 ATTATATATTTTCAAAAATCGTTTTCTAAAAACTAT
*
313787 ACTATAT
1 ATTATAT
313794 TAATATATAC
Statistics
Matches: 236, Mismatches: 31, Indels: 54
0.74 0.10 0.17
Matches are distributed among these distances:
31 5 0.02
32 3 0.01
33 7 0.03
34 49 0.21
35 33 0.14
36 59 0.25
37 27 0.11
38 36 0.15
39 7 0.03
40 10 0.04
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (36 bp):
ATTATATATTTTCAAAAATCGTTTTCTAAAAACTAT
Found at i:320900 original size:3 final size:3
Alignment explanation
Indices: 320892--320923 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
320882 AAATGTTAGA
320892 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
320924 ACATTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:321017 original size:26 final size:25
Alignment explanation
Indices: 320988--321058 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 25
320978 AAAAAATGTT
320988 AAATATTAAAAGTAATAAAATATAAA
1 AAATATTAAAA-TAATAAAATATAAA
321014 AAATATTAAGAAATAA-AAAATATAAA
1 AAATATT-A-AAATAATAAAATATAAA
*
321040 ACAATGTTTAAAATAATAA
1 A-AAT-ATTAAAATAATAA
321059 TAAAAAATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
26 24 0.62
27 10 0.26
28 5 0.13
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (25 bp):
AAATATTAAAATAATAAAATATAAA
Found at i:321029 original size:17 final size:16
Alignment explanation
Indices: 320974--321040 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
320964 TTTAAAAAAT
*
320974 AAATAAAAAATGTTAA
1 AAATAAAAAATATTAA
* * * *
320990 ATATTAAAAGTAATAA
1 AAATAAAAAATATTAA
321006 AATATAAAAAATATTAA
1 AA-ATAAAAAATATTAA
321023 GAAATAAAAAATA-TAA
1 -AAATAAAAAATATTAA
321039 AA
1 AA
321041 CAATGTTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.05
16 15 0.38
17 21 0.52
18 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (16 bp):
AAATAAAAAATATTAA
Found at i:321039 original size:33 final size:33
Alignment explanation
Indices: 320976--321040 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
320966 TAAAAAATAA
* * * *
320976 ATAAAAAATGTTAAATATTAAAAGTAATAAAAT
1 ATAAAAAATATTAAAAATAAAAAATAATAAAAT
321009 ATAAAAAATATTAAGAAATAAAAAAT-ATAAAA
1 ATAAAAAATATTAA-AAATAAAAAATAATAAAA
321041 CAATGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (33 bp):
ATAAAAAATATTAAAAATAAAAAATAATAAAAT
Found at i:321067 original size:22 final size:21
Alignment explanation
Indices: 321027--321067 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
321017 TATTAAGAAA
321027 TAAAAAATATAAAACAATGTT
1 TAAAAAATATAAAACAATGTT
321048 TAAAATAATAATAAAA-AATG
1 TAAAA-AAT-ATAAAACAATG
321068 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAAAATATAAAACAATGTT
Found at i:321091 original size:60 final size:59
Alignment explanation
Indices: 320944--321091 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 59
320934 AATCAAAGAG
* *
320944 AAAATAAAAAAAAGATTAAATTTAAAAAATAAATAAAAAATGTTAAATATTAAAAGTAAT
1 AAAATAAAAAAAATATTAAAATTAAAAAAT-AATAAAAAATGTTAAATATTAAAAGTAAT
* *
321004 AAAATATAAAAAATATTAAGAAATAAAAAAT-ATAAAACAATGTTTAAA-A-TAATAA-TAA-
1 AAAATAAAAAAAATATTAA-AATTAAAAAATAATAAAA-AATG-TTAAATATTAA-AAGTAAT
321062 AAAATGAAAAAAAATATGCTAAAATTAAAA
1 AAAAT-AAAAAAAATAT--TAAAATTAAAA
321092 GGAAAAATGA
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
58 5 0.07
59 22 0.29
60 31 0.41
61 17 0.23
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (59 bp):
AAAATAAAAAAAATATTAAAATTAAAAAATAATAAAAAATGTTAAATATTAAAAGTAAT
Found at i:321128 original size:29 final size:29
Alignment explanation
Indices: 321082--321169 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
321072 AAAATATGCT
* * *
321082 AAAATTAAAAGGA-AAAATGAATAACTAA
1 AAAATTTAAAGGATCAAATTAATAACTAA
321110 AAAATTTAAAGGATCAAATTAA-AAC-AA
1 AAAATTTAAAGGATCAAATTAATAACTAA
*
321137 ATTGAAATTT-ATGGATCAAATTAAT-ACTAA
1 A---AAATTTAAAGGATCAAATTAATAACTAA
321167 AAA
1 AAA
321170 TGAGTTGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
27 5 0.10
28 15 0.30
29 21 0.42
30 9 0.18
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (29 bp):
AAAATTTAAAGGATCAAATTAATAACTAA
Found at i:322125 original size:4 final size:4
Alignment explanation
Indices: 322111--322151 Score: 55
Period size: 4 Copynumber: 9.5 Consensus size: 4
322101 CTAAAAATGA
322111 AAAT AAAAT AAAT AAAAT AAAT AAAT AAAT AATAT AAAT AA
1 AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AA-AT AAAT AA
322152 CTAACTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 22 0.65
5 12 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:322125 original size:9 final size:9
Alignment explanation
Indices: 322111--322151 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
322101 CTAAAAATGA
322111 AAATAAAAT
1 AAATAAAAT
322120 AAATAAAAT
1 AAATAAAAT
322129 AAAT-AAAT
1 AAATAAAAT
*
322137 AAATAATAT
1 AAATAAAAT
322146 AAATAA
1 AAATAA
322152 CTAACTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:322134 original size:13 final size:13
Alignment explanation
Indices: 322105--322151 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
322095 TTAGACCTAA
322105 AAATGAAAATAAAAT
1 AAAT-AAAAT-AAAT
322120 AAATAAAATAAAT
1 AAATAAAATAAAT
322133 AAAT-AAATAATAT
1 AAATAAAATAA-AT
322146 AAATAA
1 AAATAA
322152 CTAACTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.20
13 14 0.47
14 6 0.20
15 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:322298 original size:35 final size:36
Alignment explanation
Indices: 322168--322346 Score: 173
Period size: 35 Copynumber: 5.2 Consensus size: 36
322158 TAAAAAAAAT
* * *
322168 TATACATTTTCAAAACCTC-TTTTAAAAACTATAT--
1 TATATATTTTCAAAA-ATCATTTTCAAAACTATATAA
* *
322202 TATATATTTTC-AAAATTATTTTCGAAAC--TATAA
1 TATATATTTTCAAAAATCATTTTCAAAACTATATAA
* *
322235 TATATA---TCACAAATTATTTTTCAAAACTATATAA
1 TATATATTTTCAAAAATCA-TTTTCAAAACTATATAA
*
322269 TATATATTTT-AAAAATCGTTTTCAAAACTATATAA
1 TATATATTTTCAAAAATCATTTTCAAAACTATATAA
*
322304 TATAT-TTTTCAAAAATTATTTTCAAAACTATATATA
1 TATATATTTTCAAAAATCATTTTCAAAACTATATA-A
322340 TATATAT
1 TATATAT
322347 ATATATATAT
Statistics
Matches: 120, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
30 2 0.02
31 9 0.08
32 10 0.08
33 17 0.14
34 25 0.21
35 44 0.37
36 11 0.09
37 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (36 bp):
TATATATTTTCAAAAATCATTTTCAAAACTATATAA
Found at i:322298 original size:67 final size:68
Alignment explanation
Indices: 322187--322346 Score: 193
Period size: 67 Copynumber: 2.4 Consensus size: 68
322177 TCAAAACCTC
* * * * *
322187 TTTTAAAAACTATAT--TATATATTTTCAAAATTATTTTCGAAAC-TATAATATA-TATCACAAA
1 TTTTCAAAACTATATAATATATATTTTAAAAATCATTTTCAAAACATATAATATATTATCAAAAA
322248 TTA
66 TTA
* *
322251 TTTTTCAAAACTATATAATATATATTTTAAAAATCGTTTTCAAAACTATATAATATATTTTTCAA
1 -TTTTCAAAACTATATAATATATATTTTAAAAATCATTTTCAAAAC-ATATAATATA-TTATCAA
322316 AAATTA
63 AAATTA
322322 TTTTCAAAACTATATATATATATAT
1 TTTTCAAAACTATATA-ATATATAT
322347 ATATATATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
65 14 0.17
67 24 0.30
69 9 0.11
70 16 0.20
71 18 0.22
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (68 bp):
TTTTCAAAACTATATAATATATATTTTAAAAATCATTTTCAAAACATATAATATATTATCAAAAA
TTA
Found at i:322339 original size:2 final size:2
Alignment explanation
Indices: 322332--322360 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
322322 TTTTCAAAAC
322332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
322361 TCAAAAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:322477 original size:38 final size:38
Alignment explanation
Indices: 322387--322469 Score: 118
Period size: 38 Copynumber: 2.3 Consensus size: 38
322377 TTTTTTTTAA
* *
322387 AAAAAGTATATATTATATGTTTTCAAAAACTGTTTTCT
1 AAAAACTATATATTATATGTTTTCAAAAACTATTTTCT
*
322425 AAAAACTATATATTATAT-TTTTCGAAAA-TATTTTC-
1 AAAAACTATATATTATATGTTTTCAAAAACTATTTTCT
322460 AAAAACTATA
1 AAAAACTATA
322470 CTATATTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 10 0.24
36 6 0.14
37 9 0.21
38 17 0.40
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (38 bp):
AAAAACTATATATTATATGTTTTCAAAAACTATTTTCT
Found at i:326409 original size:58 final size:56
Alignment explanation
Indices: 326346--326517 Score: 184
Period size: 58 Copynumber: 2.9 Consensus size: 56
326336 AACTATAATC
326346 CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTGTAATTTCATCTCTAAATTGAAT
1 CTCATTTTAAATTAGTCCTTAAACTTTTGAATATT-TAATTTCATC-CTAAATTGAAT
* * * * * * *
326404 TTCATTCTAAATTAATCCTTAAACATTTGGACATTCTAATTTCATCCCTAAACTATGAGT
1 CTCATTTTAAATTAGTCCTTAAACTTTTGAATATT-TAATTTCAT-CCTAAA-T-TGAAT
*
326464 CTC-TTTCTAAATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCTTAAATT
1 CTCATTT-TAAATTAGTCCTTAAACTTTTGAATATTT-AATTTCATCC-TAAATT
326518 CATCCAAATG
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
58 44 0.47
59 8 0.09
60 41 0.44
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (56 bp):
CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTTAATTTCATCCTAAATTGAAT
Found at i:326414 original size:17 final size:19
Alignment explanation
Indices: 326378--326416 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
326368 ACTTTTGAAT
326378 ATTGTAATTTCATCTCTAA
1 ATTGTAATTTCATCTCTAA
326397 ATTG-AATTTCAT-TCTAA
1 ATTGTAATTTCATCTCTAA
326414 ATT
1 ATT
326417 AATCCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 8 0.40
19 4 0.20
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTGTAATTTCATCTCTAA
Found at i:326487 original size:60 final size:57
Alignment explanation
Indices: 326346--326517 Score: 200
Period size: 60 Copynumber: 2.9 Consensus size: 57
326336 AACTATAATC
* *
326346 CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTGTAATTTCATCTCTAAATTGAAT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATT-TAATTTCATCCCTAAATTGAAT
* * * * * *
326404 TTCATTCTAAATTAATCCTTAAACATTTGGACATTCTAATTTCATCCCTAAACTATGAGT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATT-TAATTTCATCCCTAAA-T-TGAAT
* * *
326464 CTCTTTCTAAATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCTTAAATT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTT-AATTTCATCCCTAAATT
326518 CATCCAAATG
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
58 45 0.48
59 3 0.03
60 46 0.49
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (57 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTAATTTCATCCCTAAATTGAAT
Found at i:326746 original size:60 final size:60
Alignment explanation
Indices: 326667--326791 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
326657 GGTTGGTGAT
* *
326667 CAATTTAGAATGAAGGTCATAGTTT-GGGGATGAAATTGAAA-TTTTCAAAAGTTTAAGGAC
1 CAATTTAGAATGAAGGTCATAGTTTAGGGG-TGAAATTAAAACATTT-AAAAGTTTAAGGAC
*
326727 TAATTTAGAATGATA-GTCATAGTTTAGGGGTGAAATTAAAACATTTAAAAGTTTAAGGAC
1 CAATTTAGAATGA-AGGTCATAGTTTAGGGGTGAAATTAAAACATTTAAAAGTTTAAGGAC
326787 CAATT
1 CAATT
326792 CAAAATAAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
60 50 0.86
61 8 0.14
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (60 bp):
CAATTTAGAATGAAGGTCATAGTTTAGGGGTGAAATTAAAACATTTAAAAGTTTAAGGAC
Found at i:326890 original size:2 final size:2
Alignment explanation
Indices: 326885--326912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
326875 AATATATCAA
326885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
326913 TATGATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327161 original size:2 final size:2
Alignment explanation
Indices: 327154--327223 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
327144 AATTGCTTCA
327154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327196 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
327224 AATAAATAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332020 original size:14 final size:15
Alignment explanation
Indices: 331990--332022 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
331980 GGATTTGGTT
*
331990 ACTGCTGCATATTTG
1 ACTGATGCATATTTG
332005 ACTGATGCAT-TTTG
1 ACTGATGCATATTTG
332019 ACTG
1 ACTG
332023 GGGTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (15 bp):
ACTGATGCATATTTG
Found at i:336257 original size:27 final size:28
Alignment explanation
Indices: 336216--336268 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
336206 GTGTTTAAAT
336216 AATCGAATTAATTCGGTTAA-TCGATCG
1 AATCGAATTAATTCGGTTAATTCGATCG
*
336243 AATCGAATTAGTTCGGTTAATTCGAT
1 AATCGAATTAATTCGGTTAATTCGAT
336269 TTAAATTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (28 bp):
AATCGAATTAATTCGGTTAATTCGATCG
Found at i:339126 original size:20 final size:19
Alignment explanation
Indices: 339103--339252 Score: 58
Period size: 21 Copynumber: 7.3 Consensus size: 19
339093 TTCTATGAAT
339103 TAATAAATATATAAATTTTA
1 TAAT-AATATATAAATTTTA
*
339123 TAATAATTTATTAAATATTATA
1 TAATAATATA-TAAAT-TT-TA
* * *
339145 AAATGAAAATATAATATATTA
1 TAAT-AATATATAA-ATTTTA
*
339166 TAATAATATAAGTGATATTTTA
1 TAATAATAT-A-T-AAATTTTA
**
339188 TAAT-ATATA-AAA-AATA
1 TAATAATATATAAATTTTA
339204 TAATATATATTATTAAATATATTAA
1 TAATA-ATA-TA-TAAAT-T-TT-A
339229 TAAT-ATATATAAATGTTT-
1 TAATAATATATAAAT-TTTA
339247 TAATAA
1 TAATAA
339253 ATTCTTAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 37
0.65 0.10 0.25
Matches are distributed among these distances:
16 6 0.06
17 2 0.02
18 7 0.07
19 8 0.08
20 16 0.16
21 21 0.22
22 21 0.22
23 10 0.10
24 1 0.01
25 5 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TAATAATATATAAATTTTA
Found at i:339214 original size:30 final size:31
Alignment explanation
Indices: 339154--339239 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 31
339144 AAAATGAAAA
*
339154 TATAATATATTATAATAATATAAGT-GATATT-T
1 TATAATATA-TA-AATAATATAA-TATATATTAT
*
339186 TATAATATATAAAAAATATAATATATATTAT
1 TATAATATATAAATAATATAATATATATTAT
*
339217 TA-AATATATTAATAATAT-ATATA
1 TATAATATATAAATAATATAATATA
339240 AATGTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 6 0.12
30 28 0.58
31 5 0.10
32 9 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
TATAATATATAAATAATATAATATATATTAT
Found at i:339225 original size:12 final size:13
Alignment explanation
Indices: 339203--339238 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
339193 TATAAAAAAT
339203 ATAATATATATTA
1 ATAATATATATTA
*
339216 TTAA-ATATATTA
1 ATAATATATATTA
339228 ATAATATATAT
1 ATAATATATAT
339239 AAATGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAATATATATTA
Found at i:340623 original size:12 final size:14
Alignment explanation
Indices: 340604--340636 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
340594 TTTCGGAATT
340604 ACATTTTCT-GAAA
1 ACATTTTCTGGAAA
340617 A-ATTTTCTGGAAA
1 ACATTTTCTGGAAA
340630 ACATTTT
1 ACATTTT
340637 ACGTTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 6 0.33
14 5 0.28
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (14 bp):
ACATTTTCTGGAAA
Found at i:340972 original size:24 final size:23
Alignment explanation
Indices: 340943--340995 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
340933 AAATATTATT
340943 ATATTAATATTAA-ATATATAAATA
1 ATATTAATATTAATA-AT-TAAATA
* *
340967 ATATTATTATTAATAATTTAATA
1 ATATTAATATTAATAATTAAATA
340990 ATATTA
1 ATATTA
340996 TTTCTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 14 0.54
25 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTAATATTAATAATTAAATA
Found at i:340981 original size:15 final size:15
Alignment explanation
Indices: 340929--340983 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
340919 AAATATCTTC
340929 ATTAA-AATATTATT
1 ATTAATAATATTATT
*
340943 A-TATTAATATTAAATAT
1 ATTAATAATATT--AT-T
*
340960 ATAAATAATATTATT
1 ATTAATAATATTATT
340975 ATTAATAAT
1 ATTAATAAT
340984 TTAATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.06
14 7 0.22
15 9 0.28
16 4 0.12
17 2 0.06
18 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATAATATTATT
Found at i:340981 original size:23 final size:24
Alignment explanation
Indices: 340943--340997 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
340933 AAATATTATT
*
340943 ATATTAATATTAAAT-ATATAAATA
1 ATATTATTATTAAATAAT-TAAATA
*
340967 ATATTATTATT-AATAATTTAATA
1 ATATTATTATTAAATAATTAAATA
340990 ATATTATT
1 ATATTATT
340998 TCTATGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTATTATTAAATAATTAAATA
Found at i:341010 original size:23 final size:23
Alignment explanation
Indices: 340943--341013 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
340933 AAATATTATT
* * *
340943 ATATTAATATTAAATATATAAATA
1 ATATTATTATT-AATAAATTAATA
*
340967 ATATTATTATTAATAATTTAATA
1 ATATTATTATTAATAAATTAATA
340990 ATATTATT-TCT-ATGAAATTAATA
1 ATATTATTAT-TAAT-AAATTAATA
341013 A
1 A
341014 ATAATAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.08
23 27 0.68
24 10 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTATTATTAATAAATTAATA
Found at i:341102 original size:31 final size:29
Alignment explanation
Indices: 341067--341150 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
341057 AATATATATC
*
341067 TTATAATATTATAATATAAGTGATTATTTTA
1 TTATAATATTATAATATAA-T-ATTATATTA
341098 TTATAATATTA-AA-ATAATATTATATTA
1 TTATAATATTATAATATAATATTATATTA
*
341125 TTAGAAATATTAATAA-AT-ATATTATA
1 TTA-TAATATT-ATAATATAATATTATA
341151 AATGTTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.23
28 7 0.15
29 13 0.27
30 6 0.12
31 11 0.23
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
TTATAATATTATAATATAATATTATATTA
Found at i:341120 original size:19 final size:20
Alignment explanation
Indices: 341096--341133 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
341086 GTGATTATTT
341096 TATTATAATATTA-AAATAA
1 TATTATAATATTAGAAATAA
*
341115 TATTATATTATTAGAAATA
1 TATTATAATATTAGAAATA
341134 TTAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTATAATATTAGAAATAA
Found at i:344614 original size:181 final size:180
Alignment explanation
Indices: 344308--344665 Score: 682
Period size: 181 Copynumber: 2.0 Consensus size: 180
344298 ATCGATATGC
344308 TATTCGATAACTATCTTTAAGTATCGATAAGTACCAAGCCAAAACCCAAGATGTTTCAAGTTTTT
1 TATTCGATAACTATCTTTAAGTATCGATAAGTACCAAGCCAAAACCCAAGATGTTTCAAGTTTTT
344373 ATATGTAAGTTCGATGTTTCGATATACTTGAGTATGTAAACAAATTGTGTAAAATGATATATAAG
66 ATATGTAAGTTCGATGTTTCGATATACTTGAGTATGTAAACAAATTGTGTAAAATGATATATAAG
344438 AGTTATGTTATGATTTTGTAGGCGTTGTTATGTTTAAAAGTGTAGTTGGTT
131 AGTTATGTTATGATTTTGTAGGCGTTGTTATG-TTAAAAGTGTAGTTGGTT
344489 TATTCGATAACTATCTTTAAGTATCGATAAGTACCAAGCCAAAACCCAAGATGTTTCAAGTTTTT
1 TATTCGATAACTATCTTTAAGTATCGATAAGTACCAAGCCAAAACCCAAGATGTTTCAAGTTTTT
344554 ATATGTAAGTTCGATGTTTCGATATACTTGAGTATGTAAAC-AATTGTGTAAAATTGATATATAA
66 ATATGTAAGTTCGATGTTTCGATATACTTGAGTATGTAAACAAATTGTGTAAAA-TGATATATAA
*
344618 GAGTTATGTTATGATTTTGTATGCGTTGTTATGTTAAAAGTGTAGTTG
130 GAGTTATGTTATGATTTTGTAGGCGTTGTTATGTTAAAAGTGTAGTTG
344666 TTTGATTTAT
Statistics
Matches: 175, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
180 27 0.15
181 148 0.85
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (180 bp):
TATTCGATAACTATCTTTAAGTATCGATAAGTACCAAGCCAAAACCCAAGATGTTTCAAGTTTTT
ATATGTAAGTTCGATGTTTCGATATACTTGAGTATGTAAACAAATTGTGTAAAATGATATATAAG
AGTTATGTTATGATTTTGTAGGCGTTGTTATGTTAAAAGTGTAGTTGGTT
Found at i:345527 original size:36 final size:37
Alignment explanation
Indices: 345470--345564 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
345460 TATATATTCA
* *
345470 ATATAGTTTTGGAAAATATTTTTTGATAACATA-TAAT
1 ATATAATTTTGGAAAACATTTTTTGA-AACATATTAAT
* *
345507 ATTTAATTTT-GAAAACA-TTTTTGAAATATATTTAAT
1 ATATAATTTTGGAAAACATTTTTTGAAACATA-TTAAT
*
345543 ATATAGTTTTGGAAAACATTTT
1 ATATAATTTTGGAAAACATTTT
345565 AAAAATGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
34 5 0.10
35 7 0.15
36 18 0.38
37 15 0.31
38 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (37 bp):
ATATAATTTTGGAAAACATTTTTTGAAACATATTAAT
Found at i:345564 original size:37 final size:36
Alignment explanation
Indices: 345470--345666 Score: 158
Period size: 37 Copynumber: 5.6 Consensus size: 36
345460 TATATATTCA
*
345470 ATATAGTTTTGGAAAATATTTTTTGATAAC--ATATAAT
1 ATATAGTTTT-GAAAACA-TTTTTGA-AACATATATAAT
* * * *
345507 ATTTAATTTTGAAAACATTTTTGAAATATATTTAAT
1 ATATAGTTTTGAAAACATTTTTGAAACATATATAAT
** **
345543 ATATAGTTTTGGAAAACATTTTAAAAATGTATATAAT
1 ATATAGTTTT-GAAAACATTTTTGAAACATATATAAT
* *
345580 ATATAGTTTTGAAAATATTTTTG-AA-A-ATGT-AT
1 ATATAGTTTTGAAAACATTTTTGAAACATATATAAT
* ** *
345612 ATATGGTTTTGAAAACATTTTAAAAACGTATAT-AT
1 ATATAGTTTTGAAAACATTTTTGAAACATATATAAT
345647 A-ATAGTTTTTGAAAACATTT
1 ATATAG-TTTTGAAAACATTT
345667 AATATATAGT
Statistics
Matches: 130, Mismatches: 23, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
32 21 0.16
33 5 0.04
34 5 0.04
35 29 0.22
36 30 0.23
37 40 0.31
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (36 bp):
ATATAGTTTTGAAAACATTTTTGAAACATATATAAT
Found at i:345661 original size:24 final size:24
Alignment explanation
Indices: 345629--345680 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
345619 TTTGAAAACA
*
345629 TTTTAAAAACGTAT-ATATAATAGT
1 TTTTAAAAACATATAATAT-ATAGT
* *
345653 TTTTGAAAACATTTAATATATAGT
1 TTTTAAAAACATATAATATATAGT
345677 TTTT
1 TTTT
345681 TATATATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTTAAAAACATATAATATATAGT
Found at i:345772 original size:14 final size:14
Alignment explanation
Indices: 345753--345803 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
345743 TGGTTTTTCG
345753 TTATTATTATATTA
1 TTATTATTATATTA
345767 TTATTATTATA-T-
1 TTATTATTATATTA
345779 TTA-TATTAGTATTA
1 TTATTATTA-TATTA
345793 TT-TTATT-TATT
1 TTATTATTATATT
345804 TAACCATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 5 0.15
12 9 0.27
13 2 0.06
14 17 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:345782 original size:20 final size:20
Alignment explanation
Indices: 345759--345802 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
345749 TTCGTTATTA
*
345759 TTATATTATTATTATTATAT
1 TTATATTAGTATTATTATAT
*
345779 TTATATTAGTATTATTTTAT
1 TTATATTAGTATTATTATAT
345799 TTAT
1 TTAT
345803 TTAACCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATATTAGTATTATTATAT
Found at i:353732 original size:201 final size:201
Alignment explanation
Indices: 353413--353872 Score: 609
Period size: 201 Copynumber: 2.3 Consensus size: 201
353403 GGGCTATATG
* * * * *
353413 TCAATGAAAACTTTTGAGTTCAATTTCATTCAGCTCGAGGGCGTATCAACCACATGGTAGCAGCG
1 TCAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCATATCAACCACATGGTAGCAGCA
* * * * *
353478 AGGAACTACTTTTCGTTTGAAGTTTAAACTAAGGTCTTTAAGTCAATAAGAAGACC-AGGGTTGG
66 AGAAACTACTTTTCGTTTGAAGTTTAAACTAAGATCTTTAAATCAAGAAGAAGACCTA-GATTGG
* * * * *
353542 CTGCGATTTAGCAACAAGGAACTATCTCCCAACCGAATTTACAACATAGCTTAAGTCGAGAAAAG
130 ATGCGATTTAGCAACAAGAAACTATCTCCCAACCAAATTTACAACATAACTTAAGTCGAGAAAAA
*
353607 TTATCTA
195 TTATCCA
* * * *
353614 TTAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGACATATCAACTACATGGTAGCATCA
1 TCAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCATATCAACCACATGGTAGCAGCA
*
353679 AGAAACTACTTTTCAG-TTGAAGTTTAAACTGAGATCTTTAAATCAAGAAGAAGACCTAGATTGG
66 AGAAACTACTTTTC-GTTTGAAGTTTAAACTAAGATCTTTAAATCAAGAAGAAGACCTAGATTGG
* * *
353743 ATGTGATTTAGCAACAAGAAACTATCTCCCAGCCAAATTTACAGCATAACTTAAGTCGAGAAAAA
130 ATGCGATTTAGCAACAAGAAACTATCTCCCAACCAAATTTACAACATAACTTAAGTCGAGAAAAA
* *
353808 TTTTCCG
195 TTATCCA
* * * * *
353815 TCAACGAAAATTTTCGAGTTTGATTCCATTCAGCTCGAGGGCATATCAATCGCATGGT
1 TCAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCATATCAACCACATGGT
353873 GTACTTTCTA
Statistics
Matches: 223, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
201 221 0.99
202 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (201 bp):
TCAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCATATCAACCACATGGTAGCAGCA
AGAAACTACTTTTCGTTTGAAGTTTAAACTAAGATCTTTAAATCAAGAAGAAGACCTAGATTGGA
TGCGATTTAGCAACAAGAAACTATCTCCCAACCAAATTTACAACATAACTTAAGTCGAGAAAAAT
TATCCA
Found at i:354306 original size:2 final size:2
Alignment explanation
Indices: 354299--354337 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
354289 TTTTATTTAG
354299 TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
354338 GTTTTGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:354436 original size:36 final size:35
Alignment explanation
Indices: 354331--354635 Score: 253
Period size: 36 Copynumber: 8.3 Consensus size: 35
354321 ATTATATAAT
*
354331 ATATATAGTTTTGGAAAATATTTTTTCGATAACATATATA
1 ATATATAGTTTT-GAAAACA-TTTTT-GA-AA-ATATATA
*
354371 ATATATA-ATTTG--AA-ATTTTTGAAATATATATA
1 ATATATAGTTTTGAAAACATTTTTGAAA-ATATATA
354403 ATATATAGTTTTGAAAACATTTTTTGAAAATATATATA
1 ATATATAGTTTTGAAAACA-TTTTTG-AAA-ATATATA
* * *
354441 ATATATAGTTCTGGAAAATATTTTT-AAAACGTATACA
1 ATATATAGTT-TTGAAAACATTTTTGAAAA--TATATA
* *
354478 ATATGTAGTTTTGAAAACA-TTTTAAAAACGTATATA
1 ATATATAGTTTTGAAAACATTTTTGAAAA--TATATA
* **
354514 ATATATAGTTTTGAAAATATTTTTGAAAACGTATA
1 ATATATAGTTTTGAAAACATTTTTGAAAATATATA
* ** *
354549 ATATATGGTTTTGAAAACATTTTAAAAAATGTATA
1 ATATATAGTTTTGAAAACATTTTTGAAAATATATA
*
354584 TATAATATAGTTTTTGAAAACGTATTTTTGAAAACATATA
1 -AT-ATATAG-TTTTGAAAAC--ATTTTTGAAAATATATA
*
354624 ATATATAATTTT
1 ATATATAGTTTT
354636 TTTAATATTT
Statistics
Matches: 223, Mismatches: 26, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
32 16 0.07
33 6 0.03
34 5 0.02
35 42 0.19
36 43 0.19
37 37 0.17
38 42 0.19
39 12 0.05
40 20 0.09
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (35 bp):
ATATATAGTTTTGAAAACATTTTTGAAAATATATA
Found at i:354555 original size:73 final size:73
Alignment explanation
Indices: 354365--354629 Score: 291
Period size: 73 Copynumber: 3.6 Consensus size: 73
354355 TTCGATAACA
* *
354365 TATATAATATATA-ATTTG--AA-ATTTTTGAAATATATATAATATA--TAGTTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAATATTTTTGAAA-ACATATAATATATGTAGTTTTGAAAACA--
* *
354424 TTTTGAAAATA
63 TTTTAAAAATG
* *
354435 TATATAATATATAGTTCTGGAAAATATTTTT-AAAACGTATACA-ATATGTAGTTTTGAAAACAT
1 TATATAATATATAGTT-TTGAAAATATTTTTGAAAACATATA-ATATATGTAGTTTTGAAAACAT
*
354498 TTTAAAAACG
64 TTTAAAAATG
*
354508 TATATAATATATAGTTTTGAAAATATTTTTGAAAACGTATAATATATG--GTTTTGAAAACATTT
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAACATATAATATATGTAGTTTTGAAAACATTT
354571 TAAAAAATG
66 T-AAAAATG
354580 TATAT-ATAATATAGTTTTTGAAAACGTATTTTTGAAAACATATAATATAT
1 TATATAAT-ATATAG-TTTTGAAAA--TATTTTTGAAAACATATAATATAT
354630 AATTTTTTTA
Statistics
Matches: 170, Mismatches: 10, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
70 13 0.08
71 19 0.11
72 33 0.19
73 56 0.33
74 6 0.04
75 43 0.25
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (73 bp):
TATATAATATATAGTTTTGAAAATATTTTTGAAAACATATAATATATGTAGTTTTGAAAACATTT
TAAAAATG
Found at i:354746 original size:4 final size:4
Alignment explanation
Indices: 354739--354777 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
354729 TTTATATTGC
354739 TATT TA-T TATT TATTT TATTT TATT TATT TATT TATT TA
1 TATT TATT TATT TA-TT TA-TT TATT TATT TATT TATT TA
354778 ACCATTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 21 0.64
5 9 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:354773 original size:17 final size:17
Alignment explanation
Indices: 354713--354776 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
354703 TATGGTTTAG
*
354713 TATTATTATTATATTATT
1 TATT-TTATTTTATTATT
354731 TATATTGCTA-TTTATTATT
1 TAT-TT--TATTTTATTATT
354750 TATTTTATTTTATTTATT
1 TATTTTATTTTA-TTATT
354768 TA-TTTATTT
1 TATTTTATTT
354777 AACCATTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
16 2 0.05
17 11 0.28
18 13 0.32
19 12 0.30
20 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTATTTTATTATT
Found at i:358540 original size:21 final size:20
Alignment explanation
Indices: 358494--358541 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
358484 GATTCTGACT
*
358494 ATCGCATTACGATTTTTCAA
1 ATCGCATTACGATTTTCCAA
* *
358514 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTACGATTTTCC-AA
358536 ATCGCA
1 ATCGCA
358542 ATGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.82
22 3 0.14
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
ATCGCATTACGATTTTCCAA
Found at i:358793 original size:22 final size:22
Alignment explanation
Indices: 358767--358830 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
358757 CGACATCCGT
*
358767 CCCCATCTCTGACGAAATCAGC
1 CCCCATCTCCGACGAAATCAGC
*
358789 CCCCATCTCCGACGATAA-CAGT
1 CCCCATCTCCGACGA-AATCAGC
* *
358811 CTCCATCTCCGGCGAAATCA
1 CCCCATCTCCGACGAAATCA
358831 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.27, C:0.41, G:0.14, T:0.19
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCAGC
Found at i:359175 original size:14 final size:14
Alignment explanation
Indices: 359156--359189 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
359146 ACTATCGCAA
359156 TGCGATTC-TGTCGT
1 TGCGATTCTTG-CGT
359170 TGCGATTCTTGCGT
1 TGCGATTCTTGCGT
359184 TGCGAT
1 TGCGAT
359190 AGTTAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.09, C:0.21, G:0.29, T:0.41
Consensus pattern (14 bp):
TGCGATTCTTGCGT
Found at i:359271 original size:73 final size:74
Alignment explanation
Indices: 359167--359323 Score: 271
Period size: 73 Copynumber: 2.1 Consensus size: 74
359157 GCGATTCTGT
*
359167 CGTTGCGATTCTTGCGTTGCGATAGTTAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTT
1 CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTT
359232 TCA-TTTCG
66 TCATTTTCG
* *
359240 CGTTGCGATTCTTGCGTTGTGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTT
1 CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTT
359305 TCATTTTCG
66 TCATTTTCG
*
359314 TGTTGCGATT
1 CGTTGCGATT
359324 TTAAGTTTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 65 0.82
74 14 0.18
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.43
Consensus pattern (74 bp):
CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTT
TCATTTTCG
Found at i:359279 original size:34 final size:34
Alignment explanation
Indices: 359167--359282 Score: 117
Period size: 34 Copynumber: 3.3 Consensus size: 34
359157 GCGATTCTGT
*
359167 CGTTGCGATTCTTGCGTTGCGATAGTTAAATTCG
1 CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
* ** *
359201 CGTTGCGATAATCATTTTCGTGTTGCGATTTTC-ATTTCG
1 CGTTGCGAT--TC---TT-GCGTTGCGATAGTCAAATTCG
*
359240 CGTTGCGATTCTTGCGTTGTGATAGTCAAATTCG
1 CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
359274 CGTTGCGAT
1 CGTTGCGAT
359283 AGTCATTTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
33 10 0.15
34 25 0.38
36 2 0.03
37 2 0.03
39 16 0.25
40 10 0.15
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (34 bp):
CGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
Found at i:359286 original size:20 final size:20
Alignment explanation
Indices: 359180--359322 Score: 102
Period size: 20 Copynumber: 7.5 Consensus size: 20
359170 TGCGATTCTT
* *
359180 GCGTTGCGATAGTTAAATTC
1 GCGTTGCGATAGTCAATTTC
* *
359200 GCGTTGCGATAATCATTTTC
1 GCGTTGCGATAGTCAATTTC
* **
359220 GTGTTGCGATTTTC-ATTTC
1 GCGTTGCGATAGTCAATTTC
359239 GCGTTGCGAT--TC---TT-
1 GCGTTGCGATAGTCAATTTC
* *
359253 GCGTTGTGATAGTCAAATTC
1 GCGTTGCGATAGTCAATTTC
*
359273 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAATTTC
* ** *
359293 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATAGTCAATTTC
*
359313 GTGTTGCGAT
1 GCGTTGCGAT
359323 TTTAAGTTTC
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 2 0.02
17 2 0.02
19 15 0.15
20 71 0.70
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATAGTCAATTTC
Found at i:359325 original size:20 final size:20
Alignment explanation
Indices: 359197--359322 Score: 104
Period size: 20 Copynumber: 6.7 Consensus size: 20
359187 GATAGTTAAA
*
359197 TTCGCGTTGCGATAATCATT
1 TTCGCGTTGCGATATTCATT
* *
359217 TTCGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATATTCATT
359236 TTCGCGTTGCG--ATTC---
1 TTCGCGTTGCGATATTCATT
* * **
359251 TT-GCGTTGTGATAGTCAAA
1 TTCGCGTTGCGATATTCATT
*
359270 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATATTCATT
* *
359290 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATATTCATT
*
359310 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
359323 TTTAAGTTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
14 7 0.08
15 2 0.02
16 3 0.03
17 3 0.03
19 13 0.15
20 59 0.68
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGATATTCATT
Found at i:359332 original size:20 final size:20
Alignment explanation
Indices: 359289--359332 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
359279 CGATAGTCAT
* *
359289 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
359309 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
359329 TTTC
1 TTTC
359333 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:361081 original size:20 final size:20
Alignment explanation
Indices: 361056--361175 Score: 96
Period size: 20 Copynumber: 5.6 Consensus size: 20
361046 AGAATAGTTT
361056 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
361076 ACTATCGCAACGAGAAAATCG
1 ACTATCGCAATGCGAAAAT-G
* * * *
361097 CAACAACAAAATCACAACGCGAAAATA
1 -----AC--TATCGCAATGCGAAAATG
361124 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
361144 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
361164 ACTATCGCAATG
1 ACTATCGCAATG
361176 AAAGAATTGC
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
20 61 0.76
21 1 0.01
22 2 0.03
26 2 0.03
28 14 0.17
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:361098 original size:14 final size:14
Alignment explanation
Indices: 361079--361122 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
361069 GAAAATGACT
361079 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
* *
361093 ATCGCAACAACAAA
1 ATCGCAACGAGAAA
* *
361107 ATCACAACGCGAAA
1 ATCGCAACGAGAAA
361121 AT
1 AT
361123 AACTATCGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:361246 original size:20 final size:20
Alignment explanation
Indices: 361218--361366 Score: 235
Period size: 20 Copynumber: 7.5 Consensus size: 20
361208 GCGATTCTCT
*
361218 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
361238 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
**
361258 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
361278 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
361298 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
361318 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
361338 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
361358 CGTTGCGAT
1 CGTTGCGAT
361367 TTTAAGTTTC
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 116 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:361958 original size:43 final size:41
Alignment explanation
Indices: 361850--361958 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
361840 GACTCACCTG
* *
361850 TCATCGTTCAAGAGG-CCTCCCCTATCGTTCAAGAGGCTCCTA
1 TCATCGTTCAAGAGGTCCT-CCC-ACCGTTCAAGAGGCCCCTA
**
361892 TCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCCACTA
1 TCATCGTTCAAGAGGT--CCTCCCACCGTTCAAGAGGCCC-CTA
*
361935 TCATCGTTGAAGAGGTCCATCCCA
1 TCATCGTTCAAGAGGTCC-TCCCA
361959 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
41 1 0.02
42 27 0.50
43 21 0.39
44 5 0.09
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (41 bp):
TCATCGTTCAAGAGGTCCTCCCACCGTTCAAGAGGCCCCTA
Found at i:363358 original size:14 final size:14
Alignment explanation
Indices: 363339--363374 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
363329 ATTGTTTAAT
363339 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
363353 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
363367 TGATTTGT
1 TGATTTGT
363375 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:363589 original size:20 final size:20
Alignment explanation
Indices: 363564--363651 Score: 142
Period size: 20 Copynumber: 4.4 Consensus size: 20
363554 CTCTCATTGG
363564 GATAGTCATTTCCGCGTTGC
1 GATAGTCATTTCCGCGTTGC
363584 GATAGTCATTTCCGCGTTGC
1 GATAGTCATTTCCGCGTTGC
* *
363604 GATAGTCATTTCTGTGTTGC
1 GATAGTCATTTCCGCGTTGC
363624 GATAGTCATATT-CGCGTTGC
1 GATAGTCAT-TTCCGCGTTGC
363644 GATAGTCA
1 GATAGTCA
363652 AATGAATGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
GATAGTCATTTCCGCGTTGC
Found at i:366029 original size:89 final size:88
Alignment explanation
Indices: 365879--366055 Score: 345
Period size: 89 Copynumber: 2.0 Consensus size: 88
365869 TCAGGGTTAT
365879 ATGAATTACAGAATGGATGTTCAACATGTTCATTTACAGTCGTAACTTCCTCCTCATTATCATCA
1 ATGAATTACAGAATGGATGTTCAACATGTTCATTTACAGTCGTAACTTCCTCCTCATTATCATCA
365944 ACAACATCTTCCTCGGCAACGGC
66 ACAACATCTTCCTCGGCAACGGC
365967 ATGAATTACAGAATGGATGTTTCAACATGTTCATTTACAGTCGTAACTTCCTCCTCATTATCATC
1 ATGAATTACAGAATGGATG-TTCAACATGTTCATTTACAGTCGTAACTTCCTCCTCATTATCATC
366032 AACAACATCTTCCTCGGCAACGGC
65 AACAACATCTTCCTCGGCAACGGC
366056 TGTTTCATCA
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 19 0.22
89 69 0.78
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (88 bp):
ATGAATTACAGAATGGATGTTCAACATGTTCATTTACAGTCGTAACTTCCTCCTCATTATCATCA
ACAACATCTTCCTCGGCAACGGC
Found at i:367058 original size:20 final size:20
Alignment explanation
Indices: 367033--367095 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
367023 TCAGTATTGT
367033 GATAGTCAGAATCGCGTTGC
1 GATAGTCAGAATCGCGTTGC
*
367053 GATAGTCAGAATCTCGTTGC
1 GATAGTCAGAATCGCGTTGC
*
367073 GATAGTCAGATTCGCGTTGC
1 GATAGTCAGAATCGCGTTGC
367093 GAT
1 GAT
367096 TTACATATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (20 bp):
GATAGTCAGAATCGCGTTGC
Done.