Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006273.1 Hibiscus syriacus cultivar Beakdansim tig00014962_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: 71247
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:56 original size:14 final size:14
Alignment explanation
Indices: 37--66 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27 TCAAGTTTAC
37 AAACATCGAAGTTA
1 AAACATCGAAGTTA
51 AAACATCGAAGTTA
1 AAACATCGAAGTTA
65 AA
1 AA
67 TATAATGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
AAACATCGAAGTTA
Found at i:243 original size:21 final size:21
Alignment explanation
Indices: 217--264 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
207 AAATGAGTTT
*
217 CTCTCTCGATTTCTATCGCTG
1 CTCTCTCGACTTCTATCGCTG
* *
238 CTCTCTCTACTTCTTTCGCTG
1 CTCTCTCGACTTCTATCGCTG
259 CTCTCT
1 CTCTCT
265 TACTTCTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.38, G:0.10, T:0.46
Consensus pattern (21 bp):
CTCTCTCGACTTCTATCGCTG
Found at i:5562 original size:46 final size:45
Alignment explanation
Indices: 5504--5638 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 45
5494 AAATCAATTT
*
5504 CATAATTAAAATGCATGAACGGGTGCATTAAGGCATGAAAGGATGC
1 CATAATT-AAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
5550 CATAACTTAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAA-TTAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*** *
5596 CATAA--AAATGCATGAAATCATGCATTAAGGAATGAAAGGATGC
1 CATAATTAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
5639 ATTAAGGCAT
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 34 0.41
46 47 0.57
47 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.21
Consensus pattern (45 bp):
CATAATTAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:5637 original size:63 final size:65
Alignment explanation
Indices: 5564--5704 Score: 214
Period size: 66 Copynumber: 2.2 Consensus size: 65
5554 ACTTAAATGC
* *
5564 ATGAACGGATGCATTAAGGCATGAAAGGATGCCAT-A-AAAATGCATGAAATCATGCATTAAGGA
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATAAAATGCATGAAATCATGCATTAAGCA
*
5627 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAGC
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA-TAAAATGCATGAAATCATGCATTAAGC
*
5692 C
65 A
*
5693 ATGGAAGGATGC
1 ATGAAAGGATGC
5705 CATAAGTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 34 0.49
64 1 0.01
66 35 0.50
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (65 bp):
ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATAAAATGCATGAAATCATGCATTAAGCA
Found at i:5646 original size:109 final size:111
Alignment explanation
Indices: 5518--5749 Score: 353
Period size: 109 Copynumber: 2.1 Consensus size: 111
5508 ATTAAAATGC
* * *
5518 ATGAACGGGTGCATTAAGGCATGAAAGGATGCCATAACTT-AAATGCATGAACGGATGCATTAAG
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA-TTAAAATGCATGAAAGGATGCATTAAG
*
5582 GCATGAAAGGATGCCAT-A-AAAATGCATGAAATCATGCATTAAGGA
65 CCATGAAAGGATGCCATAAGAAAATGCATGAAATCATGCATTAAGGA
*
5627 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAGC
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGC
* * *
5692 CATGGAAGGATGCCATAAGTAAAATGCATGAAATGATGCATTAAGGC
66 CATGAAAGGATGCCATAAG-AAAATGCATGAAATCATGCATTAAGGA
5739 ATGAAAGGATG
1 ATGAAAGGATG
5750 AAATAAGTAA
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
108 2 0.02
109 72 0.65
110 1 0.01
112 36 0.32
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (111 bp):
ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGC
CATGAAAGGATGCCATAAGAAAATGCATGAAATCATGCATTAAGGA
Found at i:5684 original size:46 final size:46
Alignment explanation
Indices: 5627--5761 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
5617 GCATTAAGGA
* *
5627 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGC
1 ATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAGTAAAATGC
* *
5673 ATGAAATGATGCATTAAGCCATGGAAGGATGCCATAAGTAAAATGC
1 ATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAGTAAAATGC
**
5719 ATGAAATGATGCATTAAGGCATGAAAGGATGAAATAAGTAAAA
1 ATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAGTAAAA
5762 GGTATGAATG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAGTAAAATGC
Found at i:5736 original size:26 final size:26
Alignment explanation
Indices: 5645--5795 Score: 87
Period size: 26 Copynumber: 6.3 Consensus size: 26
5635 ATGCATTAAG
*
5645 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAAGTAAAAT
*
5671 GCATGAAATGATG-CAT---T--AA-
1 GCATGAAAGGATGCCATAAGTAAAAT
*
5690 GCCATGGAAGGATGCCATAAGTAAAAT
1 G-CATGAAAGGATGCCATAAGTAAAAT
* *
5717 GCATGAAATGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAGTAAAAT
** *
5737 GCATGAAAGGATGAAATAAGTAAAAG
1 GCATGAAAGGATGCCATAAGTAAAAT
* * *
5763 GTATGAATGGATGTCATAAGTAAAA-
1 GCATGAAAGGATGCCATAAGTAAAAT
*
5788 GTATGAAA
1 GCATGAAA
5796 AAAGACCATG
Statistics
Matches: 98, Mismatches: 13, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
19 1 0.01
20 26 0.27
21 5 0.05
22 2 0.02
24 2 0.02
25 13 0.13
26 48 0.49
27 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.23
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAGTAAAAT
Found at i:5742 original size:20 final size:20
Alignment explanation
Indices: 5516--5749 Score: 144
Period size: 20 Copynumber: 10.7 Consensus size: 20
5506 TAATTAAAAT
* *
5516 GCATGAACGGGTGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
5536 GCATGAAAGGATGCCATAACTTAAAT
1 GCATGAAAGGATG-C---A-TT-AAG
*
5562 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
5582 GCATGAAAGGATGCCATAAAAAT
1 GCATGAAAGGATG-CAT--TAAG
**
5605 GCATGAAATCATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
5625 GAATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
5645 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
5671 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
5691 CCATGGAAGGATGCCATAAGTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
5717 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
5737 GCATGAAAGGATG
1 GCATGAAAGGATG
5750 AAATAAGTAA
Statistics
Matches: 165, Mismatches: 28, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
20 82 0.50
21 10 0.06
22 8 0.05
23 13 0.08
24 5 0.03
25 7 0.04
26 40 0.24
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:5756 original size:20 final size:20
Alignment explanation
Indices: 5717--5756 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5707 TAAGTAAAAT
* * *
5717 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGAAATAAG
5737 GCATGAAAGGATGAAATAAG
1 GCATGAAAGGATGAAATAAG
5757 TAAAAGGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGAAATAAG
Found at i:6980 original size:18 final size:18
Alignment explanation
Indices: 6957--6992 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6947 TTTAAGTTAA
6957 CTATTTTTATGAACGTGT
1 CTATTTTTATGAACGTGT
6975 CTATTTTTATGAACGTGT
1 CTATTTTTATGAACGTGT
6993 TCATGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
CTATTTTTATGAACGTGT
Found at i:9353 original size:22 final size:22
Alignment explanation
Indices: 9325--9367 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9315 TTAATTTCTG
9325 TTTGGGTGCTA-TTTGTGTAAAC
1 TTTGGGTGCTAGTTT-TGTAAAC
*
9347 TTTGGGTGTTAGTTTTGTAAA
1 TTTGGGTGCTAGTTTTGTAAA
9368 TATTTGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.19, C:0.05, G:0.28, T:0.49
Consensus pattern (22 bp):
TTTGGGTGCTAGTTTTGTAAAC
Found at i:13136 original size:66 final size:66
Alignment explanation
Indices: 13030--13161 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
13020 CCTAAGTAAG
* * * * * *
13030 ACCTTCATTACCCGAGCGTATCACTTCTTCATCTCGTGAACCAAGTTGTTCATCAGCACCAGCAA
1 ACCTTCATTACCAGAGCGTATCACATCTTCATCTCCTGAACCAAGCTGTTCACCAGAACCAGCAA
13095 C
66 C
*
13096 ACCTTCATTACCAGA-CTGTGTCACATCTGT-ATCTCCTGAACCAAGCTGTTCACCAGAACCAGC
1 ACCTTCATTACCAGAGC-GTATCACATCT-TCATCTCCTGAACCAAGCTGTTCACCAGAACCAGC
13159 AAC
64 AAC
13162 GCTAGAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.02
66 55 0.96
67 1 0.02
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (66 bp):
ACCTTCATTACCAGAGCGTATCACATCTTCATCTCCTGAACCAAGCTGTTCACCAGAACCAGCAA
C
Found at i:15565 original size:24 final size:24
Alignment explanation
Indices: 15538--15583 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15528 AGTAAACGGA
15538 CATATCAGAAATCAAAACAGAATT
1 CATATCAGAAATCAAAACAGAATT
* *
15562 CATATCAGATATCAAAATAGAA
1 CATATCAGAAATCAAAACAGAA
15584 ATCAGAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (24 bp):
CATATCAGAAATCAAAACAGAATT
Found at i:15594 original size:24 final size:24
Alignment explanation
Indices: 15543--15595 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
15533 ACGGACATAT
* * *
15543 CAGAAATCAAAACAGAATTCATAT
1 CAGAAATCAAAACAGAAATCAGAA
* *
15567 CAGATATCAAAATAGAAATCAGAA
1 CAGAAATCAAAACAGAAATCAGAA
15591 CAGAA
1 CAGAA
15596 TTCTGATCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAAATCAGAA
Found at i:15595 original size:12 final size:12
Alignment explanation
Indices: 15543--15595 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
15533 ACGGACATAT
15543 CAGAAATCAAAA
1 CAGAAATCAAAA
* * *
15555 CAGAATTCATAT
1 CAGAAATCAAAA
*
15567 CAGATATCAAAA
1 CAGAAATCAAAA
* *
15579 TAGAAATCAGAA
1 CAGAAATCAAAA
15591 CAGAA
1 CAGAA
15596 TTCTGATCAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAAATCAAAA
Found at i:29488 original size:48 final size:48
Alignment explanation
Indices: 29432--29523 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
29422 AACGAAGATA
*
29432 TTAGAAATCAAAACAAAATTCTTATC-AGATATCAAAACAGAATTCAGG
1 TTAGAAATCAAAACAAAATTCTGATCAAG-TATCAAAACAGAATTCAGG
* * *
29480 TTAGAAATCAGAACAGAATTCTGATCAAGTATCATAACAGAATT
1 TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATT
29524 AAAATCAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (48 bp):
TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATTCAGG
Found at i:29489 original size:24 final size:24
Alignment explanation
Indices: 29431--29500 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
29421 AAACGAAGAT
* **
29431 ATTAGAAATCAAAACAAAATTCTT
1 ATTAGAAATCAAAACAGAATTCAG
* *
29455 ATCAGATATCAAAACAGAATTCAG
1 ATTAGAAATCAAAACAGAATTCAG
* *
29479 GTTAGAAATCAGAACAGAATTC
1 ATTAGAAATCAAAACAGAATTC
29501 TGATCAAGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (24 bp):
ATTAGAAATCAAAACAGAATTCAG
Found at i:33130 original size:48 final size:48
Alignment explanation
Indices: 33074--33165 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
33064 AACGAAGATA
*
33074 TTAGAAATCAAAACAAAATTCTTATC-AGATATCAAAACAGAATTCAGG
1 TTAGAAATCAAAACAAAATTCTGATCAAG-TATCAAAACAGAATTCAGG
* * *
33122 TTAGAAATCAGAACAGAATTCTGATCAAGTATCATAACAGAATT
1 TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATT
33166 AAAATCAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (48 bp):
TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATTCAGG
Found at i:33131 original size:24 final size:24
Alignment explanation
Indices: 33073--33142 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
33063 AAACGAAGAT
* **
33073 ATTAGAAATCAAAACAAAATTCTT
1 ATTAGAAATCAAAACAGAATTCAG
* *
33097 ATCAGATATCAAAACAGAATTCAG
1 ATTAGAAATCAAAACAGAATTCAG
* *
33121 GTTAGAAATCAGAACAGAATTC
1 ATTAGAAATCAAAACAGAATTC
33143 TGATCAAGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (24 bp):
ATTAGAAATCAAAACAGAATTCAG
Found at i:36770 original size:48 final size:48
Alignment explanation
Indices: 36714--36805 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
36704 AACGAAGATA
*
36714 TTAGAAATCAAAACAAAATTCTTATC-AGATATCAAAACAGAATTCAGG
1 TTAGAAATCAAAACAAAATTCTGATCAAG-TATCAAAACAGAATTCAGG
* * *
36762 TTAGAAATCAGAACAGAATTCTGATCAAGTATCATAACAGAATT
1 TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATT
36806 AAAATCAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (48 bp):
TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATTCAGG
Found at i:36771 original size:24 final size:24
Alignment explanation
Indices: 36713--36782 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
36703 AAACGAAGAT
* **
36713 ATTAGAAATCAAAACAAAATTCTT
1 ATTAGAAATCAAAACAGAATTCAG
* *
36737 ATCAGATATCAAAACAGAATTCAG
1 ATTAGAAATCAAAACAGAATTCAG
* *
36761 GTTAGAAATCAGAACAGAATTC
1 ATTAGAAATCAAAACAGAATTC
36783 TGATCAAGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (24 bp):
ATTAGAAATCAAAACAGAATTCAG
Found at i:40407 original size:48 final size:48
Alignment explanation
Indices: 40351--40442 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
40341 AACGAAGATA
*
40351 TTAGAAATCAAAACAAAATTCTTATC-AGATATCAAAACAGAATTCAGG
1 TTAGAAATCAAAACAAAATTCTGATCAAG-TATCAAAACAGAATTCAGG
* * *
40399 TTAGAAATCAGAACAGAATTCTGATCAAGTATCATAACAGAATT
1 TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATT
40443 AAAATCAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (48 bp):
TTAGAAATCAAAACAAAATTCTGATCAAGTATCAAAACAGAATTCAGG
Found at i:40408 original size:24 final size:24
Alignment explanation
Indices: 40350--40419 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
40340 AAACGAAGAT
* **
40350 ATTAGAAATCAAAACAAAATTCTT
1 ATTAGAAATCAAAACAGAATTCAG
* *
40374 ATCAGATATCAAAACAGAATTCAG
1 ATTAGAAATCAAAACAGAATTCAG
* *
40398 GTTAGAAATCAGAACAGAATTC
1 ATTAGAAATCAAAACAGAATTC
40420 TGATCAAGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (24 bp):
ATTAGAAATCAAAACAGAATTCAG
Found at i:44016 original size:24 final size:24
Alignment explanation
Indices: 43989--44060 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
43979 GTAAACGGAG
43989 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* *
44013 ATATCAGATATCAAAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
** *
44037 AGGTCAGAAATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
44061 TGATAAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:51664 original size:10 final size:10
Alignment explanation
Indices: 51649--51673 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
51639 CAAATATAAC
51649 CTAAATGAAA
1 CTAAATGAAA
51659 CTAAATGAAA
1 CTAAATGAAA
51669 CTAAA
1 CTAAA
51674 ATGTTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGAAA
Found at i:61369 original size:40 final size:39
Alignment explanation
Indices: 61313--61390 Score: 147
Period size: 40 Copynumber: 2.0 Consensus size: 39
61303 AGGTTTATAG
61313 TACACTTCGTGTATATGGTGGGCACGACCTTATATGTAA
1 TACACTTCGTGTATATGGTGGGCACGACCTTATATGTAA
61352 TACACTTCGGTGTATATGGTGGGCACGACCTTATATGTA
1 TACACTTC-GTGTATATGGTGGGCACGACCTTATATGTA
61391 GCACTACGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (39 bp):
TACACTTCGTGTATATGGTGGGCACGACCTTATATGTAA
Found at i:61545 original size:44 final size:44
Alignment explanation
Indices: 61495--61647 Score: 256
Period size: 44 Copynumber: 3.5 Consensus size: 44
61485 GTAACCATGC
61495 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
61539 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
* * *
61583 AAATAAGCTTACGAGC--ATGAAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
61626 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
61648 TTAATAAATG
Statistics
Matches: 102, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
42 6 0.06
43 33 0.32
44 60 0.59
45 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
Done.