Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002145.1 Hibiscus syriacus cultivar Beakdansim tig00004384_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: 85646
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:6039 original size:40 final size:40
Alignment explanation
Indices: 5995--6071 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
5985 ATATAAATGA
*
5995 TAGTGACACATAATTTATTGCACCCTTA-AAAATCATATGC
1 TAGTGAAACATAATTTATTGCACCC-TAGAAAATCATATGC
** *
6035 TAGTGAAAGGTAATTTATTGCGCCCTAGAAAATCATA
1 TAGTGAAACATAATTTATTGCACCCTAGAAAATCATA
6072 AAGATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (40 bp):
TAGTGAAACATAATTTATTGCACCCTAGAAAATCATATGC
Found at i:7082 original size:25 final size:25
Alignment explanation
Indices: 7054--7140 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
7044 ATTAGTCTTT
7054 TAATC-TCATCAAAAAAAGCAATCAG
1 TAATCATCATC-AAAAAAGCAATCAG
* * ** * **
7079 TAATCGTCACCCGTAAAAGTAATCTTT
1 TAATCATCA-TCAAAAAAGCAATC-AG
*
7106 TAATC-TCATCAGAAAAGCAATCAG
1 TAATCATCATCAAAAAAGCAATCAG
7130 TAATCATCATC
1 TAATCATCATC
7141 CGTAGAAAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
24 5 0.11
25 20 0.43
26 15 0.33
27 6 0.13
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (25 bp):
TAATCATCATCAAAAAAGCAATCAG
Found at i:7144 original size:51 final size:52
Alignment explanation
Indices: 7039--7144 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 52
7029 AAGTTACCAT
* * *
7039 GTAAAATTAGTCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCGTCACCC
1 GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
* *
7091 GTAAAAGTAATCTTTTAATCTCATC-AGAAAAGCAATCAGTAATCATCATCC
1 GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
7142 GTA
1 GTA
7145 GAAAACAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 26 0.53
52 23 0.47
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (52 bp):
GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
Found at i:8225 original size:34 final size:34
Alignment explanation
Indices: 8187--8266 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
8177 TATTTCAATG
8187 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
1 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
8221 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
1 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
*
8255 AATAAATTTTAA
1 AATTAATTTTAA
8267 ATAACTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (34 bp):
AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
Found at i:16904 original size:15 final size:17
Alignment explanation
Indices: 16879--16910 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16869 ATAGCCAAAG
16879 TTTAGATCTGA-TCAAT
1 TTTAGATCTGATTCAAT
16895 TTTA-ATCTGATTCAAT
1 TTTAGATCTGATTCAAT
16911 CTTATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTAGATCTGATTCAAT
Found at i:19013 original size:2 final size:2
Alignment explanation
Indices: 19006--19030 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18996 ACTTTTTAAT
19006 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
19031 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19035 original size:2 final size:2
Alignment explanation
Indices: 19030--19074 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19020 TCTCTCTCTC
19030 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
19072 TA T
1 TA T
19075 TCATCAGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22362 original size:3 final size:3
Alignment explanation
Indices: 22354--22380 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22344 CAACAGCAAC
22354 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
22381 GGGGGAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23611 original size:56 final size:56
Alignment explanation
Indices: 23549--23725 Score: 275
Period size: 56 Copynumber: 3.2 Consensus size: 56
23539 TAGAGATCCA
* **
23549 AAAAATAGGGGTTTCGAAATCGAGTATATATATCAGTTGTTGATATTAATAAGCAT
1 AAAAATAGGGGTTTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
*
23605 AAAAATAGGGGTCTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
1 AAAAATAGGGGTTTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
* * * *
23661 AAAAATAGGGGATCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACAT
1 AAAAATAGGGGTTTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
23717 -AAAATAGGG
1 AAAAATAGGG
23726 CCCCGAAATC
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 9 0.08
56 103 0.92
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (56 bp):
AAAAATAGGGGTTTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCAT
Found at i:23863 original size:32 final size:30
Alignment explanation
Indices: 23827--23903 Score: 73
Period size: 33 Copynumber: 2.4 Consensus size: 30
23817 TTTTTTTTTG
* *
23827 TAAAATTATTTAAATAATAAATTATATAATTT
1 TAAAA-TATATAAA-AATAAATGATATAATTT
*
23859 TAAAATATATAAAATTAAATGATATAAAATATT
1 TAAAATATATAAAAATAAATGATAT--AAT-TT
*
23892 TAAAAAATATAA
1 TAAAATATATAA
23904 TAATTTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 10 0.26
31 7 0.18
32 8 0.21
33 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TAAAATATATAAAAATAAATGATATAATTT
Found at i:23867 original size:15 final size:15
Alignment explanation
Indices: 23844--23904 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
23834 ATTTAAATAA
*
23844 TAAATTATATAATTT
1 TAAAATATATAATTT
**
23859 TAAAATATATAAAAT
1 TAAAATATATAATTT
*
23874 TAAATGATATAAAATATT
1 TAAA--ATATATAAT-TT
*
23892 TAAAAAATATAAT
1 TAAAATATATAAT
23905 AATTTTTTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 16 0.46
16 7 0.20
17 7 0.20
18 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TAAAATATATAATTT
Found at i:23874 original size:17 final size:17
Alignment explanation
Indices: 23845--23910 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
23835 TTTAAATAAT
*
23845 AAAT-TATATAATTTTA
1 AAATATATAAAATTTTA
23861 AAATATATAAAA--TT-
1 AAATATATAAAATTTTA
23875 AAATGATATAAAATATTTA
1 AAAT-ATATAAAAT-TTTA
*
23894 AAAAATATAATAATTTT
1 AAATATATAA-AATTTT
23911 TTCTTTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 4 0.10
15 10 0.24
16 4 0.10
17 6 0.15
18 11 0.27
19 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATATATAAAATTTTA
Found at i:24298 original size:20 final size:21
Alignment explanation
Indices: 24273--24365 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
24263 TTTTCCCAAT
*
24273 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24293 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
24314 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24334 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24355 TCGCAATGCGA
1 TCGCAATGCGA
24366 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:24318 original size:41 final size:41
Alignment explanation
Indices: 24273--24365 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
24263 TTTTCCCAAT
24273 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24314 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24355 TCGCAATGCGA
1 TCGCAATGCGA
24366 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:24378 original size:41 final size:41
Alignment explanation
Indices: 24292--24426 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
24282 GAATAAGTAA
* *
24292 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
24333 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
24374 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
24415 TTCGCAACGCGA
1 ATCGCAACGCGA
24427 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:24379 original size:20 final size:20
Alignment explanation
Indices: 24354--24448 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
24344 AATTGGGAAA
*
24354 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
24374 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
24395 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
24415 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
24435 TTCGCAACGCGATA
1 ATCGCAACGCGATA
24449 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:25362 original size:21 final size:21
Alignment explanation
Indices: 25336--25380 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25326 GATTTCTGGG
* *
25336 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
25357 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
25378 CAA
1 CAA
25381 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:26876 original size:29 final size:30
Alignment explanation
Indices: 26774--26873 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
26764 GGTTCTTCGG
*
26774 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
26805 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
26835 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
26864 GACCTCTGGA
1 GACCTCTGGA
26874 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:30021 original size:21 final size:21
Alignment explanation
Indices: 29995--30039 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29985 GATTTCTGGG
* *
29995 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
30016 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
30037 CAA
1 CAA
30040 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:30109 original size:23 final size:22
Alignment explanation
Indices: 30065--30109 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
30055 AATGCCAGAG
*
30065 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
30087 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
30110 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:31394 original size:31 final size:31
Alignment explanation
Indices: 31321--31422 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
31311 AGAGTCGAGG
*
31321 GTTTGCCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
31352 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
31384 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
31415 GTTTACCT
1 GTTTACCT
31423 GGTTCTTCGG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 33 0.55
32 27 0.45
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:31441 original size:30 final size:29
Alignment explanation
Indices: 31330--31451 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 29
31320 GGTTTGCCTA
* *
31330 TGTTCTACGGAACATATGGACAGTTTTACC
1 TGTTCTTCGGGACATATGGACAG-TTTACC
* * *
31360 TATGTCTTTCGAGACATATGGACAGTATACC
1 TGT-TC-TTCGGGACATATGGACAGTTTACC
** *
31391 TATGTTCTAAGGAACATATGGACAGTTTACC
1 --TGTTCTTCGGGACATATGGACAGTTTACC
*
31422 TGGTTCTTCGGGACCTATGGACAGTTTACC
1 T-GTTCTTCGGGACATATGGACAGTTTACC
31452 GAGGATCTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
29 1 0.01
30 26 0.36
31 26 0.36
32 17 0.24
33 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (29 bp):
TGTTCTTCGGGACATATGGACAGTTTACC
Found at i:31529 original size:29 final size:30
Alignment explanation
Indices: 31433--31529 Score: 142
Period size: 30 Copynumber: 3.2 Consensus size: 30
31423 GGTTCTTCGG
*
31433 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
31464 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
31494 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
31523 GACCTCT
1 GACCTCT
31530 AGATAGGTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.24
30 35 0.56
31 12 0.19
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:34680 original size:21 final size:21
Alignment explanation
Indices: 34654--34698 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34644 GATTTCTGGG
* *
34654 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34675 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34696 CAA
1 CAA
34699 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34768 original size:23 final size:22
Alignment explanation
Indices: 34724--34768 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34714 AATGCCAGAG
*
34724 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
34746 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
34769 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:36091 original size:31 final size:31
Alignment explanation
Indices: 35983--36114 Score: 142
Period size: 31 Copynumber: 4.2 Consensus size: 31
35973 AGAGTCGAGG
*
35983 GTTTGCCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
36014 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
36046 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
** * * *
36077 GTTTACCTGGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
36108 GTTTACC
1 GTTTACC
36115 GAGGATCTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
31 57 0.68
32 27 0.32
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:36131 original size:31 final size:29
Alignment explanation
Indices: 36069--36190 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 29
36059 CTAAGGAACA
* ***
36069 TATGGACAGTTTACCTGGGTTCTTCGGGACC
1 TATGGACAG-TTACC-GGGATCTTTATGACC
36100 TATGGACAGTTTACCGAGGATCTTTATGACC
1 TATGGACAG-TTACCG-GGATCTTTATGACC
*
36131 TCTGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCG-GGATCTTTATGACC
* * * *
36161 TCTGGATAGTTACCGGGGTCTTTGTGACC
1 TATGGACAGTTACCGGGATCTTTATGACC
36190 T
1 T
36191 CTAGATAGGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.16
30 36 0.44
31 33 0.40
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (29 bp):
TATGGACAGTTACCGGGATCTTTATGACC
Found at i:36192 original size:29 final size:30
Alignment explanation
Indices: 36096--36192 Score: 142
Period size: 30 Copynumber: 3.2 Consensus size: 30
36086 GGTTCTTCGG
*
36096 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
36127 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
36157 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36186 GACCTCT
1 GACCTCT
36193 AGATAGGTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.24
30 35 0.56
31 12 0.19
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:38582 original size:18 final size:18
Alignment explanation
Indices: 38561--38605 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
38551 TCTACTTCGG
38561 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
38579 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
38597 GAGCCATCA
1 GAGCCATCA
38606 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:39134 original size:20 final size:20
Alignment explanation
Indices: 39087--39141 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
39077 TAGTTTACTT
*
39087 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
39107 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
39127 TCGCAACGCCAAAAT
1 TCGCAACGCGAAAAT
39142 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:39145 original size:14 final size:14
Alignment explanation
Indices: 39126--39181 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
39116 GGAAATGGCT
39126 ATCGCAACGCCAAA
1 ATCGCAACGCCAAA
*
39140 ATCGCAACGCGAAATGAA
1 ATCGCAACGC--CA--AA
*
39158 ATCGCAACGACAAA
1 ATCGCAACGCCAAA
39172 ATCGCAACGC
1 ATCGCAACGC
39182 GAAACACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 21 0.62
16 2 0.06
18 11 0.32
ACGTcount: A:0.43, C:0.30, G:0.18, T:0.09
Consensus pattern (14 bp):
ATCGCAACGCCAAA
Found at i:39172 original size:32 final size:33
Alignment explanation
Indices: 39106--39185 Score: 117
Period size: 32 Copynumber: 2.4 Consensus size: 33
39096 GAAAATGACT
** *
39106 ATCGCAACGCGGAAATGGCTATCGCAACGCCAAA
1 ATCGCAACGC-GAAATGGAAATCGCAACGACAAA
39140 ATCGCAACGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGGAAATCGCAACGACAAA
39172 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
39186 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 28 0.65
33 5 0.12
34 10 0.23
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGGAAATCGCAACGACAAA
Found at i:39192 original size:19 final size:18
Alignment explanation
Indices: 39136--39202 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 18
39126 ATCGCAACGC
39136 CAAAATCGCAACGCGAAA
1 CAAAATCGCAACGCGAAA
**
39154 TGAAATCGCAA--CG--A
1 CAAAATCGCAACGCGAAA
39168 CAAAATCGCAACGCGAAA
1 CAAAATCGCAACGCGAAA
*
39186 CACAAATCGCAATGCGA
1 CA-AAATCGCAACGCGA
39203 TTTGTTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.26
16 4 0.10
18 12 0.31
19 13 0.33
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
CAAAATCGCAACGCGAAA
Found at i:39269 original size:39 final size:33
Alignment explanation
Indices: 39183--39251 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
39173 TCGCAACGCG
39183 AAACACAAATCGCAATGCGATTTGTTCAAACTC
1 AAACACAAATCGCAATGCGATTTGTTCAAACTC
*
39216 AAACACAAATCGCAATGCGATTTGTTCAAAATC
1 AAACACAAATCGCAATGCGATTTGTTCAAACTC
39249 AAA
1 AAA
39252 TCAAACACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (33 bp):
AAACACAAATCGCAATGCGATTTGTTCAAACTC
Found at i:40383 original size:24 final size:24
Alignment explanation
Indices: 40356--40409 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40346 GTATTCGAAA
* *
40356 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
40380 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
40404 TTTGAT
1 TTTGAT
40410 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:40601 original size:12 final size:12
Alignment explanation
Indices: 40584--40608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40574 ATATAATCCT
40584 GAAGAAGAAAAA
1 GAAGAAGAAAAA
40596 GAAGAAGAAAAA
1 GAAGAAGAAAAA
40608 G
1 G
40609 TCCCCGAAGA
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:42926 original size:19 final size:19
Alignment explanation
Indices: 42904--43034 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
42894 GGAAATTACT
42904 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
42923 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
42937 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
42956 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
42970 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
42989 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
43003 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43022 ATCGCAACGCGAA
1 ATCGCAATGCGAA
43035 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:42946 original size:33 final size:33
Alignment explanation
Indices: 42904--43030 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
42894 GGAAATTACT
42904 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
42937 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
42969 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
43003 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
43031 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:43011 original size:66 final size:66
Alignment explanation
Indices: 42905--43037 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
42895 GAAATTACTA
*
42905 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
42970 T
66 T
*
42971 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
43036 T
66 T
43037 T
1 T
43038 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:43052 original size:19 final size:20
Alignment explanation
Indices: 43030--43073 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43020 AAATCGCAAC
43030 GCGA-ATTTAATTTCGCGTT
1 GCGATATTTAATTTCGCGTT
* *
43049 GCGATTTTTATTTTCGCGTT
1 GCGATATTTAATTTCGCGTT
43069 GCGAT
1 GCGAT
43074 TCCCTCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATATTTAATTTCGCGTT
Found at i:43063 original size:20 final size:20
Alignment explanation
Indices: 43035--43074 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43025 GCAACGCGAA
43035 TTTAATTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
*
43055 TTTATTTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
43075 CCCTCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTAATTTCGCGTTGCGATT
Found at i:43228 original size:13 final size:14
Alignment explanation
Indices: 43212--43247 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
43202 CATCAATTAA
43212 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
43225 ACAAATCACCTTTT
1 ACAAATCAACTTTT
43239 ACAAATCAA
1 ACAAATCAA
43248 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:44339 original size:42 final size:42
Alignment explanation
Indices: 44293--44376 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
44283 CGATGACATT
* * *
44293 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
44335 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
44377 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:46462 original size:33 final size:33
Alignment explanation
Indices: 46405--46503 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
46395 ACGAGATAAT
*
46405 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
46439 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
46472 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
46504 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:46545 original size:19 final size:19
Alignment explanation
Indices: 46380--46539 Score: 133
Period size: 20 Copynumber: 8.8 Consensus size: 19
46370 TCTTTTGGTT
*
46380 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
46399 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
46419 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
46437 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
46453 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
46471 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
46486 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
46506 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
46525 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
46540 TTGCGATTTT
Statistics
Matches: 114, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.04
19 38 0.33
20 45 0.39
21 2 0.02
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:46557 original size:19 final size:19
Alignment explanation
Indices: 46535--46585 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
46525 GAAATGAAAA
* *
46535 TCGCATTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGATT
*
46554 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTGATT
46573 TCGCGTTGCGATT
1 TCGCGTTGCGATT
46586 ATCTCGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTGATT
Found at i:47163 original size:20 final size:20
Alignment explanation
Indices: 47138--47190 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
47128 GCGCTATGTA
47138 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
47158 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
47178 TATCTCGTTGCGA
1 AATCGCGTTGCGA
47191 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:47250 original size:21 final size:21
Alignment explanation
Indices: 47221--47313 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
47211 ATAGTAAGTA
47221 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
47242 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
47262 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
47283 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
47303 TCGCATTGCGA
1 TCGCATTGCGA
47314 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:47251 original size:41 final size:41
Alignment explanation
Indices: 47160--47294 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
47150 AAAGTCAGAA
* * * * ** *
47160 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
47200 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
47242 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
47283 TCGCGTTGCGAT
1 TCGCGTTGCGAT
47295 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:47295 original size:41 final size:41
Alignment explanation
Indices: 47221--47313 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
47211 ATAGTAAGTA
47221 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
47262 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
47303 TCGCATTGCGA
1 TCGCATTGCGA
47314 ATTGGGAAAA
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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:47915 original size:3 final size:3
Alignment explanation
Indices: 47907--47935 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
47897 ATAACCCATA
47907 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
47936 GGCTACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:56576 original size:20 final size:21
Alignment explanation
Indices: 56535--56577 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
56525 GATATAATCT
* *
56535 TAAAAATAAATAATTAAGTAA
1 TAAAAATAAATAATAAAATAA
56556 TAAAAATAAA-AATAAAATAA
1 TAAAAATAAATAATAAAATAA
56576 TA
1 TA
56578 GATAGGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAATAAATAATAAAATAA
Found at i:60741 original size:14 final size:14
Alignment explanation
Indices: 60722--60750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60712 AGCAAGGTTA
60722 AGAAGAAGAAAGAG
1 AGAAGAAGAAAGAG
60736 AGAAGAAGAAAGAG
1 AGAAGAAGAAAGAG
60750 A
1 A
60751 AGAGAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAAGAG
Found at i:60743 original size:17 final size:19
Alignment explanation
Indices: 60721--60757 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
60711 AAGCAAGGTT
60721 AAGAAG-AAGA-AAGAGAG
1 AAGAAGAAAGAGAAGAGAG
60738 AAGAAGAAAGAGAAGAGAG
1 AAGAAGAAAGAGAAGAGAG
60757 A
1 A
60758 TATTATCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAGAGAAGAGAG
Found at i:66049 original size:34 final size:34
Alignment explanation
Indices: 66006--66073 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
65996 TCAAGAGACA
*
66006 AAGTATGTGTTTTGGTGTCATTAGTATCTTCCTT
1 AAGTATGTGTCTTGGTGTCATTAGTATCTTCCTT
66040 AAGTATGTGTCTTGGTGTCATTAGTATCTTCCTT
1 AAGTATGTGTCTTGGTGTCATTAGTATCTTCCTT
66074 CTTGCTCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (34 bp):
AAGTATGTGTCTTGGTGTCATTAGTATCTTCCTT
Found at i:67453 original size:21 final size:21
Alignment explanation
Indices: 67424--67485 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
67414 ATAGTGACAA
67424 AAAAATTAATATATAAAATTT
1 AAAAATTAATATATAAAATTT
** *
67445 AATGATTAA-ATTAAAAAATTT
1 AAAAATTAATA-TATAAAATTT
*
67466 AAAAATATAATAAATAAAAT
1 AAAAAT-TAATATATAAAAT
67486 AAGAGAAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.65
22 9 0.29
23 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAATTAATATATAAAATTT
Found at i:67993 original size:16 final size:17
Alignment explanation
Indices: 67972--68022 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
67962 TTTTAATTTT
67972 ATTACT-TAACTTTCAA
1 ATTACTCTAACTTTCAA
67988 ATTACTCATAA-TTT--A
1 ATTACTC-TAACTTTCAA
*
68003 ATCACTCTAACTTTCAA
1 ATTACTCTAACTTTCAA
68020 ATT
1 ATT
68023 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
16 6 0.21
17 6 0.21
18 3 0.11
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTACTCTAACTTTCAA
Found at i:72820 original size:21 final size:22
Alignment explanation
Indices: 72770--72820 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
72760 CGGAAATTAG
72770 GTAGCAAAAGTAACATTTCCAA
1 GTAGCAAAAGTAACATTTCCAA
*
72792 -TAGCAAAATTAACATTT-CAA
1 GTAGCAAAAGTAACATTTCCAA
*
72812 GTAGAAAAA
1 GTAGCAAAA
72821 AATAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (22 bp):
GTAGCAAAAGTAACATTTCCAA
Done.