Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000281.1 Hibiscus syriacus cultivar Beakdansim tig00000520_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: 69660
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6446 original size:15 final size:15
Alignment explanation
Indices: 6426--6479 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
6416 TATGCTTGAA
6426 GAAGAAAAAAAAGAT
1 GAAGAAAAAAAAGAT
6441 GAAGAAAAAAAATGA-
1 GAAGAAAAAAAA-GAT
*
6456 AAAGAAAGAAAAA-AT
1 GAAGAAA-AAAAAGAT
*
6471 GAACAAAAA
1 GAAGAAAAA
6480 TATAGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 23 0.70
16 7 0.21
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (15 bp):
GAAGAAAAAAAAGAT
Found at i:6461 original size:30 final size:31
Alignment explanation
Indices: 6422--6479 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
6412 ATATTATGCT
*
6422 TGAAGAAGAAA-AAAAAGATGAAGAAAAAAAA
1 TGAAGAAGAAAGAAAAA-ATGAACAAAAAAAA
6453 TGAA-AAGAAAGAAAAAATGAACAAAAA
1 TGAAGAAGAAAGAAAAAATGAACAAAAA
6480 TATAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (31 bp):
TGAAGAAGAAAGAAAAAATGAACAAAAAAAA
Found at i:8171 original size:102 final size:105
Alignment explanation
Indices: 8011--8425 Score: 534
Period size: 113 Copynumber: 3.8 Consensus size: 105
8001 TTAGTAAAGA
8011 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
8076 AAGAAGGAAGAAGAAGTTCAT-AAG-A-TTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAAAGAATTTTAACCTTTTG
8113 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
8178 AAGAAGGAAGAAGAAGTTCATAACGAGAAGAACTTGTTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCAT----A-AAGAA--T-TTTAACCTTTTG
* *
8226 TTTTAATTCATCACTCGATGGATTAACTTTTACAGAGGAAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
*
8291 AAGATGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG
66 AAGAAGGAAGAAGAAGTTC---AT-A-AAGAA--T-TTTAACCTTTTG
* * * * * * *
8339 CTTT-AATTCATCACCCGATGGATCAGCATTTCCAGAAGAAGTTCATAATAAGAAGAATTCATCT
1 -TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCT
* *
8403 GAAGAATG-AGAAGAAATTCATAA
65 GAAGAAGGAAGAAGAAGTTCATAA
8426 TAAGAAGAAT
Statistics
Matches: 284, Mismatches: 14, Indels: 25
0.88 0.04 0.08
Matches are distributed among these distances:
102 86 0.30
107 1 0.00
108 4 0.01
109 3 0.01
112 10 0.04
113 175 0.62
114 3 0.01
116 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (105 bp):
TTTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAAAGAATTTTAACCTTTTG
Found at i:8704 original size:23 final size:23
Alignment explanation
Indices: 8676--8723 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
8666 TTTTTAATAT
8676 TTTTATTAAATATATTATTATTA
1 TTTTATTAAATATATTATTATTA
*** *
8699 TTTTATTTCTTTTATTATTATTA
1 TTTTATTAAATATATTATTATTA
8722 TT
1 TT
8724 AAATAATTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTAAATATATTATTATTA
Found at i:10027 original size:27 final size:27
Alignment explanation
Indices: 9953--10030 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
9943 TTAGTATATA
* * *
9953 ATTTTAATTATAT-TCATTGTTTAGTCAT
1 ATTTTAATTATATATGATTATTT--TAAT
*
9981 ATTTTAATTTTATATGATTATTTTAAT
1 ATTTTAATTATATATGATTATTTTAAT
*
10008 ATATTTAATTAT-TATTATTATTT
1 AT-TTTAATTATATATGATTATTT
10031 AATCATGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 15 0.36
28 20 0.48
29 7 0.17
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTTAATTATATATGATTATTTTAAT
Found at i:11697 original size:22 final size:22
Alignment explanation
Indices: 11646--11707 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
11636 CCGTTAACCA
11646 GACTCGTTGACTTTGACC--TTT
1 GACT-GTTGACTTTGACCAATTT
**
11667 GACCATTGACTTTGACCAATTT
1 GACTGTTGACTTTGACCAATTT
11689 GACTGTTGACTTTGACCAA
1 GACTGTTGACTTTGACCAA
11708 AAGTCAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.34
21 3 0.09
22 20 0.57
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (22 bp):
GACTGTTGACTTTGACCAATTT
Found at i:12492 original size:36 final size:36
Alignment explanation
Indices: 12448--12556 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
12438 ATGAAGTTTT
* ** *
12448 TATAGGTTCAGCTTCGATCAAACTGGTAATTCCTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
12484 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
* *
12520 TATAGTTTCAACACCGATCAAGCTGGTAATTCTTTA
1 TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
12556 T
1 T
12557 GGACCTAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (36 bp):
TATAGGTTCAACACCGATCAAGCTGGTAATTCCTTA
Found at i:19600 original size:16 final size:16
Alignment explanation
Indices: 19575--19609 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19565 TCATCGGATA
*
19575 TAATTTAAAAAAATAT
1 TAATTAAAAAAAATAT
*
19591 TAATTAAAAATAATAT
1 TAATTAAAAAAAATAT
19607 TAA
1 TAA
19610 AAAACTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTAAAAAAAATAT
Found at i:22192 original size:18 final size:18
Alignment explanation
Indices: 22169--22215 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
22159 ATTGGTATTA
22169 GGTATCGATACTCCTATG
1 GGTATCGATACTCCTATG
*
22187 GGTATCGAAACTCCTATG
1 GGTATCGATACTCCTATG
* *
22205 TGTATCAATAC
1 GGTATCGATAC
22216 CAATATTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (18 bp):
GGTATCGATACTCCTATG
Found at i:24635 original size:18 final size:17
Alignment explanation
Indices: 24614--24658 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
24604 TTTCATCCAT
*
24614 TTATTTTTATTTATATTG
1 TTATTATTATTT-TATTG
24632 TTATTATTATTTTATT-
1 TTATTATTATTTTATTG
*
24648 ATATTATTATT
1 TTATTATTATT
24659 AATAAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 4 0.16
18 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTATTATTTTATTG
Found at i:34660 original size:114 final size:114
Alignment explanation
Indices: 34004--34657 Score: 989
Period size: 114 Copynumber: 5.8 Consensus size: 114
33994 TCATAATAGA
*
34004 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCC-A
*
34069 AAACCAATCATTGGATTTGAAAGATCCATGTGCACATAGTAG-----A--
65 AAACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
* *
34112 AGACCCAATAGCATCTTCCGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCC-A
*
34177 AAACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGA
65 AAACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
34227 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
* * *
34292 AATCAATCATTGGATTTAAAAGATCTATGTGCTCATAGTAGAAATAAGG
66 AACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
* *
34341 AGGCCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
* * *
34406 AATCAATCATTGGATTTAAAAGATCCATGTGCTCATGGTAGAAATAAGG
66 AACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
* * * *
34455 AGGCCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATATGATCTGATTTGGTATGAATCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
* ** *
34520 AATCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGG
66 AACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
* * * * * *
34569 AGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCTCAG
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
*
34634 AACCAATCATTGGAGTTGAAAGAT
66 AACCAATCATTGGATTTGAAAGAT
34658 GAACTGCATG
Statistics
Matches: 508, Mismatches: 31, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
108 105 0.21
113 1 0.00
114 341 0.67
115 61 0.12
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (114 bp):
AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAA
AACCAATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGG
Found at i:36921 original size:22 final size:22
Alignment explanation
Indices: 36884--36938 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
36874 ATCTACACTC
* *
36884 TTCAAAGATGATAGATTCCCTT
1 TTCAAAAATGACAGATTCCCTT
* *
36906 TTTAAAAATGACAGATTCTCTT
1 TTCAAAAATGACAGATTCCCTT
*
36928 TTCAAAGATGA
1 TTCAAAAATGA
36939 AAGCTTTATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAAATGACAGATTCCCTT
Found at i:37545 original size:113 final size:113
Alignment explanation
Indices: 37375--38008 Score: 968
Period size: 113 Copynumber: 5.7 Consensus size: 113
37365 ATTTCCGGAA
*
37375 GAGTTCATAATGAGAAGAACTCATCT-------GAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* **
37433 CAACCTTTT-GCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGTC
66 CAA-ATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
*
37481 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
37546 CAACTTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
66 CAAATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
37594 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
37659 CAATTTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
66 CAAATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
*
37707 GAGTTCATAATGAGAAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
37772 CAAATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
66 CAAATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
37820 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * * ***
37885 CAACTTTTTGCGT-GAATTCATCATTCGATGGATCAACATTTCCAGAAA
66 CAAATTTTCGC-TCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
* * * *
37933 AAGTTCATAATGAGAAGAACTCATCTGAAG--AGGATAATAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
37996 CAACATTTT-GCTC
66 CAA-ATTTTCGCTC
38009 GACTCTATCG
Statistics
Matches: 494, Mismatches: 23, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
106 26 0.05
110 1 0.00
111 35 0.07
112 9 0.02
113 422 0.85
114 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAAATTTTCGCTCAAATTCATCACTCGATGGATCAGCATTGCCAGGTC
Found at i:38463 original size:18 final size:17
Alignment explanation
Indices: 38442--38486 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
38432 TTTTATCCAT
*
38442 TTATTTTTATTTATATTG
1 TTATTATTATTT-TATTG
38460 TTATTATTATTTTATT-
1 TTATTATTATTTTATTG
*
38476 ATATTATTATT
1 TTATTATTATT
38487 AATAAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 4 0.16
18 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTATTATTTTATTG
Found at i:38565 original size:17 final size:17
Alignment explanation
Indices: 38539--38578 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
38529 CAGTCCAGAT
*
38539 GACCCATTTACAAACCC
1 GACCCGTTTACAAACCC
*
38556 GACCCGTTTACAAGCCC
1 GACCCGTTTACAAACCC
*
38573 AACCCG
1 GACCCG
38579 GATCCAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.42, G:0.12, T:0.15
Consensus pattern (17 bp):
GACCCGTTTACAAACCC
Found at i:39936 original size:17 final size:19
Alignment explanation
Indices: 39908--39942 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39898 AATTTCTTTC
39908 ATTTTAATTATTA-TTTTT
1 ATTTTAATTATTACTTTTT
39926 ATTTT-ATTATTACTTTT
1 ATTTTAATTATTACTTTT
39943 GATATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTATTACTTTTT
Found at i:42566 original size:6 final size:6
Alignment explanation
Indices: 42557--42581 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42547 GGGATGATAA
42557 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
42582 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:42803 original size:12 final size:12
Alignment explanation
Indices: 42788--42822 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
42778 CGATTCTCGG
42788 CCCAATACCCGA
1 CCCAATACCCGA
*
42800 CCCAATACCCGG
1 CCCAATACCCGA
42812 CCCAATACCCG
1 CCCAATACCCG
42823 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:44250 original size:18 final size:18
Alignment explanation
Indices: 44228--44272 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
44218 AACCAAAAAT
*
44228 TTAAAATATAA-ATTTGA
1 TTAAAATATAAGATTTAA
44245 TATAAAAT-TAAGATTTAA
1 T-TAAAATATAAGATTTAA
44263 TTAAAA-ATAA
1 TTAAAATATAA
44273 TAATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
TTAAAATATAAGATTTAA
Found at i:55211 original size:7 final size:7
Alignment explanation
Indices: 55199--55227 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55189 GGGATCACGT
55199 TTGGTGC
1 TTGGTGC
55206 TTGGTGC
1 TTGGTGC
55213 TTGGTGC
1 TTGGTGC
55220 TTGGTGC
1 TTGGTGC
55227 T
1 T
55228 AGCTACAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.41, T:0.45
Consensus pattern (7 bp):
TTGGTGC
Found at i:56322 original size:14 final size:14
Alignment explanation
Indices: 56305--56370 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
56295 ATAAAATCTC
56305 TATTATAAATATAA
1 TATTATAAATATAA
56319 TATTATAAAT-TAA
1 TATTATAAATATAA
* *
56332 AAATATAATATTATAA
1 TATTATAA-A-TATAA
*
56348 -ATTAAAAATATAA
1 TATTATAAATATAA
56361 TATTATAAAT
1 TATTATAAAT
56371 TAAAAATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 14 0.33
14 20 0.47
15 6 0.14
16 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTATAAATATAA
Found at i:56330 original size:21 final size:21
Alignment explanation
Indices: 56306--56392 Score: 158
Period size: 21 Copynumber: 4.2 Consensus size: 21
56296 TAAAATCTCT
*
56306 ATTATAAATATAATATTATAA
1 ATTAAAAATATAATATTATAA
56327 ATTAAAAATATAATATTATAA
1 ATTAAAAATATAATATTATAA
56348 ATTAAAAATATAATATTATAA
1 ATTAAAAATATAATATTATAA
56369 ATTAAAAATATAATATT-TAA
1 ATTAAAAATATAATATTATAA
56389 ATTA
1 ATTA
56393 TATTTACATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
20 7 0.11
21 58 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAAAAATATAATATTATAA
Found at i:61632 original size:291 final size:288
Alignment explanation
Indices: 61078--61656 Score: 1072
Period size: 291 Copynumber: 2.0 Consensus size: 288
61068 TGACAAGCAC
61078 CGTATATTGTCAAATAAATAAGCCATTTTCTATAAGTAAGCTAAAAACGTAATAAAGAAGAAAAT
1 CGTATATTGTCAAATAAATAAGCCATTTTCTATAAGTAAGCTAAAAACGTAATAAAGAAGAAAAT
61143 GTCGATTCGTAAGAATTAAGGAGTTTTTGATGTTGAATGGTTTTGATTCTGATTTAAGTGAAAAA
66 GTCGATTCGTAAGAATTAAGGAGTTTTTGATGTTGAATGGTTTTGATTCTGATTTAAGTGAAAAA
*
61208 GCAAAAAAATGAGGGGATTTTAATTGAAATAGTAAAAAAAATGTAAAAAAAATAAAAGTAATTTT
131 GCAAAAAAATGAGGGGATTTTAATTGAAATAGTAAAAAAAATGTAAAAAAAATAAAAGTAATTGT
61273 GAAAAATTGAATATAGAAAACTAACGAAAGGAAATTTTGAGAAGAAAATCAATTAAATAAATAGC
196 GAAAAATTGAATATAGAAAACTAACGAAAGGAAATTTTGAGAAGAAAATCAATTAAATAAATAGC
61338 TTCAAGTCTCGCTTTGCCTCAATTCCAA
261 TTCAAGTCTCGCTTTGCCTCAATTCCAA
61366 CGTATATTGTCAAATAAATAAGCCATTTTCTCATATAAGTAAGCTAAAAACGTAATATAAAGAAG
1 CGTATATTGTCAAATAAATAAGCCA-TTT-TC-TATAAGTAAGCTAAAAACGT-A-ATAAAGAAG
61431 AAAATGTCGATTCGTAAGAATTAAGGAGTTTTTGATGTTGAATGGTTTTGATTCTGATTTAAGTG
61 AAAATGTCGATTCGTAAGAATTAAGGAGTTTTTGATGTTGAATGGTTTTGATTCTGATTTAAGTG
*
61496 AAAAAGCAAATAAATGAGGGGATTTTAATTGAAATAGT-AAAAAAATGT-AAAAAAATAAAAGTA
126 AAAAAGCAAAAAAATGAGGGGATTTTAATTGAAATAGTAAAAAAAATGTAAAAAAAATAAAAGTA
61559 ATTGTGAAAAATTGAATATAGAAAACTAACGAAAGGAAATTTTGAGAAGAAAATCAATTAAATAA
191 ATTGTGAAAAATTGAATATAGAAAACTAACGAAAGGAAATTTTGAGAAGAAAATCAATTAAATAA
*
61624 ATAGCTTCAGGTCTCGCTTTGCCTCAATTCCAA
256 ATAGCTTCAAGTCTCGCTTTGCCTCAATTCCAA
61657 TTGATCATCA
Statistics
Matches: 283, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
288 25 0.09
289 3 0.01
290 2 0.01
291 131 0.46
292 11 0.04
293 111 0.39
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (288 bp):
CGTATATTGTCAAATAAATAAGCCATTTTCTATAAGTAAGCTAAAAACGTAATAAAGAAGAAAAT
GTCGATTCGTAAGAATTAAGGAGTTTTTGATGTTGAATGGTTTTGATTCTGATTTAAGTGAAAAA
GCAAAAAAATGAGGGGATTTTAATTGAAATAGTAAAAAAAATGTAAAAAAAATAAAAGTAATTGT
GAAAAATTGAATATAGAAAACTAACGAAAGGAAATTTTGAGAAGAAAATCAATTAAATAAATAGC
TTCAAGTCTCGCTTTGCCTCAATTCCAA
Found at i:62399 original size:24 final size:24
Alignment explanation
Indices: 62347--62399 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
62337 AACAATTAAG
**
62347 GATAAAATCCTAAAACATTCAAAT
1 GATAAAATCCTAAAACAAACAAAT
* * *
62371 AATAAAATCCTAAAATAAACAAGT
1 GATAAAATCCTAAAACAAACAAAT
62395 GATAA
1 GATAA
62400 TTCCAAAAAT
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:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (24 bp):
GATAAAATCCTAAAACAAACAAAT
Found at i:63859 original size:21 final size:21
Alignment explanation
Indices: 63835--63883 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
63825 TAACAATTAT
*
63835 ATGTGATGAATTATTATGTTG
1 ATGTGATGAATTATTATATTG
63856 ATGTGATGAATTATTATATTG
1 ATGTGATGAATTATTATATTG
*
63877 ATATGAT
1 ATGTGAT
63884 ATTTCACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (21 bp):
ATGTGATGAATTATTATATTG
Done.