Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008742.1 Hibiscus syriacus cultivar Beakdansim tig00111831_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: 77456
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2642 original size:12 final size:12
Alignment explanation
Indices: 2625--2654 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2615 GGCTAAGGAA
2625 ATATATATATGT
1 ATATATATATGT
2637 ATATATATATGT
1 ATATATATATGT
2649 ATATAT
1 ATATAT
2655 GATAATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:2739 original size:22 final size:22
Alignment explanation
Indices: 2713--2758 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2703 CGTACACATT
*
2713 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2735 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2757 AA
1 AA
2759 CATATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:4288 original size:3 final size:3
Alignment explanation
Indices: 4270--4319 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
4260 GCAAATGTAA
* *
4270 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
4316 AAT A
1 AAT A
4320 TTTTAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:8401 original size:110 final size:110
Alignment explanation
Indices: 8208--8772 Score: 842
Period size: 110 Copynumber: 5.1 Consensus size: 110
8198 CTCGAGCCAA
*
8208 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* * *
8273 TCCTTTGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* *
8318 TTGTTTGTTGATAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
*
8383 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACCGAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * *
8428 TTGTTTGTTGACAGACAGTCGCCCCTTCGGTGTGAAGTTAAGCTTGTGTTGTCTCGAGTCCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* * * **
8493 TCCTTCACTGTGAAGTTAAAATTGATTCTGAATGAAACTGAAATT
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * * *
8538 TTTTTTGTTAACAGTCAGTCGCCCCTTCGATGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* * * * *
8603 TCCTTTGTTATGAAGTTGAAATTGACTCTGAATAAAATTGAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
* * * *
8648 TTGTTTGTTGACAGTCAGTCGCCCTTTGGCTGTGAAGTTGAGCTTGTGTTGTGTCGAGTCTAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
** *
8713 TATTTCGCTGTGAAGTTGAAATTAACTCTGAATGAAACTGAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
*
8758 TTGTTTGTTAACAGT
1 TTGTTTGTTGACAGT
8773 AAACTTTTCT
Statistics
Matches: 404, Mismatches: 51, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 404 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
Found at i:14312 original size:13 final size:13
Alignment explanation
Indices: 14294--14326 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
14284 AACAGTGATC
14294 GGTTCGGGTTATT
1 GGTTCGGGTTATT
14307 GGTTCGGGTTATT
1 GGTTCGGGTTATT
*
14320 GGATCGG
1 GGTTCGG
14327 TCATGGGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.42, T:0.39
Consensus pattern (13 bp):
GGTTCGGGTTATT
Found at i:15365 original size:2 final size:2
Alignment explanation
Indices: 15358--15395 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15348 GTGTCTTCAA
15358 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
15396 TGTACTAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17496 original size:13 final size:14
Alignment explanation
Indices: 17478--17508 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
17468 TTTATGTAAT
17478 TTTAATTTAAT-CC
1 TTTAATTTAATGCC
17491 TTTAATTTAATGCC
1 TTTAATTTAATGCC
17505 TTTA
1 TTTA
17509 TTTTCAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTAATTTAATGCC
Found at i:22308 original size:21 final size:22
Alignment explanation
Indices: 22270--22310 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22260 TTAAAAATTA
22270 TAAAGGAAGTACCGATACTCTT
1 TAAAGGAAGTACCGATACTCTT
*
22292 TAAAGGAA-TATCGATACTC
1 TAAAGGAAGTACCGATACTC
22311 CCTGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCTT
Found at i:22383 original size:20 final size:20
Alignment explanation
Indices: 22340--22383 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
22330 TTTTGTAGAA
* * *
22340 AAATTATCCCCAACGGCTCC
1 AAATCATCCCCAACGACTAC
*
22360 AAATCATCCCCAACGACTAG
1 AAATCATCCCCAACGACTAC
22380 AAAT
1 AAAT
22384 GACCAGAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.34, G:0.09, T:0.18
Consensus pattern (20 bp):
AAATCATCCCCAACGACTAC
Found at i:27627 original size:21 final size:21
Alignment explanation
Indices: 27602--27657 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
27592 TACATATATC
* *
27602 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
27623 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
27644 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
27658 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:27662 original size:21 final size:21
Alignment explanation
Indices: 27619--27662 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27609 ATTTTCTTAG
*
27619 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
27640 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
27661 CA
1 CA
27663 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:29658 original size:64 final size:62
Alignment explanation
Indices: 29525--29683 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 62
29515 TAATGAAGGT
* * *
29525 ATGCATCGATGCACTACACCATGCATCGATGAATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGAATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
29590 ATGCATCGATGCACTCCTTATGCATCGATGAATAAATTCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGAATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
29654 ATGCATCGATGCACTGCATGTGCATCGATG
1 ATGCATCGATGCACT-CCTATGCATCGATG
29684 CACCTTAAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 55 0.67
65 23 0.28
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGAATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:36738 original size:76 final size:75
Alignment explanation
Indices: 36575--36775 Score: 278
Period size: 76 Copynumber: 2.7 Consensus size: 75
36565 GTTGTACAAG
* * * * * *
36575 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGTA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCA
**
36639 AAACTGTTTA
66 AAACCATTTA
* *
36649 GAGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG-C
36714 AAAACCATTTA
65 AAAACCATTTA
* *
36725 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTG
36776 TAATTTTTGG
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 16 0.14
75 39 0.35
76 57 0.51
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCA
AAACCATTTA
Found at i:37135 original size:30 final size:30
Alignment explanation
Indices: 37089--37160 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
37079 TCCCCCTTAC
37089 TTTAACACTTCTTCAATTTATTATGTAAAACA
1 TTTAACAC--CTTCAATTTATTATGTAAAACA
37121 TTTAACACCTTCAATTTATTATGTAAAACA
1 TTTAACACCTTCAATTTATTATGTAAAACA
37151 TTTAACACCT
1 TTTAACACCT
37161 ATTCTTCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAACACCTTCAATTTATTATGTAAAACA
Found at i:39379 original size:21 final size:21
Alignment explanation
Indices: 39353--39392 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39343 CAGAACCCCA
*
39353 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
39374 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
39393 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:43286 original size:22 final size:21
Alignment explanation
Indices: 43244--43283 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43234 AGTTTGTTTT
*
43244 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
43265 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
43284 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:45303 original size:76 final size:77
Alignment explanation
Indices: 45202--45400 Score: 278
Period size: 76 Copynumber: 2.6 Consensus size: 77
45192 CCGTTGTACA
* * * *
45202 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
***
45266 -CAAAATTGTTT
66 CCAAAACCATTT
* * *
45277 AGGGGGGAATTGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
45342 CCAAAACCATTT
66 CCAAAACCATTT
*
45354 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
45401 ATCTGTAATT
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 18 0.16
76 83 0.75
77 9 0.08
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:46219 original size:18 final size:17
Alignment explanation
Indices: 46196--46229 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46186 CAGTCTGTTT
46196 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
46214 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
46230 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:48718 original size:2 final size:2
Alignment explanation
Indices: 48711--48765 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
48701 TAAAATCAGA
*
48711 AT AT AT AT AC 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
48753 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
48766 GTTGAGGATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49358 original size:2 final size:2
Alignment explanation
Indices: 49347--49375 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
49337 TAAATTAAAC
49347 TA TA -A 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
49376 ATTATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:49381 original size:8 final size:9
Alignment explanation
Indices: 49347--49382 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
49337 TAAATTAAAC
49347 TATAATATA
1 TATAATATA
49356 TAT-ATATA
1 TATAATATA
49364 TAT-ATATA
1 TATAATATA
49372 TATAAT-TA
1 TATAATATA
49380 TAT
1 TAT
49383 CAAAATGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 21 0.81
9 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATAATATA
Found at i:50015 original size:16 final size:17
Alignment explanation
Indices: 49991--50023 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
49981 TACATATTCT
*
49991 TAAATAAATA-AAAATA
1 TAAAAAAATACAAAATA
50007 TAAAAAAATACAAAATA
1 TAAAAAAATACAAAATA
50024 GTATTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAATACAAAATA
Found at i:50495 original size:22 final size:24
Alignment explanation
Indices: 50460--50511 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
50450 AAAGTAATTT
* *
50460 TTAAAAATATTTATGAAA-AATAC
1 TTAAAAAGATTTATCAAATAATAC
*
50483 TTAAAAAGA-TTATCAAATAATAT
1 TTAAAAAGATTTATCAAATAATAC
50506 TTAAAA
1 TTAAAA
50512 TTTATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAAAAAGATTTATCAAATAATAC
Found at i:52441 original size:20 final size:20
Alignment explanation
Indices: 52404--52453 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
52394 AATTTGATAA
*
52404 AAAAAATCGAAAATCGATCT
1 AAAAAATCGAAAACCGATCT
*
52424 AAAAAATCGATAACCGA--T
1 AAAAAATCGAAAACCGATCT
*
52442 AAAAAGTCGAAA
1 AAAAAATCGAAA
52454 CTGATTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (20 bp):
AAAAAATCGAAAACCGATCT
Found at i:52858 original size:45 final size:45
Alignment explanation
Indices: 52794--52892 Score: 189
Period size: 45 Copynumber: 2.2 Consensus size: 45
52784 TTAGCTTTCT
52794 GGTTTTTTTTTTGGCAAATATTCAATATATTTCTTTTACGATTAG
1 GGTTTTTTTTTTGGCAAATATTCAATATATTTCTTTTACGATTAG
*
52839 GGTTTTTTTTTTGGCAAATATTCAATATATTTCTTTTATGATTAG
1 GGTTTTTTTTTTGGCAAATATTCAATATATTTCTTTTACGATTAG
52884 GGTTTTTTT
1 GGTTTTTTT
52893 ATGAAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.22, C:0.07, G:0.14, T:0.57
Consensus pattern (45 bp):
GGTTTTTTTTTTGGCAAATATTCAATATATTTCTTTTACGATTAG
Found at i:53804 original size:19 final size:19
Alignment explanation
Indices: 53775--53814 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
53765 TTTATAATTA
*
53775 TAAAAAAATTA-GATTTTT
1 TAAAAAAATTATAATTTTT
53793 TAAAATAAATTATAATTTTT
1 TAAAA-AAATTATAATTTTT
53813 TA
1 TA
53815 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAAAAAATTATAATTTTT
Found at i:53944 original size:31 final size:31
Alignment explanation
Indices: 53886--53944 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
53876 GGTTATAGTC
**
53886 TAAACACATAAAAATATAACGTCAAAAATAT
1 TAAACACATAAAAATATAACGAAAAAAATAT
*
53917 TAAACACCTAAAAATATAACGAAAAAAA
1 TAAACACATAAAAATATAACGAAAAAAA
53945 GTTTGACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.64, C:0.14, G:0.03, T:0.19
Consensus pattern (31 bp):
TAAACACATAAAAATATAACGAAAAAAATAT
Found at i:54506 original size:2 final size:2
Alignment explanation
Indices: 54499--54592 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
54489 GATAATTTCT
54499 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
54541 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
54583 TA TA TA TA TA
1 TA TA TA TA TA
54593 GGTATTCTAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65176 original size:31 final size:31
Alignment explanation
Indices: 65088--65213 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 31
65078 GAACCTCAGC
* * * *
65088 AACTGTCCATAGGTCCCGAAGAACCTATGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
65119 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
65150 AACTATCCATATGTCCCGAACG-ACATAGGTA
1 AACTATCCATATGTCCCGAA-GAACATAGGTA
* * *
65181 ATCATGTCCATATGTCTCGAA-AGACATAGGTA
1 AAC-TATCCATATGTCCCGAAGA-ACATAGGTA
65213 A
1 A
65214 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:65630 original size:19 final size:18
Alignment explanation
Indices: 65590--65630 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
65580 TATATATATC
*
65590 CATACAAAACATATCACG
1 CATACAAAACATATAACG
*
65608 CATACAATAACATATAACT
1 CATACAA-AACATATAACG
65627 CATA
1 CATA
65631 TCACACTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (18 bp):
CATACAAAACATATAACG
Found at i:67210 original size:28 final size:29
Alignment explanation
Indices: 67139--67210 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
67129 ATGAAATTAT
*
67139 TAAAATTCCTAAAAAACACCTTAAATTCC
1 TAAAAATCCTAAAAAACACCTTAAATTCC
* *
67168 TGAAAAT-CTAAAAAA-ACTCCTAAATTCC
1 TAAAAATCCTAAAAAACAC-CTTAAATTCC
*
67196 TAAAAATCCTGAAAA
1 TAAAAATCCTAAAAA
67211 TCATAAACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.06
28 23 0.64
29 11 0.31
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.25
Consensus pattern (29 bp):
TAAAAATCCTAAAAAACACCTTAAATTCC
Found at i:73098 original size:46 final size:47
Alignment explanation
Indices: 73044--73133 Score: 155
Period size: 46 Copynumber: 1.9 Consensus size: 47
73034 CCGAATAAAT
*
73044 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTTTTGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
73090 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
73134 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 28 0.68
47 13 0.32
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Done.