Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005684.1 Hibiscus syriacus cultivar Beakdansim tig00013295_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: 67521
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:691 original size:20 final size:20
Alignment explanation
Indices: 649--691 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
639 TTTACGTCAT
* * *
649 TGATCGTTACGGTGTTGACG
1 TGATAGTTACGATGATGACG
*
669 TGATAGTTACGATGATGATG
1 TGATAGTTACGATGATGACG
689 TGA
1 TGA
692 CAGTCCACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.35
Consensus pattern (20 bp):
TGATAGTTACGATGATGACG
Found at i:9729 original size:39 final size:39
Alignment explanation
Indices: 9668--9744 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
9658 TAAAGATTCA
** ** *
9668 TCATCTTCCCAGTTGTTGTCGGCTTCACCTTCGCCATCT
1 TCATCTTCCCAGTCATCATCGGCGTCACCTTCGCCATCT
* *
9707 TCATCTTCCCAGTCATCATCGGCGTCATCTTCGTCATC
1 TCATCTTCCCAGTCATCATCGGCGTCACCTTCGCCATC
9745 AACAAACTCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.13, C:0.36, G:0.14, T:0.36
Consensus pattern (39 bp):
TCATCTTCCCAGTCATCATCGGCGTCACCTTCGCCATCT
Found at i:25933 original size:3 final size:3
Alignment explanation
Indices: 25925--26015 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
25915 TTCATTTAAA
* * * * *
25925 TAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
25973 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
26016 CAAACGGGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:27330 original size:19 final size:19
Alignment explanation
Indices: 27286--27323 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
27276 TATAATTTAG
27286 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
27305 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
27323 T
1 T
27324 TGTTTTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:32707 original size:2 final size:2
Alignment explanation
Indices: 32700--32727 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32690 TTATCCTTTA
32700 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
32728 CCTTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33028 original size:1 final size:1
Alignment explanation
Indices: 33022--33061 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
33012 CTCATCCAGC
* * *
33022 AAAAAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33062 GGAAAATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:33037 original size:10 final size:10
Alignment explanation
Indices: 33022--33067 Score: 74
Period size: 10 Copynumber: 4.4 Consensus size: 10
33012 CTCATCCAGC
33022 AAAAAAAAAG
1 AAAAAAAAAG
33032 AAAAAAAAAG
1 AAAAAAAAAG
33042 AAAAAAAAAAG
1 -AAAAAAAAAG
33053 AAAAAAAAAGG
1 AAAAAAAAA-G
33064 AAAA
1 AAAA
33068 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.56
11 15 0.44
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:33038 original size:11 final size:11
Alignment explanation
Indices: 33022--33067 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
33012 CTCATCCAGC
33022 AAAAAAAAAG-
1 AAAAAAAAAGA
33032 AAAAAAAAAGA
1 AAAAAAAAAGA
33043 AAAAAAAAAGA
1 AAAAAAAAAGA
*
33054 AAAAAAAAGGA
1 AAAAAAAAAGA
33065 AAA
1 AAA
33068 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 10 0.29
11 24 0.71
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:33048 original size:21 final size:21
Alignment explanation
Indices: 33022--33067 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
33012 CTCATCCAGC
33022 AAAAAAAAAGAAAAAAAAAGA
1 AAAAAAAAAGAAAAAAAAAGA
*
33043 AAAAAAAAAGAAAAAAAAAGG
1 AAAAAAAAAGAAAAAAAAAGA
33064 AAAA
1 AAAA
33068 TTGAATCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAAAAGA
Found at i:35517 original size:83 final size:83
Alignment explanation
Indices: 35312--35780 Score: 795
Period size: 83 Copynumber: 5.7 Consensus size: 83
35302 AATTAAATGA
35312 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
35376 AA-CAATCATTGAGTTTAG
65 AACCAATCATTGAGTTTAG
35394 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
35459 ACCAATCATTGAATTT-G
66 ACCAATCATTGAGTTTAG
*
35476 AAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 -AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
35540 GAACCAATCATTGAGTTTAG
64 GAACCAATCATTGAGTTTAG
*
35560 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
35625 ACCAATCATTGAGTTTAG
66 ACCAATCATTGAGTTTAG
35643 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* **
35708 ACCAATCATTGAATTCGG
66 ACCAATCATTGAGTTTAG
* *
35726 AACATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
35781 ATTCAGTAGG
Statistics
Matches: 369, Mismatches: 11, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
82 64 0.17
83 300 0.81
84 5 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAGTTTAG
Found at i:35749 original size:249 final size:248
Alignment explanation
Indices: 35312--35780 Score: 877
Period size: 249 Copynumber: 1.9 Consensus size: 248
35302 AATTAAATGA
*
35312 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
35377 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
35442 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATGTGTTCATAGCATCTTCTGGA
131 TGATCTGGTTTGGCAGAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTGGA
35507 AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAG
196 AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAG
35560 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAG
35624 AACCAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
65 AA-CAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
35689 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTG
129 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTG
35754 GAAGTGTTCTTTGAGTTATCTGATCTG
194 GAAGTGTTCTTTGAGTTATCTGATCTG
35781 ATTCAGTAGG
Statistics
Matches: 215, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
248 61 0.28
249 154 0.72
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (248 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAG
Found at i:38388 original size:22 final size:22
Alignment explanation
Indices: 38357--38411 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
38347 ATCTACACTC
*
38357 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
38379 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
38401 TTCAAAGATGA
1 TTCAAAGATGA
38412 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:39468 original size:17 final size:17
Alignment explanation
Indices: 39408--39468 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
39398 CAGCTTTTCC
*
39408 AGAAAAAGTTCATAATG
1 AGAAGAAGTTCATAATG
39425 AGAAGAA-TTCATCTGAA-G
1 AGAAGAAGTTCA--T-AATG
39443 AAGGAAGAAGTTCATAATG
1 -A-GAAGAAGTTCATAATG
39462 AGAAGAA
1 AGAAGAA
39469 TTTGTTCAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
16 4 0.11
17 12 0.33
18 5 0.14
19 5 0.14
20 6 0.17
21 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.20
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:39607 original size:116 final size:114
Alignment explanation
Indices: 38813--39948 Score: 1638
Period size: 113 Copynumber: 10.0 Consensus size: 114
38803 GCAAAGATTC
* *
38813 AAATCCATCA-TTCGATGGATCAACATTACCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGA
1 AAATTCATCACTT-GATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGA
* *
38876 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* ***
38926 AAA-TCTATCACTTGATGGATTATTTTTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGA
1 AAATTC-ATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGA
*
38989 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * ***
39039 GAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
39103 GAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* ***
39152 AAA-TCTATCACTTGATGGATTATTTTTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGA
1 AAATTC-ATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGA
*
39215 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * ***
39265 GAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
39329 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * * *
39378 AAATTCATCACTTGATGGATCAGCTTTTCCAGA-AAAAGTTCATAATGAGAAGAATTCATCTGAA
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
39442 GAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
*
39488 AAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCATCT
**
39552 GAAGAAAAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
*
39604 AAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCATCT
39668 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
*
39720 AAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCATTT
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATC---T
39784 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
*
39836 AAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCATCT
** ** *
39900 GAAGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
39949 AATGACTCTA
Statistics
Matches: 959, Mismatches: 42, Indels: 41
0.92 0.04 0.04
Matches are distributed among these distances:
110 90 0.09
112 6 0.01
113 488 0.51
114 7 0.01
116 362 0.38
118 1 0.00
119 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (114 bp):
AAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
Found at i:40179 original size:3 final size:3
Alignment explanation
Indices: 40171--40261 Score: 83
Period size: 3 Copynumber: 29.7 Consensus size: 3
40161 TTCATTTAAA
* * * * * *
40171 TAT TAT TAT AAT TAT TAT TAT AAT AAT TAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
40219 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
40262 CAAACGGGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:40238 original size:19 final size:19
Alignment explanation
Indices: 40169--40255 Score: 87
Period size: 19 Copynumber: 4.9 Consensus size: 19
40159 TTTTCATTTA
40169 AATATTATTA-TAATTA-T
1 AATATTATTATTAATTACT
* *
40186 --TATTA-TAATAATTATT
1 AATATTATTATTAATTACT
* *
40202 ATTATAATTA-TAATTACT
1 AATATTATTATTAATTACT
*
40220 AATATTATTATTTATTACT
1 AATATTATTATTAATTACT
40239 AATATTATTATTAATTA
1 AATATTATTATTAATTA
40256 TTATTACAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.03
15 11 0.19
16 1 0.02
18 19 0.33
19 25 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTATTAATTACT
Found at i:41567 original size:19 final size:19
Alignment explanation
Indices: 41529--41566 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41519 TATAATTTAG
41529 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
41548 TCATTTATTTTA-ATGTTT
1 TCATTTATTTTATATGTTT
41566 T
1 T
41567 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:45550 original size:35 final size:37
Alignment explanation
Indices: 45481--45552 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
45471 TTGAAAATAT
* * *
45481 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAA
1 TTATATAATTTCTTTAAAAAATTGAAAATCATAAAAA
*
45518 TTATATAATTT-TTTACAAAATTGAAAAT-ATAAAAA
1 TTATATAATTTCTTTAAAAAATTGAAAATCATAAAAA
45553 GGTTTAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 7 0.23
36 14 0.45
37 10 0.32
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
TTATATAATTTCTTTAAAAAATTGAAAATCATAAAAA
Found at i:47443 original size:31 final size:31
Alignment explanation
Indices: 47416--47476 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
47406 ACAGTCCTTT
*
47416 AATATTTAGTCTGTTTGCAATATAGTCCCCC
1 AATATTTAATCTGTTTGCAATATAGTCCCCC
* *
47447 AATATTTAATCTGTTTGTAATATGGTCCCC
1 AATATTTAATCTGTTTGCAATATAGTCCCC
47477 AACGTAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (31 bp):
AATATTTAATCTGTTTGCAATATAGTCCCCC
Found at i:57981 original size:13 final size:13
Alignment explanation
Indices: 57963--57988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57953 CTGGATGGTC
57963 ATGTCCAATGTAT
1 ATGTCCAATGTAT
57976 ATGTCCAATGTAT
1 ATGTCCAATGTAT
57989 GGAATAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTCCAATGTAT
Done.