Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004434.1 Hibiscus syriacus cultivar Beakdansim tig00009725_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: 62171
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3730 original size:54 final size:54
Alignment explanation
Indices: 3591--3732 Score: 180
Period size: 54 Copynumber: 2.6 Consensus size: 54
3581 GTAAGGGTAA
* * *
3591 TATCGATACCTTAAGGATG-ATCGATACCCTTAAAACATCGAATGCCAGATTGG
1 TATCGATACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGCCAGATTGG
* * ** *
3644 TATCGGTACCTTGAGGTGGTATCGATACCCTTGAAACATCGAATGTTA-TTTCGG
1 TATCGATACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGCCAGATT-GG
*
3698 TATCGATACCATGAGGAGGTATCGATACCCTTGAA
1 TATCGATACCTTGAGGAGGTATCGATACCCTTGAA
3733 TGGTAGTATC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
53 17 0.22
54 59 0.78
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (54 bp):
TATCGATACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATGCCAGATTGG
Found at i:4065 original size:21 final size:19
Alignment explanation
Indices: 4034--4088 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
4024 AAAACTTTAT
4034 AATTTCTTTATTATTATATTTC
1 AATTT-TTTATTATT-TA-TTC
4056 AATTTTTTATTCTATTTATTC
1 AATTTTTTA-T-TATTTATTC
4077 AATTTTATTATT
1 AATTTT-TTATT
4089 CAAGTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.03
21 14 0.47
22 11 0.37
23 4 0.13
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTTTATTATTTATTC
Found at i:4075 original size:22 final size:23
Alignment explanation
Indices: 4045--4099 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
4035 ATTTCTTTAT
4045 TATTATATTTCAATTTT-TTATTC
1 TATTATA-TTCAATTTTATTATTC
4068 TATT-TATTCAATTTTATTATTC
1 TATTATATTCAATTTTATTATTC
*
4090 AAGTTATATT
1 TA-TTATATT
4100 TTATGATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.32
22 9 0.32
23 6 0.21
24 4 0.14
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (23 bp):
TATTATATTCAATTTTATTATTC
Found at i:4300 original size:21 final size:21
Alignment explanation
Indices: 4276--4324 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
4266 AGGGTCTATA
*
4276 TGGTCATTCAGGACAATTATG
1 TGGTCATTCAGGACAAATATG
* * *
4297 TGGTCTTTCGGGATAAATATG
1 TGGTCATTCAGGACAAATATG
4318 TGG-CATT
1 TGGTCATT
4325 TTGGTGAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (21 bp):
TGGTCATTCAGGACAAATATG
Found at i:15641 original size:33 final size:33
Alignment explanation
Indices: 15599--15668 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
15589 GTAAGGAGAT
* *
15599 ACTTAAGGCTCTTGTGTTCCGTAAATATGTGAA
1 ACTTAAGGCTCTTGTGCTCCGTAAAGATGTGAA
* *
15632 ACTTAAGGCTCTTGTGCTCTGTAAAGATGTGAC
1 ACTTAAGGCTCTTGTGCTCCGTAAAGATGTGAA
15665 ACTT
1 ACTT
15669 CTCCCAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (33 bp):
ACTTAAGGCTCTTGTGCTCCGTAAAGATGTGAA
Found at i:19395 original size:90 final size:90
Alignment explanation
Indices: 19239--19405 Score: 253
Period size: 90 Copynumber: 1.9 Consensus size: 90
19229 ATTTAATTTT
* * * * * *
19239 AATTGATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATAGGACTAGGGCAACTT
19304 GGATATAAAAGGATTATTAAATTCC
66 GGATATAAAAGGATTATTAAATTCC
* *
19329 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATAGGACTAGTGCAGCTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATAGGACTAGGGCAACTT
*
19394 GGCTATAAAAGG
66 GGATATAAAAGG
19406 GTGTGTTAGG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 68 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATAGGACTAGGGCAACTT
GGATATAAAAGGATTATTAAATTCC
Found at i:21933 original size:45 final size:45
Alignment explanation
Indices: 21873--21967 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
21863 TAATTATATG
* * *
21873 TCTTTATATTGAAAGAATAAATTTATTTGAT-GTACATTATTTGTT
1 TCTTTAGATTGAAAGAATAAATTTATGTG-TGGTACATTATTTATT
* * * *
21918 TCTTTAGATTTAAAGATTATATTTGTGTGTGGTACATTATTTATT
1 TCTTTAGATTGAAAGAATAAATTTATGTGTGGTACATTATTTATT
21963 TCTTT
1 TCTTT
21968 TTATGTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (45 bp):
TCTTTAGATTGAAAGAATAAATTTATGTGTGGTACATTATTTATT
Found at i:28447 original size:51 final size:52
Alignment explanation
Indices: 28389--28508 Score: 188
Period size: 51 Copynumber: 2.3 Consensus size: 52
28379 ATCTATCTGG
* *
28389 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAGTTATCCATGTG-
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
* * *
28440 GGTATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
28492 GGCATCTTGAAGGCTCA
1 GGCATCTTGAAGGCTCA
28509 GACCCGTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
51 46 0.75
52 15 0.25
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (52 bp):
GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
Found at i:30063 original size:249 final size:249
Alignment explanation
Indices: 29610--30624 Score: 1559
Period size: 249 Copynumber: 4.1 Consensus size: 249
29600 CCTAACCAAC
* *
29610 AAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAAGAAGTTTCTTACCC---
1 AAGTTTCTCATTTAA--TTTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
* *
29672 -----A-TTCCCATAAATTTGTAAATACTTCGGGTCATCTGTTAGTCTATT-GAGCATGATGCTT
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCT-TTCGAGCATGATGCTT
*
29730 AAAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAG
128 AAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAG
29795 CCTTTGGGTAGGATGTTCACATATGATTTTCACATGAAAATGAGATAGCGATTTTCA
193 CCTTTGGGTAGGATGTTCACATATGATTTTCACATGAAAATGAGATAGCGATTTTCA
*
29852 AAGTTTCTCATTTAATTTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAATAA
1 AAGTTTCTCATTTAATTTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
* *
29917 AGTATTTCCCACAAATTTGTAAATCCTTCGAGTCATCTATTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
* * * *
29982 ACCTTTGGGCCATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCATAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
* * *
30047 TTGGGTATGCTGTTCACATATGATTTTTACATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCACATGAAAATGAGATAGCGATTTTCA
** *
30101 AAGTTTCTCATTTAATGGTCTAGAAAATCAAATTCTTAAAAAGTAAGAAGTTTCTTACCCAGTAA
1 AAGTTTCTCATTTAATTTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
* *
30166 AGTATTTCCCACAAATTTATAAATCCTCCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
* * *
30231 ACATTCGGGTCATCTGTTAGTATTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
*
30296 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCACATGAAAATGAGATAGCGATTTTCA
*
30350 AAGTTTCTCATTT-ATTGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTA
1 AAGTTTCTCATTTAATT-TTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTA
* * *
30414 AAGTATTTCCCACAAATTTGTAAATCCTTCGTGTCATCTGTAAGTCTTTCGAGCATGATGCCTAA
65 AAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAA
*
30479 AACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCC
130 AACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCC
* * * * * **
30544 TTTAGG-AAGATGTTCACATATGATTTTCGCATGAAAAATGAGAAAACGATTACCA
195 TTTGGGTAGGATGTTCACATATGATTTTCACATG-AAAATGAGATAGCGATTTTCA
* *
30599 AAGTTTCTCATTTAATGTTATAGAAA
1 AAGTTTCTCATTTAATTTTCTAGAAA
30625 TTTAAAACCT
Statistics
Matches: 708, Mismatches: 52, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
240 43 0.06
242 15 0.02
248 31 0.04
249 617 0.87
250 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (249 bp):
AAGTTTCTCATTTAATTTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
TTGGGTAGGATGTTCACATATGATTTTCACATGAAAATGAGATAGCGATTTTCA
Found at i:30739 original size:48 final size:47
Alignment explanation
Indices: 30637--30817 Score: 272
Period size: 47 Copynumber: 3.8 Consensus size: 47
30627 TAAAACCTCT
* *
30637 GGGTCATCTATAAGACCTTCAGTGTAGGATGTTTTCAAAAAGCCTTC
1 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTC
* * * *
30684 AGGTCATCCATAAGACCTTCAATACAGGATGTTTTTCAAAAAGCCTTT
1 GGGTCATCCATAAGACCTTCAGTGCAGGATG-TTTTCAAAAAGCCTTC
* *
30732 GGGTCATCCATAAGACCTTTAGTGCAAGATGTTTTCAAAAAGCCTTC
1 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTC
*
30779 GGGTCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAA
1 GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAA
30818 TGAGATTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 79 0.66
48 41 0.34
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (47 bp):
GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTC
Found at i:30807 original size:95 final size:93
Alignment explanation
Indices: 30628--30817 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 93
30618 ATAGAAATTT
* * *
30628 AAAACCTCTGGGTCATCTATAAGACCTTCAGTGTAGGATGTTTTCAAAAAGCCTTCAGGTCATCC
1 AAAACCTCTGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAAAAGCCTTCAGGTCATCC
30693 ATAAGACCTTCAATACAGGATGTTTTTCA
66 ATAAGACCTTCAATACAGGATG-TTTTCA
* * *
30722 AAAAGCCTTTGGGTCATCCATAAGACCTTTAGTGCAAGATGTTTTCAAAAAGCCTTCGGGTCATC
1 AAAA-CCTCTGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAAAAGCCTTCAGGTCATC
* * *
30787 CATAAGACCTTTAGTGCAGGATGTTTTCA
65 CATAAGACCTTCAATACAGGATGTTTTCA
30816 AA
1 AA
30818 TGAGATTTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 12 0.14
95 74 0.86
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (93 bp):
AAAACCTCTGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAAAAGCCTTCAGGTCATCC
ATAAGACCTTCAATACAGGATGTTTTCA
Found at i:40789 original size:20 final size:22
Alignment explanation
Indices: 40750--40790 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
40740 TTTTTTTTGA
*
40750 GTTTTTCAAATTATAATTTTAT
1 GTTTTTCAAATTAAAATTTTAT
40772 GTTTTT-AAA-TAAAATTTTA
1 GTTTTTCAAATTAAAATTTTA
40791 AAATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
GTTTTTCAAATTAAAATTTTAT
Found at i:43833 original size:20 final size:20
Alignment explanation
Indices: 43759--43837 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
43749 TTATGAAACA
* * *
43759 TAGTATTGATATTTTTCTTG
1 TAGTATCGATACTATTCTTG
* * *
43779 TAGTATCAATATTGTTCTTG
1 TAGTATCGATACTATTCTTG
43799 TAGTA-CGAATACTATTCTTG
1 TAGTATCG-ATACTATTCTTG
*
43819 TAGTATCGATGCTATTCTT
1 TAGTATCGATACTATTCTT
43838 ACAATATTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.94
21 2 0.04
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.49
Consensus pattern (20 bp):
TAGTATCGATACTATTCTTG
Found at i:43873 original size:45 final size:45
Alignment explanation
Indices: 43822--43909 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
43812 ATTCTTGTAG
*
43822 TATCGATGCTATTCTTACAATATTTGTATTATTATTGTAGTATAA
1 TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTATAA
* * * * * *
43867 TATCGATATTGTTCTTGCAGTATTTGTATTGTTCTTGTAGTAT
1 TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTAT
43910 CTGTAATGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (45 bp):
TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTATAA
Found at i:43898 original size:20 final size:20
Alignment explanation
Indices: 43873--43928 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
43863 ATAATATCGA
* *
43873 TATTGTTCTTGCAGTATTTG
1 TATTGTTCTTGTAGTATCTG
43893 TATTGTTCTTGTAGTATCTG
1 TATTGTTCTTGTAGTATCTG
*
43913 TAATGTTCTTGTAGTA
1 TATTGTTCTTGTAGTA
43929 ATGTCAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.54
Consensus pattern (20 bp):
TATTGTTCTTGTAGTATCTG
Found at i:45223 original size:85 final size:85
Alignment explanation
Indices: 45134--45309 Score: 228
Period size: 85 Copynumber: 2.1 Consensus size: 85
45124 CGCGCAATTA
* * * * *
45134 TGTGTCATAAATCTATGACGCGCATTTATGACGCTCATTACGCGTCATTGAAGCCCCCGTCA-TA
1 TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
*
45198 AATGAAGATGACACACATTCG
66 AA-AAAGATGACACACATTCG
* * * * *
45219 TGTGTCATAAATTTATGGCACACATGTATGACGCTCATTGCGTGTCATTGAAGTACACGTCATTA
1 TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
*
45284 AAAAAGATGACACACATTCT
66 AAAAAGATGACACACATTCG
45304 TGTGTC
1 TGTGTC
45310 GTGATTGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 74 0.95
86 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (85 bp):
TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
AAAAAGATGACACACATTCG
Found at i:46884 original size:2 final size:2
Alignment explanation
Indices: 46877--46908 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46867 GGTGCAAATG
46877 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
46909 GTCCGCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50289 original size:29 final size:29
Alignment explanation
Indices: 50257--50334 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
50247 CAGTAACGGC
**
50257 CTTTAGTGTAATTTGTGAAAAAAATAT-TT
1 CTTTAGTGTAATTTGT-AAAAAAATATAGA
* **
50286 CTTTAAT-TAATTTGTAATGAAATATAGA
1 CTTTAGTGTAATTTGTAAAAAAATATAGA
*
50314 ATTTAGTGTAATTTGTAAAAA
1 CTTTAGTGTAATTTGTAAAAA
50335 TTCGGGCCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
27 8 0.21
28 13 0.34
29 17 0.45
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (29 bp):
CTTTAGTGTAATTTGTAAAAAAATATAGA
Found at i:52265 original size:43 final size:43
Alignment explanation
Indices: 52217--52305 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
52207 TTCATCCTTT
* * * *
52217 ATCCTTAGTTTGTTTGGGTGCATACTGGAATCCATAACTTACA
1 ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
*
52260 ATCCTTAGCTTATTTGGGTGCACAGTGAAATCCATAACTTACA
1 ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
52303 ATC
1 ATC
52306 ACATGGAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (43 bp):
ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
Found at i:52565 original size:19 final size:19
Alignment explanation
Indices: 52541--52582 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
52531 GTCCATCTCA
52541 AGCTGATACGATCCAAAAT
1 AGCTGATACGATCCAAAAT
*
52560 AGCTGATACGATCCAAACT
1 AGCTGATACGATCCAAAAT
52579 AGCT
1 AGCT
52583 CCAACTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (19 bp):
AGCTGATACGATCCAAAAT
Found at i:54432 original size:23 final size:24
Alignment explanation
Indices: 54404--54448 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54394 AAAGAAATCG
54404 AAGCACTC-AAAAGAAGAAAAGTC
1 AAGCACTCAAAAAGAAGAAAAGTC
54427 AAGCACTCAAAAAGAAGAAAAG
1 AAGCACTCAAAAAGAAGAAAAG
54449 AAAAGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.60, C:0.16, G:0.18, T:0.07
Consensus pattern (24 bp):
AAGCACTCAAAAAGAAGAAAAGTC
Found at i:54454 original size:24 final size:23
Alignment explanation
Indices: 54404--54455 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
54394 AAAGAAATCG
**
54404 AAGCACTCAAAAGAAGAAAAGTC
1 AAGCACTCAAAAGAAGAAAAGAA
54427 AAGCACTCAAAAAGAAGAAAAGAA
1 AAGCACTC-AAAAGAAGAAAAGAA
54451 AAGCA
1 AAGCA
54456 AAGACATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.62, C:0.15, G:0.17, T:0.06
Consensus pattern (23 bp):
AAGCACTCAAAAGAAGAAAAGAA
Found at i:55669 original size:24 final size:21
Alignment explanation
Indices: 55635--55677 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
55625 TCCACAAGAC
*
55635 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
55657 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
55678 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:60152 original size:21 final size:21
Alignment explanation
Indices: 60128--60170 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60118 GACACACATA
* * *
60128 TTTAATGAATAAAATTTGAAT
1 TTTAAAGAAGAAAATTTAAAT
60149 TTTAAAGAAGAAAATTTAAAT
1 TTTAAAGAAGAAAATTTAAAT
60170 T
1 T
60171 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTAAAGAAGAAAATTTAAAT
Done.