Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002215.1 Hibiscus syriacus cultivar Beakdansim tig00004509_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: 63714
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:189 original size:55 final size:55
Alignment explanation
Indices: 126--234 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
116 TTTAATAAAA
126 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTTT
1 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTTT
*
181 TATTAAAAATATTGGTGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
1 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
235 GTGTAATTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (55 bp):
TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTTT
Found at i:3745 original size:117 final size:112
Alignment explanation
Indices: 3531--3823 Score: 393
Period size: 117 Copynumber: 2.6 Consensus size: 112
3521 AAGCGTTGGA
3531 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
3595 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAAT-AAA--AA-G
3648 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * * **
3713 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
* *
3761 --GAACAAGTTCTTCTCATTATGAAC-T-TTC-CC-CTTTAGGACGAGTTATTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTT-GGATGAGTTCTTCTCATTATGAAC
3820 TCTT
65 TCTT
3824 AATTAGAATG
Statistics
Matches: 165, Mismatches: 8, Indels: 16
0.87 0.04 0.08
Matches are distributed among these distances:
106 4 0.02
107 28 0.17
109 3 0.02
110 1 0.01
111 24 0.15
113 1 0.01
114 2 0.01
116 1 0.01
117 96 0.58
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
Found at i:5192 original size:19 final size:18
Alignment explanation
Indices: 5170--5211 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5160 CCCTTTTCTC
5170 TTTTCATTTCATTTTTTTT
1 TTTTCATTT-ATTTTTTTT
*
5189 TTTTCATTTTTTTTTTTT
1 TTTTCATTTATTTTTTTT
5207 TTTTC
1 TTTTC
5212 TTTTTGTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTCATTTATTTTTTTT
Found at i:5200 original size:9 final size:8
Alignment explanation
Indices: 5181--5231 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
5171 TTTCATTTCA
5181 TTTTT-TT
1 TTTTTCTT
5188 TTTTTCATTT
1 TTTTTC--TT
*
5198 TTTTTTTT
1 TTTTTCTT
5206 TTTTTCTT
1 TTTTTCTT
5214 TTTGTTCCTT
1 TTT-TT-CTT
5224 TTTTTCTT
1 TTTTTCTT
5232 CAAGCATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 5 0.14
8 15 0.41
9 4 0.11
10 13 0.35
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5200 original size:10 final size:9
Alignment explanation
Indices: 5181--5231 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
5171 TTTCATTTCA
5181 TTTT-TTTT
1 TTTTCTTTT
5189 TTTTCATTTT
1 TTTTC-TTTT
5199 TTTT-TTTT
1 TTTTCTTTT
5207 TTTTCTTTT
1 TTTTCTTTT
* *
5216 TGTTCCTTT
1 TTTTCTTTT
5225 TTTTCTT
1 TTTTCTT
5232 CAAGCATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 12 0.33
9 16 0.44
10 8 0.22
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:5203 original size:15 final size:14
Alignment explanation
Indices: 5176--5228 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
5166 TCTCTTTTCA
5176 TTTCATTTTTTTTT
1 TTTCATTTTTTTTT
5190 TTTCATTTTTTTTT
1 TTTCATTTTTTTTT
5204 TTT--TTTTCTTTTT
1 TTTCATTTT-TTTTT
* *
5217 GTTCCTTTTTTT
1 TTTCATTTTTTT
5229 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 4 0.11
13 7 0.20
14 20 0.57
15 4 0.11
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTCATTTTTTTTT
Found at i:19621 original size:7 final size:7
Alignment explanation
Indices: 19609--19635 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19599 GCAAATGCAG
19609 TGCACAC
1 TGCACAC
19616 TGCACAC
1 TGCACAC
19623 TGCACAC
1 TGCACAC
19630 TGCACA
1 TGCACA
19636 AAGCAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (7 bp):
TGCACAC
Found at i:21453 original size:27 final size:29
Alignment explanation
Indices: 21409--21464 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
21399 TTTATTAATA
*
21409 ATATGTTTTTTCTCTAAAATCT-TATAAGT
1 ATATGTTTTTTCTATAAAAT-TATATAAGT
21438 ATAT-TTTTTT-TATAAAATTATATAAGT
1 ATATGTTTTTTCTATAAAATTATATAAGT
21465 TCATCACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 14 0.56
28 6 0.24
29 4 0.16
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (29 bp):
ATATGTTTTTTCTATAAAATTATATAAGT
Found at i:25621 original size:8 final size:8
Alignment explanation
Indices: 25608--25648 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
25598 CTCATTTTCA
25608 GAGAATTT
1 GAGAATTT
25616 GAGAATTT
1 GAGAATTT
*
25624 -AGAGTTT
1 GAGAATTT
*
25631 GAGGATTT
1 GAGAATTT
25639 GAGAATTT
1 GAGAATTT
25647 GA
1 GA
25649 AAGTTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:25706 original size:12 final size:14
Alignment explanation
Indices: 25681--25712 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
25671 TTTGAAAGTT
25681 TATAATACGTTGTA
1 TATAATACGTTGTA
25695 TATAATA-G-TGTA
1 TATAATACGTTGTA
25707 TATAAT
1 TATAAT
25713 TGGGGTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (14 bp):
TATAATACGTTGTA
Found at i:25959 original size:128 final size:127
Alignment explanation
Indices: 25729--26079 Score: 594
Period size: 128 Copynumber: 2.7 Consensus size: 127
25719 ACTATTCACA
* * *
25729 TGAAGGCGCTTTCCCGGGGGCGCGCATTCCATTATTTTATCAGAGAATATGTTATTATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGC-TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
25794 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAAGAGACT
*
25857 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCG-CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
25922 TTATGTCACTCATGTCCCTCGGGGATACTATTTATATCAGTACCTATTATTTCTCAAGAGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAAGAGACT
*
25985 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCG-CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
26050 TTATGTCACTCATGTCCCTCGGGGACACTA
65 TTATGTCACTCATGTCCCTCGGGGACACTA
26080 GATGGATTGT
Statistics
Matches: 210, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
128 209 1.00
129 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (127 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAAGAGACT
Found at i:26540 original size:29 final size:27
Alignment explanation
Indices: 26498--26555 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
26488 TTGGAATACT
26498 ATAATTTATATTTTAATTTTAATTTTCAA
1 ATAATTTATATTTT-ATTTTAATTTT-AA
*
26527 ATAATATTAT-TTTTATTTTTATTTTAA
1 ATAAT-TTATATTTTATTTTAATTTTAA
26554 AT
1 AT
26556 TTCGAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 10 0.37
29 9 0.33
30 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATAATTTATATTTTATTTTAATTTTAA
Found at i:26544 original size:34 final size:34
Alignment explanation
Indices: 26475--26581 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
26465 TAAGTTGAAA
* ** *
26475 TTTAATGTTAAATTTGGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCAAATAATATAATTTATAT
* * *
26509 TTTAATTTTAATTTTCAAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCAAATAATATAATTTATAT
* * *
26543 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCAAATAATATAATTTATAT
26577 TTTAA
1 TTTAA
26582 AAACATTTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCAAATAATATAATTTATAT
Found at i:27126 original size:21 final size:21
Alignment explanation
Indices: 27108--27168 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
27098 ATAAAACCCT
* *
27108 GCAGGCTATGCATGTAACCTG
1 GCAGGCTAGGAATGTAACCTG
*
27129 GCGGGCTAGGAATGTAACCTG
1 GCAGGCTAGGAATGTAACCTG
*
27150 GCGGGCTAGGAATGTAACC
1 GCAGGCTAGGAATGTAACC
27169 CTGCAGGTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.20
Consensus pattern (21 bp):
GCAGGCTAGGAATGTAACCTG
Found at i:27467 original size:17 final size:17
Alignment explanation
Indices: 27447--27485 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
27437 TGAATCAAAT
27447 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
27464 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
27481 -AATTA
1 TAATTA
27486 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:27787 original size:21 final size:21
Alignment explanation
Indices: 27743--27783 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27733 GCGGAGATGA
*
27743 CATATGAACTGGTGGGCTTGG
1 CATATGAACTGGAGGGCTTGG
*
27764 CATATGAAGTGGAGGG-TTGG
1 CATATGAACTGGAGGGCTTGG
27784 GCATGTACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.10, G:0.41, T:0.27
Consensus pattern (21 bp):
CATATGAACTGGAGGGCTTGG
Found at i:29332 original size:26 final size:27
Alignment explanation
Indices: 29302--29366 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
29292 GTATCCTAAA
*
29302 TAATATACATT-ATAAAAAATTAAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
* * *
29328 TAATATAAATTCATAATAACTTTAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
*
29355 TAAAAATAAATT
1 T-AATATAAATT
29367 TAAATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.31
27 13 0.41
28 9 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATATAAATTCATAAAAAATTAAAAT
Found at i:29355 original size:17 final size:17
Alignment explanation
Indices: 29318--29371 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
29308 ACATTATAAA
* *
29318 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
29334 AAATTCATAATAACTTT
1 AAATTAAAAATAAATTT
29351 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
29368 AAAT
1 AAAT
29372 ATTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:29558 original size:35 final size:32
Alignment explanation
Indices: 29519--29603 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
29509 AATTCTAAAT
*
29519 AAATAATAATTATATCAATATTATTTTAATAAAAA
1 AAATAATAATTATAT-AA-A-TATATTAATAAAAA
* *
29554 AAATAATATTTATATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* * *
29586 ATATAATAACTATTTAAA
1 AAATAATAATTATATAAA
29604 AAAATACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 26 0.60
33 1 0.02
34 2 0.05
35 14 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:29580 original size:32 final size:35
Alignment explanation
Indices: 29519--29594 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 35
29509 AATTCTAAAT
*
29519 AAATAATAATTATATCAATATTATTTTAATAAAAA
1 AAATAATAATTATATCAATATTATATTAATAAAAA
* *
29554 AAATAATATTTATAT-AA-A-TATATTAATATAAA
1 AAATAATAATTATATCAATATTATATTAATAAAAA
*
29586 ATATAATAA
1 AAATAATAA
29595 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 19 0.53
33 1 0.03
34 2 0.06
35 14 0.39
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
AAATAATAATTATATCAATATTATATTAATAAAAA
Found at i:29587 original size:15 final size:15
Alignment explanation
Indices: 29553--29590 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29543 TTTAATAAAA
*
29553 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
29569 -AAATATATTAATAT
1 AAAATATATTAATAT
29583 AAAATATA
1 AAAATATA
29591 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:29619 original size:34 final size:34
Alignment explanation
Indices: 29547--29624 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
29537 TATTATTTTA
* * * *
29547 ATAAAAAAAATAATATTTATATAAATATATTAAT
1 ATAAAAATAATAATATTTATATAAAAATACTAAC
29581 ATAAAATATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTATATAAAAATACTAAC
29615 ATAAAAATAA
1 ATAAAAATAA
29625 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 21 0.55
35 7 0.18
36 6 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAATAATAATATTTATATAAAAATACTAAC
Found at i:33171 original size:84 final size:83
Alignment explanation
Indices: 33012--33181 Score: 288
Period size: 84 Copynumber: 2.0 Consensus size: 83
33002 ATATTTGAAA
*
33012 GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCAGATAATTATGGAACTTATTGATATT
1 GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCAGATAATTAAGGAACTTATTGATATT
*
33077 TATTGAGGTTTTTGGTTT
66 TATTGAGGTTTTGGGTTT
33095 GAGTTTGATCATAACTATTTAAGCACGAACCAAACAATCTC-GATAATTAAGGAACTTATTGATA
1 GAGTTTGATCATAACTATTTAAGCACGAACCAAA-AATC-CAGATAATTAAGGAACTTATTGATA
*
33159 TTTCTTGAGGTTTTGGGTTT
64 TTTATTGAGGTTTTGGGTTT
33179 GAG
1 GAG
33182 CACCGTAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
83 34 0.41
84 47 0.57
85 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (83 bp):
GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCAGATAATTAAGGAACTTATTGATATT
TATTGAGGTTTTGGGTTT
Found at i:37613 original size:15 final size:15
Alignment explanation
Indices: 37593--37623 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37583 TCAAAGTGCT
37593 AGCATATAAGTAAGA
1 AGCATATAAGTAAGA
37608 AGCATATAAGTAAGA
1 AGCATATAAGTAAGA
37623 A
1 A
37624 AAAGATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AGCATATAAGTAAGA
Found at i:38318 original size:24 final size:24
Alignment explanation
Indices: 38291--38349 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
38281 CTATTCTTTC
*
38291 GCTTCAATCGATATTGAATTTCAG
1 GCTTCAATCGATATTGAATTTCAA
*
38315 GCTTCAATCGATCTTGAATTTCAA
1 GCTTCAATCGATATTGAATTTCAA
38339 GCTTCAATCGA
1 GCTTCAATCGA
38350 GCTTCTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (24 bp):
GCTTCAATCGATATTGAATTTCAA
Found at i:38750 original size:13 final size:13
Alignment explanation
Indices: 38715--38754 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
38705 TCTTTTTCCC
38715 TCTTCTCTC-TTT
1 TCTTCTCTCTTTT
*
38727 TC-TCTCCCTTTT
1 TCTTCTCTCTTTT
38739 TCTTCTCTCTTTT
1 TCTTCTCTCTTTT
38752 TCT
1 TCT
38755 GTGTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 7 0.29
13 12 0.50
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TCTTCTCTCTTTT
Found at i:39033 original size:15 final size:15
Alignment explanation
Indices: 39013--39043 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39003 CCATGATTAG
*
39013 TGTAAACGAATTCTC
1 TGTAAACGAACTCTC
39028 TGTAAACGAACTCTC
1 TGTAAACGAACTCTC
39043 T
1 T
39044 TGCATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (15 bp):
TGTAAACGAACTCTC
Found at i:50481 original size:16 final size:16
Alignment explanation
Indices: 50448--50486 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
50438 TCTAGTTAAC
50448 TTATAAATTGTTTATTA
1 TTAT-AATTGTTTATTA
* *
50465 TTATAATTTTTTGTTA
1 TTATAATTGTTTATTA
50481 TTATAA
1 TTATAA
50487 GATAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTATAATTGTTTATTA
Found at i:51041 original size:16 final size:16
Alignment explanation
Indices: 51012--51049 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
51002 GTATTATCCA
*
51012 ACCTGCTATCAACCTG
1 ACCTGTTATCAACCTG
*
51028 ACCTGTTATGAACCTG
1 ACCTGTTATCAACCTG
51044 ACCTGT
1 ACCTGT
51050 AAATGATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.29
Consensus pattern (16 bp):
ACCTGTTATCAACCTG
Done.