Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003248.1 Hibiscus syriacus cultivar Beakdansim tig00006829_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: 72141
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:8867 original size:31 final size:31
Alignment explanation
Indices: 8798--8900 Score: 190
Period size: 31 Copynumber: 3.4 Consensus size: 31
8788 GAAACTTTCT
8798 TTTTTATTTAACTAAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
8829 -TTTTATTTAACTAAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
*
8859 TTTTTATTTAACTGAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
8890 TTTTTATTTAA
1 TTTTTATTTAA
8901 TTAATATGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 30 0.43
31 40 0.57
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTTTATTTAACTAAGATATGATTATATTCA
Found at i:17610 original size:20 final size:21
Alignment explanation
Indices: 17585--17625 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
17575 AATTATTCCT
*
17585 ATTAAAAAACTAAA-AGAAAA
1 ATTAAAAAAATAAATAGAAAA
17605 ATTAAAAAAATAAATAGAAAA
1 ATTAAAAAAATAAATAGAAAA
17626 GATAATAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (21 bp):
ATTAAAAAAATAAATAGAAAA
Found at i:18231 original size:2 final size:2
Alignment explanation
Indices: 18221--18252 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
18211 AACGCAAAAA
18221 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
18253 AACGTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21362 original size:18 final size:18
Alignment explanation
Indices: 21330--21369 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21320 AATTCTTTCC
** *
21330 TTTAATTCTGTCTTATTA
1 TTTAATTCTAACTTATCA
21348 TTTAATTCTAACTTATCA
1 TTTAATTCTAACTTATCA
21366 TTTA
1 TTTA
21370 TTCCAGACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTAATTCTAACTTATCA
Found at i:24007 original size:21 final size:21
Alignment explanation
Indices: 23973--24012 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23963 TTTTGGATCG
23973 ATCCCACGAGGAAAATGATAT
1 ATCCCACGAGGAAAATGATAT
* *
23994 ATCCCTCGATGAAAATGAT
1 ATCCCACGAGGAAAATGAT
24013 TGATCTCTTT
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:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCCCACGAGGAAAATGATAT
Found at i:28400 original size:21 final size:22
Alignment explanation
Indices: 28347--28401 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
28337 AAGTATATTT
*
28347 AATATTTTTAATAATAATTTAAA
1 AATATTTTTAAAAATAA-TTAAA
*
28370 AATA--TATAAAAATAA-TAAA
1 AATATTTTTAAAAATAATTAAA
28389 AATATTTTTAAAA
1 AATATTTTTAAAA
28402 TTATATCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.30
21 15 0.56
23 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATTTTTAAAAATAATTAAA
Found at i:28847 original size:2 final size:2
Alignment explanation
Indices: 28840--28872 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28830 GCAATTCATA
28840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28873 GAGGTTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32460 original size:20 final size:20
Alignment explanation
Indices: 32435--32472 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32425 ATCATATTCT
32435 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
*
32455 CTGATAATCTTATATTCC
1 CTGATAATCTTACATTCC
32473 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:38026 original size:28 final size:28
Alignment explanation
Indices: 37993--38048 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
37983 CCCATTTTAT
37993 TAATAAAAATATTAAGATTCCAGATTGC
1 TAATAAAAATATTAAGATTCCAGATTGC
*
38021 TAATAAAAATATTAAGATTCCATATTGC
1 TAATAAAAATATTAAGATTCCAGATTGC
38049 AACATACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (28 bp):
TAATAAAAATATTAAGATTCCAGATTGC
Found at i:38507 original size:264 final size:262
Alignment explanation
Indices: 38024--39064 Score: 1323
Period size: 264 Copynumber: 3.9 Consensus size: 262
38014 AGATTGCTAA
* * * * *
38024 TAAAAATATTAAGATTCCATATTGCAACATACTTTCTTACTGAACCATGACATTTTTTGACGGAA
1 TAAAAATAGTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACGTAA
* * *
38089 CATTTTTTATTAATAAAAATATTAACATTAAATAAAT-AAACCCTATTTCTTATTGAACCATGAC
66 CCTATTTTATTAATAAAAATATTAACATT--ACAAATCAAA-CCTATTTCTTATTGAACCATGAC
* * * * *
38153 ATTATTGGGCGCAACCGTATTTATTATACTTATTTATAACATTTGAAACTTTTAACTTATTTTCT
128 ATTATTGGACACAACCGTATTTATTATACATATTCATAACATTT-TAACTTTTAACTTATTTTCT
* ** * * * *
38218 TATCGTGATAAACTCCAAAGCTCCATCAGCTTAAACTTTGATAATATTTTAGGTGCAACCCATTT
192 TATCATGGGAAACTCCAAGGCTCCATCATCTTAAACTCTGATAATATTTTAGGCGCAACCCATTT
*
38283 TAATAT
257 TATTAT
** * *
38289 TAAAAATAGTAAGATTCCAGATTGCAACATGTTTTCTTAGTGAACCATGACATTCTTGGATGTAA
1 TAAAAATAGTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACGTAA
* * * *
38354 CTTATTTTATTAGTAAAAATATTAACATTACAAATCACAACCTATTTTTTATTGAACAATGACAT
66 CCTATTTTATTAATAAAAATATTAACATTACAAATCA-AACCTATTTCTTATTGAACCATGACAT
* *
38419 TATTGGGCACAACCGTATTTATTATACATATTCATAACATTTTCAACTTTTAACTTATGTTCTTA
130 TATTGGACACAACCGTATTTATTATACATATTCATAACATTTT-AACTTTTAACTTATTTTCTTA
* * * * *
38484 TCATGTGAAACTTCAAGGCTCCATCAACTTAAACTCTGATAATATTTTAAGCGGAACCCATTTTA
194 TCATGGGAAACTCCAAGGCTCCATCATCTTAAACTCTGATAATATTTTAGGCGCAACCCATTTTA
38549 TTAT
259 TTAT
* * * **
38553 TAAAAATATTAAGATTTCAGATTGCAACATACTTTCTTACTGAACCAT-AGCATTCTTGGGCACA
1 TAAAAATAGTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGA-CATTCTTGGACGTA
*
38617 ACCTATTTTATTAATAAAAATATTAACATTAAAAATCTAAACCTATTTCTTATTGAACCATGACA
65 ACCTATTTTATTAATAAAAATATTAACATTACAAATC-AAACCTATTTCTTATTGAACCATGACA
* *
38682 TTATTGGACACAACTGTATTTATTATACATATTCATAACATTTTAAGCTTTTAACTTATTTTATT
129 TTATTGGACACAACCGTATTTATTATACATATTCATAACATTTTAA-CTTTTAACTTATTTTCTT
** * * *
38747 ATCGCGGGAAACTCCAAGGCTCAATCATCTTAAACTTTGATAATATTTTAGGCGCAACTCATTTT
193 ATCATGGGAAACTCCAAGGCTCCATCATCTTAAACTCTGATAATATTTTAGGCGCAACCCATTTT
38812 ATTAT
258 ATTAT
* * * * * *
38817 TAAAAATAGTAAGATTCCATAATGCAACTTGCTTTCTTAATGAACCATGACATTCTTGGGCGTAA
1 TAAAAATAGTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACGTAA
* *
38882 CCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCTATTTCTTATTGAATCATAACAT
66 CCTATTTTATTAATAAAAATATTAACATTACAAATCA-AACCTATTTCTTATTGAACCATGACAT
* ** * * * *
38947 TATTGTATGCAATCGTATTTATTATACATATTTATAACATTTTGAGTTTTAAACTTATTTTCTTA
130 TATTGGACACAACCGTATTTATTATACATATTCATAACATTTTAACTTTT-AACTTATTTTCTTA
* * ** * *
39012 TAATGGGAAATTAAAAGAC-CTTATCATCTTAAACTCTGATAATATTTTAGGCG
194 TCATGGGAAACTCCAAGGCTC-CATCATCTTAAACTCTGATAATATTTTAGGCG
39065 TTTTATTATT
Statistics
Matches: 677, Mismatches: 89, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
263 14 0.02
264 577 0.85
265 86 0.13
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (262 bp):
TAAAAATAGTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACGTAA
CCTATTTTATTAATAAAAATATTAACATTACAAATCAAACCTATTTCTTATTGAACCATGACATT
ATTGGACACAACCGTATTTATTATACATATTCATAACATTTTAACTTTTAACTTATTTTCTTATC
ATGGGAAACTCCAAGGCTCCATCATCTTAAACTCTGATAATATTTTAGGCGCAACCCATTTTATT
AT
Found at i:39045 original size:528 final size:529
Alignment explanation
Indices: 38024--39060 Score: 1494
Period size: 528 Copynumber: 2.0 Consensus size: 529
38014 AGATTGCTAA
* * * **
38024 TAAAAATATTAAGATTCCATATTGCAACATACTTTCTTACTGAACCATGACATTTTTTGACGGAA
1 TAAAAATATTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACACAA
*
38089 CATTTTTTATTAATAAAAATATTAACATTAAATAAATAAACCCTATTTCTTATTGAACCATGACA
66 CATATTTTATTAATAAAAATATTAACATTAAATAAATAAACCCTATTTCTTATTGAACCATGACA
* * * * *
38154 TTATTGGGCGCAACCGTATTTATTATACTTATTTATAACATTTGAAACTTTTAACTTATTTTCTT
131 TTATTGGACACAACCGTATTTATTATACATATTCATAACATTTGAAACTTTTAACTTATTTTATT
* * * *
38219 ATCGTGATAAACTCCAAAGCTCCATCAGCTTAAACTTTGATAATATTTTAGGTGCAACCCATTTT
196 ATCGCGAGAAACTCCAAAGCTCAATCAGCTTAAACTTTGATAATATTTTAGGCGCAACCCATTTT
* * *
38284 AATATTAAAAATAGTAAGATTCCAGATTGCAACATGTTTTCTTAGTGAACCATGACATTCTTGGA
261 AATATTAAAAATAGTAAGATTCCAGAATGCAACATGCTTTCTTAATGAACCATGACATTCTTGGA
* * * *
38349 TGTAACTTATTTTATTAGTAAAAATATTAACATTACAAATCACAACCTATTTTTTATTGAACAAT
326 CGTAACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCTATTTCTTATTGAACAAT
* *
38414 GACATTATTGGGCACAACCGTATTTATTATACATATTCATAACATTTTCAACTTTTAACTTATGT
391 AACATTATTGGACACAACCGTATTTATTATACATATTCATAACATTTTCAACTTTTAACTTATGT
* * * *
38479 TCTTATCATGTGAAACTTCAAGGCTCCATCAACTTAAACTCTGATAATATTTTAAGCGGAACCCA
456 TCTTATAATGGGAAACTTAAAGCCTCCATCAACTTAAACTCTGATAATATTTTAAGCGGAACCCA
38544 TTTTATTAT
521 TTTTATTAT
* *
38553 TAAAAATATTAAGATTTCAGATTGCAACATACTTTCTTACTGAACCAT-AGCATTCTTGGGCACA
1 TAAAAATATTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGA-CATTCTTGGACACA
* *
38617 ACCTATTTTATTAATAAAAATATTAACATTAAA-AATCTAAA-CCTATTTCTTATTGAACCATGA
65 ACATATTTTATTAATAAAAATATTAACATTAAATAA-ATAAACCCTATTTCTTATTGAACCATGA
* * *
38680 CATTATTGGACACAACTGTATTTATTATACATATTCATAACATTTTAAGCTTTTAACTTATTTTA
129 CATTATTGGACACAACCGTATTTATTATACATATTCATAACATTTGAAACTTTTAACTTATTTTA
* * * *
38745 TTATCGCGGGAAACTCCAAGGCTCAATCATCTTAAACTTTGATAATATTTTAGGCGCAACTCATT
194 TTATCGCGAGAAACTCCAAAGCTCAATCAGCTTAAACTTTGATAATATTTTAGGCGCAACCCATT
* * *
38810 TTATTATTAAAAATAGTAAGATTCCATAATGCAACTTGCTTTCTTAATGAACCATGACATTCTTG
259 TTAATATTAAAAATAGTAAGATTCCAGAATGCAACATGCTTTCTTAATGAACCATGACATTCTTG
*
38875 GGCGTAACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCTATTTCTTATTGAATC
324 GACGTAACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCTATTTCTTATTGAA-C
* ** * * * *
38940 -ATAACATTATTGTATGCAATCGTATTTATTATACATATTTATAACATTTT-GAGTTTTAAACTT
388 AATAACATTATTGGACACAACCGTATTTATTATACATATTCATAACATTTTCAACTTTT-AACTT
* * *
39003 ATTTTCTTATAATGGGAAA-TTAAAAGACCT-TATCATCTTAAACTCTGATAATATTTTA
452 ATGTTCTTATAATGGGAAACTT-AAAG-CCTCCATCAACTTAAACTCTGATAATATTTTA
39061 GGCGTTTTAT
Statistics
Matches: 449, Mismatches: 53, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
527 7 0.02
528 349 0.78
529 93 0.21
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (529 bp):
TAAAAATATTAAGATTCCAGATTGCAACATACTTTCTTACTGAACCATGACATTCTTGGACACAA
CATATTTTATTAATAAAAATATTAACATTAAATAAATAAACCCTATTTCTTATTGAACCATGACA
TTATTGGACACAACCGTATTTATTATACATATTCATAACATTTGAAACTTTTAACTTATTTTATT
ATCGCGAGAAACTCCAAAGCTCAATCAGCTTAAACTTTGATAATATTTTAGGCGCAACCCATTTT
AATATTAAAAATAGTAAGATTCCAGAATGCAACATGCTTTCTTAATGAACCATGACATTCTTGGA
CGTAACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCTATTTCTTATTGAACAAT
AACATTATTGGACACAACCGTATTTATTATACATATTCATAACATTTTCAACTTTTAACTTATGT
TCTTATAATGGGAAACTTAAAGCCTCCATCAACTTAAACTCTGATAATATTTTAAGCGGAACCCA
TTTTATTAT
Found at i:39318 original size:188 final size:187
Alignment explanation
Indices: 38880--39427 Score: 580
Period size: 188 Copynumber: 3.0 Consensus size: 187
38870 TCTTGGGCGT
* * * * * * * * * * *
38880 AACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACCT-ATTTCTTATTGAATC-ATA
1 AACCCATTTTATTATTAAAAAGATTAAGATTCCATATTACAAACTCATTCCTTACTGAAACAAT-
*** * * * * * * *
38943 ACATTATTGTATGCAATCGTATTTATTATACATATTTATAACATTTTGAGTTTTAAACTTATTTT
65 ACATTATTGGGCGCAATCATACTTATTATATATGTTCATAACATTTTCAGTTTTTAACTTATTTT
** * * * * *
39008 CTTATAATGGGAAATTAAAAGAC-CTTATCATCTTA-AACTCTGATAATATTTTAGG---
130 CTTATCGTAGGAAATTAAAAGGCTC-CATCA-GTTATAACTCTGATAACATTTTAGGCAC
* * * * **
39063 ----CGTTTTATTATTTAAAATATTAAGATTTCATATTACAAACTCATTTTTTACTGAAACAATA
1 AACCCATTTTATTATTAAAAAGATTAAGATTCCATATTACAAACTCATTCCTTACTGAAACAATA
* * *
39124 CATTATTGGGTGCGATCATACTTATTATATATGTTCATAATATTTTTCAGTTTTTAACTTATTTT
66 CATTATTGGGCGCAATCATACTTATTATATATGTTCATAACA-TTTTCAGTTTTTAACTTATTTT
39189 CTTATCGTAGGAAATTAAAAGGCTCCATCAGTT-TAAACTCTGATAACATTTTAGGCAC
130 CTTATCGTAGGAAATTAAAAGGCTCCATCAGTTAT-AACTCTGATAACATTTTAGGCAC
* *
39247 AACCCATTTTATTATTAAAAAGATTAAGATTCCATATTACAACCTCCTTCCTTACTGAAACAATA
1 AACCCATTTTATTATTAAAAAGATTAAGATTCCATATTACAAACTCATTCCTTACTGAAACAATA
* * *
39312 CATTATTGGGCGCAATCGTATTTGTTATATATGTTCATAACATTTTCAGTTTTTAACTTATTTTC
66 CATTATTGGGCGCAATCATACTTATTATATATGTTCATAACATTTTCAGTTTTTAACTTATTTTC
*
39377 TTATCGTAGGAAATTAAAAGGCTCCGTCAGTTATAACTCTGATAACATTTT
131 TTATCGTAGGAAATTAAAAGGCTCCATCAGTTATAACTCTGATAACATTTT
39428 TGATGCAACC
Statistics
Matches: 306, Mismatches: 45, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
179 32 0.10
180 48 0.16
181 64 0.21
182 1 0.00
187 71 0.23
188 90 0.29
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (187 bp):
AACCCATTTTATTATTAAAAAGATTAAGATTCCATATTACAAACTCATTCCTTACTGAAACAATA
CATTATTGGGCGCAATCATACTTATTATATATGTTCATAACATTTTCAGTTTTTAACTTATTTTC
TTATCGTAGGAAATTAAAAGGCTCCATCAGTTATAACTCTGATAACATTTTAGGCAC
Found at i:40809 original size:46 final size:47
Alignment explanation
Indices: 40759--40877 Score: 125
Period size: 46 Copynumber: 2.6 Consensus size: 47
40749 ATTTAAGTTG
* * * *
40759 CATTTAAGTTTATAACACTTTAATTTTTCTCAAAT-TATAATAAAAT
1 CATTTAAGTTTATAACATTTTAATTTTCCCCAAATCTATAACAAAAT
* * * **
40805 CATTTAATTTTGTAACAATTTTAA-TTTCCCCAAGTCTATAACAAGTT
1 CATTTAAGTTTATAAC-ATTTTAATTTTCCCCAAATCTATAACAAAAT
*
40852 CATTTAAGTTTATACCATTTTAATTT
1 CATTTAAGTTTATAACATTTTAATTT
40878 AAAGATTATT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
46 29 0.50
47 29 0.50
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.46
Consensus pattern (47 bp):
CATTTAAGTTTATAACATTTTAATTTTCCCCAAATCTATAACAAAAT
Found at i:40937 original size:79 final size:79
Alignment explanation
Indices: 40806--40952 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 79
40796 TAATAAAATC
* * * *
40806 ATTTAATTTTGTAACAATTTTAATTTCCCCAAGTCTATAACAAGTTCATTTAAGTTTATACCATT
1 ATTTAAGTTTGTAACAATTTTAATTTCCCCAAATCTATAACAAATTCATTTAAGTTTATAACATT
40871 TTAATTTAAAGATT
66 TTAATTTAAAGATT
*** *
40885 ATTTAAGTTTGTAACAATTTTAATTTCTTTAAATCTATAATAAATT-ATTTTAAGTTTATAACAT
1 ATTTAAGTTTGTAACAATTTTAATTTCCCCAAATCTATAACAAATTCA-TTTAAGTTTATAACAT
40949 TTTA
65 TTTA
40953 CTTATTTTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 1 0.02
79 58 0.98
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (79 bp):
ATTTAAGTTTGTAACAATTTTAATTTCCCCAAATCTATAACAAATTCATTTAAGTTTATAACATT
TTAATTTAAAGATT
Found at i:47060 original size:2 final size:2
Alignment explanation
Indices: 47053--47083 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47043 TTAGATAATC
47053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47084 ATTATCCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64467 original size:44 final size:46
Alignment explanation
Indices: 64401--64497 Score: 135
Period size: 44 Copynumber: 2.1 Consensus size: 46
64391 TATTTTCGTT
* *
64401 TTTTTCGAATAAATGCATGCGAACTAGGTATCATGCGGTTAGGTTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTA
* *
64448 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTA
64492 TTTTTG
1 TTTTTG
64498 TGGATAACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 35 0.76
45 2 0.04
46 4 0.09
47 5 0.11
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (46 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTA
Done.