Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003127.1 Hibiscus syriacus cultivar Beakdansim tig00006549_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: 73841
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:12052 original size:20 final size:20
Alignment explanation
Indices: 12027--12273 Score: 341
Period size: 20 Copynumber: 12.3 Consensus size: 20
12017 ATTTCCCTTA
*
12027 AATTTGTAAAGCCTCCGAGT
1 AATTTGTAAAGCCTCCGGGT
*
12047 AATTTGTAAAGCCTCTGGGT
1 AATTTGTAAAGCCTCCGGGT
12067 AATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
12087 AATTTGTAAAGCCTCCAGGT
1 AATTTGTAAAGCCTCCGGGT
* *
12107 AATTTGTAAAGCCACCAGGT
1 AATTTGTAAAGCCTCCGGGT
*
12127 AATTTGTAAATCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
* * *
12147 CATTTGTAAATCCTCCGAGT
1 AATTTGTAAAGCCTCCGGGT
* *
12167 AATTTATAAAGCCTTCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
12187 CATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
12207 CATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
12227 AATTTGTAAAGCCTCCAGGT
1 AATTTGTAAAGCCTCCGGGT
* * *
12247 CATTTGTAAAACCTTCGGGT
1 AATTTGTAAAGCCTCCGGGT
12267 AATTTGT
1 AATTTGT
12274 GAATCTTTTG
Statistics
Matches: 202, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 202 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
AATTTGTAAAGCCTCCGGGT
Found at i:12936 original size:65 final size:64
Alignment explanation
Indices: 12801--12956 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 64
12791 ATACCCCATT
* *
12801 TCGAATGAATTTTATGCACCGATGCACAGCCATGCATCGATGCACTCATGATTTTATTGAAACA
1 TCGAATGAATTTTATGCATCGATGCACAGCCATGCATCGATGCACTCATGATTTTATAGAAACA
* * *
12865 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCTTGGCTTTT-TAGAAAC
1 TCGAATGAATTTTATGCATCGATGCACAG-CCATGCATCGATGCACTCAT-GATTTTATAGAAAC
12929 A
64 A
* *
12930 TTGAATGTAA-TTAATGCATCGATGCAC
1 TCGAATG-AATTTTATGCATCGATGCAC
12957 CCCTAGTGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.33
65 48 0.59
66 6 0.07
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGAATTTTATGCATCGATGCACAGCCATGCATCGATGCACTCATGATTTTATAGAAACA
Found at i:19320 original size:26 final size:27
Alignment explanation
Indices: 19265--19318 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
19255 TTATTGTTGG
*
19265 AACATTGTTTTCAAAAATAATTTTTCA
1 AACATTGTTTTCAAAAATAAGTTTTCA
*
19292 AACATTGTTTT-ATAAAT-AGTTTTCA
1 AACATTGTTTTCAAAAATAAGTTTTCA
19317 AA
1 AA
19319 ACTATGCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
26 5 0.20
27 11 0.44
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (27 bp):
AACATTGTTTTCAAAAATAAGTTTTCA
Found at i:21412 original size:65 final size:64
Alignment explanation
Indices: 21286--21441 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 64
21276 ATACCCCATT
* * *
21286 TCGAATGTATTTTATGCACCGATGTACAACCATGCATCGATGCACTCAGGATTTTATTGAAACA
1 TCGAATGTATTTTATGCATCGATGCACAACCATGCATCGATGCACTCAGGATTGTATTGAAACA
* * * *
21350 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCATTCTTGGCTTGT-TTGAAAC
1 TCGAATGTATTTTATGCATCGATGCACA-ACCATGCATCGATGCACTC-AGGATTGTATTGAAAC
21414 A
64 A
* * *
21415 TCGAATGTAATTAATGCATTGATGCAC
1 TCGAATGTATTTTATGCATCGATGCAC
21442 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 25 0.32
65 49 0.62
66 5 0.06
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGTATTTTATGCATCGATGCACAACCATGCATCGATGCACTCAGGATTGTATTGAAACA
Found at i:22195 original size:36 final size:36
Alignment explanation
Indices: 22109--22202 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
22099 TTAATCCAGT
*
22109 CTTCACAAAAGAGTATTGAAG-AAATACAATCAAAC
1 CTTCACAAAAGAGTAGTGAAGTAAATACAATCAAAC
**
22144 CTTCACGGAAGAGTAGTGAAGTAAAT-CAAATTC-AAC
1 CTTCACAAAAGAGTAGTGAAGTAAATAC-AA-TCAAAC
*
22180 CTTCACAAAATAGTAGTGAAGTA
1 CTTCACAAAAGAGTAGTGAAGTA
22203 TTCCAACTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 19 0.38
36 29 0.58
37 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (36 bp):
CTTCACAAAAGAGTAGTGAAGTAAATACAATCAAAC
Found at i:22362 original size:124 final size:124
Alignment explanation
Indices: 22141--22377 Score: 393
Period size: 124 Copynumber: 1.9 Consensus size: 124
22131 AATACAATCA
* * *
22141 AACCTTCACGGAAGAGTAGTGAAGTAAATCAAATTCAACCTTCACAAAATAGTAGTGAAGTATTC
1 AACCTTCACGGAACAGTAGTGAAGTAAATCAAATTCAACCTTCACAAAAGAGTAGTGAAGTAATC
* ** *
22206 CAACTTCGAGTTTGATCTTCATGAAAGTGTAGTGAAACAGATTCTTCTTATTCAAGATC
66 CAACTTCGAGTCTGATCTTCACAAAAGAGTAGTGAAACAGATTCTTCTTATTCAAGATC
*
22265 AACCTTCACGGAACAGTAGTGAAGTAAATCAAATTCAACCTTCACAGAAGAGTAGTGAAGTAATC
1 AACCTTCACGGAACAGTAGTGAAGTAAATCAAATTCAACCTTCACAAAAGAGTAGTGAAGTAATC
*
22330 CAACTTCGTGTCTGATCTTCACAAAAGAGTAGTGAAACAGATTCTTCT
66 CAACTTCGAGTCTGATCTTCACAAAAGAGTAGTGAAACAGATTCTTCT
22378 CAAGTCAATC
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 104 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (124 bp):
AACCTTCACGGAACAGTAGTGAAGTAAATCAAATTCAACCTTCACAAAAGAGTAGTGAAGTAATC
CAACTTCGAGTCTGATCTTCACAAAAGAGTAGTGAAACAGATTCTTCTTATTCAAGATC
Found at i:22451 original size:93 final size:93
Alignment explanation
Indices: 22298--22479 Score: 292
Period size: 93 Copynumber: 2.0 Consensus size: 93
22288 GTAAATCAAA
* ** *
22298 TTCAACCTTCACAGAAGAGTAGTGAAGTAATCCAACTTCGTGTCTGATCTTCACAAAAGAGTAGT
1 TTCAACCTTCACAGAAGAATAGTGAAGTAATCCAACTTCGAATATGATCTTCACAAAAGAGTAGT
22363 GAAACAGATTCTTCTCAAGTCAATCATT
66 GAAACAGATTCTTCTCAAGTCAATCATT
***
22391 TTCAACCTTCACAGAAGAATAGTGAAGTAATCCAACTTCGAATATGATCTTCATGGAAGAGTAGT
1 TTCAACCTTCACAGAAGAATAGTGAAGTAATCCAACTTCGAATATGATCTTCACAAAAGAGTAGT
*
22456 GAAACAGATTCTTTTCAAGTCAAT
66 GAAACAGATTCTTCTCAAGTCAAT
22480 TCAACCTTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (93 bp):
TTCAACCTTCACAGAAGAATAGTGAAGTAATCCAACTTCGAATATGATCTTCACAAAAGAGTAGT
GAAACAGATTCTTCTCAAGTCAATCATT
Found at i:22702 original size:11 final size:11
Alignment explanation
Indices: 22671--22710 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
22661 CGAGTGTTAT
22671 TATTATTATAAA
1 TATTATTAT-AA
22683 TATTA-TATAA
1 TATTATTATAA
*
22693 TATTATTATAT
1 TATTATTATAA
22704 TATTATT
1 TATTATT
22711 TACAAAGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 14 0.54
12 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTATTATAA
Found at i:27337 original size:17 final size:17
Alignment explanation
Indices: 27315--27348 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27305 TTCATGAGGG
*
27315 CAGTATCGATACTCCTT
1 CAGTATCGATACCCCTT
27332 CAGTATCGATACCCCTT
1 CAGTATCGATACCCCTT
27349 GAAGGAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (17 bp):
CAGTATCGATACCCCTT
Found at i:29208 original size:22 final size:22
Alignment explanation
Indices: 29183--29234 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
29173 GGTTTAAATC
*
29183 TTAATATTTATATATTTATATT
1 TTAATATTTATATAATTATATT
* * * *
29205 TTAAAATTAATTTAATTATCTT
1 TTAATATTTATATAATTATATT
29227 TT-ATATTT
1 TTAATATTT
29235 TTCCTATAAG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAATATTTATATAATTATATT
Found at i:32204 original size:19 final size:19
Alignment explanation
Indices: 32167--32205 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32157 GCAATACCAC
*
32167 CAGCAGTCCACTCCGGTTT
1 CAGCAGTCCACTCAGGTTT
32186 CAGCAGTCCAC-CAGTGTTT
1 CAGCAGTCCACTCAG-GTTT
32205 C
1 C
32206 CCAAACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.26
Consensus pattern (19 bp):
CAGCAGTCCACTCAGGTTT
Found at i:33926 original size:5 final size:5
Alignment explanation
Indices: 33907--33965 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
33897 GTCCGTCCGT
* * * *
33907 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
33957 CTCGG CTCG
1 CTCGG CTCG
33966 TGGTCGTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.05, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:33974 original size:6 final size:6
Alignment explanation
Indices: 33963--34029 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
33953 TCGGCTCGGC
* *
33963 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
34011 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
34030 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:34329 original size:22 final size:22
Alignment explanation
Indices: 34304--34358 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
34294 TCAGGAGTTA
* *
34304 CAGGAGTTATTTGATCTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
34326 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
34348 CGGGAGTTATA
1 CAGGAGTTATA
34359 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:34639 original size:19 final size:19
Alignment explanation
Indices: 34602--34640 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34592 GCAATACCAC
*
34602 CAGCAGTCCACTCCGGTTT
1 CAGCAGTCCACTCAGGTTT
34621 CAGCAGTCCAC-CAGTGTTT
1 CAGCAGTCCACTCAG-GTTT
34640 C
1 C
34641 CCAAACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.26
Consensus pattern (19 bp):
CAGCAGTCCACTCAGGTTT
Found at i:36364 original size:5 final size:5
Alignment explanation
Indices: 36345--36403 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
36335 GTCCGTCCGT
* * * *
36345 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
36395 CTCGG CTCG
1 CTCGG CTCG
36404 TGGTCGTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.05, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:36412 original size:6 final size:6
Alignment explanation
Indices: 36401--36467 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
36391 TCGGCTCGGC
* *
36401 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
36449 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
36468 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:36767 original size:22 final size:22
Alignment explanation
Indices: 36742--36796 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
36732 TCAGGAGTTA
* *
36742 CAGGAGTTATTTGATCTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
36764 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
36786 CGGGAGTTATA
1 CAGGAGTTATA
36797 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:37077 original size:19 final size:19
Alignment explanation
Indices: 37040--37078 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
37030 GCAATACCAC
*
37040 CAGCAGTCCACTCCGGTTT
1 CAGCAGTCCACTCAGGTTT
37059 CAGCAGTCCAC-CAGTGTTT
1 CAGCAGTCCACTCAG-GTTT
37078 C
1 C
37079 CCAAACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.26
Consensus pattern (19 bp):
CAGCAGTCCACTCAGGTTT
Found at i:38801 original size:5 final size:5
Alignment explanation
Indices: 38782--38850 Score: 102
Period size: 5 Copynumber: 13.8 Consensus size: 5
38772 GTCCGTCCGT
* * * *
38782 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
38832 CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCG
38851 TGGTCGTGGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.04, C:0.41, G:0.38, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:38859 original size:6 final size:6
Alignment explanation
Indices: 38848--38896 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
38838 TCGGCTCGGC
* *
38848 TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
38896 T
1 T
38897 AATACGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:39196 original size:22 final size:22
Alignment explanation
Indices: 39171--39225 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
39161 TCAGGAGTTA
* *
39171 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
39193 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
39215 CGGGAGTTATA
1 CAGGAGTTATA
39226 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:42883 original size:13 final size:13
Alignment explanation
Indices: 42865--42891 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42855 TGATTAATTC
42865 ATTTTATTTATTT
1 ATTTTATTTATTT
42878 ATTTTATTTATTT
1 ATTTTATTTATTT
42891 A
1 A
42892 GATGCATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:48504 original size:39 final size:39
Alignment explanation
Indices: 48450--48538 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
48440 CTTGAATGAT
*
48450 ATTGTAGTTTGTGATTGGAGGAGAAAGGATTTTGGTTTC
1 ATTGTATTTTGTGATTGGAGGAGAAAGGATTTTGGTTTC
* *
48489 ATTGTATTTTGTGATTGGAGGAGGAAGGGTTTTGGTTTC
1 ATTGTATTTTGTGATTGGAGGAGAAAGGATTTTGGTTTC
48528 ATTGTATTTTG
1 ATTGTATTTTG
48539 GATAAGAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (39 bp):
ATTGTATTTTGTGATTGGAGGAGAAAGGATTTTGGTTTC
Found at i:53835 original size:2 final size:2
Alignment explanation
Indices: 53828--53856 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53818 AATGCATTGA
53828 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 A
53857 CTTCATCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54953 original size:9 final size:9
Alignment explanation
Indices: 54939--55009 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
54929 GGGCTAGAAA
*
54939 ACCGGTCTG
1 ACCGGTTTG
*
54948 ACCGGTTTTCA
1 ACCGG-TTT-G
54959 ACCGGTTTTG
1 ACCGG-TTTG
*
54969 ACTGGTTTG
1 ACCGGTTTG
54978 ACCGGTTTTG
1 ACCGG-TTTG
*
54988 ACCGGTCTG
1 ACCGGTTTG
*
54997 AACCGGTCTG
1 -ACCGGTTTG
55007 ACC
1 ACC
55010 CGACCCGACC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 19 0.37
10 24 0.46
11 9 0.17
ACGTcount: A:0.14, C:0.27, G:0.28, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:54987 original size:10 final size:10
Alignment explanation
Indices: 54946--54993 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
54936 AAAACCGGTC
54946 TGACCGGTTT
1 TGACCGGTTT
*
54956 TCAACCGGTTT
1 T-GACCGGTTT
*
54967 TGACTGG-TT
1 TGACCGGTTT
54976 TGACCGGTTT
1 TGACCGGTTT
54986 TGACCGGT
1 TGACCGGT
54994 CTGAACCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (10 bp):
TGACCGGTTT
Found at i:55008 original size:19 final size:20
Alignment explanation
Indices: 54938--55009 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
54928 AGGGCTAGAA
*
54938 AACCGG-TCTGACCGGTTTTC
1 AACCGGTTCTGACCGG-TTTG
* *
54958 AACCGGTTTTGACTGGTTTG
1 AACCGGTTCTGACCGGTTTG
* *
54978 -ACCGGTTTTGACCGGTCTG
1 AACCGGTTCTGACCGGTTTG
54997 AACCGG-TCTGACC
1 AACCGGTTCTGACC
55010 CGACCCGACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 23 0.52
20 14 0.32
21 7 0.16
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (20 bp):
AACCGGTTCTGACCGGTTTG
Found at i:55016 original size:5 final size:5
Alignment explanation
Indices: 55006--55046 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
54996 GAACCGGTCT
*
55006 GACCC GACCC GACCC GACCC AACCGC TGACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACC-C -GACCC GACCC GACC
55047 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 27 0.84
6 2 0.06
7 3 0.09
ACGTcount: A:0.22, C:0.56, G:0.20, T:0.02
Consensus pattern (5 bp):
GACCC
Found at i:55038 original size:17 final size:17
Alignment explanation
Indices: 55016--55053 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
55006 GACCCGACCC
55016 GACCCGACCCAACCGCT
1 GACCCGACCCAACCGCT
* *
55033 GACCCGACCCGACCGTT
1 GACCCGACCCAACCGCT
55050 GACC
1 GACC
55054 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.08
Consensus pattern (17 bp):
GACCCGACCCAACCGCT
Found at i:55729 original size:21 final size:21
Alignment explanation
Indices: 55683--55730 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
55673 TACACCGATT
* *
55683 TATTGTTGATGATTTATGGAC
1 TATTGATGATGATATATGGAC
55704 T-TTGATGACTGATATATGGA-
1 TATTGATGA-TGATATATGGAC
55724 TATTGAT
1 TATTGAT
55731 TTTGGGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (21 bp):
TATTGATGATGATATATGGAC
Found at i:64474 original size:176 final size:176
Alignment explanation
Indices: 64180--64530 Score: 558
Period size: 176 Copynumber: 2.0 Consensus size: 176
64170 ACTTCTGAAC
* * * *
64180 CAGATGCCCATATTTTCCACACAACTGACACTGTGGTCGATTATTAAATTGTCCGCGGCCGCGAC
1 CAGATGCCCATATTTTCCACACAACTGACACTGTGGTCGATTATTAAACTGTCCACGGCCACCAC
* * * * * *
64245 TATGGCCACCACCACGACGATTGCCTTGAGACGTGTCCGATGTTCCAGAGGAAAGATGAAATCCA
66 CACGGCCACCACCACCACGATTGCCTTGAGACGTGTCCAACGTTCCAGAGGAAAAATGAAATCCA
*
64310 GACGAATTCTTCCCAGCATAAGCACCATTCTCATTATACGAGGCAG
131 GACGAATTCTTCCCAACATAAGCACCATTCTCATTATACGAGGCAG
**
64356 CAGATGCCCATATTTTCCACACAACTGACACTGTGGTCGATTATTAAACTGTCCACGGTTACCAC
1 CAGATGCCCATATTTTCCACACAACTGACACTGTGGTCGATTATTAAACTGTCCACGGCCACCAC
* *
64421 CACGGCCACCACCACCACGATTGCCTTGAGACGTGTCTAACGTTTCAGAGGAAAAATGAAATCCA
66 CACGGCCACCACCACCACGATTGCCTTGAGACGTGTCCAACGTTCCAGAGGAAAAATGAAATCCA
*
64486 GACGAATTCTTCCCAACATAAGCACCATTCTCATTATGCGAGGCA
131 GACGAATTCTTCCCAACATAAGCACCATTCTCATTATACGAGGCA
64531 ACATTTGCCT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 159 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (176 bp):
CAGATGCCCATATTTTCCACACAACTGACACTGTGGTCGATTATTAAACTGTCCACGGCCACCAC
CACGGCCACCACCACCACGATTGCCTTGAGACGTGTCCAACGTTCCAGAGGAAAAATGAAATCCA
GACGAATTCTTCCCAACATAAGCACCATTCTCATTATACGAGGCAG
Done.