Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002356.1 Hibiscus syriacus cultivar Beakdansim tig00004810_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: 318585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:241520 original size:23 final size:23
Alignment explanation
Indices: 241492--241577 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 23
241482 AAATATTGTA
241492 TTTTAATTAATTTATATTTATAT
1 TTTTAATTAATTTATATTTATAT
* *
241515 TTTTAACTAATTTATAATTATAT
1 TTTTAATTAATTTATATTTATAT
* * *
241538 GTTT-AGTAATTTATAATTTAATGT
1 TTTTAATTAATTTAT-ATTT-ATAT
241562 TTTATAAATTAATTTA
1 TTT-T-AATTAATTTA
241578 ATGGTGTTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 9 0.18
23 27 0.54
24 5 0.10
25 1 0.02
27 8 0.16
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTTAATTAATTTATATTTATAT
Found at i:241561 original size:22 final size:24
Alignment explanation
Indices: 241493--241563 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 24
241483 AATATTGTAT
* *
241493 TTTAATTAATTTAT-ATTTATATT
1 TTTAACTAATTTATAATTTATATG
241516 TTTAACTAATTTATAA-TTATATG
1 TTTAACTAATTTATAATTTATATG
*
241539 TTT-AGTAATTTATAATTTA-ATG
1 TTTAACTAATTTATAATTTATATG
241561 TTT
1 TTT
241564 TATAAATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 17 0.40
23 25 0.58
24 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTAACTAATTTATAATTTATATG
Found at i:244042 original size:3 final size:3
Alignment explanation
Indices: 244036--244215 Score: 247
Period size: 3 Copynumber: 60.7 Consensus size: 3
244026 TTTTTATCCA
* * *
244036 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
244084 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
244132 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TGT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
244180 TAT T-T T-T TAT TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
244216 AATATATTAA
Statistics
Matches: 154, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
2 4 0.03
3 150 0.97
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:245623 original size:22 final size:23
Alignment explanation
Indices: 245598--245642 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
245588 TAGTGATATT
**
245598 TTTTTTAT-TATATTGTTAAATA
1 TTTTTTATATATATTCATAAATA
245620 -TTTTTATATATATTCATAAATA
1 TTTTTTATATATATTCATAAATA
245642 T
1 T
245643 GCATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTTATATATATTCATAAATA
Found at i:246336 original size:17 final size:17
Alignment explanation
Indices: 246311--246362 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
246301 TTCTTTTCAA
*
246311 ATTTTTTATTTTTATTT
1 ATTTATTATTTTTATTT
*
246328 ATTTATTATTTTTATAAT
1 ATTTATTATTTTTAT-TT
246346 ATTTA-TATGTTTTATTT
1 ATTTATTAT-TTTTATTT
246363 GCAAGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTATTATTTTTATTT
Found at i:257001 original size:33 final size:33
Alignment explanation
Indices: 256964--257037 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
256954 TTATGCTTGA
*
256964 AAAAAAAAAAAAGAAAAGAA-AAAGAAGAGAAAG
1 AAAAAAAAAAAAGAAAAGAAGAAA-AAGAAAAAG
*
256997 AAAAAAAAAAAGGAAAAGAAGAAAAAGAAAAAG
1 AAAAAAAAAAAAGAAAAGAAGAAAAAGAAAAAG
257030 AAAAAAAA
1 AAAAAAAA
257038 GGGTCAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAAGAAAAGAAGAAAAAGAAAAAG
Found at i:257008 original size:27 final size:27
Alignment explanation
Indices: 256962--257035 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
256952 TATTATGCTT
*
256962 GAAAAAAAAAAAAAGAAAAGAAAAAGAA
1 GAAAAAGAAAAAAA-AAAAGAAAAAGAA
* *
256990 GAGAAAGAAAAAAAAAAAGGAAAAGAA
1 GAAAAAGAAAAAAAAAAAGAAAAAGAA
257017 GAAAAAGAAAAAGAAAAAA
1 GAAAAAGAAAAA-AAAAAA
257036 AAGGGTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (27 bp):
GAAAAAGAAAAAAAAAAAGAAAAAGAA
Found at i:258078 original size:52 final size:53
Alignment explanation
Indices: 258013--258371 Score: 613
Period size: 52 Copynumber: 6.9 Consensus size: 53
258003 ATGGAAAAGC
*
258013 ATCAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
258065 ATCATAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
258118 A-CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
258169 ATCATAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
258222 A-CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
258273 ATCATAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
* *
258326 A-CAGAACATAGCATTTTCTGGAAGTGTTCTTTGAGATATCTGATCT
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
258372 AATTGGATAG
Statistics
Matches: 291, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
51 4 0.01
52 281 0.97
53 6 0.02
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.38
Consensus pattern (53 bp):
ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
Found at i:258391 original size:104 final size:104
Alignment explanation
Indices: 258015--258371 Score: 678
Period size: 104 Copynumber: 3.4 Consensus size: 104
258005 GGAAAAGCAT
258015 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
1 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
258080 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
66 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
258119 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
1 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
258184 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
66 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
258223 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
1 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
258288 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
66 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
* * *
258327 CAGAACATAGCATTTTCTGGAAGTGTTCTTTGAGATATCTGATCT
1 CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
258372 AATTGGATAG
Statistics
Matches: 248, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 248 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.38
Consensus pattern (104 bp):
CAGAACATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAACATAGCAT
CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
Found at i:259164 original size:115 final size:114
Alignment explanation
Indices: 259001--259910 Score: 1316
Period size: 115 Copynumber: 7.8 Consensus size: 114
258991 CAAAGATTTG
* *
259001 AATTCATCAAATTGATGGATCATTCATTTTCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCAT
1 AATTCATC-ACTTGATGGATCATT--TTTTC-CA-G-AGAGTTCATAATGAGAAGAACTCGTCAT
259066 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
60 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
259121 AATTCATCACTTGATGGATCATTTGTTTCCAGAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 AATTCATCACTTGATGGATCATTT-TTTCCAGAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
259186 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
259236 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCATT-TTTTCC--AG-AGAGTTCATAATGAGAAGAACTCGTCATCT
*
259301 GAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
259354 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTG
1 AATTCATCACTTGATGGATCATT-TTTTCCAGAG-A-GTTCATAATGAGAAGAACTCGTCATCTG
* *
259416 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* *
259468 AATTCATCAAATTGATGGATCATTGTTTCCAGAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 AATTCATC-ACTTGATGGATCATTTTTTCCAGAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
*
259533 GAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
259583 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTG
1 AATTCATCACTTGATGGATCATT-TTTTCCAGAG-A-GTTCATAATGAGAAGAACTCGTCATCTG
* *
259645 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* ** *
259697 AATTCATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGTCATC
1 AATTCATC-ACTTGATGGATCATTTTTTCC--A-G-AGAGTTCATAATGAGAAGAACTCGTCATC
* * *
259762 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* *** * *
259816 AATTCATCATTTGATGGATCAACATTACCAGGTAAAGTTCATAATGAGAAGAA--C-TCATCTGA
1 AATTCATCACTTGATGGATCATTTTTTCCA-G-AGAGTTCATAATGAGAAGAACTCGTCATCTGA
*
259878 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
259911 CATCAAGAGC
Statistics
Matches: 738, Mismatches: 30, Indels: 51
0.90 0.04 0.06
Matches are distributed among these distances:
112 17 0.02
113 40 0.05
114 158 0.21
115 215 0.29
116 44 0.06
117 40 0.05
118 136 0.18
119 80 0.11
120 8 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (114 bp):
AATTCATCACTTGATGGATCATTTTTTCCAGAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
Found at i:259485 original size:233 final size:234
Alignment explanation
Indices: 258998--259910 Score: 1528
Period size: 233 Copynumber: 3.9 Consensus size: 234
258988 TAGCAAAGAT
* *
258998 TTGAATTCATCAAATTGATGGATCATTCATTTTCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 TTGAATTCATCAAATTGATGGATCATTCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
259063 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
259128 CACTTGATGGATCATT-TGTTTCCAGAG-A-GTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
131 CACTTGATGGATCATTCT-TTTCCAGAGAAGGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
*
259190 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGT
192 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
259233 TTAAATTCATC-ACTTGATGGATCATTCTTTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGT
1 TTGAATTCATCAAATTGATGGATCATTCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
*
259296 CATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
259361 CACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
131 CACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
259426 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
196 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
259465 TTGAATTCATCAAATTGATGGATCATT-GTTTCC--A-G-AGAGTTCATAATGAGAAGAACTCGT
1 TTGAATTCATCAAATTGATGGATCATTCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
*
259525 CATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
259590 CACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
131 CACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
259655 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
196 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
259694 TTGAATTCATCAAATTGATGGATCA-TCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGT
1 TTGAATTCATCAAATTGATGGATCATTCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
* * *
259758 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCAT
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
* * * * *
259823 CATTTGATGGATCA-ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
131 CACTTGATGGATCATTCTTTTCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
259886 GAAAAAGTTCATAATGAGAAGAACT
195 GAAGAAGTTCATAATGAGAAGAACT
259911 CATCAAGAGC
Statistics
Matches: 646, Mismatches: 22, Indels: 23
0.93 0.03 0.03
Matches are distributed among these distances:
228 1 0.00
229 223 0.35
230 2 0.00
231 2 0.00
232 138 0.21
233 229 0.35
234 24 0.04
235 27 0.04
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (234 bp):
TTGAATTCATCAAATTGATGGATCATTCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCAT
CACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:260166 original size:3 final size:3
Alignment explanation
Indices: 260160--260336 Score: 250
Period size: 3 Copynumber: 59.7 Consensus size: 3
260150 TTTTTATCCA
*
260160 TAT TAT TAT TAT TA- TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
260206 TAT TAT TAA TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
260254 TAT TAT TAT TAA TAT TAT TAT TAT CAT TGT TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
260302 TAT TTT TAT TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
260337 AATATATTAA
Statistics
Matches: 152, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
2 4 0.03
3 148 0.97
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:261764 original size:22 final size:21
Alignment explanation
Indices: 261725--261767 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
261715 GATATTTTTA
**
261725 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
261746 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
261768 GCATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:262804 original size:6 final size:6
Alignment explanation
Indices: 262793--262817 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
262783 TCTGGTTTTG
262793 GGGATT GGGATT GGGATT GGGATT G
1 GGGATT GGGATT GGGATT GGGATT G
262818 TGATCTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGATT
Found at i:266304 original size:2 final size:2
Alignment explanation
Indices: 266297--266325 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
266287 TCCAATCCAA
266297 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
266326 AGATCAATTA
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:274714 original size:2 final size:2
Alignment explanation
Indices: 274707--274753 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
274697 AAAAATCAAG
274707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
274749 TA TA T
1 TA TA T
274754 CGTCTGAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:287494 original size:3 final size:3
Alignment explanation
Indices: 287488--287534 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
287478 CAAAAAAACG
287488 TTA TTA -TA TTA TTA TT- TTA TTA TCTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
287531 TTA T
1 TTA T
287535 CTTATTACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.15
3 32 0.80
4 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:287517 original size:20 final size:20
Alignment explanation
Indices: 287488--287541 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
287478 CAAAAAAACG
287488 TTATTATATTATTATT-TTA
1 TTATTATATTATTATTATTA
287507 TTATCTATATTATTATTATTA
1 TTAT-TATATTATTATTATTA
*
287528 TTATTATCTTATTA
1 TTATTATATTATTA
287542 CTAATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 4 0.12
20 21 0.66
21 7 0.22
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATATTATTATTATTA
Found at i:287540 original size:32 final size:29
Alignment explanation
Indices: 287488--287548 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 29
287478 CAAAAAAACG
*
287488 TTATTATATTATTATTTTATTATCTATATTA
1 TTATTATATTATTATCTTATTA-CTA-ATTA
287519 TTATTATTATTATTATCTTATTACTAATTA
1 TTATTA-TATTATTATCTTATTACTAATTA
287549 ATTACATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 9 0.32
32 15 0.54
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATTATATTATTATCTTATTACTAATTA
Found at i:290608 original size:29 final size:29
Alignment explanation
Indices: 290566--290639 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
290556 TTTCATATGT
290566 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
290594 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
290623 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
290640 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:291058 original size:27 final size:26
Alignment explanation
Indices: 291028--291086 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
291018 TAAAAGGTAT
*
291028 TCGATGTAGT-ATTATTGATGGGATGCA
1 TCGATGT-GTCATTATTAAT-GGATGCA
*
291055 TCGATGTTTCATTATTAATGGATGCA
1 TCGATGTGTCATTATTAATGGATGCA
291081 TCGATG
1 TCGATG
291087 CACTACTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (26 bp):
TCGATGTGTCATTATTAATGGATGCA
Found at i:297626 original size:29 final size:29
Alignment explanation
Indices: 297584--297655 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
297574 TCATATGTTT
297584 ATGTA-CTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
*
297612 ATGTAGCTCGTGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
297641 ATGTAGCTCATGTCA
1 ATGTAGCTCATGTCA
297656 CTTCATATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (29 bp):
ATGTAGCTCATGTCATTTCTCTTGTGATC
Found at i:298062 original size:27 final size:27
Alignment explanation
Indices: 298032--298091 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
298022 TAAAAGGTAT
**
298032 TCGATGTAGT-ATTATTGCTGGGATGCA
1 TCGATGT-GTCATTATTAATGGGATGCA
*
298059 TCGATGTTTCATTATTAATGGGATGCA
1 TCGATGTGTCATTATTAATGGGATGCA
298086 TCGATG
1 TCGATG
298092 CACTACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (27 bp):
TCGATGTGTCATTATTAATGGGATGCA
Found at i:298127 original size:64 final size:63
Alignment explanation
Indices: 298055--298176 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 63
298045 ATTGCTGGGA
* * **
298055 TGCATCGATG-TTTCATTATT-AATGGGATGCATCGATGCACTACTTATGCATCGATGCATGAAT
1 TGCATCGATGTTTTCATT-TTAAAAGAG-TGCATCGATGCACTACCAATGCATCGATGCATGAAT
*
298118 TGCATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACCAATGCATCGATGCA
1 TGCA-TCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACCAATGCATCGATGCA
298177 CATTCAAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
63 4 0.08
64 37 0.73
65 10 0.20
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
TGCATCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACCAATGCATCGATGCATGAAT
Found at i:299379 original size:22 final size:21
Alignment explanation
Indices: 299351--299395 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
299341 AATGTTATTA
299351 TATTATTATT-TTATATCTATAT
1 TATTATTATTATTA-ATCT-TAT
299373 TATTATTATTATTAATCTTAT
1 TATTATTATTATTAATCTTAT
299394 TA
1 TA
299396 CTAATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 14 0.64
23 3 0.14
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTATTATTAATCTTAT
Found at i:312471 original size:13 final size:13
Alignment explanation
Indices: 312453--312477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312443 AATAAAATAA
312453 AAAATATATATTT
1 AAAATATATATTT
312466 AAAATATATATT
1 AAAATATATATT
312478 AATTTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATATATATTT
Found at i:313232 original size:19 final size:19
Alignment explanation
Indices: 313176--313234 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
313166 AAAACCGAAA
* *
313176 TCGGTTTTTTCGGTTCGGT
1 TCGGGTTTTTCGATTCGGT
* * *
313195 TCGAGTTTTT-TA-ACGGT
1 TCGGGTTTTTCGATTCGGT
313212 TCGGGTTTTTCGATTCGGT
1 TCGGGTTTTTCGATTCGGT
313231 TCGG
1 TCGG
313235 TTCGATTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 13 0.43
18 1 0.03
19 16 0.53
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TCGGGTTTTTCGATTCGGT
Found at i:315244 original size:31 final size:31
Alignment explanation
Indices: 315206--315330 Score: 196
Period size: 31 Copynumber: 4.0 Consensus size: 31
315196 CCCGAAGGAC
* * * *
315206 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
315237 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
315268 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
315299 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
315330 C
1 C
315331 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Done.