Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004109.1 Hibiscus syriacus cultivar Beakdansim tig00008994_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: 163315
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:1426 original size:3 final size:3
Alignment explanation
Indices: 1418--1461 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1408 GTCCGGGATA
*
1418 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA- TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
1462 ATACTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5428 original size:125 final size:123
Alignment explanation
Indices: 5198--5491 Score: 421
Period size: 125 Copynumber: 2.4 Consensus size: 123
5188 GGCCAAGATG
* * * * * *
5198 TTTGGGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAACATTGGGGCACGACTGAGC
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
* * *
5263 CCACATCATGTTGAGATGACAAAATTCATACCAAGGAGGCA-TGAAGAATGAGCCTTACAA
66 CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTG-AGAATGAGCCTT--AA
5323 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
* * *
5388 CCACATCATGTTGATATGGCAAGATTCAGAACAAGAAGGCATTGAGAATGAGCCTTAA
66 CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTGAGAATGAGCCTTAA
* *
5446 TTTGAGGTG-TTGGGCATTTTGAAGGCTCGTACCAATATAAGATAAT
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAAT
5492 GTTGTGGCAC
Statistics
Matches: 154, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
122 35 0.23
123 11 0.07
125 106 0.69
126 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (123 bp):
TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTGAGAATGAGCCTTAA
Found at i:6467 original size:22 final size:22
Alignment explanation
Indices: 6426--6468 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6416 TTTCAATATG
*
6426 CATATATATATATATTTCATGA
1 CATATATATATATATGTCATGA
6448 CATATATATA-ATCATGTCATG
1 CATATATATATAT-ATGTCATG
6469 CACACATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
CATATATATATATATGTCATGA
Found at i:6697 original size:15 final size:15
Alignment explanation
Indices: 6677--6726 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
6667 CCGTAGGACC
6677 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
6692 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
6707 ACTACATCCCGAAGG
1 ACTACGTCCCGAAGG
6722 ACTAC
1 ACTAC
6727 AATACCCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.30, C:0.34, G:0.22, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:9143 original size:42 final size:42
Alignment explanation
Indices: 9071--9167 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
9061 ACTTAGTATG
* * *
9071 TCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
* * * *
9113 TCCTTAGGGTCATCTGTAAGCCTTTTGAGCAAGATGA-TAAG
1 TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
* *
9154 TACTTCGGGCCATC
1 TCCTTAGGGCCATC
9168 CATAAGACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 14 0.31
42 31 0.69
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
Found at i:9242 original size:215 final size:214
Alignment explanation
Indices: 8852--9785 Score: 1081
Period size: 225 Copynumber: 4.3 Consensus size: 214
8842 CCAAAATTTA
* * *
8852 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAATCCTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * *
8917 GCCTTTTGAGCAAGACGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAA
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
*
8982 AGGAATTTG-AAAATGAGAAAATGATGTTTTAAAGAGATGAAATTTTTGAAAACTAAGAATGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAAA-AGATGAAA-TTTTGAAAACTAAGAATGCGA
*
9046 TTTCCAAAATTTCACACTTAG
194 TTTCCAAAATTTCACAATTAG
* * *
9067 TATGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * *
9132 GCCTTTTGAGCAAGATGATAAGTACTTCGGGCCATCCATAAGACCTTC-AGTAGGATGTTTTCAA
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
*
9196 AAGAATTTG-AAAATGAGAAAATGATGTTTTAAGAAGATGAAAATTTTGAAAACTATGAATGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAA-AAGATG-AAATTTTGAAAACTAAGAATGCGA
*
9260 TTTCC-AAATTTCACATTTAG
194 TTTCCAAAATTTCACAATTAG
* * * *
9280 TAAGTCCTTCGGGCCATCAATAAGTCTTTTGAACATGATGCTTAAATCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * *
9345 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTTGGGCATGATGTTTTCAC
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
** * * ** * **
9410 AAGTCTATCGAAAAATGAG-AAA-GATTTCTCATTAAAATCTGAAGA-TTTGAAAAGTAAGAAAA
131 AAGAAT-TTGAAAAATGAGAAAATGATGT-T--TTAAAAGATGAA-ATTTTGAAAACTAAGAATG
*** * *
9472 ATTTCTTACCTAGTAAATTATTTCCAAAATTGG
191 CGAT-TT-CC----AAA--ATTT-CACAATTAG
* * * * *
9505 TATGTCATTCGGGCCATCAGTAAGTCTTTCGAGTATGATGTTTAAACCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * * *
9570 ACCTTTTGATCAAGGTGATAAGTCCTTCTGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAC
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
* * ** * * *
9635 AATAAGTTGAAAAATGAGAAAGCGATGTTTTAAGAAAATGAAATATTTGAAAACTACGAAGGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAA-AAGATGAAAT-TTTGAAAACTAAGAATGCGA
* **
9700 TTTCCAAATTTTTGCAATTAG
194 TTTCCAAAATTTCACAATTAG
* * *
9721 TAAGTCCTTCGGGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
9786 CTTCACGAAA
Statistics
Matches: 609, Mismatches: 86, Indels: 47
0.82 0.12 0.06
Matches are distributed among these distances:
213 117 0.19
214 96 0.16
215 131 0.22
216 77 0.13
217 9 0.01
219 3 0.00
222 2 0.00
223 7 0.01
224 23 0.04
225 140 0.23
226 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (214 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
AAGAATTTGAAAAATGAGAAAATGATGTTTTAAAAGATGAAATTTTGAAAACTAAGAATGCGATT
TCCAAAATTTCACAATTAG
Found at i:9351 original size:42 final size:41
Alignment explanation
Indices: 9284--9392 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
9274 ATTTAGTAAG
* * * *
9284 TCCTTCGGGCCATCAATAAGTCTTTTGAACATGATGCTTAAA
1 TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATG-ATAAA
* ** * *
9326 TCCTTCGGGTCATCTGTAAGCCTTTTGAGCAAGATGATAAG
1 TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATGATAAA
*
9367 TCCTTCGGGACATCCATAAGACCTTT
1 TCCTTCGGGACATCAATAAG-CCTTT
9393 GGGCATGATG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.36
42 35 0.64
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATGATAAA
Found at i:9978 original size:37 final size:37
Alignment explanation
Indices: 9937--10089 Score: 227
Period size: 37 Copynumber: 4.2 Consensus size: 37
9927 GGCCTTCGGG
9937 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
9974 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-GAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * *
10010 CCATTTTAAGCTTTCACCGAAGAGTAGTAAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
10047 CCATCTTAAGCCTTCATCGAAGAGTGGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
10084 CAATCT
1 CCATCT
10090 CGAGTCTGAT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 31 0.30
37 71 0.70
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (37 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:10030 original size:73 final size:73
Alignment explanation
Indices: 9937--10079 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
9927 GGCCTTCGGG
*
9937 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCA-CAGAAGAGTAG
1 CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATC-GAAGAGTAG
10001 TGAAGCGAT
65 TGAAGCGAT
* * *
10010 CCATTTTAAGCTTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTGGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
10075 GAAGC
66 GAAGC
10080 AAATCAATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
73 64 0.98
74 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (73 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
GAAGCGAT
Found at i:16155 original size:13 final size:13
Alignment explanation
Indices: 16137--16161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16127 ATTACAGACG
16137 TGCATATGAAGAT
1 TGCATATGAAGAT
16150 TGCATATGAAGA
1 TGCATATGAAGA
16162 CTGTTCAACT
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:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
TGCATATGAAGAT
Found at i:24329 original size:29 final size:29
Alignment explanation
Indices: 24297--24353 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
24287 AGAATAATAT
*
24297 TATA-CATTAAATTAATAATTAATATTTTG
1 TATATCATTAAATT-ATAATTAAAATTTTG
* *
24326 TATATCTTTCAATTATAATTAAAATTTT
1 TATATCATTAAATTATAATTAAAATTTT
24354 ATTTTGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (29 bp):
TATATCATTAAATTATAATTAAAATTTTG
Found at i:34339 original size:48 final size:48
Alignment explanation
Indices: 34266--34407 Score: 268
Period size: 48 Copynumber: 3.0 Consensus size: 48
34256 ACGCGAAGTC
*
34266 ATTAATTAAAATATTAAATTGTATTCTTTAAAAAATATATCCACGTTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
34314 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
34362 ATTAATTAAAATATTAAATTATATTCTTT-AAAAATATATCCACGTT
1 ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTT
34408 GAAGAAAACT
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
47 17 0.18
48 76 0.82
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (48 bp):
ATTAATTAAAATATTAAATTATATTCTTTAAAAAATATATCCACGTTT
Found at i:34370 original size:26 final size:26
Alignment explanation
Indices: 34293--34372 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 26
34283 ATTGTATTCT
34293 TTAAAAAATATATCCACGTTTATTAA
1 TTAAAAAATATATCCACGTTTATTAA
** **
34319 TT--AAAATAT-T--AAATTATATTCT
1 TTAAAAAATATATCCACGTT-TATTAA
34341 TTAAAAAATATATCCACGTTTATTAA
1 TTAAAAAATATATCCACGTTTATTAA
34367 TTAAAA
1 TTAAAA
34373 TATTAAATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
21 3 0.08
22 6 0.15
23 1 0.03
24 14 0.35
25 1 0.03
26 12 0.30
27 3 0.08
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (26 bp):
TTAAAAAATATATCCACGTTTATTAA
Found at i:34392 original size:22 final size:22
Alignment explanation
Indices: 34319--34394 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 22
34309 CGTTTATTAA
34319 TTAAAATATTAAATTATATTCT
1 TTAAAATATTAAATTATATTCT
** **
34341 TTAAAAAATATATCCACGTT-TATTAA
1 TT--AAAATAT-T--AAATTATATTCT
34367 TTAAAATATTAAATTATATTCT
1 TTAAAATATTAAATTATATTCT
34389 TTAAAA
1 TTAAAA
34395 ATATATCCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
21 3 0.08
22 12 0.30
23 1 0.03
24 14 0.35
25 1 0.03
26 6 0.15
27 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (22 bp):
TTAAAATATTAAATTATATTCT
Found at i:38367 original size:19 final size:20
Alignment explanation
Indices: 38343--38390 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
38333 TCTAGCAAAT
*
38343 GATCGATTCATTT-CAAAAG
1 GATCGATCCATTTACAAAAG
* *
38362 GATCGATCCCTTTACAAAAT
1 GATCGATCCATTTACAAAAG
38382 GATCGATCC
1 GATCGATCC
38391 TTTCTCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (20 bp):
GATCGATCCATTTACAAAAG
Found at i:38385 original size:20 final size:19
Alignment explanation
Indices: 38339--38394 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
38329 TTTGTCTAGC
*
38339 AAATGATCGATTCATTTCA
1 AAATGATCGATCCATTTCA
* *
38358 AAAGGATCGATCCCTTTACA
1 AAATGATCGATCCATTT-CA
38378 AAATGATCGATCC-TTTC
1 AAATGATCGATCCATTTC
38395 TCTGTTTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 14 0.44
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (19 bp):
AAATGATCGATCCATTTCA
Found at i:45173 original size:21 final size:21
Alignment explanation
Indices: 45147--45186 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45137 CAGAACCCCA
*
45147 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
45168 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
45187 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:45221 original size:20 final size:21
Alignment explanation
Indices: 45167--45229 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
45157 GATTCCCCTG
45167 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
45191 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
45211 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
45230 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:58333 original size:37 final size:37
Alignment explanation
Indices: 58280--58353 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
58270 TAGGTTTTGT
*
58280 ATTATTATATACAAATATTATAAAACATATAAGTTGC
1 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
58317 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
1 ATTATTATATAAAAATATTATAAAACATATAAGTTGC
58354 CAAATAGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (37 bp):
ATTATTATATAAAAATATTATAAAACATATAAGTTGC
Found at i:58655 original size:13 final size:13
Alignment explanation
Indices: 58637--58661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58627 CATAGTTGAA
58637 CAGTCTTCATATG
1 CAGTCTTCATATG
58650 CAGTCTTCATAT
1 CAGTCTTCATAT
58662 ACGCGTCTGT
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:65808 original size:16 final size:17
Alignment explanation
Indices: 65785--65824 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
65775 GTTTATTTGA
65785 AAATTTAAA-ATTTTAT
1 AAATTTAAATATTTTAT
* *
65801 ATATTTAAATGTTTTAT
1 AAATTTAAATATTTTAT
65818 AAATTTA
1 AAATTTA
65825 TTTATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTTAAATATTTTAT
Found at i:68024 original size:15 final size:13
Alignment explanation
Indices: 67993--68017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67983 ATAAATATCG
67993 AATACAAATATTA
1 AATACAAATATTA
68006 AATACAAATATT
1 AATACAAATATT
68018 TTAAATAATG
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AATACAAATATTA
Found at i:69439 original size:28 final size:28
Alignment explanation
Indices: 69399--69455 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
69389 TATAAAAGGA
69399 AAGAAGAACAAAAGTATCATAGGAAAAT
1 AAGAAGAACAAAAGTATCATAGGAAAAT
69427 AAGAAGAACAAAAGTATCATAGGAAAAT
1 AAGAAGAACAAAAGTATCATAGGAAAAT
69455 A
1 A
69456 TGGCAACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (28 bp):
AAGAAGAACAAAAGTATCATAGGAAAAT
Found at i:74333 original size:15 final size:17
Alignment explanation
Indices: 74298--74335 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
74288 ATTAAATAAC
74298 TTAATATAATACTAATA
1 TTAATATAATACTAATA
*
74315 TTAATATAA-A-TATTA
1 TTAATATAATACTAATA
74330 TTAATA
1 TTAATA
74336 CTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATATAATACTAATA
Found at i:75560 original size:3 final size:3
Alignment explanation
Indices: 75552--75624 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
75542 AACTATTAAG
75552 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
75600 AAT AAT -AT AAT -AT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
75625 TTTATTATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 6 0.09
3 61 0.91
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:75883 original size:36 final size:36
Alignment explanation
Indices: 75821--75925 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
75811 TGATCTAATC
75821 TTGCTTCACTACTCTTTTTGTGAAGGCT-GAATTTGCA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTAG-ATTTGCA
75858 TTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCA
*
75894 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTAGATT
75926 AACTTGAGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
36 51 0.77
37 15 0.23
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCA
Found at i:76350 original size:18 final size:18
Alignment explanation
Indices: 76319--76353 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
76309 TGAATTCCAC
76319 CAATACAAATTATTTCAT
1 CAATACAAATTATTTCAT
76337 CAATGACAAA-TATTTCA
1 CAAT-ACAAATTATTTCA
76354 GATTATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (18 bp):
CAATACAAATTATTTCAT
Found at i:77993 original size:3 final size:3
Alignment explanation
Indices: 77985--78010 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
77975 TCAAGGTTTC
77985 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
78011 AATGTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:87050 original size:20 final size:20
Alignment explanation
Indices: 87012--87095 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
87002 ATTTGTTTTC
*
87012 TAAAT-TAAATAACTTAATA-
1 TAAATATAAAT-ATTTAATAT
87031 TAAATACTAAATATTTAATAT
1 TAAATA-TAAATATTTAATAT
* *
87052 TTAATATAAATATTATTAATAC
1 TAAATATAAATA-T-TTAATAT
* *
87074 T-ATTAT-AATATTTAACAT
1 TAAATATAAATATTTAATAT
87092 TAAA
1 TAAA
87096 ACTATATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
18 6 0.12
19 7 0.13
20 17 0.33
21 15 0.29
22 7 0.13
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATAAATATTTAATAT
Found at i:87194 original size:20 final size:23
Alignment explanation
Indices: 87155--87203 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 23
87145 ACTAGTATTA
87155 ATTAATTATAATAATAATTAATG
1 ATTAATTATAATAATAATTAATG
*
87178 ATTAA-TATAA-AAT-ATTAA-A
1 ATTAATTATAATAATAATTAATG
87197 ATTAATT
1 ATTAATT
87204 GACCCAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 3 0.12
22 5 0.21
23 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAATTATAATAATAATTAATG
Found at i:87289 original size:14 final size:14
Alignment explanation
Indices: 87269--87303 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
87259 TTATGAATAT
87269 GACTAAAATATAAA
1 GACTAAAATATAAA
*
87283 TACTAAAATATAAA
1 GACTAAAATATAAA
87297 GACTAAA
1 GACTAAA
87304 TGTATGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.23
Consensus pattern (14 bp):
GACTAAAATATAAA
Found at i:88489 original size:3 final size:3
Alignment explanation
Indices: 88481--88518 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
88471 AACTATTAAG
*
88481 AAT AAT AAT AAT AAT AAT -AT AAT TAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
88519 TTTATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:88508 original size:11 final size:11
Alignment explanation
Indices: 88481--88518 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
88471 AACTATTAAG
88481 AATAATAATAAT
1 AATAAT-ATAAT
88493 AATAATATAAT
1 AATAATATAAT
*
88504 TATAATATAAT
1 AATAATATAAT
88515 AATA
1 AATA
88519 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAATATAAT
Found at i:89018 original size:14 final size:14
Alignment explanation
Indices: 88981--89010 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88971 TCATTTGTGC
88981 AAATCCCTTTATGT
1 AAATCCCTTTATGT
*
88995 AAATCCCTTTGTGT
1 AAATCCCTTTATGT
89009 AA
1 AA
89011 TTCGCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (14 bp):
AAATCCCTTTATGT
Found at i:93610 original size:9 final size:9
Alignment explanation
Indices: 93598--93646 Score: 61
Period size: 8 Copynumber: 5.9 Consensus size: 9
93588 AAAAACATAA
*
93598 AAAAGAGAG
1 AAAAGAAAG
93607 AAAAGAAAG
1 AAAAGAAAG
93616 -AAAGAAA-
1 AAAAGAAAG
93623 AAAAGAAAG
1 AAAAGAAAG
93632 -AAAGAAAG
1 AAAAGAAAG
93640 -AAAGAAA
1 AAAAGAAA
93647 ACCAATCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
8 29 0.78
9 8 0.22
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:93617 original size:4 final size:4
Alignment explanation
Indices: 93608--93646 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
93598 AAAAGAGAGA
*
93608 AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
93647 ACCAATCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:101135 original size:24 final size:23
Alignment explanation
Indices: 101107--101166 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 23
101097 CCAGCGGGTT
101107 TAGAATCGGATGCGCGAGCTTTA
1 TAGAATCGGATGCGCGAGCTTTA
*
101130 GTAGAATCGGATGCACGAGCTTTA
1 -TAGAATCGGATGCGCGAGCTTTA
101154 T--AATCGGATGCGC
1 TAGAATCGGATGCGC
101167 TCGCCCAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 11 0.32
23 1 0.03
24 22 0.65
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (23 bp):
TAGAATCGGATGCGCGAGCTTTA
Found at i:101796 original size:33 final size:33
Alignment explanation
Indices: 101754--101816 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
101744 GCACGGGATG
*
101754 GTAGTTGGATGATAGCACAAAGTCAGTTGCTGA
1 GTAGTTGGATGATAGCACAAAGTAAGTTGCTGA
101787 GTAGTTGGATGATAGCACAAAGTAAGTTGC
1 GTAGTTGGATGATAGCACAAAGTAAGTTGC
101817 AGCTAGGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (33 bp):
GTAGTTGGATGATAGCACAAAGTAAGTTGCTGA
Found at i:103114 original size:19 final size:19
Alignment explanation
Indices: 103090--103127 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
103080 ACGGGTAACG
103090 TGATCAGCAGGACAAATAA
1 TGATCAGCAGGACAAATAA
* *
103109 TGATCAGCGGGACACATAA
1 TGATCAGCAGGACAAATAA
103128 CGTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (19 bp):
TGATCAGCAGGACAAATAA
Found at i:140796 original size:13 final size:13
Alignment explanation
Indices: 140778--140803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
140768 TTTTGGGGGA
140778 ATAATATATATAT
1 ATAATATATATAT
140791 ATAATATATATAT
1 ATAATATATATAT
140804 CGCTTTTCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATATATATAT
Done.