Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000633.1 Hibiscus syriacus cultivar Beakdansim tig00001229_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: 57238
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:295 original size:40 final size:41
Alignment explanation
Indices: 216--452 Score: 340
Period size: 42 Copynumber: 5.8 Consensus size: 41
206 GAGCTTAGAA
*
216 AAACTGTAAGGCTTTATCCTTGCACACAACAAGGAACCTGGG
1 AAACTGTAAGGC-TTACCCTTGCACACAACAAGGAACCTGGG
258 AAACTGTAAGGCTTACCCTTGCAC-CAACAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAGGAACCTGGG
* *
298 AAACTGTAA-GCTTACCCTTGCACACAAAAAAGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAGGAACCT-GGG
*
339 GAACTGTAAGGCTTACCCTTGCACAGCAA-AAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACA-CAACAAGGAACCT-GGG
*
381 GAACTGTAAGGCTTACCCTTGCACACAAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACAC-AAC-AAGGAACCTGGG
424 -AA-TGTAAGGCTTACCCTTGCACACAACAA
1 AAACTGTAAGGCTTACCCTTGCACACAACAA
453 AGCCTGCTGT
Statistics
Matches: 183, Mismatches: 5, Indels: 17
0.89 0.02 0.08
Matches are distributed among these distances:
39 16 0.09
40 39 0.21
41 45 0.25
42 68 0.37
43 6 0.03
44 9 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (41 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAGGAACCTGGG
Found at i:3408 original size:10 final size:11
Alignment explanation
Indices: 3383--3411 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3373 CCCTGATATC
3383 GAAAAATTCCT
1 GAAAAATTCCT
3394 GAAAAATTCCT
1 GAAAAATTCCT
3405 -AAAAATT
1 GAAAAATT
3412 ATTTTAAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (11 bp):
GAAAAATTCCT
Found at i:6428 original size:24 final size:24
Alignment explanation
Indices: 6306--6413 Score: 171
Period size: 24 Copynumber: 4.5 Consensus size: 24
6296 TTCAGTTATT
* *
6306 ATACCTGACCTGGATTATGATATG
1 ATACTTGACCTGGATTTTGATATG
* *
6330 ATACTTGACTTGGATTTTGGTATG
1 ATACTTGACCTGGATTTTGATATG
6354 ATACTTGACCTGGATTTTGATATG
1 ATACTTGACCTGGATTTTGATATG
*
6378 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATATG
6402 ATACTTGACCTG
1 ATACTTGACCTG
6414 AATTATGCTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATATG
Found at i:7516 original size:17 final size:18
Alignment explanation
Indices: 7483--7516 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7473 GCCAAAGCAA
*
7483 GAAAAATAAATGGCATTG
1 GAAAAATAAATGACATTG
7501 GAAAAATAAAT-ACATT
1 GAAAAATAAATGACATT
7517 CTTCATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (18 bp):
GAAAAATAAATGACATTG
Found at i:10625 original size:30 final size:30
Alignment explanation
Indices: 10589--10647 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
10579 CAACTTCTCT
* *
10589 AAAATTACCAAATTGGTTCCC-AATTTTTCA
1 AAAATTA-CAAAATGGTCCCCAAATTTTTCA
10619 AAAATTACAAAATGGTCCCCAAATTTTTC
1 AAAATTACAAAATGGTCCCCAAATTTTTC
10648 TAAGGCTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (30 bp):
AAAATTACAAAATGGTCCCCAAATTTTTCA
Found at i:11383 original size:31 final size:31
Alignment explanation
Indices: 11340--11402 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11330 AATCACCATT
11340 AAACCAAGACACCTCAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
*
11371 AAACCAATACACCTCAACCTTATCATCTTCC
1 AAACCAAGACACCTCAACCTTATCATCTTCC
11402 A
1 A
11403 TAAGTAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.38, G:0.02, T:0.24
Consensus pattern (31 bp):
AAACCAAGACACCTCAACCTTATCATCTTCC
Found at i:16906 original size:12 final size:12
Alignment explanation
Indices: 16881--16941 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
16871 AATGCTGAAA
16881 TTACTGTAGCAG
1 TTACTGTAGCAG
* *
16893 TTATTGTAGTAG
1 TTACTGTAGCAG
16905 TTACTGTAG-ATG
1 TTACTGTAGCA-G
*
16917 TTACTGTAGCGG
1 TTACTGTAGCAG
*
16929 TTACTATAGCAG
1 TTACTGTAGCAG
16941 T
1 T
16942 ACATCGATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 1 0.02
12 40 0.98
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:16961 original size:21 final size:21
Alignment explanation
Indices: 16935--16974 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16925 GCGGTTACTA
16935 TAGCAGTACATCGATGCACTG
1 TAGCAGTACATCGATGCACTG
**
16956 TAGCAGTGTATCGATGCAC
1 TAGCAGTACATCGATGCAC
16975 AATTAAATTT
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:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TAGCAGTACATCGATGCACTG
Found at i:17779 original size:15 final size:15
Alignment explanation
Indices: 17759--17796 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
17749 CAAGTCACAT
17759 GGGAATTCTTTCTAA
1 GGGAATTCTTTCTAA
*
17774 GGGAATTCTTTCTGA
1 GGGAATTCTTTCTAA
17789 GGGAATTC
1 GGGAATTC
17797 AAGGAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (15 bp):
GGGAATTCTTTCTAA
Found at i:23650 original size:2 final size:2
Alignment explanation
Indices: 23645--23679 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23635 AATTTTTTTA
23645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23680 TATTAAGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:25354 original size:16 final size:16
Alignment explanation
Indices: 25323--25353 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
25313 TAGATATAAA
25323 CTTTTCTCTTTTTTTT
1 CTTTTCTCTTTTTTTT
25339 CTTTTCT-TTTTTTTT
1 CTTTTCTCTTTTTTTT
25354 TAAAACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTCTCTTTTTTTT
Found at i:37824 original size:12 final size:12
Alignment explanation
Indices: 37807--37840 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
37797 CAGAAATTAT
37807 TGTAGCAGTTAC
1 TGTAGCAGTTAC
37819 TGTAGCAG-TAC
1 TGTAGCAGTTAC
37830 TGTAGCAGTTA
1 TGTAGCAGTTA
37841 GCAGCACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (12 bp):
TGTAGCAGTTAC
Found at i:38280 original size:81 final size:81
Alignment explanation
Indices: 38142--38534 Score: 606
Period size: 81 Copynumber: 4.9 Consensus size: 81
38132 GGGTGTTACG
* * *
38142 GAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAACGGCTT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
38207 AGTTGTGCATTTGACA
66 AGCTGTGCATTTGACA
* * * **
38223 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACATTTGAGTAAACGATTAATGTTCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* *
38288 AGTTGTGCATTTGATA
66 AGCTGTGCATTTGACA
*
38304 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
38369 AGCTGTGCATTTGATA
66 AGCTGTGCATTTGACA
* * * * *
38385 GAAATGTGTCAATTATGCTAGTTATATGAAAGGTTAAATATCTTTGAGTAAAAGTTTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
38450 AGCTGTGCATTTGACA
66 AGCTGTGCATTTGACA
* *
38466 GAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
38531 AGCT
66 AGCT
38535 AAGATTAATG
Statistics
Matches: 282, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 282 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (81 bp):
GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
AGCTGTGCATTTGACA
Found at i:38416 original size:162 final size:162
Alignment explanation
Indices: 38142--39349 Score: 1588
Period size: 162 Copynumber: 7.3 Consensus size: 162
38132 GGGTGTTACG
* * *
38142 GAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAACGGCTT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * *
38207 AGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACATTTGAGT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
* ** * *
38272 AAACGATTAATGTTCTAGTTGTGCATTTGATA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
*
38304 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * * * *
38369 AGCTGTGCATTTGATAGAAATGTGTCAATTATGCTAGTTATATGAAAGGTTAAATATCTTTGAGT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
*
38434 AAAAGTTTAATGGCCTAGCTGTGCATTTGACA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
* *
38466 GAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * *
38531 AGCTAAGATTAATGGCCTAGCTATGCATTTCATAGAAATGTGTCAATTATGCCAGTTAAATGAAA
66 AGCT--G-----T-G-C-A--TTTG-A---C--AGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
38596 GGTTAAATACCTTTGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACA
113 GGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * * *
38646 GAAAGGTGTCAATTTTGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAATGGCAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * * * * *
38711 AGATGTCCATTTGACAGAAAGATGGCAATTATACCAGTTATATGAAAGGTTAAATACCTTTGAGT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
* *
38776 AAATGATTAATGGCATAGCTGTGCATTTGACA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * * *
38808 GAAAGGTGTCAATTATGCCAGTTAGATGAAAAGTTAAATACCTTTGAGTAAAAGGTTAACGGCTT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* *** * * *
38873 AGTTGTGCGCCTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTTGAAT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
* * *
38938 TAAAGATTAATGGCCTAGTTGTGCATTTGAAA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
* *
38970 GAAAGGTTTTAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
*
39035 AGCTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
* *
39100 AAAAGATTAATGGTCTAGCTGTGCATTTGATA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * * * *
39132 GAAAGGTGTCGATTATTCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAAGGTCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
* * ** ** *
39197 AGCTTTGCATTTGACATAAATATGTCAATTATGTTAGTTAGATGAAATGTTAAATACCTTTGAGT
66 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
**
39262 AAAAGATTAATAACCTAGCTGTGCATTTGACA
131 AAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * * *
39294 GAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAATTCCTTTGGGTAAAAGAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAT
39350 GAAATACTTA
Statistics
Matches: 915, Mismatches: 113, Indels: 36
0.86 0.11 0.03
Matches are distributed among these distances:
162 759 0.83
164 2 0.00
167 1 0.00
168 3 0.00
169 1 0.00
170 2 0.00
171 2 0.00
172 1 0.00
173 1 0.00
174 3 0.00
175 1 0.00
178 1 0.00
180 138 0.15
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (162 bp):
GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCT
AGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
AAAAGATTAATGGCCTAGCTGTGCATTTGACA
Found at i:38540 original size:18 final size:18
Alignment explanation
Indices: 38517--38553 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38507 CTTTGAGTAA
38517 AAGATTAATGGCCTAGCT
1 AAGATTAATGGCCTAGCT
38535 AAGATTAATGGCCTAGCT
1 AAGATTAATGGCCTAGCT
38553 A
1 A
38554 TGCATTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (18 bp):
AAGATTAATGGCCTAGCT
Found at i:38611 original size:99 final size:99
Alignment explanation
Indices: 38440--38631 Score: 312
Period size: 99 Copynumber: 1.9 Consensus size: 99
38430 GAGTAAAAGT
* * * * *
38440 TTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAAT
1 TTAATGGCCTAGCTATGCATTTCACAGAAAGGTGTCAATTATGCCAGTTAAATGAAAGGTTAAAT
38505 ACCTTTGAGTAAAAGATTAATGGCCTAGCTAAGA
66 ACCTTTGAGTAAAAGATTAATGGCCTAGCTAAGA
* *
38539 TTAATGGCCTAGCTATGCATTTCATAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGTTAAAT
1 TTAATGGCCTAGCTATGCATTTCACAGAAAGGTGTCAATTATGCCAGTTAAATGAAAGGTTAAAT
*
38604 ACCTTTGAGTAAAATATTAATGGCCTAG
66 ACCTTTGAGTAAAAGATTAATGGCCTAG
38632 TTGTGCATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (99 bp):
TTAATGGCCTAGCTATGCATTTCACAGAAAGGTGTCAATTATGCCAGTTAAATGAAAGGTTAAAT
ACCTTTGAGTAAAAGATTAATGGCCTAGCTAAGA
Found at i:39370 original size:81 final size:81
Alignment explanation
Indices: 38535--39349 Score: 1126
Period size: 81 Copynumber: 10.1 Consensus size: 81
38525 TGGCCTAGCT
* * * * *
38535 AAGATTAATGGCCTAGCTATGCATTTCATAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
38600 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
* * *
38616 AATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTTTGCCAGTTAGATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
*
38681 AAATACATTTGAGTAA
66 AAATACCTTTGAGTAA
* * * * * * * *
38697 AATATTAATGGCATAGATGTCCATTTGACAGAAAGATGGCAATTATACCAGTTATATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
38762 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
* * *
38778 ATGATTAATGGCATAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
38843 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
* * * * *** * *
38859 AAGGTTAACGGCTTAGTTGTGCGCCTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
* *
38924 AAATACCTTTGAATTA
66 AAATACCTTTGAGTAA
* * * *
38940 AAGATTAATGGCCTAGTTGTGCATTTGAAAGAAAGGTTTTAATTATGCCAGTTAGATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
39005 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
*
39021 AAGATTAATGGCCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
39086 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
* * * * *
39102 AAGATTAATGGTCTAGCTGTGCATTTGATAGAAAGGTGTCGATTATTCCAATTAGATGAAAGGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
39167 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
* * * * ** ** *
39183 AAGATTAAAGGTCTAGCTTTGCATTTGACATAAATATGTCAATTATGTTAGTTAGATGAAATGTT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
39248 AAATACCTTTGAGTAA
66 AAATACCTTTGAGTAA
** * *
39264 AAGATTAATAACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCT
1 AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
* *
39329 AAATTCCTTTGGGTAA
66 AAATACCTTTGAGTAA
39345 AAGAT
1 AAGAT
39350 GAAATACTTA
Statistics
Matches: 646, Mismatches: 88, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 646 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
AAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTT
AAATACCTTTGAGTAA
Found at i:40595 original size:134 final size:134
Alignment explanation
Indices: 40345--41136 Score: 853
Period size: 134 Copynumber: 5.9 Consensus size: 134
40335 AGTTTGAGAA
* * *
40345 ACGTTGATTTATTCCACTGTT-CTTCAGGGAAGATTGAATTGAGGCAGATTTGTTCCACTGTTAC
1 ACGTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
* * * ** *
40409 TCAGGGAATATTAAATCTTGAATGAGAGGGATCTATTCCTCTTTTTCTTGAGGGAAAATCATATC
65 TCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCAGCTTTTTCTTGAGGGAAAATCAGATC
40474 TGGGG
130 TGGGG
* * * * * * * *
40479 ACGTTGATTCATTCAACTATTACACAAGGAAGATTGAATTGAGGTAAACTTGTTCCACTATTACT
1 ACGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * *
40544 CAGGGAATATCAAATCATGAAAGAGAGGGATTTGTTCAGCTTATTCCTGAGGGAAAATTAGA-CT
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCAGCTTTTTCTTGAGGGAAAATCAGATCT
*
40608 AGGG
131 GGGG
** * * * *
40612 TTGTTGATTCGTTCCATTGTT-CTTTAGGGAAGATTGAATCGAGGCAGACTTATTCCACTG-TAC
1 ACGTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
* * * * * * *
40675 TTAGGGAATATCAAATATTGAAAGAAAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATTAGATC
65 TCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCAGCTTTTTCTTGAGGGAAAATCAGATC
***
40740 CAAGG
130 TGGGG
* * * * * *
40745 AAGTTGATTCATTCCACTGTCACTCA-TGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACT
1 ACGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* ** * ** *
40809 CAGGGAATATCAAATCTTGAAAGATATAGATTTGTTTTGCTTTTTCTTGAGGGAAAATCATATCT
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCAGCTTTTTCTTGAGGGAAAATCAGATCT
*
40874 GAGG
131 GGGG
* * *
40878 ACGTTGATTTATTCCACTGTTACTTAGGGAAGATTGAATCGAGGCAGACTTGTTTCACTGTTACT
1 ACGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * * *
40943 TAGGGAATATCAAATCTTGAAAGGGATGGATCTATCTC-GCTTTTTCTTAAGGGAAAATTAGATC
66 CAGGGAATATCAAATCTTGAAAGAGAGGGATCTGT-TCAGCTTTTTCTTGAGGGAAAATCAGATC
41007 TGGGG
130 TGGGG
* * * *
41012 ACAGTT-ATTCATTCCAATGTTACTCAGGGAAGATTGAATTGAGGTAGACTTGTTCCACTTTTAC
1 AC-GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
* * * *
41076 TCAAGAAATATCAAATCTTGAAAGAGATGGATCTGTTCCA-CTTCTTCTTGAGGGAAAATCA
65 TCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT-CAGCTTTTTCTTGAGGGAAAATCA
41137 TATATAAAAA
Statistics
Matches: 546, Mismatches: 102, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
132 89 0.16
133 154 0.28
134 298 0.55
135 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (134 bp):
ACGTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
CAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCAGCTTTTTCTTGAGGGAAAATCAGATCT
GGGG
Found at i:42903 original size:9 final size:9
Alignment explanation
Indices: 42891--42989 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 9
42881 TTCTTACCTA
42891 TCTTTTCTT
1 TCTTTTCTT
42900 TC-TTTCTT
1 TCTTTTCTT
*
42908 TTTATTTC-T
1 TCT-TTTCTT
42917 TCTTTTCTT
1 TCTTTTCTT
42926 T-TTCTTCTT
1 TCTT-TTCTT
42935 T-TTCTTCTTTT
1 TCTT-TTC--TT
42946 TCTTTTCTT
1 TCTTTTCTT
** *
42955 TAATTCCTTT
1 TCTTTTC-TT
42965 TCTTTTCTT
1 TCTTTTCTT
42974 T-TTCTTCTT
1 TCTT-TTCTT
*
42983 TTTTTTC
1 TCTTTTC
42990 AAATGTGGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
8 15 0.21
9 37 0.51
10 12 0.17
11 6 0.08
12 2 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (9 bp):
TCTTTTCTT
Found at i:42910 original size:14 final size:14
Alignment explanation
Indices: 42893--42989 Score: 66
Period size: 14 Copynumber: 7.4 Consensus size: 14
42883 CTTACCTATC
42893 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
*
42907 TTTTATTTC-TTC-
1 TTTTCTTTCTTTCT
*
42919 TTTTCTTTTTCTTCT
1 TTTTCTTTCT-TTCT
*
42934 TTTTC-TTCTTTTT
1 TTTTCTTTCTTTCT
** *
42947 CTTTTCTTTAATTCC
1 -TTTTCTTTCTTTCT
42962 TTTTC--T-TTTCT
1 TTTTCTTTCTTTCT
42973 TTTTC-TTCTTT-T
1 TTTTCTTTCTTTCT
42985 TTTTC
1 TTTTC
42990 AAATGTGGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.12
12 15 0.23
13 9 0.14
14 24 0.37
15 9 0.14
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:42915 original size:18 final size:17
Alignment explanation
Indices: 42893--42989 Score: 70
Period size: 18 Copynumber: 5.3 Consensus size: 17
42883 CTTACCTATC
42893 TTTTCTTTCTTTCTTTT
1 TTTTCTTTCTTTCTTTT
42910 TATTTC-TTCTTTTCTTTT
1 T-TTTCTTTC-TTTCTTTT
* *
42928 TCTTCTTTTTCTTCTTTTT
1 TTTTCTTTCT-TTC-TTTT
* *
42947 CTTTTCTTTAATTCCTTTT
1 -TTTTCTTT-CTTTCTTTT
*
42966 CTTTTCTTTTTCTTCTTTT
1 -TTTTCTTTCT-TTCTTTT
42985 TTTTC
1 TTTTC
42990 AAATGTGGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.12
18 24 0.37
19 23 0.35
20 9 0.14
21 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTTTCTTTCTTTT
Found at i:44696 original size:22 final size:22
Alignment explanation
Indices: 44670--44718 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
44660 TCTCGACTTC
44670 TTATCCGTGAGATAAGACCTTA
1 TTATCCGTGAGATAAGACCTTA
44692 TTATCCGTGAGATAAGACCTTA
1 TTATCCGTGAGATAAGACCTTA
44714 TTATC
1 TTATC
44719 TTGTTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCCGTGAGATAAGACCTTA
Found at i:44978 original size:10 final size:10
Alignment explanation
Indices: 44965--44997 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
44955 AAGTGTCAAA
44965 AATGATAAAG
1 AATGATAAAG
44975 AATG-TAAAG
1 AATGATAAAG
*
44984 AATGACAAAG
1 AATGATAAAG
44994 AATG
1 AATG
44998 TGAAAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (10 bp):
AATGATAAAG
Found at i:54129 original size:41 final size:42
Alignment explanation
Indices: 54011--54133 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
54001 ACAAAATTGG
*
54011 TAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGGGCCATCTA-TAAGTCTTTCGAGCAAGATGAT
* * * * * *
54053 TAAATCCTTCGGGTCATTTGTCAGTCTTTCAAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATGAT
* * *
54094 TAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATG
1 TAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATG
54134 TTTTCATATG
Statistics
Matches: 64, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
41 31 0.48
42 33 0.52
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATGAT
Found at i:54267 original size:259 final size:258
Alignment explanation
Indices: 53629--54530 Score: 1246
Period size: 259 Copynumber: 3.5 Consensus size: 258
53619 TTGTTTTTAT
** * *
53629 ATAATTTGAAAAATGAGAAA-CAATTTTCAAAGTTTCTCATTTAGA-ATTTTTAGAAAATAAAAA
1 ATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTA-ATATTTTCAGAAAAT-GAAA
53692 TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACC-AGTAAACTATTTCCAAAATTGGTA
64 TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTA
* * *
53756 AGTCCTTCGGGCGATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGT
129 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTCAGT
* * * ** * * * * *
53821 CTTTTGAGAAAGATTATAAGTCCTTCAGACTATCTATAAGACCTTCGGGTAATATGCTTT-TATG
194 CTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCTATG
* *
53885 ATAATTTGAAAAATAAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAACT
1 ATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATT
* * * *
53950 TTTGAAAAGTAAGAAAGCAATTACCAAAGTTTCTTACCTAGTAAATTACTTACAAAATTGGTAAG
66 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
54015 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTCAGTCT
131 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTCAGTCT
* *
54080 TTCAAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGTTTTCATATG
196 TTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTC-TATG
* * * *
54144 ATAACTTGAAAAATGAGAAAGTGATTTTCAAAGTTTTTCATTTAGTATTTTCAGAATAT-AAATT
1 ATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAA-T
* *
54208 TTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGCAA
65 TTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAA
* * * *
54273 GTCCTTCAGGCCATCAGAAAGTTTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTT-TCAGT
130 GTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCAT-TTGTCAGT
* * * * *
54337 CTTTCGAGCATGACGATAAGTCATTTGGGCCATCTATAAGATCTTTGAGCAAGATGCTTTC-AT-
194 CTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCTATG
* * * *
54400 ATAATTTGAAAATTGAGAAAG-CAGTTTTCAAAGCTTCTCATTTAATATTTTTAGAAAATGAAAT
1 ATAATTTGAAAAATGAGAAAGTGA-TTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAAT
** * * *
54464 TTTTGAAAAGTAAGAAAGTGATTTCCAAAGGTTCTTACCTAGTAAACTATTTCTAAAATTGTTAA
65 TTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAA
54529 GT
130 GT
54531 ATTCCAGTTC
Statistics
Matches: 576, Mismatches: 61, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
255 1 0.00
256 173 0.30
257 169 0.29
258 3 0.01
259 228 0.40
260 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (258 bp):
ATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATT
TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTCAGTCT
TTCGAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCTATG
Found at i:54700 original size:176 final size:173
Alignment explanation
Indices: 54387--54706 Score: 498
Period size: 176 Copynumber: 1.8 Consensus size: 173
54377 ATCTTTGAGC
* * *
54387 AAGATGCTTTCATATAATTTGAAAATTGAGAAAGCAGTTTTCAAAGCTTCTCATTTAATATTTTT
1 AAGATGCTTTCATATAATTTGAAAAATAAGAAAGCAGTTTTCAAAGCTTCTCATTTAATATTTTC
* *
54452 AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGGTTCTTACCTAGTAAACTATTTC
66 AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATCTCCAAAGGTTCTTACCTAGTAAAATATTTC
* *
54517 TAAAATTGTTAAGTATTCCAGTTCATCAATAAGACCTTCGGGA
131 CAAAATTGGTAAGTATTCCAGTTCATCAATAAGACCTTCGGGA
* *
54560 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGC-GATTTTCAAAGTTTCTCATTTAGTAT
1 AAGATGCTTTC--AT-ATAATTTGAAAAATAAGAAAGCAG-TTTTCAAAGCTTCTCATTTAATAT
* *
54624 TTTCAGAATATGAAATTTTTGAAAAGTAAGAAAGTGATCTCCAAAGTTTCTTACCTAGTAAAATA
62 TTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATCTCCAAAGGTTCTTACCTAGTAAAATA
54689 TTTCCAAAATTGGTAAGT
127 TTTCCAAAATTGGTAAGT
54707 TCTTCAGGCC
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
173 11 0.08
175 3 0.02
176 118 0.89
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (173 bp):
AAGATGCTTTCATATAATTTGAAAAATAAGAAAGCAGTTTTCAAAGCTTCTCATTTAATATTTTC
AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATCTCCAAAGGTTCTTACCTAGTAAAATATTTC
CAAAATTGGTAAGTATTCCAGTTCATCAATAAGACCTTCGGGA
Found at i:55181 original size:2 final size:2
Alignment explanation
Indices: 55174--55252 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
55164 AATATTAGAT
55174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
55215 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55253 CCAAATCAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 73 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55212 original size:31 final size:31
Alignment explanation
Indices: 55174--55252 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
55164 AATATTAGAT
55174 TATATATATATATATATATATATATATATAA
1 TATATATATATATATATATATATATATATAA
55205 TATATATATATATATATATATATATATATAA
1 TATATATATATATATATATATATATATATAA
55236 TATATATATATATATAT
1 TATATATATATATATAT
55253 CCAAATCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATATATATATATATATATATATATATAA
Done.