Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004461.1 Hibiscus syriacus cultivar Beakdansim tig00009833_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: 113503
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:17467 original size:23 final size:22
Alignment explanation
Indices: 17439--17488 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
17429 TAGACACAAT
17439 TAAAATTTTAAGATAAATATAAA
1 TAAAATTTTAAGATAAA-ATAAA
*
17462 TAAAATTTTAAGATGAAATAAA
1 TAAAATTTTAAGATAAAATAAA
17484 -AAAAT
1 TAAAAT
17489 AGCTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (22 bp):
TAAAATTTTAAGATAAAATAAA
Found at i:17611 original size:17 final size:18
Alignment explanation
Indices: 17572--17618 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
17562 TGTTTCTGAG
17572 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
17590 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
17607 GGAATTGGAATC
1 GGAATTGGAATC
17619 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:18512 original size:256 final size:251
Alignment explanation
Indices: 17999--18507 Score: 710
Period size: 256 Copynumber: 2.0 Consensus size: 251
17989 ATTTTTATTC
*
17999 AATATATGAATTAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
1 AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
* *
18064 AAAACATTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATAT
66 AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATAT
* * * * *
18129 ATAAGGTAAAATAATATATTTTTTTTCGGGTCGGGTCCGATTTTTTTCACCCTAAACCCGACCAA
131 ATAAGGTAAAAT-ATATATATATTTTCAGGTC--GTCAGATATTTTTCACCCTAAACCCGACCAA
18194 CCCGAATATCACACTTAAAAAACCAGACCCGACCCGAACAAAATAAAGTTTCACCCGACCCG
193 CCCGAATATCACACTTAAAAAACCAGACCCGA-CC--ACAAAATAAAGTTTCACCCGACCCG
* * * *
18256 AATATATGAAATAGAAATCCGACCCGACCCGACCCGAAATAA-AAAAAATTATTTTTATTCAATA
1 AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
* *
18320 AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCTTAATTAT
66 AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATAT
18385 ATAAGGTAAAAT-TATATATATTTTCAGGTC-T-AG-TATTTTTCACCCTAAACCCGAACTCGAT
131 ATAAGGTAAAATATATATATATTTTCAGGTCGTCAGATATTTTTCACCCTAAACCCG-A--C---
18446 CAGACCCGAATATCACACTTAAAAAAACCA-ACCCGA-C-CAAAATAAAGTTTCACCCGACCCG
190 CA-ACCCGAATATCACACTT-AAAAAACCAGACCCGACCACAAAATAAAGTTTCACCCGACCCG
18507 A
1 A
18508 CCCGACCCGA
Statistics
Matches: 230, Mismatches: 14, Indels: 22
0.86 0.05 0.08
Matches are distributed among these distances:
249 19 0.08
250 2 0.01
251 26 0.11
252 1 0.00
254 16 0.07
255 2 0.01
256 117 0.51
257 47 0.20
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (251 bp):
AATATATGAAATAGAAACCCGACCCGACACGACACGAAATAATAAAAAAATATTTTTATTCAATA
AAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTACTGTAATTATTCCTAAATAT
ATAAGGTAAAATATATATATATTTTCAGGTCGTCAGATATTTTTCACCCTAAACCCGACCAACCC
GAATATCACACTTAAAAAACCAGACCCGACCACAAAATAAAGTTTCACCCGACCCG
Found at i:20983 original size:29 final size:30
Alignment explanation
Indices: 20951--21007 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
20941 TCATTTTCGG
*
20951 TCATTTAAATTTTAAA-AATTATAAAATAA
1 TCATTCAAATTTTAAACAATTATAAAATAA
** *
20980 TCATTCATTTTTTAAACGATTATAAAAT
1 TCATTCAAATTTTAAACAATTATAAAAT
21008 TATGATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (30 bp):
TCATTCAAATTTTAAACAATTATAAAATAA
Found at i:24641 original size:18 final size:17
Alignment explanation
Indices: 24618--24652 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
24608 TTAAGGAGTA
24618 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACA-AGTG
*
24636 GTCCTTTGGGACAAGTG
1 GTCCTTCGGGACAAGTG
24653 TTCAGTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (17 bp):
GTCCTTCGGGACAAGTG
Found at i:27140 original size:19 final size:19
Alignment explanation
Indices: 27105--27143 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27095 TAAGGAACCT
*
27105 AAAATCTAAGGCTTAATTA
1 AAAATCTAAGACTTAATTA
27124 AAAATCTAAAGAC-TAATTA
1 AAAATCT-AAGACTTAATTA
27143 A
1 A
27144 TATTTAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (19 bp):
AAAATCTAAGACTTAATTA
Found at i:28846 original size:17 final size:17
Alignment explanation
Indices: 28824--28857 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28814 ATTATTTAAT
28824 ATGCAATGCAACATGAA
1 ATGCAATGCAACATGAA
**
28841 ATGCAATTTAACATGAA
1 ATGCAATGCAACATGAA
28858 TTAATATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:33960 original size:18 final size:19
Alignment explanation
Indices: 33937--33975 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33927 TTAATGTTTT
* *
33937 ATTTTTTACA-AATTTTAA
1 ATTTTTGACATAAATTTAA
33955 ATTTTTGACATAAATTTAA
1 ATTTTTGACATAAATTTAA
33974 AT
1 AT
33976 GTTTATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTTTTGACATAAATTTAA
Found at i:34964 original size:20 final size:20
Alignment explanation
Indices: 34936--34979 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34926 TTTTGCAGAA
* *
34936 AAATTATCCCTAACGGCTAC
1 AAATCATCCCCAACGGCTAC
*
34956 AAATCATCCCCAACGGCTAG
1 AAATCATCCCCAACGGCTAC
34976 AAAT
1 AAAT
34980 GGCCACAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (20 bp):
AAATCATCCCCAACGGCTAC
Found at i:36980 original size:32 final size:31
Alignment explanation
Indices: 36927--37021 Score: 147
Period size: 31 Copynumber: 3.0 Consensus size: 31
36917 CCCGAAGGAC
* *
36927 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
36958 CAGTCCATATGTCCCCGAAGAACATAGGTAAA
1 CAGTCCATATGT-CCCGAAGAACATAGGTAAA
36990 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37021 C
1 C
37022 CCTCGACCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.50
32 30 0.50
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:37874 original size:64 final size:63
Alignment explanation
Indices: 37678--37883 Score: 184
Period size: 64 Copynumber: 3.2 Consensus size: 63
37668 AATAAAGGTA
* * ** * * *
37678 TGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCT-GAGA
1 TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA-T-TTATT-TTAAAGA
37742 -
63 G
* * * ** * * * *
37742 CGCATCGATGCACTCCTTATACATCGATGCACCAATTGCATTCGATGT-TTCACTATTAATGGG
1 TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTA-TTTTAAAGAG
*
37805 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATTTTAAAAGAG
1 -TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTTT-AAAGAG
37870 TGCATCGATGCACT
1 TGCATCGATGCACT
37884 TCCAATGCAT
Statistics
Matches: 111, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
61 3 0.03
62 3 0.03
64 98 0.88
65 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTTATTTTAAAGAG
Found at i:37892 original size:64 final size:64
Alignment explanation
Indices: 37738--37901 Score: 172
Period size: 64 Copynumber: 2.6 Consensus size: 64
37728 TATTATTGCT
* * *
37738 GAGACGCATCGATGCAC-TCCTTATACATCGATGCACCAATTGCATTCGATGTTTCACTATTAAT
1 GAGATGCATCGATGCACTTCC-TATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAA
* * * ** * *
37802 GGGATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTA-TTTTAAA
1 GAGATGCATCGATGCACTTCCTATGCATCGATGCACCAATTGCATTCGATGT-TTCACTATTAAA
* *
37866 -AGAGTGCATCGATGCACTTCCAATGCATCGGTGCAC
1 GAGA-TGCATCGATGCACTTCCTATGCATCGATGCAC
37902 ATTCAAACAA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
63 2 0.02
64 75 0.93
65 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (64 bp):
GAGATGCATCGATGCACTTCCTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAA
Found at i:39888 original size:36 final size:36
Alignment explanation
Indices: 39823--39992 Score: 108
Period size: 36 Copynumber: 4.9 Consensus size: 36
39813 CGTTTCAAGG
* * *
39823 GAAAACTATCTCAAGCGAGA-CAAAATTTGTTTTTAC
1 GAAAACAATCTCAAGCGAGATC-AATTTTGTTTTTAA
*
39859 GAAAACAATCTCAAGCGAGATCAATTTTG-TTTCAA
1 GAAAACAATCTCAAGCGAGATCAATTTTGTTTTTAA
* * * ** *
39894 GTGAAACAATTTCAA---A-AT---TTGTGTTTCGAGT
1 G-AAAACAATCTCAAGCGAGATCAATTTTGTTTTTA-A
* * *
39925 GAAAACTATCTCAAGCGAGA-CAAAATTTGTTTTTAG
1 GAAAACAATCTCAAGCGAGATC-AATTTTGTTTTTAA
*
39961 GAAAACAATCTCAAGAGAGATCAATTTTGTTT
1 GAAAACAATCTCAAGCGAGATCAATTTTGTTT
39993 CAAGTGAAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
29 4 0.04
30 13 0.13
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 5 0.05
36 63 0.63
37 9 0.09
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
GAAAACAATCTCAAGCGAGATCAATTTTGTTTTTAA
Found at i:39920 original size:102 final size:102
Alignment explanation
Indices: 39779--40154 Score: 457
Period size: 102 Copynumber: 3.7 Consensus size: 102
39769 TATGAGATAA
* *
39779 AATTTTGTTTCGAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
*
39844 AAAATTTGTTTTTACGAAAACAATCTCAAGCGAGATC
66 AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
* *
39881 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGTGAAAACTATCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
*
39946 AAAATTTGTTTTTAGGAAAACAATCTCAAGAGAGATC
66 AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
* * *
39983 AATTTTGTTTCAAGTGAAAAAATTTCAAAATTTATGTTTCAAGGG-AAACTGTCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
* ** * *
40047 GAAACTTTGTTTCGA-GAGAATCAATCTCAA-A-TG-T-
66 -AAAATTTGTTTTTACGA-AAACAATCTCAAGAGAGATC
* * * * * *
40081 --TTATGTTTCAAGAGAAACAATCT-AAAAGGTTTATGTTTCAAGAG-AAACTGTCTCAAGCGAG
1 AATTTTGTTTCAAGTGAAACAATTTCAAAA--TTTGTGTTTCAAGGGAAAACTATCTCAAGCGAG
*
40142 ATAAAATTTGTTT
64 ACAAAATTTGTTT
40155 CAAGAGAAAC
Statistics
Matches: 247, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
95 4 0.02
96 29 0.12
97 32 0.13
99 1 0.00
100 1 0.00
101 21 0.09
102 159 0.64
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (102 bp):
AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
AAAATTTGTTTTTACGAAAACAATCTCAAGAGAGATC
Found at i:40095 original size:30 final size:30
Alignment explanation
Indices: 40054--40194 Score: 122
Period size: 30 Copynumber: 4.5 Consensus size: 30
40044 GACGAAACTT
* * * *
40054 TGTTTCGAGAGAATCAATCTCAAATGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
40084 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
** * *
40114 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATT-
1 TGTTTCAAGAGAAACAATCT-AA--AAGGT----TTA
* *
40150 TGTTTCAAGAGAAACAATGTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTA
40180 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
40195 TGTCTCAAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
29 2 0.02
30 59 0.66
31 2 0.02
33 6 0.07
35 1 0.01
36 17 0.19
37 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTAAAAGGTTTA
Found at i:40154 original size:36 final size:35
Alignment explanation
Indices: 40114--40240 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 35
40104 AAAAGGTTTA
40114 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGATAAAATT
** * *
40150 TGTTTCAAGAGAAACAATGTCAA--AGGT----TT
1 TGTTTCAAGAGAAACTGTCTCAAGGAGATAAAATT
*
40179 ATGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAG-GAGATAAAATT
* *
40216 TGTTTCAAGAAAAATTGTCTCAAGG
1 TGTTTCAAGAGAAACTGTCTCAAGG
40241 GAGACAGACA
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
29 2 0.03
30 20 0.28
33 5 0.07
35 1 0.01
36 42 0.58
37 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGATAAAATT
Found at i:40190 original size:66 final size:66
Alignment explanation
Indices: 40084--40225 Score: 248
Period size: 66 Copynumber: 2.2 Consensus size: 66
40074 CAAATGTTTA
*
40084 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
40149 T
66 T
* * *
40150 TGTTTCAAGAGAAACAATGTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAAT
1 TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
40215 T
66 T
40216 TGTTTCAAGA
1 TGTTTCAAGA
40226 AAAATTGTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATCTAAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAAT
T
Found at i:42370 original size:8 final size:8
Alignment explanation
Indices: 42354--42483 Score: 56
Period size: 8 Copynumber: 15.9 Consensus size: 8
42344 CTCCTTTCAG
*
42354 TTTTATTT
1 TTTTCTTT
42362 TTTTC--T
1 TTTTCTTT
42368 TTTTCTTT
1 TTTTCTTT
42376 TTTT-TTT
1 TTTTCTTT
42383 TTATT-TTT
1 TT-TTCTTT
*
42391 TTCTCTATAT
1 TTTTCT-T-T
42401 TGTTTCTCTAT
1 T-TTTCT-T-T
42412 ATTTTTCCTTT
1 --TTTT-CTTT
*
42423 TTTTATTT
1 TTTTCTTT
42431 TTTTC-TT
1 TTTTCTTT
**
42438 TTTTCCCT
1 TTTTCTTT
**
42446 TTTTCCCT
1 TTTTCTTT
42454 TTTTC-TT
1 TTTTCTTT
42461 TTTTCTTT
1 TTTTCTTT
* *
42469 TTTTATTC
1 TTTTCTTT
42477 TTTTCTT
1 TTTTCTT
42484 CAAGTGTAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
6 6 0.06
7 19 0.19
8 52 0.53
9 5 0.05
10 2 0.02
11 8 0.08
12 4 0.04
13 3 0.03
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTCTTT
Found at i:42376 original size:19 final size:19
Alignment explanation
Indices: 42354--42390 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42344 CTCCTTTCAG
*
42354 TTTTATTTTTTTCTTTTTC
1 TTTTATTTTTTTATTTTTC
*
42373 TTTTTTTTTTTTATTTTT
1 TTTTATTTTTTTATTTTT
42391 TTCTCTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.89
Consensus pattern (19 bp):
TTTTATTTTTTTATTTTTC
Found at i:44249 original size:31 final size:31
Alignment explanation
Indices: 44211--44366 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
44201 CCCGAAGGAC
* * *
44211 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
44242 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
44273 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
44304 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
44335 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
44366 C
1 C
44367 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:44608 original size:23 final size:24
Alignment explanation
Indices: 44582--44628 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
44572 ATATACTTGT
*
44582 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
44605 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
44629 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:46476 original size:22 final size:24
Alignment explanation
Indices: 46427--46477 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
46417 TGTATGAAAT
*
46427 GAATGAAATAATAAAAATGTCAAA
1 GAATGAAATAACAAAAATGTCAAA
*
46451 -AATGAAAT-ACAATAATGT-AAA
1 GAATGAAATAACAAAAATGTCAAA
46472 GAATGA
1 GAATGA
46478 TAAAGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
23 8 0.33
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.22
Consensus pattern (24 bp):
GAATGAAATAACAAAAATGTCAAA
Found at i:55521 original size:16 final size:16
Alignment explanation
Indices: 55502--55535 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55492 CAATATACGA
55502 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
55518 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
55534 AT
1 AT
55536 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:56278 original size:130 final size:130
Alignment explanation
Indices: 56074--56321 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
56064 AATTTTCTTC
* *
56074 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
56139 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
56204 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTTAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
56269 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
56322 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:56761 original size:35 final size:35
Alignment explanation
Indices: 56718--56793 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
56708 AATTGAATTT
* *
56718 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
* *
56753 ATTTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
56788 AATTGA
1 AATTGA
56794 GGACTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:63482 original size:3 final size:3
Alignment explanation
Indices: 63476--63502 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
63466 CATCATCATC
63476 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
63503 TAAATTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:63540 original size:3 final size:3
Alignment explanation
Indices: 63532--63565 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
63522 CATAATGATT
63532 TTA TTA TTA TTA TTA TTGA TTAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TT
63566 TAAGTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:63568 original size:63 final size:61
Alignment explanation
Indices: 63476--63596 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 61
63466 CATCATCATC
*
63476 ATTATTATTATTATTATTATTATTATTTAAATTACAATCAATGATACATAATGATTTTATT
1 ATTATTATTATTATTATTATTATTATTTAAATAACAATCAATGATACATAATGATTTTATT
* * *
63537 ATTATTATTATTGATTAATTATTATTATTTAAGTAATAATCAATGATATATAATGATTTT
1 ATTATTATTATT-ATT-ATTATTATTATTTAAATAACAATCAATGATACATAATGATTTT
63597 TAAGATACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.22
62 3 0.06
63 39 0.72
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (61 bp):
ATTATTATTATTATTATTATTATTATTTAAATAACAATCAATGATACATAATGATTTTATT
Found at i:63802 original size:31 final size:31
Alignment explanation
Indices: 63764--63824 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
63754 GAAACGGTCT
*
63764 CTAACATTATCGATTCGTTCGATTTTAATCC
1 CTAACATTATCGATTCGTTAGATTTTAATCC
*
63795 CTAACATTATTGATTCGTTAGATTTTAATC
1 CTAACATTATCGATTCGTTAGATTTTAATC
63825 TCTCAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (31 bp):
CTAACATTATCGATTCGTTAGATTTTAATCC
Found at i:65612 original size:104 final size:103
Alignment explanation
Indices: 65432--65637 Score: 270
Period size: 104 Copynumber: 2.0 Consensus size: 103
65422 TTCCGGGAAA
* *
65432 GCTATTTAAGAGCCATTGGCTAACCAGAGCATGTAGAAAAATTGCCTTTAGGAACAATTCAGGGT
1 GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTGCCTTTA-GAACAATTCAGGGT
* * * *
65497 CAGAACTTGAATCAGCCAATGATTTAAATCAATAAGGTC
65 CAAAACTTGAATCAACCAATGACTAAAATCAATAAGGTC
* * * * *
65536 GCTATTTAAGAGTAATTGGCTAATCAGAGCATGTTCAAAGATTGTTCTTTCA-AACAATTCAGGG
1 GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTG-CCTTT-AGAACAATTCAGGG
*
65600 TCAAAACTTGAATCAACCAGTGACTAAAATCAATAAGG
64 TCAAAACTTGAATCAACCAATGACTAAAATCAATAAGG
65638 CCTCAGTGTT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
104 83 0.94
105 4 0.05
106 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (103 bp):
GCTATTTAAGAGCAATTGGCTAACCAGAGCATGTACAAAAATTGCCTTTAGAACAATTCAGGGTC
AAAACTTGAATCAACCAATGACTAAAATCAATAAGGTC
Found at i:74019 original size:166 final size:169
Alignment explanation
Indices: 73742--74074 Score: 611
Period size: 166 Copynumber: 2.0 Consensus size: 169
73732 TGCGGTATAA
*
73742 TCCTCCGAACATGAACACCCAAACTTAGGAATGATATTGCTTCATTCCGTCAAGCTGATGACGAG
1 TCCTCCGAACATGAACACCC-AACTTAGGAATGACATTGCTTCATTCCGTCAAGCTGATGACGAG
73807 TCGATGCATGAGTGCTGGGATAGATACAAAGCATTGCTTCGCAAGTGTTCAAACCATGGTTTTCA
65 TCGATGCATGAGTGCTGGGATAGATACAAAGCATTGCTTCGCAAGTGTTCAAACCATGG-TTTCA
73872 AGATTGG-ACACAAGTAGTGATGTTCTAT-ATGGGTAACGC
129 AGATTGGCACACAAGTAGTGATGTTCTATAATGGGTAACGC
73911 TCCTCCGAACATGAACA-CC-ACTTAGGAATGACATTGCTTCATTCCGTCAAGCTGATGACGAGT
1 TCCTCCGAACATGAACACCCAACTTAGGAATGACATTGCTTCATTCCGTCAAGCTGATGACGAGT
73974 CGATGCATGAGTGCTGGGATAGATACAAAGCATTGCTTCGCAAGTGTTCAAACCATGGTTTCAAG
66 CGATGCATGAGTGCTGGGATAGATACAAAGCATTGCTTCGCAAGTGTTCAAACCATGGTTTCAAG
74039 ATTGGCACACAAGTAGTGATGTTCTATAATGGGTAA
131 ATTGGCACACAAGTAGTGATGTTCTATAATGGGTAA
74075 ACGCACCCAC
Statistics
Matches: 161, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
165 12 0.07
166 122 0.76
167 8 0.05
168 2 0.01
169 17 0.11
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (169 bp):
TCCTCCGAACATGAACACCCAACTTAGGAATGACATTGCTTCATTCCGTCAAGCTGATGACGAGT
CGATGCATGAGTGCTGGGATAGATACAAAGCATTGCTTCGCAAGTGTTCAAACCATGGTTTCAAG
ATTGGCACACAAGTAGTGATGTTCTATAATGGGTAACGC
Found at i:88488 original size:24 final size:21
Alignment explanation
Indices: 88445--88491 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
88435 ACAGTATTAA
88445 ATATTTAAATTATTTATAAAT
1 ATATTTAAATTATTTATAAAT
*
88466 ATATTTAGATATATATTATTAAAT
1 ATATTTAAAT-TAT-TTA-TAAAT
88490 AT
1 AT
88492 TAATATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 3 0.14
24 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTTAAATTATTTATAAAT
Found at i:90411 original size:37 final size:37
Alignment explanation
Indices: 90329--90447 Score: 181
Period size: 36 Copynumber: 3.3 Consensus size: 37
90319 TGGTAACCAA
*
90329 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
90366 CTTT-AAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
90402 CTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
90439 -ATTGAAAAA
1 CTTTGAAAAA
90448 TGATAATGAG
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
36 46 0.61
37 30 0.39
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:94864 original size:21 final size:21
Alignment explanation
Indices: 94840--94901 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
94830 AACTTTGAAA
94840 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
**
94861 AAAT-G-TTTC----TTTGAA
1 AAATGGTTTTCAAAGTTTGGT
*
94876 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
94897 AAATG
1 AAATG
94902 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 8 0.27
16 1 0.03
17 4 0.13
19 4 0.13
20 1 0.03
21 12 0.40
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:94932 original size:37 final size:36
Alignment explanation
Indices: 94832--94951 Score: 188
Period size: 36 Copynumber: 3.3 Consensus size: 36
94822 TGGTAACCAA
*
94832 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
94869 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
94905 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
94942 -GTTGAAAAAT
1 CTTTGAAAAAT
94952 GATAATGGGA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
36 52 0.66
37 27 0.34
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:100775 original size:19 final size:19
Alignment explanation
Indices: 100751--100792 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
100741 TTCTGTTAAA
100751 AAATTGATTCATCAAAATT
1 AAATTGATTCATCAAAATT
100770 AAATTGATTCATCAAAATT
1 AAATTGATTCATCAAAATT
100789 AAAT
1 AAAT
100793 GTGTGATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTGATTCATCAAAATT
Found at i:104488 original size:90 final size:90
Alignment explanation
Indices: 104335--104501 Score: 307
Period size: 90 Copynumber: 1.9 Consensus size: 90
104325 CCTAACACAC
*
104335 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
104400 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
* *
104425 CCTTTTATATCCAAGTTACCCTAATCGTATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
104490 ATTTAATTAATT
66 ATTTAATTAATT
104502 AAAATTAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:104499 original size:20 final size:20
Alignment explanation
Indices: 104474--104543 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 20
104464 TATTATTTCA
104474 AATTAATT-AAATCTATATTT
1 AATTAATTAAAAT-TATATTT
104494 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAATT--ATATTT
104516 GATATT-ATTAAAATATATATTT
1 -A-ATTAATTAAAAT-TATATTT
104538 AATTAA
1 AATTAA
104544 CTCTAGATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
20 12 0.28
21 6 0.14
22 12 0.28
23 9 0.21
24 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (20 bp):
AATTAATTAAAATTATATTT
Found at i:104513 original size:22 final size:21
Alignment explanation
Indices: 104474--104543 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
104464 TATTATTTCA
**
104474 AATTAATT-AAATCTATATTT
1 AATTAATTAAAATAAATATTT
104494 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAA-TAAATATTT
*
104516 GATATT-ATTAAAATATATATTT
1 -A-ATTAATTAAAATAAATATTT
104538 AATTAA
1 AATTAA
104544 CTCTAGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 15 0.36
23 8 0.19
24 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
AATTAATTAAAATAAATATTT
Done.