Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009197.1 Hibiscus syriacus cultivar Beakdansim tig00112780_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: 62007
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4735 original size:17 final size:17
Alignment explanation
Indices: 4715--4756 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
4705 AAGCATGCTC
4715 GGGTAGATATCATGATA
1 GGGTAGATATCATGATA
4732 GGGTAGATATCATGATA
1 GGGTAGATATCATGATA
4749 GGGTAGAT
1 GGGTAGAT
4757 GTTATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.29
Consensus pattern (17 bp):
GGGTAGATATCATGATA
Found at i:6932 original size:24 final size:28
Alignment explanation
Indices: 6882--6941 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 28
6872 AGTTAACAAC
6882 ACAGAAAGAAAAAGAAGAGATATAAAA-A
1 ACAGAAA-AAAAAGAAGAGATATAAAAGA
*
6910 ACAGAAAAAAGAGAA-AGA-A-AAAAGA
1 ACAGAAAAAAAAGAAGAGATATAAAAGA
6935 A-AGAAAA
1 ACAGAAAA
6942 CGAGAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 10 0.33
25 3 0.10
26 3 0.10
27 7 0.23
28 7 0.23
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (28 bp):
ACAGAAAAAAAAGAAGAGATATAAAAGA
Found at i:6947 original size:12 final size:11
Alignment explanation
Indices: 6916--6972 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
6906 AAAAACAGAA
6916 AAAAGAGAAAG
1 AAAAGAGAAAG
*
6927 AAAAAAGAAAG
1 AAAAGAGAAAG
6938 AAAACGAG-AA-
1 AAAA-GAGAAAG
*
6948 AAAATAGAAA-
1 AAAAGAGAAAG
6958 AAAAGA-AGAAG
1 AAAAGAGA-AAG
6969 AAAA
1 AAAA
6973 TAGACAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.08
10 13 0.34
11 20 0.53
12 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:6957 original size:32 final size:30
Alignment explanation
Indices: 6907--6972 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 30
6897 AGAGATATAA
6907 AAAACAGAAAAAAGAGAAAGAAAA-AAGAAAG
1 AAAACAGAAAAAAGAGAAA-AAAAGAAG-AAG
*
6938 AAAACGAGAAAAAATAGAAAAAAAGAAGAAG
1 AAAAC-AGAAAAAAGAGAAAAAAAGAAGAAG
6969 AAAA
1 AAAA
6973 TAGACAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (30 bp):
AAAACAGAAAAAAGAGAAAAAAAGAAGAAG
Found at i:6958 original size:8 final size:8
Alignment explanation
Indices: 6905--6964 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 8
6895 GAAGAGATAT
6905 AAAAAACAG
1 AAAAAA-AG
6914 AAAAAAGAG
1 AAAAAA-AG
*
6923 AAAGAAA-
1 AAAAAAAG
*
6930 AAAGAAAG
1 AAAAAAAG
**
6938 AAAACGAG
1 AAAAAAAG
6946 AAAAAATAG
1 AAAAAA-AG
6955 AAAAAAAG
1 AAAAAAAG
6963 AA
1 AA
6965 GAAGAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.17
8 14 0.33
9 21 0.50
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9204 original size:36 final size:36
Alignment explanation
Indices: 9136--9212 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
9126 TGTTTTTCTC
* **
9136 AAAACATGTTTTGTCTCTCTTAAGACTGTTTCTCTT
1 AAAACATGTTTTATCTCTCTTAAGACAATTTCTCTT
* * *
9172 GAAACATGTTTTATCTCTTTTGAGACAATTTCTCTT
1 AAAACATGTTTTATCTCTCTTAAGACAATTTCTCTT
9208 AAAAC
1 AAAAC
9213 GCCAACCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (36 bp):
AAAACATGTTTTATCTCTCTTAAGACAATTTCTCTT
Found at i:9301 original size:36 final size:36
Alignment explanation
Indices: 9229--9377 Score: 226
Period size: 36 Copynumber: 4.1 Consensus size: 36
9219 CTTTGATATT
*
9229 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTAAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
9266 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
9302 GTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
9338 GTTTCACTTGAAACAAATTTTGTCTCGCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
9374 GTTT
1 GTTT
9378 TTTTAAACAA
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 85 0.83
37 17 0.17
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:9438 original size:46 final size:45
Alignment explanation
Indices: 9353--9444 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
9343 ACTTGAAACA
* * * *
9353 AATTTTGTCTCGCTTGAGATAGTTTTTTTAAACAAAAAAATCTTTG
1 AATTTTGTCTCCCTTGAGACAATTTTTTGAAAC-AAAAAATCTTTG
9399 AATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAAAATCTTT
1 AATTTTGTCTCCCTTGAGACAATTT-T-TTGAAACAAAAAATCTTT
9445 AAGGTCGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 22 0.55
47 12 0.30
48 6 0.15
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (45 bp):
AATTTTGTCTCCCTTGAGACAATTTTTTGAAACAAAAAATCTTTG
Found at i:9575 original size:216 final size:223
Alignment explanation
Indices: 9302--9717 Score: 573
Period size: 216 Copynumber: 1.9 Consensus size: 223
9292 CCTTGAGACA
*
9302 GTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACAGTTTCACTTGAAACAAATTTTGTCTCGCT
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAAATTTTGTCTCGCT
* *
9367 TGAGATAGTTT-TTTT-AAACAAA-AA-A-A-TCT-TTG--AATTTTGTCTCCCTTGAGACAATT
66 TGAGATAGTTTCTTTTGAAAAAAATAATATATTCTCTTGAAAATTTTGTCTCCCTTAAGACAATT
* * *
9423 TCTCTTGAAACAAAAAATCTTTAAGGTCGTTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGACAA
131 TCTCTTGAAACAAAAAATCTTTAAGGTCG-TTCCCTTGAAACGAGCTTAGTCTCTCTTGAGACAA
9488 TTTTTCTTGAAACGCCAACCTTTGATATT
195 TTTTTCTTGAAACGCCAACCTTTGATATT
*
9517 GTTTCTCTTGAAAC-AAGGTTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAAATTTTGTCTCG
1 GTTTCCCTTGAAACGAA--TTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAAATTTTGTCTCG
9581 CTTGAGATAGTTTCTTTTGAAAAAAATCTTTGAATATATTTCTCTTGAAACAAATTTTGTCTCCC
64 CTTGAGATAGTTTCTTTTGAAAAAAA----T-AATATA-TTCTCTTG--A-AAATTTTGTCTCCC
* *
9646 TTAAGACATTTTCTCTTGAAACAAAAAATCTTTGAGGTCGTTCCCTTGAAACGAGCTTAGTCTCT
120 TTAAGACAATTTCTCTTGAAACAAAAAATCTTTAAGGTCGTTCCCTTGAAACGAGCTTAGTCTCT
9711 CTTGAGA
185 CTTGAGA
9718 TAGTTTTCCT
Statistics
Matches: 172, Mismatches: 9, Indels: 22
0.85 0.04 0.11
Matches are distributed among these distances:
214 2 0.01
215 13 0.08
216 58 0.34
217 4 0.02
218 6 0.03
224 2 0.01
225 1 0.01
226 1 0.01
228 3 0.02
229 3 0.02
233 29 0.17
234 50 0.29
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (223 bp):
GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAAATTTTGTCTCGCT
TGAGATAGTTTCTTTTGAAAAAAATAATATATTCTCTTGAAAATTTTGTCTCCCTTAAGACAATT
TCTCTTGAAACAAAAAATCTTTAAGGTCGTTCCCTTGAAACGAGCTTAGTCTCTCTTGAGACAAT
TTTTCTTGAAACGCCAACCTTTGATATT
Found at i:9585 original size:36 final size:36
Alignment explanation
Indices: 9517--9612 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 36
9507 CTTTGATATT
* *
9517 GTTTCTCTTGAAACAAGGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAA-ATTTTGTCTCGCTTGAGACA
* *
9554 GTTTCACTTGAAACAAATTTTGTCTCGCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
* *
9590 GTTTCTTTTGAAAAAAATCTTTG
1 GTTTCTCTTGAAACAAAT-TTTG
9613 AATATATTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 32 0.63
37 19 0.37
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
Found at i:9639 original size:64 final size:66
Alignment explanation
Indices: 9555--9680 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 66
9545 CTTGAGACAG
* * * *
9555 TTTCACTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTTTTG-A-AAAAAATCTTTGAATAT
1 TTTCACTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAACAAAAAATCTTTGAATAT
9618 A
66 A
* *
9619 TTTCTCTTGAAACAAATTTTGTCTCCCTTAAGACATTTTCTCTTGAAACAAAAAATCTTTGA
1 TTTCACTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTG-AACAAAAAATCTTTGA
9681 GGTCGTTCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 39 0.74
66 1 0.02
67 13 0.25
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (66 bp):
TTTCACTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAACAAAAAATCTTTGAATAT
A
Found at i:10384 original size:91 final size:91
Alignment explanation
Indices: 10172--10536 Score: 554
Period size: 91 Copynumber: 4.0 Consensus size: 91
10162 TATAAATCGA
* * *
10172 TCAACATTGCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAATGAGGGAGAAGAAGGTT-AT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAA-GTTCAT
10236 AATGAGAAGAACTTG-TCAACCTTGGC
65 AATGAGAAGAACTTGTTCAACCTTGGC
*
10262 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
10327 ATGAGAAGAAATTGTTCAACCTTAGC
66 ATGAGAAGAACTTGTTCAACCTTGGC
** * *
10353 TCAACATTTCCAACGAAGAGTTCATAATGAGAAGAACTCGTCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
10418 ATGAGAAGAACTTGTTCAACTTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGC
* * * *
10444 TCAAGATTTCCAGTGGAGAGTTTATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTTATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
10509 ATGAGAAGAACTTGTTCAACCTTTGC
66 ATGAGAAGAACTTGTTCAACCTTGGC
10535 TC
1 TC
10537 GATTCATCAC
Statistics
Matches: 249, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
89 3 0.01
90 72 0.29
91 174 0.70
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGC
Found at i:11933 original size:24 final size:26
Alignment explanation
Indices: 11915--11962 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
11905 AATTTGTTAT
11915 TTTTTATGT-A-TGTATATTTATATA
1 TTTTTATGTAAGTGTATATTTATATA
11939 TTTTTATGTAAGTGTATA-TTATAT
1 TTTTTATGTAAGTGTATATTTATAT
11963 TAGATTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 7 0.32
26 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTTTATGTAAGTGTATATTTATATA
Found at i:12107 original size:2 final size:2
Alignment explanation
Indices: 12100--12160 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
12090 TTATTATTTC
12100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12142 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
12161 AATCATGTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13338 original size:20 final size:20
Alignment explanation
Indices: 13313--13365 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
13303 TTTTCCTAAT
13313 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
13333 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
13353 TCGCAACGCGAAT
1 TCGCAATGCGAAT
13366 CTAACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:13375 original size:20 final size:20
Alignment explanation
Indices: 13352--13458 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
13342 GAATACGTAA
* * *
13352 ATCGCAACGCGAATCTAACT
1 ATCGCAACGAGATTCTGACT
13372 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
13392 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
13412 ATCGTAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
13432 ATTGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
13452 ATCGCAA
1 ATCGCAA
13459 TACTGAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:14320 original size:24 final size:24
Alignment explanation
Indices: 14293--14346 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
14283 GTATTCGAAA
*
14293 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* * * *
14317 TTTGATCTTAGTTAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
14341 TTTGAT
1 TTTGAT
14347 GATTTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:16855 original size:14 final size:14
Alignment explanation
Indices: 16836--16889 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
16826 GGAATTGACT
16836 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
16850 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
16869 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
16883 ATCGCAA
1 ATCGCAA
16890 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:16878 original size:33 final size:34
Alignment explanation
Indices: 16836--16911 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
16826 GGAATTGACT
16836 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
16869 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
16903 ATCGCAACG
1 ATCGCAACG
16912 CGAATTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:16907 original size:20 final size:19
Alignment explanation
Indices: 16849--16915 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
16839 GCAACGAGAG
16849 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
16868 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
16882 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
16902 AATCGCAACGCGAA
1 AATCGCAATGCGAA
16916 TTTAGTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:16967 original size:14 final size:14
Alignment explanation
Indices: 16948--17001 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
16938 CATTTTTGCA
16948 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
16962 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
16979 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
16995 TTGCGAT
1 TTGCGAT
17002 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:16971 original size:34 final size:34
Alignment explanation
Indices: 16926--17021 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
16916 TTTAGTTTCG
* *
16926 CGTTGCAATTTTCATTTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
16960 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** *
16993 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
17022 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:17146 original size:14 final size:14
Alignment explanation
Indices: 17127--17163 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17117 CATCAATTAA
17127 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
17141 ACAAATCATCTTTT
1 ACAAATCAACATTT
17155 ACAAATCAA
1 ACAAATCAA
17164 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:18641 original size:42 final size:42
Alignment explanation
Indices: 18562--18654 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
18552 CCTCTTCAAC
* * *
18562 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
18604 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
18646 GATGACAGG
1 GATGACAGG
18655 TGAATCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:19252 original size:20 final size:20
Alignment explanation
Indices: 19227--19316 Score: 153
Period size: 20 Copynumber: 4.5 Consensus size: 20
19217 GATTCTTTCG
**
19227 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
19247 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
19267 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
19287 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
19307 TTGCGATAGT
1 TTGCGATAGT
19317 AAACTATTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:19708 original size:6 final size:6
Alignment explanation
Indices: 19697--19738 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
19687 AACTCATCCC
*
19697 GTGGAG GTGGAG GTGGAG GTGGAA GTGGAG GTGGAG GTGGAG
1 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG
19739 AATAGGGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.64, T:0.17
Consensus pattern (6 bp):
GTGGAG
Found at i:21293 original size:19 final size:20
Alignment explanation
Indices: 21227--21298 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
21217 TCTGAAACTT
* *
21227 AAAATCGCAACACAAAAAATG
1 AAAATCGCAACGC-GAAAATG
*
21248 AAAATCGCAACACGAAAAT-
1 AAAATCGCAACGCGAAAATG
*
21267 AACTATCGCAACGCG-AAATG
1 AA-AATCGCAACGCGAAAATG
21287 AAAATCGCAACG
1 AAAATCGCAACG
21299 ACAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.33
20 17 0.38
21 13 0.29
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:21697 original size:22 final size:22
Alignment explanation
Indices: 21635--21700 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
21625 TGACCGTGAA
* *
21635 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
21657 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
21679 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
21701 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:21920 original size:20 final size:20
Alignment explanation
Indices: 21897--21989 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
21887 CGATAGTCAG
*
21897 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
21917 ATTCGCATTGCGATATACGT
1 ATTCGCATTGCGATTTACGT
21937 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
21957 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
21977 ATTCGCATTGCGA
1 ATTCGCATTGCGA
21990 ATTAGGAAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:21941 original size:40 final size:40
Alignment explanation
Indices: 21879--21989 Score: 172
Period size: 40 Copynumber: 2.8 Consensus size: 40
21869 GCTATGTAAA
*
21879 TCGCATTGCGATAGT-CAG-ATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATA-TAC-GTATTCGCATTGCGATTTACGTAT
21919 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGTAT
*
21959 TCGCATTGCGATTTACGTATTCGCATTGCGA
1 TCGCATTGCGATATACGTATTCGCATTGCGA
21990 ATTAGGAAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
39 2 0.03
40 65 0.97
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATATACGTATTCGCATTGCGATTTACGTAT
Found at i:22010 original size:21 final size:21
Alignment explanation
Indices: 21986--22031 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21976 TATTCGCATT
*
21986 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
22007 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
22028 GCGA
1 GCGA
22032 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:26865 original size:13 final size:14
Alignment explanation
Indices: 26841--26869 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
26831 TCATACATCA
26841 AATTTATTTTAATC
1 AATTTATTTTAATC
26855 AATTT-TTTTAATC
1 AATTTATTTTAATC
26868 AA
1 AA
26870 ATTCGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTATTTTAATC
Found at i:26872 original size:14 final size:15
Alignment explanation
Indices: 26837--26872 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
26827 GTATTCATAC
26837 ATCAAATTTATTTTA
1 ATCAAATTTATTTTA
26852 ATC-AATTT-TTTTA
1 ATCAAATTTATTTTA
26865 ATCAAATT
1 ATCAAATT
26873 CGAAGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.40
14 9 0.45
15 3 0.15
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
ATCAAATTTATTTTA
Found at i:30955 original size:38 final size:38
Alignment explanation
Indices: 30913--31014 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 38
30903 TTCTTAAAAC
* *
30913 TTTCGATTAAACCGAAAATGTTACATTCTTCGTAACAT
1 TTTCGATTAAACAGAAAATGTTACATTCTTCATAACAT
* * **
30951 TTTCGATTAACAACAAAAAAATATTATTTTCTTCATAACAT
1 TTTCGATT-A-AAC-AGAAAATGTTACATTCTTCATAACAT
* *
30992 TTTCGATTCAACTGAAAATGTTA
1 TTTCGATTAAACAGAAAATGTTA
31015 GAAAAAGTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
38 16 0.31
39 4 0.08
40 3 0.06
41 28 0.55
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (38 bp):
TTTCGATTAAACAGAAAATGTTACATTCTTCATAACAT
Found at i:31325 original size:2 final size:2
Alignment explanation
Indices: 31318--31350 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31308 TATCTGACAT
31318 TA TA TA TA TA TA TA TA 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 T
31351 TTTGTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31584 original size:52 final size:52
Alignment explanation
Indices: 31506--31608 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
31496 TTATAATATT
31506 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
31558 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
31609 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:36185 original size:52 final size:52
Alignment explanation
Indices: 36107--36209 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
36097 TTATAATATT
36107 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
36159 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
36210 TGCCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:45717 original size:31 final size:32
Alignment explanation
Indices: 45681--45751 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 32
45671 AAAAGCACAC
45681 CCCTTCTCCT-TCC-TCTCATCCTCCTAC-CCCT
1 CCCTTCTCCTCTCCTTCTC-TCCTCCT-CTCCCT
*
45712 CCCTTC-CCTCTCCTTCTCTCGTCCTCTCCCT
1 CCCTTCTCCTCTCCTTCTCTCCTCCTCTCCCT
45743 CCCTCTCTC
1 CCCT-TCTC
45752 GATAGATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
30 4 0.12
31 23 0.68
32 6 0.18
33 1 0.03
ACGTcount: A:0.03, C:0.59, G:0.01, T:0.37
Consensus pattern (32 bp):
CCCTTCTCCTCTCCTTCTCTCCTCCTCTCCCT
Found at i:49679 original size:2 final size:2
Alignment explanation
Indices: 49672--49883 Score: 173
Period size: 2 Copynumber: 108.5 Consensus size: 2
49662 AAGCTGAACC
*
49672 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
49713 AG AG AG AG AG GG AG AG AG AG GG AG AG AG AG AG AG GG AG AG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * * * * *
49755 AG AG AG AG GG AG GG GG AG GG GG AG GG GG AG GG GG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
49797 -G AG AG GG AG AG GG AG AG -G GG AG AG GG AG -G AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
49835 GG AG AG GG AG AG GG AG AG GG AG GG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
49877 AG AG AG A
1 AG AG AG A
49884 TCTTAAAAAT
Statistics
Matches: 167, Mismatches: 38, Indels: 10
0.78 0.18 0.05
Matches are distributed among these distances:
1 5 0.03
2 162 0.97
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (2 bp):
AG
Done.