Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001897.1 Hibiscus syriacus cultivar Beakdansim tig00003844_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: 45113
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2842 original size:5 final size:5
Alignment explanation
Indices: 2832--2861 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2822 TGTTGAAATT
2832 TAATC TAATC TAATC TAATC TAATC TAATC
1 TAATC TAATC TAATC TAATC TAATC TAATC
2862 AAACAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATC
Found at i:12894 original size:2 final size:2
Alignment explanation
Indices: 12887--12919 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12877 CAAGTCTGAA
12887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12920 CAATACAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13277 original size:5 final size:5
Alignment explanation
Indices: 12917--13275 Score: 466
Period size: 5 Copynumber: 71.8 Consensus size: 5
12907 ATATATATAT
12917 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
12967 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
** ** * ** **
13017 ATACA ATGTA ATGTA ATACA ATATA ATGTA ATACA ATGTA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
13067 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
*
13117 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACC ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
* * * * * * *
13167 ATACA ATACA ATACA ATACC ATACC ATACC ATACC ATACC ATACC ATACC
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
* * * * * * * * * *
13217 ATACC ATACC ATACC ATACC ATACC ATACC ATACC ATACC ATACC ATACC
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
*
13267 ATACC ATAC
1 ATACA ATAC
13276 CACTCGCAAG
Statistics
Matches: 339, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 339 1.00
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.21
Consensus pattern (5 bp):
ATACA
Found at i:15036 original size:34 final size:36
Alignment explanation
Indices: 14992--15093 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
14982 TTTCGTCATA
*
14992 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
15027 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
15062 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
15094 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:15117 original size:37 final size:37
Alignment explanation
Indices: 14990--15127 Score: 156
Period size: 37 Copynumber: 3.8 Consensus size: 37
14980 TTTTTCGTCA
* *
14990 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
*
15026 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
15061 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
15098 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
15128 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:15661 original size:15 final size:15
Alignment explanation
Indices: 15615--15662 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
15605 TTTTTATTAT
*
15615 TATTTTACTTATATA
1 TATTTTACTTATTTA
*
15630 TATGCTTTACTTTTTTA
1 TAT--TTTACTTATTTA
*
15647 TATTTTACTCATTTA
1 TATTTTACTTATTTA
15662 T
1 T
15663 TTATCTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTTACTTATTTA
Found at i:15681 original size:16 final size:18
Alignment explanation
Indices: 15660--15694 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
15650 TTTACTCATT
15660 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
15676 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
15694 T
1 T
15695 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:18889 original size:8 final size:7
Alignment explanation
Indices: 18860--18947 Score: 61
Period size: 7 Copynumber: 11.7 Consensus size: 7
18850 AATCAAGAAC
18860 AAAAAAG
1 AAAAAAG
18867 AAAAGAAG
1 AAAA-AAG
18875 CAAAAAAG
1 -AAAAAAG
18883 TAAAAAA-
1 -AAAAAAG
18890 AAACAAAG
1 AAA-AAAG
*
18898 AAAAGAG
1 AAAAAAG
*
18905 AAACAAG
1 AAAAAAG
*
18912 AACAAAAA
1 AA-AAAAG
18920 AAAAAAG
1 AAAAAAG
*
18927 AGCAAAAAT
1 A--AAAAAG
*
18936 CAAAAAG
1 AAAAAAG
18943 AAAAA
1 AAAAA
18948 GGGACAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
6 3 0.05
7 31 0.49
8 20 0.32
9 9 0.14
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:18901 original size:31 final size:29
Alignment explanation
Indices: 18860--18927 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
18850 AATCAAGAAC
18860 AAAAAAGAAAAGAAGCAAAAAAGTAA-AAAAA
1 AAAAAAGAAAAG-AG-AAAAAAG-AACAAAAA
* *
18891 AACAAAGAAAAGAGAAACAAGAACAAAAA
1 AAAAAAGAAAAGAGAAAAAAGAACAAAAA
18920 AAAAAAGA
1 AAAAAAGA
18928 GCAAAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 18 0.55
30 2 0.06
31 11 0.33
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (29 bp):
AAAAAAGAAAAGAGAAAAAAGAACAAAAA
Found at i:18927 original size:15 final size:14
Alignment explanation
Indices: 18860--18947 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 14
18850 AATCAAGAAC
*
18860 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAA-AA-A
18876 AAAAAAGTAAAAAAA
1 AAAAAAG-AAAAAAA
* * *
18891 AACAAAGAAAAGAG
1 AAAAAAGAAAAAAA
*
18905 AAACAAGAACAAAAA
1 AAAAAAGAA-AAAAA
*
18920 AAAAAAGAGCAAAAAT
1 AAAAAAGA--AAAAAA
*
18936 CAAAAAGAAAAA
1 AAAAAAGAAAAA
18948 GGGACAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
14 16 0.28
15 16 0.28
16 20 0.35
17 5 0.09
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:18939 original size:22 final size:23
Alignment explanation
Indices: 18914--18957 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
18904 GAAACAAGAA
18914 CAAAAAAAAAAAGAG-CAAAAAT
1 CAAAAAAAAAAAGAGACAAAAAT
* *
18936 CAAAAAGAAAAAGGGACAAAAA
1 CAAAAAAAAAAAGAGACAAAAA
18958 GCACATGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.75, C:0.09, G:0.14, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAAAAGAGACAAAAAT
Found at i:19600 original size:22 final size:22
Alignment explanation
Indices: 19575--19623 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
19565 CCATCAATCT
* *
19575 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
19597 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
19619 TTTGA
1 TTTGA
19624 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:20448 original size:71 final size:73
Alignment explanation
Indices: 20365--20688 Score: 212
Period size: 72 Copynumber: 4.6 Consensus size: 73
20355 GTTTTTCTTA
* * * * * *
20365 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
20427 TTTCCCTTG
65 TTTCCCTTG
* * * *
20436 AAACAAATTTTGTCTCTTTTGAGATAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
20500 TTCCCTTG
66 TTCCCTTG
* * * * *
20508 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
20564 TTTTCTTTG
65 TTTCCCTTG
** * ** * * * * *
20573 AAACAAATTCCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
20637 TTTCTCTTG
65 TTTCCCTTG
* * * *
20646 AAAC-AATTTTCGTCTATCTTGAGACA-ATTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
20689 ACCTTTGAAT
Statistics
Matches: 198, Mismatches: 40, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
64 2 0.01
65 45 0.23
66 5 0.03
70 8 0.04
71 23 0.12
72 75 0.38
73 38 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:20450 original size:36 final size:36
Alignment explanation
Indices: 20407--20688 Score: 285
Period size: 36 Copynumber: 8.0 Consensus size: 36
20397 ACTAGAAGAG
20407 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
20443 TTTTGTCTCTTTTGAGATAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
20479 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
20515 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
20551 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
20580 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
20617 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
20652 TTTTCGTCTATCTTGAGACAATTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
20689 ACCTTTGAAT
Statistics
Matches: 200, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 137 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:20648 original size:102 final size:103
Alignment explanation
Indices: 20405--20651 Score: 304
Period size: 101 Copynumber: 2.4 Consensus size: 103
20395 TCACTAGAAG
* *
20405 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAGATAGTTTCTCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----TATCATTTGAGATAGTTTCTCT
* *
20470 TGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATA
61 TGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATA
*
20513 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-AT-ATTTGA-ATATGTTT-TCTTTGA
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATCATTTGAGATA-GTTTCTC-TTGA
* ** *
20574 AACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
64 AACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATA
*
20615 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
20652 TTTTCGTCTA
Statistics
Matches: 125, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
100 5 0.04
101 42 0.34
102 41 0.33
108 37 0.30
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (103 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATCATTTGAGATAGTTTCTCTTGAAA
CAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATA
Found at i:20680 original size:138 final size:137
Alignment explanation
Indices: 20427--20751 Score: 409
Period size: 138 Copynumber: 2.4 Consensus size: 137
20417 CTTGAGACAG
** *
20427 TTTCCCTTGAAACAAATTTTGTCTCTTTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* * *
20492 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAAAACATTT
*
20557 GAATATG
131 GAATATA
* * ** * * * * *
20564 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
20629 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAATTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAATTTCCCTTGAAACAAAACAT
*
20693 TTGAATTTA
129 TTGAATATA
* * * *
20702 TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
20752 CAAAATCTTA
Statistics
Matches: 156, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
137 47 0.30
138 109 0.70
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:21652 original size:105 final size:105
Alignment explanation
Indices: 21463--22399 Score: 1434
Period size: 105 Copynumber: 9.0 Consensus size: 105
21453 GCACTCGAGG
* * * * * *
21463 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
21528 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21569 CAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
21634 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
21674 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * * *
21739 GCCTATTTCAACTTTACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
21779 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGTTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21844 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGG
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
21884 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
21949 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
21989 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
22054 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
22094 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
22159 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
22199 CAACGCAAGTTCAACTTCACGACGAAGGGACCTCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
22259 TTCAATTTCAACTTCATAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
22299 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
22364 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
22400 TGGAACAATG
Statistics
Matches: 772, Mismatches: 53, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
100 81 0.10
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 604 0.78
106 74 0.10
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:22991 original size:34 final size:36
Alignment explanation
Indices: 22947--23048 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
22937 TTTCGTCATA
*
22947 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
22982 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
23017 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
23049 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:23072 original size:37 final size:37
Alignment explanation
Indices: 22945--23082 Score: 156
Period size: 37 Copynumber: 3.8 Consensus size: 37
22935 TTTTTCGTCA
* *
22945 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
*
22981 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
23016 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
23053 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
23083 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:23640 original size:16 final size:18
Alignment explanation
Indices: 23619--23653 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
23609 TTTACTCATT
23619 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
23635 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
23653 T
1 T
23654 GTTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:27698 original size:2 final size:2
Alignment explanation
Indices: 27691--27742 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
27681 TTAATTGTAA
27691 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
27733 AT AT AT AT AT
1 AT AT AT AT AT
27743 TCATAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31095 original size:5 final size:5
Alignment explanation
Indices: 31085--31110 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31075 ACAAGGTTTC
31085 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
31111 ATATATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:32134 original size:23 final size:23
Alignment explanation
Indices: 32101--32162 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
32091 CTCGTATAAA
*
32101 TGCACCTAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
**
32124 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
32147 TGCACCGAAGTGCCAT
1 TGCACCGAAGTGCCAT
32163 ATAAAATGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:40953 original size:19 final size:20
Alignment explanation
Indices: 40916--40953 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40906 CTATTGAAAA
*
40916 GAAATATTTAAAATTATAAT
1 GAAATATTTAAAATCATAAT
*
40936 GAAA-ATTTATAATCATAA
1 GAAATATTTAAAATCATAA
40954 ATGTAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (20 bp):
GAAATATTTAAAATCATAAT
Found at i:41414 original size:22 final size:21
Alignment explanation
Indices: 41385--41431 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
41375 TAAAAATAGA
*
41385 AAAAAAATATTTCATATAAAAG
1 AAAAAAATATGTCATA-AAAAG
* *
41407 AAAAAAATGTGTCATAAAAAT
1 AAAAAAATATGTCATAAAAAG
41428 AAAA
1 AAAA
41432 TTATTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAAAATATGTCATAAAAAG
Found at i:43821 original size:22 final size:23
Alignment explanation
Indices: 43785--43827 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
43775 TAGCATTTCG
43785 AAAAAATAAATTATAATTTATTC
1 AAAAAATAAATTATAATTTATTC
*
43808 AAAAAATAAA-TATATTTTAT
1 AAAAAATAAATTATAATTTAT
43828 AATTTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAAATAAATTATAATTTATTC
Done.