Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004947.1 Hibiscus syriacus cultivar Beakdansim tig00011122_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: 135033
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:368 original size:35 final size:35
Alignment explanation
Indices: 315--428 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
305 ACTATCTGTT
315 CATCACCATCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAA
* *
351 CATCACCAT-TTCCATCACCATTGCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAA
* *
385 CATCACCATCTTCTATTACCATTTCACGCCTATATA
1 CATCACCATCTTCCATCACCATTTCACGCCTATA-A
421 -ATCACCAT
1 CATCACCAT
429 TCCCTTACCA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
34 21 0.30
35 40 0.57
36 9 0.13
ACGTcount: A:0.28, C:0.37, G:0.04, T:0.32
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAA
Found at i:4027 original size:19 final size:17
Alignment explanation
Indices: 3988--4037 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
3978 TTGGAGTGCA
*
3988 AAAAGAAAGAAAAAGAC
1 AAAAGAAAGAAAAACAC
*
4005 AAAAGAAGAGAAAAATCAG
1 AAAAGAA-AGAAAAA-CAC
4024 AAAAGAAAAGAAAA
1 AAAAG-AAAGAAAA
4038 GAAAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 12 0.43
20 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAACAC
Found at i:9143 original size:19 final size:19
Alignment explanation
Indices: 9119--9160 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9109 AAAACCCCTT
* *
9119 TGAAAACATATTATTTTAA
1 TGAAAACACATAATTTTAA
*
9138 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
9157 TGAA
1 TGAA
9161 GATAAATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:14866 original size:15 final size:15
Alignment explanation
Indices: 14846--14878 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14836 GTGCTTCAAC
14846 TTTCTTTCCTTTCCT
1 TTTCTTTCCTTTCCT
*
14861 TTTCTTTCCTTTTCT
1 TTTCTTTCCTTTCCT
14876 TTT
1 TTT
14879 TTTTAAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTTCCTTTCCT
Found at i:14867 original size:10 final size:10
Alignment explanation
Indices: 14845--14877 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
14835 AGTGCTTCAA
*
14845 CTTT-CTTTC
1 CTTTCCTTTT
14854 CTTTCCTTTT
1 CTTTCCTTTT
14864 CTTTCCTTTT
1 CTTTCCTTTT
14874 CTTT
1 CTTT
14878 TTTTTAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:17757 original size:16 final size:18
Alignment explanation
Indices: 17726--17769 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
17716 AAGGTAATGA
17726 AATAAGAAAGAATGAAAG
1 AATAAGAAAGAATGAAAG
*
17744 AATAA-AAA-AATGAAAT
1 AATAAGAAAGAATGAAAG
*
17760 AGTAAGAAAG
1 AATAAGAAAG
17770 TGAAGATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.50
17 6 0.27
18 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
AATAAGAAAGAATGAAAG
Found at i:17930 original size:14 final size:14
Alignment explanation
Indices: 17900--17948 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
17890 TTGCAACTTG
*
17900 CTTCTATTT-TTTT
1 CTTCTTTTTCTTTT
17913 -TTCTTTTTCTTTT
1 CTTCTTTTTCTTTT
17926 CTTCTTTTTCTTTT
1 CTTCTTTTTCTTTT
17940 CTTTCTTTT
1 C-TTCTTTT
17949 GCACTCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.22
13 4 0.12
14 14 0.44
15 7 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTCTTTTTCTTTT
Found at i:20744 original size:20 final size:20
Alignment explanation
Indices: 20702--20772 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
20692 CGGCCAATAG
* * *
20702 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAC
20721 CATGTATTTTCATCAAAAAC
1 CATGTATTTTCATCAAAAAC
20741 CATGTATTTTCATCAAAAAC
1 CATGTATTTTCATCAAAAAC
20761 CATGTATTTTCA
1 CATGTATTTTCA
20773 AAGGGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 12 0.25
20 36 0.75
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAC
Found at i:26604 original size:19 final size:20
Alignment explanation
Indices: 26580--26622 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
26570 AGCATTTATC
*
26580 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
26599 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
26619 TTCA
1 TTCA
26623 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:28273 original size:20 final size:20
Alignment explanation
Indices: 28248--28286 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28238 TTTTTTTTTT
28248 CAAAAAAAACAAAAAAAAAC
1 CAAAAAAAACAAAAAAAAAC
**
28268 CAAAAAAGGCAAAAAAAAA
1 CAAAAAAAACAAAAAAAAA
28287 AGGCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (20 bp):
CAAAAAAAACAAAAAAAAAC
Found at i:28287 original size:15 final size:15
Alignment explanation
Indices: 28269--28313 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
28259 AAAAAAAACC
28269 AAAAAAGGC--AAAA
1 AAAAAAGGCAAAAAA
28282 AAAAAAGGCAAAAAA
1 AAAAAAGGCAAAAAA
28297 AAAAAAGAGCCAAAAAA
1 AAAAAAG-G-CAAAAAA
28314 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.32
15 11 0.39
16 1 0.04
17 7 0.25
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAGGCAAAAAA
Found at i:28301 original size:14 final size:13
Alignment explanation
Indices: 28269--28300 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28259 AAAAAAAACC
28269 AAAAAAGGCAAAA
1 AAAAAAGGCAAAA
28282 AAAAAAGGCAAAA
1 AAAAAAGGCAAAA
28295 AAAAAA
1 AAAAAA
28301 AAGAGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGGCAAAA
Found at i:28301 original size:20 final size:19
Alignment explanation
Indices: 28248--28302 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
28238 TTTTTTTTTT
28248 CAAAAAAAACAAAAAAAAAC
1 CAAAAAAAA-AAAAAAAAAC
**
28268 CAAAAAAGGCAAAAAAAAAAGG
1 CAAAAAA---AAAAAAAAAAAC
28290 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
28303 GAGCCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
22 15 0.50
23 2 0.07
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAAC
Found at i:36621 original size:20 final size:19
Alignment explanation
Indices: 36586--36626 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
36576 AGCATTTATC
*
36586 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
36605 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
36625 TT
1 TT
36627 TAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:44298 original size:17 final size:17
Alignment explanation
Indices: 44276--44308 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44266 TCAGCTTAAA
44276 AGAAATGGTTAGGGTAT
1 AGAAATGGTTAGGGTAT
*
44293 AGAAATGGTTATGGTA
1 AGAAATGGTTAGGGTA
44309 GAGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (17 bp):
AGAAATGGTTAGGGTAT
Found at i:44619 original size:6 final size:6
Alignment explanation
Indices: 44600--44640 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
44590 TGTAGGAGTA
* *
44600 TTTTCT TTTGCT TTTTCT TTTTCT TCTTTCT TTTACT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
44641 GTTGCAACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:45052 original size:35 final size:35
Alignment explanation
Indices: 45008--45119 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
44998 AATGGAATGC
* **
45008 TGATTATATAGGCGTGAAATGGTGATATAAGATGG
1 TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
*
45043 TGATGATATAGGCGTGCAATGGTGATGGAAGATGG
1 TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
* *
45078 TGATGTTATAGGCGTGAAAATGGTGATGGAAGATGC
1 TGATGATATAGGCGTG-AAATGGTGATGGAAGATGG
45114 TGATGA
1 TGATGA
45120 ACAGATAGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 46 0.68
36 22 0.32
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
Found at i:49701 original size:19 final size:20
Alignment explanation
Indices: 49677--49727 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
49667 CGGCCAAGAG
* *
49677 CATGTATCTTCATTA-AAAT
1 CATGTATTTTCATCAGAAAT
49696 CATGTATTTTCATCAGAAAT
1 CATGTATTTTCATCAGAAAT
49716 CATGTATTTTCA
1 CATGTATTTTCA
49728 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAGAAAT
Found at i:50460 original size:19 final size:19
Alignment explanation
Indices: 50438--50506 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
50428 AATTGGAGTG
50438 CAAAAAGAAAAGAAAAATA
1 CAAAAAGAAAAGAAAAATA
*
50457 CAAAAAGAAGAAGAAAATTCA
1 CAAAAAGAA-AAGAAAAAT-A
*
50478 GAAAAAGAAAAGAAGAAA-A
1 CAAAAAGAAAAGAA-AAATA
*
50497 GAAAAAGAAA
1 CAAAAAGAAA
50507 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
19 20 0.45
20 13 0.30
21 11 0.25
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAATA
Found at i:50482 original size:34 final size:32
Alignment explanation
Indices: 50443--50518 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
50433 GAGTGCAAAA
*
50443 AGAAAAGAAAA-ATACAAAAAGAAGAAGAAAATTC
1 AGAAAAGAAAAGA-A-AAAAAGAAAAAG-AAATTC
*
50477 AGAAAAAGAAAAGAAGAAAAGAAAAAGAAATTC
1 AG-AAAAGAAAAGAAAAAAAGAAAAAGAAATTC
50510 A-AAAAGAAA
1 AGAAAAGAAA
50519 GCAAGCCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 8 0.21
33 7 0.18
34 12 0.32
35 10 0.26
36 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (32 bp):
AGAAAAGAAAAGAAAAAAAGAAAAAGAAATTC
Found at i:53766 original size:19 final size:20
Alignment explanation
Indices: 53742--53792 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
53732 CGGCCAAGAG
* *
53742 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
53761 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
53781 CATGTATTTTCA
1 CATGTATTTTCA
53793 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:55901 original size:22 final size:22
Alignment explanation
Indices: 55875--55916 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55865 ATATTAAATT
55875 ATATT-AAAATTAATCAATATAA
1 ATATTGAAAATTAA-CAATATAA
*
55897 ATATTGAAAATTCACAATAT
1 ATATTGAAAATTAACAATAT
55917 TTACAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTGAAAATTAACAATATAA
Found at i:57933 original size:16 final size:16
Alignment explanation
Indices: 57908--57949 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
57898 AGAGATGTCT
57908 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
57924 AGTGGGGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
57940 ACTGGAGACA
1 AGTGGAGACA
57950 TGCTCCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.33, T:0.07
Consensus pattern (16 bp):
AGTGGAGACAAAGCCA
Found at i:58187 original size:23 final size:23
Alignment explanation
Indices: 58147--58191 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58137 TAATATATAT
58147 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
58171 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
58192 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:61087 original size:13 final size:12
Alignment explanation
Indices: 61069--61110 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
61059 GCTTTCTTTC
61069 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
61082 TCTTTTT-CTTT
1 TCTTTTTGATTT
61093 TCTTTTCTGATTT
1 TCTTTT-TGATTT
61106 TCTTT
1 TCTTT
61111 CTTTTTGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:61105 original size:24 final size:25
Alignment explanation
Indices: 61061--61110 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
61051 TTTCCTTGGC
61061 TTTCTTTCTCTTTTTGAATTTTCTT
1 TTTCTTTCTCTTTTTGAATTTTCTT
61086 TTTCTTT-TCTTTTCTG-ATTTTCTT
1 TTTCTTTCTCTTTT-TGAATTTTCTT
61110 T
1 T
61111 CTTTTTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTCTTTCTCTTTTTGAATTTTCTT
Found at i:62596 original size:23 final size:23
Alignment explanation
Indices: 62556--62600 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
62546 TAATATATAT
62556 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
62580 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
62601 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:64748 original size:16 final size:16
Alignment explanation
Indices: 64727--64765 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
64717 AGAGATGTCT
64727 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
64743 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
64759 ACTGGAG
1 AGTGGAG
64766 TCAAGTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.33, T:0.08
Consensus pattern (16 bp):
AGTGGAGACAAAGCCA
Found at i:65862 original size:17 final size:17
Alignment explanation
Indices: 65819--65885 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
65809 CAATAAAGGA
* **
65819 TTAATAAATGAACTGGT
1 TTAATTAATGAACTACT
* *
65836 TTGATGAATGAACTACT
1 TTAATTAATGAACTACT
65853 TTAATTAATGAACTAACT
1 TTAATTAATGAACT-ACT
65871 TT-ATTCAATGAACTA
1 TTAATT-AATGAACTA
65886 GATACTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
TTAATTAATGAACTACT
Found at i:65873 original size:18 final size:18
Alignment explanation
Indices: 65842--65885 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
65832 TGGTTTGATG
65842 AATGAACT-ACTTTAATT-
1 AATGAACTAACTTT-ATTC
65859 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
65877 AATGAACTA
1 AATGAACTA
65886 GATACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:68426 original size:16 final size:16
Alignment explanation
Indices: 68405--68449 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
68395 CAAGAGATGT
68405 CTAGTGGAGACAAAGC
1 CTAGTGGAGACAAAGC
*
68421 CTAGTGGAGATAAAGC
1 CTAGTGGAGACAAAGC
* *
68437 CAAGTGAAGACAA
1 CTAGTGGAGACAA
68450 GTAATCTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.29, T:0.13
Consensus pattern (16 bp):
CTAGTGGAGACAAAGC
Found at i:69541 original size:17 final size:17
Alignment explanation
Indices: 69498--69564 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
69488 CAATTAAGGA
* **
69498 TTAATAAATGAACTGGT
1 TTAATTAATGAACTACT
* *
69515 TTGATGAATGAACTACT
1 TTAATTAATGAACTACT
69532 TTAATTAATGAACTAACT
1 TTAATTAATGAACT-ACT
69550 TT-ATTCAATGAACTA
1 TTAATT-AATGAACTA
69565 GATACTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
TTAATTAATGAACTACT
Found at i:69552 original size:18 final size:18
Alignment explanation
Indices: 69521--69564 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
69511 TGGTTTGATG
69521 AATGAACT-ACTTTAATT-
1 AATGAACTAACTTT-ATTC
69538 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
69556 AATGAACTA
1 AATGAACTA
69565 GATACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:72289 original size:24 final size:24
Alignment explanation
Indices: 72243--72289 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
72233 TCTTGGCACT
* * *
72243 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
*
72267 TCAAGTGGCATAGCTGTTGGAAC
1 TCAAGTGGCACAGCTGTTGGAAC
72290 GTTAAAGGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:81526 original size:23 final size:24
Alignment explanation
Indices: 81484--81536 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
81474 TTTCTTTCTT
81484 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
81508 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
81531 TTTCTT
1 TTTCTT
81537 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:84792 original size:30 final size:31
Alignment explanation
Indices: 84740--84799 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
84730 CTTAGCTTTA
**
84740 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
84770 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
84800 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:85700 original size:19 final size:20
Alignment explanation
Indices: 85676--85725 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
85666 GGCCAAGAGC
* *
85676 ATGTATCTTCAT-TAAAATA
1 ATGTATTTTCATCAAAAATA
*
85695 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCATCAAAAATA
85715 ATGTATTTTCA
1 ATGTATTTTCA
85726 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCATCAAAAATA
Found at i:86489 original size:22 final size:23
Alignment explanation
Indices: 86433--86491 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
86423 ATTGGAGTGC
86433 AAAAAG-AAAGAAAAAGACAAAA
1 AAAAAGAAAAGAAAAAGACAAAA
* * *
86455 AAAAAGAAGAGAAAAA-TCAGAA
1 AAAAAGAAAAGAAAAAGACAAAA
*
86477 AAGAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
86492 GAAAAAGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAAGACAAAA
Found at i:89898 original size:19 final size:20
Alignment explanation
Indices: 89874--89924 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
89864 CGGCCAAGAG
* *
89874 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
89893 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
89913 CATGTATTTTCA
1 CATGTATTTTCA
89925 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:93405 original size:13 final size:12
Alignment explanation
Indices: 93389--93430 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
93379 GTGCAAAAAG
93389 AAAGAAAATCAGA
1 AAAGAAAATCA-A
*
93402 AAAGAAAA-GAA
1 AAAGAAAATCAA
93413 AAAGAAAATTCAA
1 AAAGAAAA-TCAA
93426 AAAGA
1 AAAGA
93431 GAAAGCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:93420 original size:24 final size:25
Alignment explanation
Indices: 93389--93435 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
93379 GTGCAAAAAG
93389 AAAGAAAA-TCAGAAAAGA-AAAGAA
1 AAAGAAAATTCA-AAAAGAGAAAGAA
93413 AAAGAAAATTCAAAAAGAGAAAG
1 AAAGAAAATTCAAAAAGAGAAAG
93436 CAAGCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAGAAAATTCAAAAAGAGAAAGAA
Found at i:101522 original size:15 final size:15
Alignment explanation
Indices: 101504--101536 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
101494 ACATAAAGGG
*
101504 AGCTATCTTAAAGCT
1 AGCTAACTTAAAGCT
101519 AGCTAACTTAAAGCT
1 AGCTAACTTAAAGCT
101534 AGC
1 AGC
101537 ATTGGAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (15 bp):
AGCTAACTTAAAGCT
Found at i:103007 original size:18 final size:18
Alignment explanation
Indices: 102984--103018 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
102974 ACAAACATAA
102984 AAAAGA-AAGAAGAAAAAC
1 AAAAGAGAA-AAGAAAAAC
103002 AAAAGAGAAAAGAAAAA
1 AAAAGAGAAAAGAAAAA
103019 GACTCCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAAAGAAAAAC
Found at i:109737 original size:10 final size:11
Alignment explanation
Indices: 109715--109739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109705 CAACAACAGC
109715 AAAAATACAAA
1 AAAAATACAAA
109726 AAAAATACAAA
1 AAAAATACAAA
109737 AAA
1 AAA
109740 GAAGTGACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATACAAA
Found at i:109803 original size:20 final size:19
Alignment explanation
Indices: 109762--109803 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
109752 AGTGCTAGTG
*
109762 AAGAAATCCAGATTCAACA
1 AAGAAATCCAGACTCAACA
109781 AAGAAATTCCAGTACTCAA-A
1 AAGAAA-TCCAG-ACTCAACA
109801 AAG
1 AAG
109804 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (19 bp):
AAGAAATCCAGACTCAACA
Found at i:118329 original size:11 final size:11
Alignment explanation
Indices: 118313--118368 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
118303 ATTGGAGTGC
118313 AAAAAGAAAAG
1 AAAAAGAAAAG
118324 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
118335 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
118349 AAAAAGAAAAG
1 AAAAAGAAAAG
118360 AAAAAGAAA
1 AAAAAGAAA
118369 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:131576 original size:23 final size:22
Alignment explanation
Indices: 131537--131590 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
131527 TAATTCATTC
*
131537 ATTATCATATGCATGAGTTGTT
1 ATTATTATATGCATGAGTTGTT
*
131559 ATTATTATGATGCTTGAGTTGTT
1 ATTATTAT-ATGCATGAGTTGTT
131582 ATTATTATA
1 ATTATTATA
131591 ACCTATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (22 bp):
ATTATTATATGCATGAGTTGTT
Done.