Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008347.1 Hibiscus syriacus cultivar Beakdansim tig00111078_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: 63082
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2444 original size:53 final size:53
Alignment explanation
Indices: 2364--2542 Score: 268
Period size: 53 Copynumber: 3.4 Consensus size: 53
2354 TTGCTTCAGG
* * *
2364 AGAATTCGAATAATCTTCTGCTTACGGGTTCGCTCCCTCTTGTTTCAGGGAGT
1 AGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT
* * * *
2417 AGAACTCGAACAATATTCTACTTACGGGTTCGCTCCCTCTTACTTCAAGGAGT
1 AGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT
* *
2470 AGAACTCGAACAATCGTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT
1 AGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT
*
2523 AGAACTCGAACAATTTTCTG
1 AGAACTCGAACAATCTTCTG
2543 GTGTAATTCT
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 111 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (53 bp):
AGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT
Found at i:3005 original size:41 final size:42
Alignment explanation
Indices: 2953--3061 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
2943 GGTGTGAAAA
* *
2953 CATCTTACCCGAAGGACTTA-TGGATGACAC-GAAGGATTT-AT
1 CATCTTGCCCGAAAGACTTACT-GATGAC-CTGAAGGATTTCAT
* *
2994 CATCTTGCCCGAACGACTTACTGATGGCCTGAAGGATTTCAT
1 CATCTTGCCCGAAAGACTTACTGATGACCTGAAGGATTTCAT
* *
3036 CATCATGCTCGAAAGACTTACTGATG
1 CATCTTGCCCGAAAGACTTACTGATG
3062 GCACTTACTG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.02
41 32 0.54
42 26 0.44
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
CATCTTGCCCGAAAGACTTACTGATGACCTGAAGGATTTCAT
Found at i:3054 original size:42 final size:41
Alignment explanation
Indices: 2983--3063 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
2973 TGGATGACAC
* *
2983 GAAGGATTTATCATCTTGCCCGAACGACTTACTGATGGCCT
1 GAAGGATTTATCATCATGCCCGAAAGACTTACTGATGGCCT
*
3024 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 GAAGGATTT-ATCATCATGCCCGAAAGACTTACTGATGGC
3064 ACTTACTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 9 0.25
42 27 0.75
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
GAAGGATTTATCATCATGCCCGAAAGACTTACTGATGGCCT
Found at i:3069 original size:13 final size:13
Alignment explanation
Indices: 3051--3075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3041 TGCTCGAAAG
3051 ACTTACTGATGGC
1 ACTTACTGATGGC
3064 ACTTACTGATGG
1 ACTTACTGATGG
3076 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:3131 original size:93 final size:92
Alignment explanation
Indices: 3024--3238 Score: 385
Period size: 93 Copynumber: 2.3 Consensus size: 92
3014 CTGATGGCCT
3024 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
1 GAAGGATTT-ATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
3089 CTCTTCCGTGAAGGCTTACAAATTACCC
65 CTCTTCCGTGAAGGCTTACAAATTACCC
* *
3117 GAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCACTA
1 GAAGGATTT-ATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTA
*
3182 CTCTTCGGTGAAGGCTTACAAATTACCC
65 CTCTTCCGTGAAGGCTTACAAATTACCC
3210 GAAGGATTTATCATCATGCTCGAAAGACT
1 GAAGGATTTATCATCATGCTCGAAAGACT
3239 GATGGCCTGA
Statistics
Matches: 117, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 20 0.17
93 97 0.83
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (92 bp):
GAAGGATTTATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTAC
TCTTCCGTGAAGGCTTACAAATTACCC
Found at i:3162 original size:13 final size:13
Alignment explanation
Indices: 3144--3168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3134 TGCTCGAAAG
3144 ACTTACTGATGGC
1 ACTTACTGATGGC
3157 ACTTACTGATGG
1 ACTTACTGATGG
3169 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:19704 original size:11 final size:11
Alignment explanation
Indices: 19690--19761 Score: 74
Period size: 11 Copynumber: 6.3 Consensus size: 11
19680 CAATTTAGTC
*
19690 ATTTTATTATT
1 ATTTTATTTTT
19701 ATTTTTATTTTT
1 A-TTTTATTTTT
*
19713 TTTCTTATTTCTT
1 ATT-TTATTT-TT
19726 A-TTTATTGTTT
1 ATTTTATT-TTT
19737 ATTTTATTTTT
1 ATTTTATTTTT
*
19748 ACTTTATTTTT
1 ATTTTATTTTT
19759 ATT
1 ATT
19762 ATTTTTTCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 26 0.51
12 23 0.45
13 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:19723 original size:7 final size:6
Alignment explanation
Indices: 19691--19828 Score: 63
Period size: 6 Copynumber: 22.3 Consensus size: 6
19681 AATTTAGTCA
*
19691 TTTTAT TATTAT TTTTAT TTTT-T TTCTTAT TTCTTA- -TTTAT TGTTTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TT-TTAT TTTTAT T-TTTAT
* * *
19738 TTTTAT TTTTA- CTTTAT TTTTAT TATTT-T TTCTAAT ATTTTAT TTATACGT
1 TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TT-TTAT -TTTTAT TTTTA--T
* * * * *
19789 TTATAT ATATAT ATATAT TACTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT T--TTTAT TTTTAT TTTTAT TT
19829 GTTTTTACCT
Statistics
Matches: 107, Mismatches: 10, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.03
5 13 0.12
6 60 0.56
7 18 0.17
8 13 0.12
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:19743 original size:23 final size:24
Alignment explanation
Indices: 19704--19770 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
19694 TATTATTATT
* *
19704 TTTATTTTTTTTCTTATTTCTTA-
1 TTTATTTTTATTATTATTTCTTAC
19727 TTTATTGTTTATT-TTATTT-TTAC
1 TTTATT-TTTATTATTATTTCTTAC
*
19750 TTTATTTTTATTATTTTTTCT
1 TTTATTTTTATTATTATTTCT
19771 AATATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 9 0.24
23 23 0.61
24 6 0.16
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTATTTTTATTATTATTTCTTAC
Found at i:19904 original size:48 final size:44
Alignment explanation
Indices: 19792--19906 Score: 106
Period size: 48 Copynumber: 2.4 Consensus size: 44
19782 TATACGTTTA
*
19792 TATATATATATATATTACTTTATTTTTATTTTTATTTGTTTTTACC
1 TATAT-TATATATA-TACTTTATTATTATTTTTATTTGTTTTTACC
19838 TAGTATTTCATATGTATATA-TTTATTATTATTTTTATTTGTTTTATTAAACAC
1 TA-TA-TT-ATA--TATATACTTTATTATTATTTTTATTTG-TTT-TT--AC-C
19891 TATATTATATATATAC
1 TATATTATATATATAC
19907 ACACATTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
46 2 0.04
47 3 0.05
48 29 0.51
49 5 0.09
50 9 0.16
51 2 0.04
52 4 0.07
53 3 0.05
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.60
Consensus pattern (44 bp):
TATATTATATATATACTTTATTATTATTTTTATTTGTTTTTACC
Found at i:19961 original size:14 final size:14
Alignment explanation
Indices: 19912--20129 Score: 96
Period size: 14 Copynumber: 15.4 Consensus size: 14
19902 TATACACACA
19912 TTATTTTTATTTTT
1 TTATTTTTATTTTT
* *
19926 ATT-TTTTTCTTTAAT
1 -TTATTTTTATTT-TT
* *
19941 TT-CTTTTACTTTT
1 TTATTTTTATTTTT
*
19954 TTATTTTTTTTGTTT
1 TTATTTTTATT-TTT
* *
19969 TTGTTTTTGTTTTT
1 TTATTTTTATTTTT
**
19983 TTA-TTTTACTTCCT
1 TTATTTTTA-TTTTT
*
19997 TTACTTTTT-TTTCT
1 TTA-TTTTTATTTTT
*
20011 TTATCTTTATTTTT
1 TTATTTTTATTTTT
20025 TTATTTTGT-TTTGTT
1 TTATTTT-TATTT-TT
*
20040 TTATTTTTATTTATG
1 TTATTTTTATTT-TT
*
20055 TTACCATTTTATTTTAT
1 TTA--TTTTTATTTT-T
20072 TTA--TTTATTTTT
1 TTATTTTTATTTTT
* *
20084 TTA--CTTATTTTA
1 TTATTTTTATTTTT
*
20096 TTATTTTT-TTGTT
1 TTATTTTTATTTTT
*
20109 TTGTTTATTATTTTT
1 TTATTT-TTATTTTT
*
20124 ATATTT
1 TTATTT
20130 ACACACTTTC
Statistics
Matches: 154, Mismatches: 32, Indels: 34
0.70 0.15 0.15
Matches are distributed among these distances:
12 14 0.09
13 27 0.18
14 57 0.37
15 40 0.26
16 5 0.03
17 11 0.07
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.77
Consensus pattern (14 bp):
TTATTTTTATTTTT
Found at i:20085 original size:38 final size:38
Alignment explanation
Indices: 20028--20125 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 38
20018 TATTTTTTTA
*
20028 TTTTGTTTT-GTT-TTATTTTTATTTATGTTACCATTT
1 TTTTGTTTTATTTATTATTTTTATTTATGTTACCATTT
* * **
20064 TATTT-TATTTATTTATT-TTTTTACTTATTTTATTATTT
1 T-TTTGT-TTTATTTATTATTTTTATTTATGTTACCATTT
*
20102 TTTTGTTTTGTTTATTATTTTTAT
1 TTTTGTTTTATTTATTATTTTTAT
20126 ATTTACACAC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
36 2 0.04
37 18 0.37
38 27 0.55
39 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (38 bp):
TTTTGTTTTATTTATTATTTTTATTTATGTTACCATTT
Found at i:20091 original size:12 final size:13
Alignment explanation
Indices: 20063--20097 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
20053 TGTTACCATT
*
20063 TTATTTTATTTAT
1 TTATTTTATTTAC
20076 TTATTTT-TTTAC
1 TTATTTTATTTAC
20088 TTATTTTATT
1 TTATTTTATT
20098 ATTTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTAC
Found at i:20091 original size:20 final size:20
Alignment explanation
Indices: 20071--20123 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
20061 TTTTATTTTA
20071 TTTATTTATTTTTTTACTTAT
1 TTTA-TTATTTTTTTACTTAT
* *
20092 TTTATTATTTTTTT-GTTTT
1 TTTATTATTTTTTTACTTAT
20111 GTTTATTATTTTT
1 -TTTATTATTTTT
20124 ATATTTACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTATTATTTTTTTACTTAT
Found at i:25385 original size:33 final size:33
Alignment explanation
Indices: 25348--25417 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
25338 TATCTTTGGA
* * * *
25348 TCTGTGTGGTATATTTTTTAAGCTACCTATGGT
1 TCTGTATGATATACTTTTTAAGCTACCTATGAT
* * *
25381 TCTGTATGATATGCTTTTTAAGTTACCTTTGAT
1 TCTGTATGATATACTTTTTAAGCTACCTATGAT
25414 TCTG
1 TCTG
25418 CGCTGTATGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (33 bp):
TCTGTATGATATACTTTTTAAGCTACCTATGAT
Found at i:26286 original size:2 final size:2
Alignment explanation
Indices: 26275--26303 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
26265 CTCCAATTCT
26275 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26304 ATTATCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30898 original size:29 final size:29
Alignment explanation
Indices: 30866--30924 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
30856 TTAATTTGTA
30866 ATTTCATT-TAAACAATGGAACAA-TTATTT
1 ATTT-ATTATAAA-AATGGAACAATTTATTT
*
30895 ATTTATTGATAGAAATGGAACAATTTATTT
1 ATTTATT-ATAAAAATGGAACAATTTATTT
30925 GCTTTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 3 0.12
29 14 0.54
30 9 0.35
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (29 bp):
ATTTATTATAAAAATGGAACAATTTATTT
Found at i:34851 original size:83 final size:80
Alignment explanation
Indices: 34703--34865 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
34693 TCAAGGTATG
*
34703 ATGAATAGTAACTATTTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
1 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
34768 TAAGATAGACTACAT
66 TAAGATAGACTACAT
34783 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTCTTGTGATAAAGTAGCTTCT
1 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTG---TCTTGTGATAAAGTAGCTTCT
34848 TTTTAAGATAGACTACAT
63 TTTTAAGATAGACTACAT
34866 TCATTATGGT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
80 40 0.51
83 39 0.49
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (80 bp):
ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
TAAGATAGACTACAT
Found at i:38951 original size:20 final size:20
Alignment explanation
Indices: 38926--38965 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38916 AGCAACAGAA
*
38926 TAAAAATGATTATATCTAAT
1 TAAAAATGATCATATCTAAT
*
38946 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCATATCTAAT
38966 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:39008 original size:20 final size:21
Alignment explanation
Indices: 38979--39018 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
38969 TAATAGAATA
*
38979 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
39000 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
39019 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:39057 original size:20 final size:20
Alignment explanation
Indices: 39032--39070 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39022 TAATAGAATA
39032 AAAACTGAT-TCTATCTAATT
1 AAAACTGATCT-TATCTAATT
39052 AAAACTGATCTTATCTAAT
1 AAAACTGATCTTATCTAAT
39071 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCTTATCTAATT
Found at i:39061 original size:52 final size:52
Alignment explanation
Indices: 38922--39071 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
38912 AATTAGCAAC
*
38922 AGAATAAAAA-TGATTATATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
38973 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
39026 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCTTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
39072 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.47
53 45 0.48
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:43663 original size:20 final size:20
Alignment explanation
Indices: 43638--43677 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43628 AGCAACAGAA
*
43638 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
43658 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
43678 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:43706 original size:53 final size:53
Alignment explanation
Indices: 43634--43784 Score: 270
Period size: 53 Copynumber: 2.9 Consensus size: 53
43624 AATTAGCAAC
43634 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
43685 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
43738 AGAATAAAAAACTGATTCTATCTAATTAAAACTGATCCAATCTAATA
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
43785 TTTAATTTAG
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 5 0.05
52 5 0.05
53 86 0.90
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (53 bp):
AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:43720 original size:20 final size:21
Alignment explanation
Indices: 43691--43730 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
43681 TAATAGAATA
*
43691 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
43712 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
43731 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:43770 original size:20 final size:20
Alignment explanation
Indices: 43745--43783 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43735 AATAGAATAA
* *
43745 AAAACTGATTCTATCTAATT
1 AAAACTGATCCAATCTAATT
43765 AAAACTGATCCAATCTAAT
1 AAAACTGATCCAATCTAAT
43784 ATTTAATTTA
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:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAACTGATCCAATCTAATT
Found at i:44162 original size:128 final size:128
Alignment explanation
Indices: 43938--44194 Score: 392
Period size: 128 Copynumber: 2.0 Consensus size: 128
43928 CTCTACCAAG
* * *
43938 CAAGGTATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTTTCATCTTTCCTACCTAGCTCCTCAA
1 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAG--TTTTCATCTTTCCTACCAAGCACCTCAA
* * *
44003 TGGAAAAAATATATGAACTCTCAATCTTTTACTAATCTCCTCTAATTTTTCATCTTTCCAATTTT
64 TGGAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
44068 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAG-TTT-ATCTTTCCTACCAAGCACACCTCAA
1 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTCATCTTTCCTACCAAG--CACCTCAA
* *
44131 TGGAAAAAATATATGCACTTTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTT
64 TGGAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTT
44195 CCTTTATGTT
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
126 14 0.12
127 3 0.03
128 66 0.56
130 34 0.29
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (128 bp):
CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTCATCTTTCCTACCAAGCACCTCAATG
GAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
Found at i:47192 original size:57 final size:57
Alignment explanation
Indices: 47099--47213 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
47089 ATACTAAATC
* *
47099 TGTTCAAGTTTTACATTTAGCAAGTCCTGACCATCAGCATCTCTTACAACACCCATT
1 TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
*
47156 TGTTCAAGTTTTACATTTAGCAACTCCTAACTATCAGCATCTCTTACAACACCCATT
1 TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
47213 T
1 T
47214 CTCTATCTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (57 bp):
TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
Found at i:57741 original size:2 final size:2
Alignment explanation
Indices: 57734--57759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57724 AGCTTAATAA
57734 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
57760 TTGGTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60866 original size:6 final size:6
Alignment explanation
Indices: 60855--60893 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
60845 ACTGTGATTG
* * *
60855 GCACTA GCACTA GCACTA GCACTA CCATTA CCACTA GCA
1 GCACTA GCACTA GCACTA GCACTA GCACTA GCACTA GCA
60894 ATATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (6 bp):
GCACTA
Found at i:62857 original size:16 final size:17
Alignment explanation
Indices: 62836--62867 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
62826 GTTTCTCTTC
62836 TCTTTTCT-TTTTTTTT
1 TCTTTTCTGTTTTTTTT
62852 TCTTTTCTGTTTTTTT
1 TCTTTTCTGTTTTTTT
62868 CTGCGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (17 bp):
TCTTTTCTGTTTTTTTT
Done.