Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008834.1 Hibiscus syriacus cultivar Beakdansim tig00112028_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: 48937
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3740 original size:30 final size:30
Alignment explanation
Indices: 3706--3763 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3696 TATTATGCTT
3706 AAAAGAAAA-AAAAGAATAAAAAATAAAAGA
1 AAAAGAAAAGAAAA-AATAAAAAATAAAAGA
* *
3736 AAAAGAAAAGAAAAAGTAGAAAATAAAA
1 AAAAGAAAAGAAAAAATAAAAAATAAAA
3764 AGAAGGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (30 bp):
AAAAGAAAAGAAAAAATAAAAAATAAAAGA
Found at i:4137 original size:18 final size:18
Alignment explanation
Indices: 4111--4148 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4101 CAAGTTCATC
*
4111 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
*
4129 TTTTCGAAATTTAATTTA
1 TTTTCGAAATTCAATTTA
4147 TT
1 TT
4149 CTTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:4798 original size:22 final size:22
Alignment explanation
Indices: 4766--4832 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
4756 TATCCACATC
4766 TACATTCTTCAAAAATAATAGA
1 TACATTCTTCAAAAATAATAGA
* * *
4788 TACATTTTTCAAAGATGATAGA
1 TACATTCTTCAAAAATAATAGA
* * *
4810 TTC-TCTCTTCAAAGATGATAGA
1 TACAT-TCTTCAAAAATAATAGA
4832 T
1 T
4833 TCTCTTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (22 bp):
TACATTCTTCAAAAATAATAGA
Found at i:4833 original size:22 final size:22
Alignment explanation
Indices: 4795--4843 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
4785 AGATACATTT
4795 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTC
*
4817 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTC
4839 TTCAA
1 TTCAA
4844 TTAAGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTC
Found at i:5559 original size:123 final size:123
Alignment explanation
Indices: 5259--5803 Score: 769
Period size: 123 Copynumber: 4.5 Consensus size: 123
5249 AATAATAAAG
**
5259 AGAACTCATCTGAAGAATAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
1 AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
* * * **
5324 ACTATCACA-AGAGGAGATAGATCAGCATAAACATTTCCAGA-AGTGTTCATAATGAGA
66 TCTATCACAGA-AGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
* *
5381 AGAACTCATCTGAAG-AGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTATGAT
1 AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
*
5445 TCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGCTCATAATGAGA
66 TCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
5503 AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATG-C
1 AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
* * *
5567 TTCTATCACAGAAGGAGATAGATCATCATCAAATTTTGCAGAGAAAGTTCATAATGAGA
66 -TCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
* * * * *
5626 AGAACTCATATGAAGAAGGAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGGC
1 AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
* * * * *
5691 TCTATCACAGAAAGAGATAGATCAACACCAACGTTTCCAGATAAAGTTCATAATGA-A
66 TCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
* * * * *
5748 AAAACTTATCTGAAG-AGGAAGAAGAAGTTCGTAATGAGAATAACTTGTTCGACCTT
1 AGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
5804 AGCTTGATTC
Statistics
Matches: 382, Mismatches: 35, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
121 84 0.22
122 89 0.23
123 208 0.54
124 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
AGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAC
TCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
Found at i:5886 original size:17 final size:17
Alignment explanation
Indices: 5864--5896 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5854 GATCAATGTT
*
5864 TTCATAATGAGAAGAAG
1 TTCATAATAAGAAGAAG
5881 TTCATAATAAGAAGAA
1 TTCATAATAAGAAGAA
5897 CTTATTCAAC
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:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
TTCATAATAAGAAGAAG
Found at i:6141 original size:3 final size:3
Alignment explanation
Indices: 6135--6208 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
6125 TCATTTGGTT
* *
6135 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TAA TTA -TA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
6181 ATA TTA TTA TTA ATA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA
6209 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.06
3 57 0.90
4 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:6162 original size:23 final size:23
Alignment explanation
Indices: 6136--6206 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
6126 CATTTGGTTT
6136 TATTATTATTATTATTATTATTA
1 TATTATTATTATTATTATTATTA
* * *
6159 TATTATTATTATAATTATAATAA
1 TATTATTATTATTATTATTATTA
*
6182 TATTATTATTAATATTTATTATTA
1 TATTATTATTATTA-TTATTATTA
6206 T
1 T
6207 TACAGGCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 32 0.80
24 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTATTATTATTATTATTA
Found at i:7573 original size:17 final size:18
Alignment explanation
Indices: 7551--7584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7541 GTCACTACTT
*
7551 ATTTA-TATTTTAATTTA
1 ATTTATTATTTAAATTTA
7568 ATTTATTATTTAAATTT
1 ATTTATTATTTAAATTT
7585 CAATATGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATTATTTAAATTTA
Found at i:7753 original size:15 final size:16
Alignment explanation
Indices: 7722--7754 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
7712 AATTCCTATT
7722 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
*
7738 TATAAA-TTACTTTTA
1 TATAAATTTAATTTTA
7753 TA
1 TA
7755 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:7962 original size:43 final size:44
Alignment explanation
Indices: 7896--7979 Score: 152
Period size: 43 Copynumber: 1.9 Consensus size: 44
7886 TTATTTTTAT
7896 AGAAATACTTTATTAATATTTTATTTATTTTTTAATATTAAGAA
1 AGAAATACTTTATTAATATTTTATTTATTTTTTAATATTAAGAA
*
7940 AGAAATATTTTATTAATA-TTTATTTATTTTTTAATATTAA
1 AGAAATACTTTATTAATATTTTATTTATTTTTTAATATTAA
7980 AAAAATGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 22 0.56
44 17 0.44
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (44 bp):
AGAAATACTTTATTAATATTTTATTTATTTTTTAATATTAAGAA
Found at i:8080 original size:18 final size:19
Alignment explanation
Indices: 8043--8084 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
8033 ATAAATATCT
8043 TATTTATAAAAATTATATA
1 TATTTATAAAAATTATATA
*
8062 TATTTATAAAAGTTA-ATA
1 TATTTATAAAAATTATATA
8080 TATTT
1 TATTT
8085 TTCTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTATAAAAATTATATA
Found at i:10691 original size:26 final size:28
Alignment explanation
Indices: 10654--10726 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 28
10644 ATCCTATATT
*
10654 AATTTAATATTAATTA-AATAAATATAA
1 AATTTAATATTAATTATAATAAAAATAA
* *
10681 AATTTAA-ATTATTTATGATAAAAATAA
1 AATTTAATATTAATTATAATAAAAATAA
* *
10708 ATTTTAATATTTATT-TAAT
1 AATTTAATATTAATTATAAT
10727 TTTAAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 7 0.19
27 25 0.68
28 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
AATTTAATATTAATTATAATAAAAATAA
Found at i:14873 original size:3 final size:3
Alignment explanation
Indices: 14865--14932 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
14855 TTATCCATAA
*
14865 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
14913 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
14933 AATATATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:16279 original size:19 final size:18
Alignment explanation
Indices: 16243--16291 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
16233 TAGATTTTTA
*
16243 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
16260 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
16279 ATTTTATTGTTTT
1 ATTTTATTGTTTT
16292 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:17101 original size:18 final size:18
Alignment explanation
Indices: 17056--17103 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
17046 TTTCAAATTA
17056 TTTA-TTTATTTATTATT
1 TTTATTTTATTTATTATT
**
17073 TTTATAATATTTA-TATGT
1 TTTATTTTATTTATTAT-T
17091 TTTATTTTATTTA
1 TTTATTTTATTTA
17104 CAAGTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTTATTATT
Found at i:17124 original size:13 final size:15
Alignment explanation
Indices: 17093--17129 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
17083 TTATATGTTT
17093 TATTTTATTTACAAG
1 TATTTTATTTACAAG
17108 TATTTTATTT-C-AG
1 TATTTTATTTACAAG
17121 TA-TTTATTT
1 TATTTTATTT
17130 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTTTATTTACAAG
Found at i:27740 original size:11 final size:10
Alignment explanation
Indices: 27723--27782 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 10
27713 TGAAGAGAAT
27723 AGAAAAAAAA
1 AGAAAAAAAA
27733 AGGAAAAAAAA
1 A-GAAAAAAAA
27744 TAGAAAATAAAA
1 -AGAAAA-AAAA
*
27756 AAAAATAAAAA
1 AGAAA-AAAAA
*
27767 AGAGAAGAAAA
1 AGA-AAAAAAA
27778 AGAAA
1 AGAAA
27783 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
10 3 0.07
11 31 0.74
12 8 0.19
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:27765 original size:22 final size:21
Alignment explanation
Indices: 27720--27782 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
27710 GCTTGAAGAG
27720 AATAGAAAAAAAAAGGAAAAAA
1 AATAGAAAAAAAAA-GAAAAAA
27742 AATAGAAAATAAAAA-AAAATAA
1 AATAGAAAA-AAAAAGAAAA-AA
* *
27764 AAAAGAGAAGAAAAAGAAA
1 AATAGA-AAAAAAAAGAAA
27783 GGGGGTCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 4 0.11
22 21 0.60
23 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (21 bp):
AATAGAAAAAAAAAGAAAAAA
Found at i:29312 original size:165 final size:166
Alignment explanation
Indices: 28904--29389 Score: 868
Period size: 165 Copynumber: 2.9 Consensus size: 166
28894 TATCTTAGTC
*
28904 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
28969 TGATCTGGTTGGACATAATCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
65 TGATCTGGTTGGACAGAA-CAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
* * *
29034 AAGTGTTCTTTGAGTTATATAATCTGGTTGGACATAAT
129 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
29072 CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
29137 GATCTGGTTGGACAGAACAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAA
66 GATCTGGTTGGACAGAACAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAA
*
29202 GTATTCTTTGAGTTATCTGATCTGGTTGGACAGAA-
131 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
29237 CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
* *
29302 GATCTGGTTGGACAGAACAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAA
66 GATCTGGTTGGACAGAACAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAA
29366 GTGTTCTTTGAGTTATCTGATCTG
131 GTGTTCTTTGAGTTATCTGATCTG
29390 ATTCAGTAGG
Statistics
Matches: 309, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
164 41 0.13
165 109 0.35
166 79 0.26
167 52 0.17
168 28 0.09
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (166 bp):
CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
GATCTGGTTGGACAGAACAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAA
GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
Found at i:29321 original size:82 final size:83
Alignment explanation
Indices: 28904--29389 Score: 843
Period size: 82 Copynumber: 5.9 Consensus size: 83
28894 TATCTTAGTC
28904 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
28969 TGATCTGGTTGGACATAA
66 TGATCTGGTTGGACAGAA
*
28987 TCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 -CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
29052 ATAATCTGGTTGGACATAA
65 CTGATCTGGTTGGACAGAA
*
29071 TCAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 -CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
29135 CTGATCTGGTTGGACAGAA
65 CTGATCTGGTTGGACAGAA
* *
29154 CAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATC
1 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
29219 TGATCTGGTTGGACAGAA
66 TGATCTGGTTGGACAGAA
*
29237 CAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
29301 TGATCTGGTTGGACAGAA
66 TGATCTGGTTGGACAGAA
*
29319 CAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
29383 TGATCTG
66 TGATCTG
29390 ATTCAGTAGG
Statistics
Matches: 387, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
82 150 0.39
83 129 0.33
84 108 0.28
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
CAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGGACAGAA
Found at i:30331 original size:113 final size:113
Alignment explanation
Indices: 30133--31137 Score: 1818
Period size: 113 Copynumber: 8.9 Consensus size: 113
30123 TCAAATCCAC
* *
30133 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
30197 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
30246 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30311 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
30359 TTGATGGATCAACATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30423 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
30471 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30536 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
30584 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30649 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
30697 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30762 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
30810 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
30875 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
30923 TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
30988 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *** *
31037 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
31102 AGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
31138 GATACTATCA
Statistics
Matches: 867, Mismatches: 22, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
112 128 0.15
113 636 0.73
114 103 0.12
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:31460 original size:3 final size:3
Alignment explanation
Indices: 31452--31514 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
31442 TTTTTATCCA
*
31452 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31500 TAT TAT TATT TAT TA
1 TAT TAT TA-T TAT TA
31515 AATATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:32301 original size:23 final size:23
Alignment explanation
Indices: 32275--32325 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
32265 GGCCACCGAA
32275 GACGGTGGCCGGCGGCGGTGGTT
1 GACGGTGGCCGGCGGCGGTGGTT
32298 GACGGTGGCCGGCGGCGGTGGTT
1 GACGGTGGCCGGCGGCGGTGGTT
32321 GACGG
1 GACGG
32326 CGGATGAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.06, C:0.22, G:0.57, T:0.16
Consensus pattern (23 bp):
GACGGTGGCCGGCGGCGGTGGTT
Found at i:32883 original size:19 final size:18
Alignment explanation
Indices: 32847--32895 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
32837 TAGATTTTTA
*
32847 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
32864 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
32883 ATTTTATTGTTTT
1 ATTTTATTGTTTT
32896 TAATATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:32904 original size:19 final size:19
Alignment explanation
Indices: 32863--32904 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
32853 TTTTTTCGTT
* *
32863 TATTTTATATGTTTTCATT
1 TATTTTATATGTTTTAATA
32882 TATTTTAT-TGTTTTTAATA
1 TATTTTATATG-TTTTAATA
32901 TATT
1 TATT
32905 GTTTTAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTATATGTTTTAATA
Found at i:32961 original size:13 final size:13
Alignment explanation
Indices: 32933--32967 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
32923 TTTTATTATA
32933 TTATTAAATA-TT
1 TTATTAAATATTT
32945 TTATTAAATATTT
1 TTATTAAATATTT
32958 TTA-TAAATAT
1 TTATTAAATAT
32968 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:36261 original size:2 final size:2
Alignment explanation
Indices: 36254--36285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36244 CAATTTTGTA
36254 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
36286 TATGAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36493 original size:18 final size:19
Alignment explanation
Indices: 36470--36512 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
36460 CAGTAATCCT
36470 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
36488 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
36508 ATTCC
1 ATTCC
36513 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:36500 original size:20 final size:20
Alignment explanation
Indices: 36475--36512 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
36465 ATCCTATTCC
36475 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
36495 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
36513 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:48484 original size:18 final size:17
Alignment explanation
Indices: 48456--48491 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
48446 ATTATAAAGT
48456 AAATATTAAATAAATTA
1 AAATATTAAATAAATTA
48473 AAATACTTAAATAAATTA
1 AAATA-TTAAATAAATTA
48491 A
1 A
48492 TACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATTAAATAAATTA
Found at i:48516 original size:18 final size:18
Alignment explanation
Indices: 48456--48519 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
48446 ATTATAAAGT
48456 AAATATT-AAATA-AATTA
1 AAATATTAAAATATAA-TA
*
48473 AAATACTTAAATAAATTAATACA
1 AAATA-TTAAA-ATA-TAAT--A
48496 AAATATTAAAATATAATA
1 AAATATTAAAATATAATA
48514 AAATAT
1 AAATAT
48520 ACCTTAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
17 5 0.13
18 9 0.24
19 2 0.05
20 6 0.16
21 3 0.08
22 7 0.18
23 6 0.16
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATTAAAATATAATA
Found at i:48562 original size:10 final size:10
Alignment explanation
Indices: 48549--48594 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
48539 AGAGTATTTA
*
48549 AGAGAAGTTG
1 AGAGAAATTG
48559 AGAGAAATTG
1 AGAGAAATTG
*
48569 AGAGAATTTG
1 AGAGAAATTG
48579 AGAGAAATTG
1 AGAGAAATTG
48589 AGAGAA
1 AGAGAA
48595 TTTGGTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.20
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:48595 original size:20 final size:20
Alignment explanation
Indices: 48549--48598 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
48539 AGAGTATTTA
*
48549 AGAGAAGTTGAGAGAAATTG
1 AGAGAATTTGAGAGAAATTG
48569 AGAGAATTTGAGAGAAATTG
1 AGAGAATTTGAGAGAAATTG
48589 AGAGAATTTG
1 AGAGAATTTG
48599 GTGTGATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (20 bp):
AGAGAATTTGAGAGAAATTG
Done.