Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008968.1 Hibiscus syriacus cultivar Beakdansim tig00112310_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: 112859
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:4130 original size:19 final size:19
Alignment explanation
Indices: 4106--4162 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
4096 TCTTTTTGAA
4106 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
* *
4125 TTCTTTTCTTTTTTCTTTTT
1 TTCTTTT-TCTTTTCTTTTC
4145 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
4163 TGCACTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.45
20 12 0.36
21 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:4140 original size:15 final size:15
Alignment explanation
Indices: 4112--4162 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
4102 TGAATTCTTT
4112 TTCTTTTC--TTTTC
1 TTCTTTTCTTTTTTC
4125 TTCTTTTCTTTTTTC
1 TTCTTTTCTTTTTTC
*
4140 TT-TTTTGTCTTTTTC
1 TTCTTTTCT-TTTTTC
4155 TTTCTTTT
1 -TTCTTTT
4163 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.25
14 5 0.16
15 13 0.41
16 2 0.06
17 4 0.12
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (15 bp):
TTCTTTTCTTTTTTC
Found at i:4144 original size:13 final size:12
Alignment explanation
Indices: 4109--4143 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
4099 TTTTGAATTC
4109 TTTTTCTTTTCT
1 TTTTTCTTTTCT
4121 TTTCTTCTTTTCT
1 TTT-TTCTTTTCT
4134 TTTTTCTTTT
1 TTTTTCTTTT
4144 TTGTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:4163 original size:19 final size:18
Alignment explanation
Indices: 4106--4163 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 18
4096 TCTTTTTGAA
*
4106 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTC-TTTCTTTTT
*
4125 TTCTTTTCTTTTTTCTTTTT
1 TTC-TTT-TTCTTTCTTTTT
4145 TGTCTTTTTCTTTCTTTTT
1 T-TCTTTTTCTTTCTTTTT
4164 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.42
20 15 0.45
21 4 0.12
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (18 bp):
TTCTTTTTCTTTCTTTTT
Found at i:8709 original size:19 final size:19
Alignment explanation
Indices: 8685--8740 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
8675 TCTTTTTGAA
8685 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
8704 TTC-TTTTCTTTTTCTTTTT
1 TTCTTTTTC-TTTTCTTTTC
8723 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
8741 TGCACTCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.15
19 21 0.64
20 2 0.06
21 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:8730 original size:15 final size:14
Alignment explanation
Indices: 8694--8740 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
8684 ATTCTTTTTC
*
8694 TTTTC-TTTTCTTC
1 TTTTCTTTTTCTTT
8707 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
8721 TTTGTCTTTTTCTTT
1 TTT-TCTTTTTCTTT
8736 CTTTT
1 -TTTT
8741 TGCACTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 5 0.17
14 10 0.33
15 12 0.40
16 3 0.10
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:11660 original size:16 final size:17
Alignment explanation
Indices: 11639--11679 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
11629 AAGATATGGT
11639 AATGAAATAA-TAATA-A
1 AATGAAATAACTAA-AGA
11655 AATGAAA-AACTAAAGA
1 AATGAAATAACTAAAGA
11671 AATGAAATA
1 AATGAAATA
11680 GTAAGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (17 bp):
AATGAAATAACTAAAGA
Found at i:11927 original size:18 final size:19
Alignment explanation
Indices: 11893--11948 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
11883 TAGGAGTCTT
*
11893 TTCTTTC-TCTTTTTTTTG
1 TTCTTTCTTCTTTCTTTTG
11911 TT-TTTCTTCTTTCTTTT-
1 TTCTTTCTTCTTTCTTTTG
*
11928 TCTCTTT-TTGTTTCTTTTG
1 T-TCTTTCTTCTTTCTTTTG
11947 TT
1 TT
11949 GCAGCACTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.16
18 23 0.72
19 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (19 bp):
TTCTTTCTTCTTTCTTTTG
Found at i:18185 original size:30 final size:31
Alignment explanation
Indices: 18133--18192 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
18123 CTTAGCTTTA
**
18133 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
18163 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
18193 GGCAGCATGT
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:19126 original size:19 final size:21
Alignment explanation
Indices: 19102--19153 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
19092 CGGCCAAGAG
*
19102 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
19121 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
19142 CATGTATTTTCA
1 CATGTATTTTCA
19154 AAGGGTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:29747 original size:20 final size:20
Alignment explanation
Indices: 29719--29759 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
29709 AAAGACTTAT
*
29719 GCATGGGAGGAATTAATGAA
1 GCATAGGAGGAATTAATGAA
29739 GCATAGGAGGAATTAATGAA
1 GCATAGGAGGAATTAATGAA
29759 G
1 G
29760 ACATGCATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.34, T:0.20
Consensus pattern (20 bp):
GCATAGGAGGAATTAATGAA
Found at i:35282 original size:13 final size:11
Alignment explanation
Indices: 35259--35380 Score: 79
Period size: 11 Copynumber: 10.2 Consensus size: 11
35249 AATATAGGCG
35259 TGATAATGGTGA
1 TGAT-ATGGTGA
35271 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
35284 TGATATAGGCG-
1 TGATAT-GGTGA
35295 TGATAATGGTGA
1 TGAT-ATGGTGA
35307 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
35320 TGATATAGGCG-
1 TGATAT-GGTGA
35331 TGATAATGGTGA
1 TGAT-ATGGTGA
35343 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
35356 TGATATAGGCG-
1 TGATAT-GGTGA
35367 TGATAATGGTGA
1 TGAT-ATGGTGA
35379 TG
1 TG
35381 GACAGATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
11 31 0.35
12 25 0.28
13 29 0.33
14 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:35283 original size:36 final size:36
Alignment explanation
Indices: 35242--35383 Score: 266
Period size: 36 Copynumber: 3.9 Consensus size: 36
35232 ATTTATAAGT
*
35242 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
35278 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
35314 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
35350 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
35384 AGATTGTATC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:35304 original size:23 final size:24
Alignment explanation
Indices: 35266--35380 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
35256 GCGTGATAAT
35266 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
*
35292 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
35315 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
35338 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
35364 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
35381 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 11 0.15
25 13 0.18
26 3 0.04
27 10 0.14
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:39802 original size:13 final size:11
Alignment explanation
Indices: 39779--39900 Score: 79
Period size: 11 Copynumber: 10.2 Consensus size: 11
39769 AATATAGGCG
39779 TGATAATGGTGA
1 TGAT-ATGGTGA
39791 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
39804 TGATATAGGCG-
1 TGATAT-GGTGA
39815 TGATAATGGTGA
1 TGAT-ATGGTGA
39827 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
39840 TGATATAGGCG-
1 TGATAT-GGTGA
39851 TGATAATGGTGA
1 TGAT-ATGGTGA
39863 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
39876 TGATATAGGCG-
1 TGATAT-GGTGA
39887 TGATAATGGTGA
1 TGAT-ATGGTGA
39899 TG
1 TG
39901 GACAGATTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
11 31 0.35
12 25 0.28
13 29 0.33
14 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:39803 original size:36 final size:36
Alignment explanation
Indices: 39762--39903 Score: 266
Period size: 36 Copynumber: 3.9 Consensus size: 36
39752 ATTTATAAGT
*
39762 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
39798 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
39834 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
39870 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
39904 AGATTGTATC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:39824 original size:23 final size:24
Alignment explanation
Indices: 39786--39900 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
39776 GCGTGATAAT
39786 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
*
39812 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
39835 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
39858 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
39884 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
39901 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 11 0.15
25 13 0.18
26 3 0.04
27 10 0.14
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:44364 original size:13 final size:13
Alignment explanation
Indices: 44346--44371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44336 AACAACTATC
44346 ACATACCTTTTCA
1 ACATACCTTTTCA
44359 ACATACCTTTTCA
1 ACATACCTTTTCA
44372 TATTTGTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:46809 original size:5 final size:5
Alignment explanation
Indices: 46795--46824 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
46785 GTGTTTCAAC
46795 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
46825 CTTTTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:46844 original size:27 final size:28
Alignment explanation
Indices: 46814--46878 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
46804 TTTCTTTTCT
* *
46814 TTTCTTTTCTTCTTTTTGAATGC-TGAA
1 TTTCTTTTCTTCTTTTGGAATGCTTCAA
*
46841 TTTC-TTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTC-TTCTTTTGGAATGCTTCAA
46869 TTTCTTTTCT
1 TTTCTTTTCT
46879 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 8 0.25
29 4 0.12
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTTCTTTTGGAATGCTTCAA
Found at i:48653 original size:13 final size:14
Alignment explanation
Indices: 48633--48671 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
48623 CAGCCATCTC
48633 TATCATTTCTTTAT
1 TATCATTTCTTTAT
*
48647 T-TCATTTCATTAT
1 TATCATTTCTTTAT
*
48660 TATTATTTCTTT
1 TATCATTTCTTT
48672 TCATTACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
TATCATTTCTTTAT
Found at i:48667 original size:19 final size:20
Alignment explanation
Indices: 48643--48682 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
48633 TATCATTTCT
48643 TTATTTCATTTCATTA-TTA
1 TTATTTCATTTCATTACTTA
*
48662 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
48682 T
1 T
48683 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:48685 original size:19 final size:19
Alignment explanation
Indices: 48635--48685 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
48625 GCCATCTCTA
*
48635 TCATTTCTT-TATTTCATT
1 TCATTACTTATATTTCATT
*
48653 TCATTA-TTATTATTTCTTT
1 TCATTACTTA-TATTTCATT
48672 TCATTACTTATATT
1 TCATTACTTATATT
48686 ATTATTCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 18 0.64
20 3 0.11
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (19 bp):
TCATTACTTATATTTCATT
Found at i:48977 original size:19 final size:18
Alignment explanation
Indices: 48946--48993 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
48936 AATTGGAGTG
48946 CAAAAAGAA-AGAAAAAGA
1 CAAAAAGAAGAGAAAAA-A
*
48964 CAAAAAGAAGAGAAAAAT
1 CAAAAAGAAGAGAAAAAA
48982 CAGAAAAGAAGA
1 CA-AAAAGAAGA
48994 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAGAGAAAAAA
Found at i:51819 original size:19 final size:19
Alignment explanation
Indices: 51777--51816 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51767 TATCTTTTCT
*
51777 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCCTA
*
51796 TTATTTCTTTTCATTACCTA
1 TTATTTCATTTCATT-CCTA
51816 T
1 T
51817 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTCATTTCATTCCTA
Found at i:52840 original size:17 final size:17
Alignment explanation
Indices: 52818--52851 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52808 CGGCTTAAAA
52818 AAATGGTTATGGTATAG
1 AAATGGTTATGGTATAG
52835 AAATGGTTATGGTATAG
1 AAATGGTTATGGTATAG
52852 GGGTAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (17 bp):
AAATGGTTATGGTATAG
Found at i:53156 original size:7 final size:6
Alignment explanation
Indices: 53127--53167 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
53117 TGTAGGAGTC
* *
53127 TTTTCT TTCTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
53168 GTAGCTTTTG
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:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:53160 original size:19 final size:18
Alignment explanation
Indices: 53127--53167 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
53117 TGTAGGAGTC
*
53127 TTTTCTTTCTCTTTTTGT
1 TTTTCTTTCTCTTTTTCT
*
53145 TTTTCTTCTTTCTTTTTCT
1 TTTTCTT-TCTCTTTTTCT
53164 TTTT
1 TTTT
53168 GTAGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTCTTTTTCT
Found at i:53609 original size:13 final size:13
Alignment explanation
Indices: 53591--53626 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
53581 ATAGGCGTGC
53591 AATGGTGATGGAA
1 AATGGTGATGGAA
53604 AATGGTGATGGAA
1 AATGGTGATGGAA
*
53617 GATGGTGATG
1 AATGGTGATG
53627 TTATAGGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:53632 original size:48 final size:49
Alignment explanation
Indices: 53555--53662 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 49
53545 TATAAGCGTG
* * *
53555 AAATGGTGATAGAAGTTGATGATAATATAGGCGTG-CAATGGTGATGGA
1 AAATGGTGATGGAAGATGATGATAATATAGGCGTGAAAATGGTGATGGA
* **
53603 AAATGGTGATGGAAGATGGTGATGTTATAGGCGTGAAAATGGTGATGGA
1 AAATGGTGATGGAAGATGATGATAATATAGGCGTGAAAATGGTGATGGA
**
53652 AGGTGGTGATG
1 AAATGGTGATG
53663 TTATAGGTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 30 0.59
49 21 0.41
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.27
Consensus pattern (49 bp):
AAATGGTGATGGAAGATGATGATAATATAGGCGTGAAAATGGTGATGGA
Found at i:53641 original size:36 final size:36
Alignment explanation
Indices: 53601--53669 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
53591 AATGGTGATG
53601 GAAAATGGTGATGGAAGATGGTGATGTTATAGGCGT
1 GAAAATGGTGATGGAAGATGGTGATGTTATAGGCGT
*
53637 GAAAATGGTGATGGAAGGTGGTGATGTTATAGG
1 GAAAATGGTGATGGAAGATGGTGATGTTATAGG
53670 TAGTATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.01, G:0.41, T:0.28
Consensus pattern (36 bp):
GAAAATGGTGATGGAAGATGGTGATGTTATAGGCGT
Found at i:58013 original size:20 final size:21
Alignment explanation
Indices: 57976--58014 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
57966 GATGGTCTTG
*
57976 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
57997 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
58015 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:62190 original size:8 final size:8
Alignment explanation
Indices: 62177--62202 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
62167 TCTTTTTCTT
62177 TTCTTTTC
1 TTCTTTTC
62185 TTCTTTTC
1 TTCTTTTC
62193 TTCTTTTC
1 TTCTTTTC
62201 TT
1 TT
62203 ATTCTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:68059 original size:17 final size:17
Alignment explanation
Indices: 68032--68064 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
68022 AAAAGACAAA
*
68032 AAGAAGAAGAAAAGAAG
1 AAGAAAAAGAAAAGAAG
68049 AAGAAAAAGAAAAGAA
1 AAGAAAAAGAAAAGAA
68065 TTCAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAGAAG
Found at i:68063 original size:11 final size:12
Alignment explanation
Indices: 68029--68064 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
68019 AGAAAAAGAC
68029 AAAAAGAAGAAG
1 AAAAAGAAGAAG
68041 -AAAAGAAGAAG
1 AAAAAGAAGAAG
68052 AAAAAGAA-AAG
1 AAAAAGAAGAAG
68063 AA
1 AA
68065 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:74381 original size:19 final size:20
Alignment explanation
Indices: 74331--74373 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
74321 GAAATCCCTT
*
74331 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
74351 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
74370 TGAA
1 TGAA
74374 GATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:78279 original size:54 final size:54
Alignment explanation
Indices: 78197--78487 Score: 213
Period size: 54 Copynumber: 5.5 Consensus size: 54
78187 ATTCTATGGT
* * *
78197 TTGCACACGTAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTAC-TGAGG
* * * *
78252 TTGCACACATAGTGCC-ATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTACTGAGG
* * * * * *
78305 TTACACACACAGTGCCAATACAGAAATT--C--A-T-A--ATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTACTGAGG
* * * * * * * *
78351 TTGCACACACATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTACTGAGG
* * * * * * * *
78405 TTGCACACACAGTGCAAATACGAAAACTTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAA-TTCACAAACTCATTATGAATTACTGAGG
* * *
78460 TTGTACACACAGTGCCAATACGAAAATT
1 TTGCACACATAGTGCCAATACGGAAATT
78488 TATAAACAAT
Statistics
Matches: 205, Mismatches: 21, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
46 37 0.18
48 1 0.00
49 1 0.00
50 2 0.01
51 1 0.00
52 1 0.00
53 17 0.08
54 78 0.38
55 67 0.33
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTACTGAGG
Found at i:78358 original size:46 final size:49
Alignment explanation
Indices: 78251--78487 Score: 223
Period size: 55 Copynumber: 4.6 Consensus size: 49
78241 ATTACGTGGG
* * *
78251 GTTGCACACATAGTGCC-ATACGGAAATTCATAAACTTATTATGAATTTCTTAG
1 GTTGCACACACAGTGCCAATACGAAAATTC---AAC-TA-TATGAATTTCTTAA
*
78304 GTTACACACACAGTGCCAATAC-AGAAATTC-A-TA-ATGAATTTCTTAA
1 GTTGCACACACAGTGCCAATACGA-AAATTCAACTATATGAATTTCTTAA
*
78350 GTTGCACACACATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAA
1 GTTGCACACACAGTGCCAATACGAAAATTC---AAC-TA-TATGAATTTCTTAA
*
78404 GTTGCACACACAGTGCAAATACGAAAACTTCATAAACTTATTATGAATTTCTTAA
1 GTTGCACACACAGTGCCAATACGAAAA-TTC---AAC-TA-TATGAATTTCTTAA
*
78459 GTTGTACACACAGTGCCAATACGAAAATT
1 GTTGCACACACAGTGCCAATACGAAAATT
78488 TATAAACAAT
Statistics
Matches: 162, Mismatches: 10, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
46 38 0.23
47 1 0.01
48 2 0.01
50 2 0.01
52 2 0.01
53 15 0.09
54 50 0.31
55 52 0.32
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (49 bp):
GTTGCACACACAGTGCCAATACGAAAATTCAACTATATGAATTTCTTAA
Found at i:78494 original size:54 final size:54
Alignment explanation
Indices: 78337--78494 Score: 271
Period size: 55 Copynumber: 2.9 Consensus size: 54
78327 GAAATTCATA
*
78337 ATGAATTTCTTAAGTTGCACACACATTGCCAATACGAAAATTCATAAACTTATT
1 ATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATT
*
78391 ATGAATTTCTTAAGTTGCACACACAGTGCAAATACGAAAACTTCATAAACTTATT
1 ATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA-TTCATAAACTTATT
* *
78446 ATGAATTTCTTAAGTTGTACACACAGTGCCAATACGAAAATTTATAAAC
1 ATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAAC
78495 AATAATCACA
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 46 0.47
55 52 0.53
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (54 bp):
ATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATT
Found at i:82540 original size:26 final size:26
Alignment explanation
Indices: 82511--82568 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
82501 GGTTAGGGTC
82511 TAGAAATGATTAGGATAGGGGTAGGA
1 TAGAAATGATTAGGATAGGGGTAGGA
* * *
82537 TAGAAATGGTTATGATAGGGTTAGGA
1 TAGAAATGATTAGGATAGGGGTAGGA
82563 TAGAAA
1 TAGAAA
82569 AGGTTAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (26 bp):
TAGAAATGATTAGGATAGGGGTAGGA
Found at i:82573 original size:26 final size:26
Alignment explanation
Indices: 82524--82574 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
82514 AAATGATTAG
*
82524 GATAGGGGTAGGATAGAAATGGTTAT
1 GATAGGGGTAGGATAGAAAAGGTTAT
*
82550 GATAGGGTTAGGATAGAAAAGGTTA
1 GATAGGGGTAGGATAGAAAAGGTTA
82575 AGAAATGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.25
Consensus pattern (26 bp):
GATAGGGGTAGGATAGAAAAGGTTAT
Found at i:82864 original size:10 final size:10
Alignment explanation
Indices: 82843--82882 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
82833 GATGTAGGAG
82843 TCTTTTTCTTT
1 TCTTTTT-TTT
82854 TCTTTTTTTT
1 TCTTTTTTTT
82864 TCTTTTTTTT
1 TCTTTTTTTT
82874 TCTCTTTTT
1 TCT-TTTTT
82883 GTTGCTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:82865 original size:15 final size:14
Alignment explanation
Indices: 82845--82874 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
82835 TGTAGGAGTC
82845 TTTTTCTTTTCTTTT
1 TTTTTCTTTT-TTTT
82860 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
82874 T
1 T
82875 CTCTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:82871 original size:12 final size:12
Alignment explanation
Indices: 82843--82882 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
82833 GATGTAGGAG
*
82843 TCTTTTTCTTT-
1 TCTTTTTTTTTC
82854 TC-TTTTTTTT-
1 TCTTTTTTTTTC
82864 TCTTTTTTTTTC
1 TCTTTTTTTTTC
82876 TCTTTTT
1 TCTTTTT
82883 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:82890 original size:22 final size:21
Alignment explanation
Indices: 82844--82891 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
82834 ATGTAGGAGT
*
82844 CTTTTTCTTTTCTTTTTTTTT
1 CTTTTTCTTTTCTTTTTTTTG
82865 CTTTTT-TTTTCTCTTTTTGTTG
1 CTTTTTCTTTTCT-TTTTT-TTG
82887 CTTTT
1 CTTTT
82892 GTTGCAGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
22 7 0.29
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (21 bp):
CTTTTTCTTTTCTTTTTTTTG
Found at i:94076 original size:26 final size:26
Alignment explanation
Indices: 94047--94136 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
94037 GGTTAGGGTC
* *
94047 TAGAAATGATTATGATAGGGGTAGGA
1 TAGAAAAGGTTATGATAGGGGTAGGA
94073 TAGAAAAGGTTATGATAGGGGTAGGA
1 TAGAAAAGGTTATGATAGGGGTAGGA
*
94099 TAGAAAAGGTTATGATAGGGTTAGGA
1 TAGAAAAGGTTATGATAGGGGTAGGA
94125 TAGAAAAGGTTA
1 TAGAAAAGGTTA
94137 AGAAATGGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (26 bp):
TAGAAAAGGTTATGATAGGGGTAGGA
Found at i:94135 original size:15 final size:15
Alignment explanation
Indices: 94068--94136 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
94058 ATGATAGGGG
94068 TAGGATAGAAAAGGT
1 TAGGATAGAAAAGGT
* *
94083 TATGATAG----GGG
1 TAGGATAGAAAAGGT
94094 TAGGATAGAAAAGGT
1 TAGGATAGAAAAGGT
*
94109 TATGATAG----GGT
1 TAGGATAGAAAAGGT
94120 TAGGATAGAAAAGGT
1 TAGGATAGAAAAGGT
94135 TA
1 TA
94137 AGAAATGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
11 19 0.47
15 21 0.52
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.25
Consensus pattern (15 bp):
TAGGATAGAAAAGGT
Found at i:94186 original size:15 final size:17
Alignment explanation
Indices: 94150--94190 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
94140 AATGGATAAG
94150 GAAATGAAATAAGAAAA
1 GAAATGAAATAAGAAAA
94167 G--ATGAAA-AA-AAAA
1 GAAATGAAATAAGAAAA
94180 GAAATGAAATA
1 GAAATGAAATA
94191 GTAAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.24
14 2 0.10
15 12 0.57
16 1 0.05
17 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
GAAATGAAATAAGAAAA
Found at i:110668 original size:29 final size:28
Alignment explanation
Indices: 110636--110705 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
110626 ATTGGAGTGC
*
110636 AAAAAGAAAGAAATAGAAAA-AAGAAGAG
1 AAAAAG-AAGAAATAGAAAAGAAGAAAAG
** *
110664 AAAAATCAGAAAAAAGAAAAGAAGAAAAG
1 AAAAAGAAG-AAATAGAAAAGAAGAAAAG
110693 AAAAAGAAGAAAT
1 AAAAAGAAGAAAT
110706 TCAAAAAGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
27 2 0.06
28 17 0.52
29 14 0.42
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (28 bp):
AAAAAGAAGAAATAGAAAAGAAGAAAAG
Found at i:110676 original size:21 final size:21
Alignment explanation
Indices: 110639--110702 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
110629 GGAGTGCAAA
110639 AAGA-AAGAAATAGAAAAAAG
1 AAGAGAAGAAATAGAAAAAAG
110659 AAGAGAA-AAATCAGAAAAAAG
1 AAGAGAAGAAAT-AGAAAAAAG
*
110680 AAAAGAAGAAA-AG-AAAAAG
1 AAGAGAAGAAATAGAAAAAAG
110699 AAGA
1 AAGA
110703 AATTCAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.23
20 10 0.26
21 17 0.44
22 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (21 bp):
AAGAGAAGAAATAGAAAAAAG
Found at i:110711 original size:14 final size:14
Alignment explanation
Indices: 110636--110704 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 14
110626 ATTGGAGTGC
110636 AAAAAGAAAGAAATAG
1 AAAAAG-AAGAAA-AG
110652 AAAAAAGAAGAGAAA-
1 -AAAAAGAAGA-AAAG
**
110667 AATCAGAA-AAAAG
1 AAAAAGAAGAAAAG
110680 -AAAAGAAGAAAAG
1 AAAAAGAAGAAAAG
110693 AAAAAGAAGAAA
1 AAAAAGAAGAAA
110705 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
12 8 0.18
13 6 0.14
14 17 0.39
16 5 0.11
17 8 0.18
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Done.