Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004824.1 Hibiscus syriacus cultivar Beakdansim tig00010869_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: 65246
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:12195 original size:25 final size:25
Alignment explanation
Indices: 12154--12210 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
12144 TATGCATATC
* *
12154 TTATTTTATGTCGATATCGCTTTAA
1 TTATTTTATGTCAATATAGCTTTAA
* * *
12179 TTGTTTTATGTTAATATAGCTTTGA
1 TTATTTTATGTCAATATAGCTTTAA
12204 TTATTTT
1 TTATTTT
12211 TGTGCTCTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.58
Consensus pattern (25 bp):
TTATTTTATGTCAATATAGCTTTAA
Found at i:13015 original size:18 final size:18
Alignment explanation
Indices: 12992--13054 Score: 92
Period size: 18 Copynumber: 3.5 Consensus size: 18
12982 TCACGGAATG
12992 TAAGATTACCAGTGGGAA
1 TAAGATTACCAGTGGGAA
13010 TAAGATTACCAGTGGGAA
1 TAAGATTACCAGTGGGAA
* *
13028 TAGGATTACC-GACGGGAA
1 TAAGATTACCAG-TGGGAA
13046 TAAGATTAC
1 TAAGATTAC
13055 TAGGAATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 1 0.02
18 40 0.98
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGTGGGAA
Found at i:18167 original size:21 final size:21
Alignment explanation
Indices: 18143--18203 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
18133 AACTTTGAAA
18143 AAATAGTTTTCAAAGTTTGGT
1 AAATAGTTTTCAAAGTTTGGT
*
18164 AAAT-G-TTTC----TTT-GA
1 AAATAGTTTTCAAAGTTTGGT
18178 AAATAGTTTTCAAAGTTTGGT
1 AAATAGTTTTCAAAGTTTGGT
18199 AAATA
1 AAATA
18204 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (21 bp):
AAATAGTTTTCAAAGTTTGGT
Found at i:18249 original size:36 final size:36
Alignment explanation
Indices: 18135--18253 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
18125 TGGTAACCAA
18135 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
18172 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
18207 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
18244 -GTTGAAAAAT
1 CTTTGAAAAAT
18254 GATAATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 16 0.21
37 26 0.34
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:21940 original size:21 final size:21
Alignment explanation
Indices: 21916--21976 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
21906 AACTTTGAAA
21916 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
21937 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
21951 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
21972 AAATG
1 AAATG
21977 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:22025 original size:36 final size:35
Alignment explanation
Indices: 21915--22023 Score: 175
Period size: 35 Copynumber: 3.1 Consensus size: 35
21905 CAACTTTGAA
21915 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
21950 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
21985 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
22020 AAAA
1 AAAA
22024 ATGATAATGG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 47 0.67
36 23 0.33
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:27898 original size:29 final size:29
Alignment explanation
Indices: 27863--27944 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
27853 AAACTAAATT
*
27863 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
27892 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
27921 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
27945 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:28304 original size:10 final size:10
Alignment explanation
Indices: 28289--28318 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28279 AATCTGAGTA
*
28289 ACGCACCGCT
1 ACGCACCGCC
28299 ACGCACCGCC
1 ACGCACCGCC
28309 ACGCACCGCC
1 ACGCACCGCC
28319 GGAAGACTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.57, G:0.20, T:0.03
Consensus pattern (10 bp):
ACGCACCGCC
Found at i:32554 original size:29 final size:29
Alignment explanation
Indices: 32519--32600 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
32509 AAACTAAATT
*
32519 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
32548 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
32577 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
32601 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:33771 original size:2 final size:2
Alignment explanation
Indices: 33766--33790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33756 TTAGATAGTA
33766 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
33791 CACTATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35145 original size:41 final size:42
Alignment explanation
Indices: 35080--35161 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
35070 TTTTTCTTCA
35080 TTTAGGTCTAGGGAAATTTATTAACAAAGCCCCGATCGTGTG
1 TTTAGGTCTAGGGAAATTTATTAACAAAGCCCCGATCGTGTG
** * *
35122 TTTA-GTCTAGGGAGGTTTTTTAACAAAGCTCCGATCGTGT
1 TTTAGGTCTAGGGAAATTTATTAACAAAGCCCCGATCGTGT
35162 CTTTTGTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
TTTAGGTCTAGGGAAATTTATTAACAAAGCCCCGATCGTGTG
Found at i:35679 original size:24 final size:26
Alignment explanation
Indices: 35652--35702 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
35642 TCGATAATTT
*
35652 ATTC-TCACCC-CTAAAATTTTATAA
1 ATTCGTCACCCTCTAAAATTGTATAA
**
35676 ATTCGTGTCCCTCTAAAATTGTATAA
1 ATTCGTCACCCTCTAAAATTGTATAA
35702 A
1 A
35703 CCTCTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 14 0.64
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (26 bp):
ATTCGTCACCCTCTAAAATTGTATAA
Found at i:42036 original size:12 final size:12
Alignment explanation
Indices: 42019--42046 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42009 AACTATTTGA
42019 TTTCTTTAACTG
1 TTTCTTTAACTG
42031 TTTCTTTAACTG
1 TTTCTTTAACTG
42043 TTTC
1 TTTC
42047 AATCAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.18, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTCTTTAACTG
Found at i:42855 original size:29 final size:29
Alignment explanation
Indices: 42821--42879 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42811 CCTAAATTAA
42821 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42850 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42879 T
1 T
42880 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:47540 original size:29 final size:29
Alignment explanation
Indices: 47506--47564 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47496 CCTAAATTAA
47506 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
47535 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
47564 T
1 T
47565 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:47842 original size:3 final size:3
Alignment explanation
Indices: 47834--47858 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47824 TTCAACAGGG
47834 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
47859 TTGTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:49790 original size:91 final size:89
Alignment explanation
Indices: 49635--49813 Score: 268
Period size: 91 Copynumber: 2.0 Consensus size: 89
49625 TCTATAAAAA
* * ** *
49635 ATTTGTTGTTTGTAGACACTTATTTTCGTCTGGGACTTTGAGGGTTTTTATTATATATTTTATAT
1 ATTTGTTGTTTGTAGACACTTATTTTCGTCCGAGACTTCAAGGGTTTTTATTACATATTTTATAT
*
49700 GTAATATAGTATATAATAATATATAT
66 ATAATATA-TATATAAT-ATATATAT
*
49726 ATTTGTTGTTTGTAGACACTTATTTTCGTCCGAGACTTCAAGGGTTTTTATTACATTTTTTATAT
1 ATTTGTTGTTTGTAGACACTTATTTTCGTCCGAGACTTCAAGGGTTTTTATTACATATTTTATAT
*
49791 ATATTATATATATAATATATATA
66 ATAATATATATATAATATATATA
49814 GTTTTTGAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 7 0.09
90 8 0.10
91 65 0.81
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.50
Consensus pattern (89 bp):
ATTTGTTGTTTGTAGACACTTATTTTCGTCCGAGACTTCAAGGGTTTTTATTACATATTTTATAT
ATAATATATATATAATATATATAT
Found at i:49854 original size:21 final size:24
Alignment explanation
Indices: 49800--49857 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 24
49790 TATATTATAT
49800 ATATAATATATATAGTTTTTGAAA
1 ATATAATATATATAGTTTTTGAAA
* *
49824 ACATATTATAT-TA-TTTTTG-AA
1 ATATAATATATATAGTTTTTGAAA
49845 ATATAATATATAT
1 ATATAATATATAT
49858 TATATAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.38
22 7 0.24
23 2 0.07
24 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (24 bp):
ATATAATATATATAGTTTTTGAAA
Found at i:49860 original size:28 final size:30
Alignment explanation
Indices: 49826--49890 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
49816 TTTTGAAAAC
49826 ATATTATATTA-TTTTTGAA-ATATA-ATAT
1 ATATTATATTAGTTTTT-AATATATACATAT
49854 ATATTATA-TAGTTTTTAATATATACATAT
1 ATATTATATTAGTTTTTAATATATACATAT
49883 -TATTATAT
1 ATATTATAT
49891 ATTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
27 4 0.12
28 25 0.76
29 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (30 bp):
ATATTATATTAGTTTTTAATATATACATAT
Found at i:49891 original size:28 final size:26
Alignment explanation
Indices: 49796--49891 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 26
49786 TATATATATT
* * *
49796 ATATATATAATATATATAGTTTTTGA
1 ATATACATATTATATATAGTTTTTAA
49822 A-A-ACATATTATAT-TA-TTTTTGAA
1 ATATACATATTATATATAGTTTTT-AA
49845 ATATA-ATATATATTATATAGTTTTTAA
1 ATATACATAT-TA-TATATAGTTTTTAA
49872 TATATACATATTATTATATA
1 -ATATACATATTA-TATATA
49892 TTATTATTAG
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
22 5 0.09
23 4 0.07
24 14 0.24
25 4 0.07
26 4 0.07
27 4 0.07
28 19 0.33
29 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
ATATACATATTATATATAGTTTTTAA
Found at i:51146 original size:26 final size:28
Alignment explanation
Indices: 51117--51174 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
51107 ACCCATAATA
51117 TTTTAAT-TCTTTTTAATTTAAT-CAGT
1 TTTTAATATCTTTTTAATTTAATGCAGT
* *
51143 TTTTAATATTTTTTTAATTTAATGCATT
1 TTTTAATATCTTTTTAATTTAATGCAGT
51171 TTTT
1 TTTT
51175 TATTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 14 0.50
28 7 0.25
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTAATATCTTTTTAATTTAATGCAGT
Found at i:51163 original size:16 final size:17
Alignment explanation
Indices: 51144--51181 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
51134 TTAATCAGTT
51144 TTTAAT-ATTTTTTTAA
1 TTTAATCATTTTTTTAA
*
51160 TTTAATGCATTTTTTTAT
1 TTTAAT-CATTTTTTTAA
51178 TTTA
1 TTTA
51182 TTTTTTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAATCATTTTTTTAA
Found at i:51941 original size:25 final size:25
Alignment explanation
Indices: 51910--51964 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
51900 TCCTATTTCA
51910 CCATCTCTGCAGGCAAGTATGTTTT
1 CCATCTCTGCAGGCAAGTATGTTTT
51935 CCATCTCTGCAGGCAAGTATGTTTT
1 CCATCTCTGCAGGCAAGTATGTTTT
51960 CCATC
1 CCATC
51965 GCTGGACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (25 bp):
CCATCTCTGCAGGCAAGTATGTTTT
Found at i:59849 original size:15 final size:15
Alignment explanation
Indices: 59829--59861 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
59819 TTTTTAAATA
59829 AAAAAT-AGAGGGATT
1 AAAAATAAGAGGG-TT
59844 AAAAATAAGAGGGTT
1 AAAAATAAGAGGGTT
59859 AAA
1 AAA
59862 TTCCAAACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (15 bp):
AAAAATAAGAGGGTT
Found at i:60712 original size:21 final size:21
Alignment explanation
Indices: 60686--60735 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
60676 ATTATATAAT
* *
60686 AAAATCTTAGGTCTCCATTAC
1 AAAATCTTAGGTCTACATCAC
*
60707 AAAATCTTAGGTCTACGTCAC
1 AAAATCTTAGGTCTACATCAC
60728 AAAATCTT
1 AAAATCTT
60736 TTTGAAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAATCTTAGGTCTACATCAC
Found at i:62316 original size:2 final size:2
Alignment explanation
Indices: 62309--62338 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62299 AATCGTAATT
62309 TA TA TA 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
62339 ATAATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63390 original size:3 final size:3
Alignment explanation
Indices: 63382--63434 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
63372 ATGGTAGCGG
63382 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63430 TTA TT
1 TTA TT
63435 TTCTTAATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.