Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001100.1 Hibiscus syriacus cultivar Beakdansim tig00002181_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: 30417
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Found at i:6266 original size:16 final size:16
Alignment explanation
Indices: 6224--6279 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
6214 ACCATAAACA
6224 TAAATAAATT-TTAA-
1 TAAATAAATTATTAAT
* *
6238 -AATTAAATCATTAAT
1 TAAATAAATTATTAAT
6253 TAAATAAATTATTAAT
1 TAAATAAATTATTAAT
*
6269 TAAAAAAATTA
1 TAAATAAATTA
6280 AATTTTAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
16 23 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAAATTATTAAT
Found at i:8329 original size:2 final size:2
Alignment explanation
Indices: 8317--8351 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
8307 TTCTCTAACC
*
8317 AT AT A- AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8352 TATTCTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13752 original size:3 final size:3
Alignment explanation
Indices: 13744--13843 Score: 120
Period size: 3 Copynumber: 34.7 Consensus size: 3
13734 TTTTTATCCA
*
13744 TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT TAT TAT CA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
13788 TA- TAT TAT TAT TTT TAT TAT TAT TAT TAT ATAT TAT TAT TTT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
13833 TAT TAT TAT TA
1 TAT TAT TAT TA
13844 AATATATTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
2 9 0.11
3 71 0.86
4 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:13820 original size:28 final size:29
Alignment explanation
Indices: 13744--13852 Score: 143
Period size: 28 Copynumber: 3.8 Consensus size: 29
13734 TTTTTATCCA
*
13744 TATTATTATTATTATTATATTATTA-TAT
1 TATTATTATTATTATTATATTATTATTTT
13772 TATTATCATATTA-TATTATATTATTATTTT
1 TATTAT--TATTATTATTATATTATTATTTT
13802 TATTATTATTATTA-TATATTATTATTTT
1 TATTATTATTATTATTATATTATTATTTT
* *
13830 TACTATTATTATTAAATATATTA
1 TATTATTATTATT-ATTATATTA
13853 AATACATATA
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
28 37 0.51
29 16 0.22
30 20 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTATTATTATTATTATATTATTATTTT
Found at i:13852 original size:46 final size:45
Alignment explanation
Indices: 13744--13844 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 45
13734 TTTTTATCCA
*
13744 TATTATTATT-ATTATTATATTATTATATTATTATCATATTATAT
1 TATTATTATTAATTATTATATTATTATATTATTATCATATTATAC
* * *
13788 TA-TATTATT-ATTTTTATTATTATTATTATATATTATTAT-TTTTAC
1 TATTATTATTAATTATTA-TATTATTA-TAT-TATTATCATATTATAC
13833 TATTATTATTAA
1 TATTATTATTAA
13845 ATATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 13 0.27
44 10 0.21
45 9 0.19
46 15 0.31
47 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (45 bp):
TATTATTATTAATTATTATATTATTATATTATTATCATATTATAC
Found at i:26421 original size:1 final size:1
Alignment explanation
Indices: 26415--26458 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
26405 ATGCTTGAAG
* *
26415 AAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26459 GAGAAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:26438 original size:18 final size:18
Alignment explanation
Indices: 26415--26472 Score: 89
Period size: 18 Copynumber: 3.1 Consensus size: 18
26405 ATGCTTGAAG
26415 AAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAGAA
26433 AAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAGAA
26451 AAAAAAAAGAGAAGAAAAGAA
1 AAAAAAAA-A-AA-AAAAGAA
26472 A
1 A
26473 GAAAGGGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
18 26 0.70
19 1 0.03
20 2 0.05
21 8 0.22
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGAA
Found at i:26441 original size:21 final size:21
Alignment explanation
Indices: 26415--26476 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
26405 ATGCTTGAAG
26415 AAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAGAAAAA
26436 AAAAAAAAAAAAGAAA-AAAAA
1 AAAAAAAAAAAA-AAAGAAAAA
* * *
26457 AAGAGAAGAAAAGAAAGAAA
1 AA-AAAAAAAAAAAAAGAAA
26477 GGGGTCAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAGAAAAA
Found at i:26477 original size:18 final size:16
Alignment explanation
Indices: 26412--26468 Score: 80
Period size: 16 Copynumber: 3.4 Consensus size: 16
26402 ATTATGCTTG
26412 AAGAAAAAAAAAAAAA
1 AAGAAAAAAAAAAAAA
26428 AAGAAAAAAAAAAAAA
1 AAGAAAAAAAAAAAAA
26444 AA-AAGAAAAAAAAAAGA
1 AAGAA-AAAAAAAAAA-A
26461 GAAGAAAA
1 -AAGAAAA
26469 GAAAGAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.05
16 28 0.76
17 1 0.03
18 4 0.11
19 2 0.05
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAAAA
Found at i:26477 original size:29 final size:29
Alignment explanation
Indices: 26416--26476 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 29
26406 TGCTTGAAGA
26416 AAAAAAAAAAAAAAGAAAAAAAAAA-AAAA
1 AAAAAAAA-AAAAAGAAAAAAAAAAGAAAA
26445 AAAGAAAAAAAAAAGAGAAGAAAAGAAAGAAA
1 AAA-AAAAAAAAAAGA-AA-AAAA-AAAGAAA
26477 GGGGTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 10 0.37
30 7 0.26
31 4 0.15
32 3 0.11
33 3 0.11
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAAGAAAAAAAAAAGAAAA
Found at i:27683 original size:52 final size:52
Alignment explanation
Indices: 27605--27842 Score: 420
Period size: 52 Copynumber: 4.7 Consensus size: 52
27595 CAAATGAATC
27605 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
27657 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G---G-A
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
27704 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
27756 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
27808 CATAGCATCTTCTGGAA--G-TCTTTGAGTTATCTGAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
27843 GGACAGAATC
Statistics
Matches: 181, Mismatches: 0, Indels: 13
0.93 0.00 0.07
Matches are distributed among these distances:
47 45 0.25
48 2 0.01
49 17 0.09
50 1 0.01
51 2 0.01
52 114 0.63
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:27776 original size:99 final size:102
Alignment explanation
Indices: 27605--27842 Score: 416
Period size: 99 Copynumber: 2.4 Consensus size: 102
27595 CAAATGAATC
27605 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
27670 GGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G-G-A
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAGAA
27704 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
27769 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG--AGAA
27808 CATAGCATCTTCTGGAA--G-TCTTTGAGTTATCTGAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
27843 GGACAGAATC
Statistics
Matches: 134, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
99 96 0.72
100 1 0.01
101 17 0.13
102 1 0.01
103 1 0.01
104 18 0.13
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (102 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAGAA
Found at i:28726 original size:107 final size:110
Alignment explanation
Indices: 28469--29186 Score: 1072
Period size: 110 Copynumber: 6.7 Consensus size: 110
28459 CATTGCAGAG
*
28469 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
28534 AACCTTTTACTGAAT-CATCA-TTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTT--TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
28579 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAA-TTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
28640 AACCTTTTACTGAATCCATCA-TT-G-GGATCATC-TTTCCAGAGAA
66 AACCTTTT--TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
28683 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG-AGAA-TTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
28746 AACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACC--TT-TTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
28794 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
28858 AA-CTTTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
28902 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC--AATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
28965 AACTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AAC-CTT-TTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
29012 AGTTCATAATGAGAAGAACTCATCTGAA-AAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
29075 AA-CTTTTTGAAATTCATCATTTGATGGATCA---TTGCTAGAG-A
66 AACCTTTTTG-AATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
29116 AGTTCATGAATGA-AA-AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
29179 CAACCTTT
65 CAACCTTT
29187 GTTTGATATT
Statistics
Matches: 572, Mismatches: 12, Indels: 52
0.90 0.02 0.08
Matches are distributed among these distances:
103 12 0.02
104 62 0.11
105 47 0.08
106 39 0.07
107 81 0.14
108 99 0.17
109 31 0.05
110 146 0.26
111 47 0.08
112 8 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (110 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
Found at i:29003 original size:218 final size:219
Alignment explanation
Indices: 28469--29190 Score: 1117
Period size: 218 Copynumber: 3.3 Consensus size: 219
28459 CATTGCAGAG
*
28469 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA-AATGAGAAGAACTTGTTC
** * *
28534 AACCTTTT-ACTGAAT-CATCA-TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
65 AACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
28596 ACTCATCTGAAGAAG--GAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACTGAATCCA
130 ACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT--TGAATCCA
28658 TCA-TT-G-GGATCATCTTTCCAGAGAA
192 TCATTTGGTGGATCATCTTTCCAGAGAA
28683 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG-AGAA-TTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA-AATGAGAAGAACTTGTTC
28746 AACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
65 AACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
28811 ACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATCCATCA
130 ACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATCCATCA
28876 TTTGGTGGATCATCTTTTCCAGAGAA
195 TTTGGTGGATCATC-TTTCCAGAGAA
28902 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC-AATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAATGAGAAGAACTTGTTCA
28966 A-CTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
29030 CTCATCTGAA-AAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAAATTCATC
131 CTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-AATCCATC
* * *
29093 ATTTGATGGATCA--TTGCTAGAG-A
194 ATTTGGTGGATCATCTTTCCAGAGAA
*
29116 AGTTCATGAATGA-AA-AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA-AATGAGAAGAACTTGTT
29179 CAACC-TTTGTTT
64 CAACCTTTTGTTT
29191 GATATTATCT
Statistics
Matches: 481, Mismatches: 9, Indels: 35
0.92 0.02 0.07
Matches are distributed among these distances:
212 14 0.03
213 37 0.08
214 68 0.14
215 105 0.22
216 3 0.01
217 71 0.15
218 119 0.25
219 64 0.13
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (219 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAATGAGAAGAACTTGTTCA
ACCTTTTGTTTAAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATCCATCAT
TTGGTGGATCATCTTTCCAGAGAA
Found at i:29483 original size:3 final size:3
Alignment explanation
Indices: 29475--29577 Score: 147
Period size: 3 Copynumber: 34.7 Consensus size: 3
29465 ATTTTTTCCA
*
29475 TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT TAT TAT CAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * *
29520 TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TA- TAT TAT TTT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29567 TAT TAT TAT TA
1 TAT TAT TAT TA
29578 AATATATTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 4 0.04
3 82 0.92
4 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Done.