Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001512.1 Hibiscus syriacus cultivar Beakdansim tig00002958_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: 66852
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1318 original size:23 final size:23
Alignment explanation
Indices: 1269--1318 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1259 CGGAAACAAC
* ** * *
1269 TCTTGGCACTTCAAGTGACGTTC
1 TCTTGGAACTTCAAACGACATTA
1292 TCTTGGAACTTCAAACGACATTA
1 TCTTGGAACTTCAAACGACATTA
1315 TCTT
1 TCTT
1319 TGAAACATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (23 bp):
TCTTGGAACTTCAAACGACATTA
Found at i:2649 original size:37 final size:36
Alignment explanation
Indices: 2593--2664 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
2583 CTTTTGCACT
*
2593 TTTCTTTTCTTTGCTTTTTGTTTTTCTTCTTTCTTC
1 TTTCTTTGCTTTGCTTTTTGTTTTTCTTCTTTCTTC
2629 TTTCTTTGCTTTTGCTTTTTGTTTTTCTTCTTTCTT
1 TTTCTTTGC-TTTGCTTTTTGTTTTTCTTCTTTCTT
2665 TTCTTTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 8 0.24
37 26 0.76
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75
Consensus pattern (36 bp):
TTTCTTTGCTTTGCTTTTTGTTTTTCTTCTTTCTTC
Found at i:2655 original size:54 final size:51
Alignment explanation
Indices: 2539--2657 Score: 123
Period size: 53 Copynumber: 2.3 Consensus size: 51
2529 TTTCTTCACT
*
2539 TTTTTTTTTTTTTTAATTTTTTTTCTCTTCTTTTTCTTGTCGTTCTTTTGC
1 TTTTTTTTTTCTTTAATTTTTTTTCTCTTCTTTTTCTTGTCGTTCTTTTGC
* * ** * *
2590 ACTTTTCTTTTCTTTGCTTTTTGTTTTTCTTCTTTCTTCTT-TCTTTGCTTTTGC
1 -TTTTTTTTTTCTTTAATTTTT-TTTCTCTTCTTT-TTCTTGTCGTT-CTTTTGC
2644 TTTTTGTTTTTCTT
1 TTTTT-TTTTTCTT
2658 CTTTCTTTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
52 16 0.30
53 19 0.35
54 19 0.35
ACGTcount: A:0.03, C:0.16, G:0.07, T:0.75
Consensus pattern (51 bp):
TTTTTTTTTTCTTTAATTTTTTTTCTCTTCTTTTTCTTGTCGTTCTTTTGC
Found at i:2656 original size:30 final size:30
Alignment explanation
Indices: 2598--2671 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 30
2588 GCACTTTTCT
2598 TTTCTTTGCTTTTTGTTTTTCTTCTTTCTTC
1 TTTCTTTGC-TTTTGTTTTTCTTCTTTCTTC
*
2629 TTTCTTTGCTTTTGCTTTTTGTT-TTTCTTC
1 TTTCTTTGCTTTTG-TTTTTCTTCTTTCTTC
*
2659 TTTCTTTTCTTTT
1 TTTCTTTGCTTTT
2672 TGTTGCAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.60
31 16 0.40
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.76
Consensus pattern (30 bp):
TTTCTTTGCTTTTGTTTTTCTTCTTTCTTC
Found at i:3449 original size:20 final size:20
Alignment explanation
Indices: 3424--3497 Score: 130
Period size: 20 Copynumber: 3.6 Consensus size: 20
3414 AAACCCTTTG
3424 AAATACATGATTTTTTATGA
1 AAATACATGATTTTTTATGA
*
3444 AAATACATAATTTTTTATGA
1 AAATACATGATTTTTTATGA
3464 AAATACATGATTTTTTTATGA
1 AAATACATGA-TTTTTTATGA
3485 AAATACATGATTT
1 AAATACATGATTT
3498 AAATGAAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 31 0.61
21 20 0.39
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
AAATACATGATTTTTTATGA
Found at i:3504 original size:40 final size:40
Alignment explanation
Indices: 3424--3512 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
3414 AAACCCTTTG
**
3424 AAATACATGATTTTTTATGAAAATACATAATTTTTTATGA
1 AAATACATGATTTTTTATGAAAATACATAATTTTAAATGA
*
3464 AAATACATGATTTTTTTATGAAAATACATGA-TTTAAATGA
1 AAATACATGA-TTTTTTATGAAAATACATAATTTTAAATGA
*
3504 AGATACATG
1 AAATACATG
3513 CTCTTGGCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 25 0.57
41 19 0.43
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (40 bp):
AAATACATGATTTTTTATGAAAATACATAATTTTAAATGA
Found at i:14844 original size:19 final size:20
Alignment explanation
Indices: 14820--14859 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
14810 TATCATTTCT
14820 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
14839 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
14859 T
1 T
14860 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:14862 original size:19 final size:18
Alignment explanation
Indices: 14816--14862 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
14806 TCTCTATCAT
14816 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
14833 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
14852 TTACTTATATT
1 TT-CTTATATT
14863 ATTATCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:20423 original size:23 final size:23
Alignment explanation
Indices: 20395--20449 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
20385 ACAATTTGTC
*
20395 CATCACCATTATCATGCCTATAT
1 CATCACCATTATCACGCCTATAT
20418 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
20441 CATCACCAT
1 CATCACCAT
20450 ATTCCATCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.31
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:20451 original size:11 final size:11
Alignment explanation
Indices: 20395--20467 Score: 60
Period size: 11 Copynumber: 6.3 Consensus size: 11
20385 ACAATTTGTC
20395 CATCACCATTAT
1 CATCACCA-TAT
*
20407 CATGC-CTATAT
1 CAT-CACCATAT
20418 CATCACCATTAT
1 CATCACCA-TAT
*
20430 CA-CGCCTATAT
1 CATCACC-ATAT
20441 CATCACCATATT
1 CATCACCATA-T
20453 CCATCACCATAT
1 -CATCACCATAT
20465 CAT
1 CAT
20468 GCCTATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 1 0.02
11 22 0.44
12 16 0.32
13 11 0.22
ACGTcount: A:0.32, C:0.34, G:0.03, T:0.32
Consensus pattern (11 bp):
CATCACCATAT
Found at i:20894 original size:12 final size:11
Alignment explanation
Indices: 20867--20910 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
20857 GCTACAACAA
20867 AAAAAGCAAGAAG
1 AAAAAG-AA-AAG
20880 AAAGAAGAAAAG
1 AAA-AAGAAAAG
20892 AAAAGAGAAAAG
1 AAAA-AGAAAAG
20904 AAAAAGA
1 AAAAAGA
20911 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:26143 original size:13 final size:11
Alignment explanation
Indices: 26102--26186 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
26092 ACAATTTGTC
26102 CATCACCATTAT
1 CATCACCA-TAT
*
26114 CA-CGCCTATAT
1 CATCACC-ATAT
26125 CATCACCATAGT
1 CATCACCATA-T
26137 CCATCACCATTAT
1 -CATCACCA-TAT
*
26150 CA-CGCCTATAT
1 CATCACC-ATAT
26161 CATCACCATATT
1 CATCACCATA-T
26173 CCATCACCATAT
1 -CATCACCATAT
26185 CA
1 CA
26187 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:26146 original size:36 final size:36
Alignment explanation
Indices: 26099--26203 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
26089 GATACAATTT
26099 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
26135 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
26171 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
26204 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:27855 original size:13 final size:13
Alignment explanation
Indices: 27837--27861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27827 GATACTATCT
27837 TTCCATCACCATA
1 TTCCATCACCATA
27850 TTCCATCACCAT
1 TTCCATCACCAT
27862 TCACGCCTAT
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:39065 original size:14 final size:15
Alignment explanation
Indices: 39031--39077 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
39021 AATTTGGAGT
39031 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
39046 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
39060 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
39077 G
1 G
39078 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:50939 original size:26 final size:28
Alignment explanation
Indices: 50901--50952 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
50891 GAAATATGAA
50901 ATAAGAAATGGAAAGATGG-AATGAAATG
1 ATAAGAAATGGAAA-ATGGAAATGAAATG
50929 ATAAG-AA-GGAAAATGGAAATGAAA
1 ATAAGAAATGGAAAATGGAAATGAAA
50953 GAAATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 2 0.09
28 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (28 bp):
ATAAGAAATGGAAAATGGAAATGAAATG
Found at i:51147 original size:13 final size:13
Alignment explanation
Indices: 51129--51153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51119 ATAGGTGTGA
51129 ATAGTGATGGAAT
1 ATAGTGATGGAAT
51142 ATAGTGATGGAA
1 ATAGTGATGGAA
51154 AGATATTATC
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:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
ATAGTGATGGAAT
Found at i:52306 original size:20 final size:21
Alignment explanation
Indices: 52269--52307 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52259 AATATGGAGT
*
52269 TTATAATAATAACTTCATACA
1 TTATAATAATAACATCATACA
*
52290 TTAT-ATAATATCATCATA
1 TTATAATAATAACATCATA
52308 GCTATAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATAATAATAACATCATACA
Found at i:65281 original size:19 final size:20
Alignment explanation
Indices: 65257--65307 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
65247 CGGCCAAGAG
* *
65257 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
65276 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
65296 CATGTATTTTCA
1 CATGTATTTTCA
65308 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Done.