Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006077.1 Hibiscus syriacus cultivar Beakdansim tig00014390_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: 76092
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2421 original size:16 final size:16
Alignment explanation
Indices: 2400--2433 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2390 ATTTGATCGG
2400 AAAAAA-AAAAAGACGA
1 AAAAAATAAAAAGA-GA
2416 AAAAAATAAAAAGAGA
1 AAAAAATAAAAAGAGA
2432 AA
1 AA
2434 TCAAGGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAATAAAAAGAGA
Found at i:7102 original size:12 final size:12
Alignment explanation
Indices: 7068--7110 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
7058 TATTTTAACC
*
7068 GGTTAAAAAATC
1 GGTTAAAAAATT
7080 GGTTTGAAAAAAATT
1 GG-TT--AAAAAATT
7095 GGTTAAAAAATT
1 GGTTAAAAAATT
7107 GGTT
1 GGTT
7111 TTTATCTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 14 0.52
13 2 0.07
14 2 0.07
15 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (12 bp):
GGTTAAAAAATT
Found at i:9414 original size:21 final size:21
Alignment explanation
Indices: 9390--9431 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9380 AGTTTATTTT
9390 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
9411 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
9432 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:9476 original size:33 final size:33
Alignment explanation
Indices: 9426--9524 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
9416 TTTGTTTCAA
9426 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
9458 TTATTGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
9491 TTATCAAACTTGGAAGTATTTAAGTATTTTAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
9524 T
1 T
9525 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 10 0.16
33 51 0.84
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.47
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:13579 original size:23 final size:23
Alignment explanation
Indices: 13553--13622 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
13543 CACTTTTTAA
13553 TTGAAGAACAAAAAGAATAATCC
1 TTGAAGAACAAAAAGAATAATCC
* ***
13576 TTGAATG-AC-CACTTAATAA---
1 TTGAA-GAACAAAAAGAATAATCC
13595 TTGAAGAACAAAAAGAATAATCC
1 TTGAAGAACAAAAAGAATAATCC
13618 TTGAA
1 TTGAA
13623 TGACCACTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 6 0.18
22 6 0.18
23 12 0.36
24 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (23 bp):
TTGAAGAACAAAAAGAATAATCC
Found at i:13602 original size:42 final size:42
Alignment explanation
Indices: 13550--13661 Score: 215
Period size: 42 Copynumber: 2.7 Consensus size: 42
13540 CATCACTTTT
13550 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
1 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
*
13592 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAT
1 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
13634 TAATTGAAGAACAAAAAGAATAATCCTT
1 TAATTGAAGAACAAAAAGAATAATCCTT
13662 TAACGACTGA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (42 bp):
TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
Found at i:26602 original size:18 final size:18
Alignment explanation
Indices: 26579--26619 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
26569 AAAAGGAGGG
26579 TGAGTTCTAAGCATGTTA
1 TGAGTTCTAAGCATGTTA
*
26597 TGAGTTCTACGCATGTTA
1 TGAGTTCTAAGCATGTTA
26615 T-AGTT
1 TGAGTT
26620 AGGTCCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGAGTTCTAAGCATGTTA
Found at i:30604 original size:16 final size:16
Alignment explanation
Indices: 30562--30604 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
30552 TGGATAATAG
*
30562 AAATTCATAATATTGT
1 AAATTTATAATATTGT
* *
30578 AATTTTTTAATATTGT
1 AAATTTATAATATTGT
30594 AAATTTATAAT
1 AAATTTATAAT
30605 TCTTTTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
AAATTTATAATATTGT
Found at i:31617 original size:13 final size:13
Alignment explanation
Indices: 31599--31631 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
31589 TTTTCCCTTT
*
31599 TTTTCCTTGTTTA
1 TTTTCCTTATTTA
31612 TTTTCCTTATTTA
1 TTTTCCTTATTTA
31625 TTTTCCT
1 TTTTCCT
31632 ACAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTCCTTATTTA
Found at i:32301 original size:18 final size:17
Alignment explanation
Indices: 32278--32311 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
32268 AATTAGTTAA
32278 TTTTATTAAAAATAATAG
1 TTTTATTAAAAA-AATAG
32296 TTTTATTAAAAAAATA
1 TTTTATTAAAAAAATA
32312 ACTAGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTTATTAAAAAAATAG
Found at i:32322 original size:21 final size:21
Alignment explanation
Indices: 32285--32332 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
32275 TAATTTTATT
** *
32285 AAAAATAATAGTTTTATTA-A
1 AAAAATAATAGAATTATAATA
32305 AAAAATAACTAGAATTATAATA
1 AAAAATAA-TAGAATTATAATA
32327 AAAAAT
1 AAAAAT
32333 TACAATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATAATAGAATTATAATA
Found at i:34465 original size:16 final size:17
Alignment explanation
Indices: 34444--34475 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34434 AACTTAAAAC
34444 TTTAAAAATTT-AGAGG
1 TTTAAAAATTTGAGAGG
34460 TTTAAAAATTTGAGAG
1 TTTAAAAATTTGAGAG
34476 ACTTAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
TTTAAAAATTTGAGAGG
Found at i:36393 original size:27 final size:28
Alignment explanation
Indices: 36362--36416 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
36352 TCAAAGCTAT
**
36362 TAAATCAAATTATCAA-TAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
* *
36389 TAAATTATATTAGAAATTAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
36417 AGTAAAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAATCAAATTAGAAATTAAAAAACATC
Found at i:43491 original size:18 final size:18
Alignment explanation
Indices: 43468--43508 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
43458 AAAAGGAGGG
43468 TGAGTTCTAAGCATGTTA
1 TGAGTTCTAAGCATGTTA
*
43486 TGAGTTCTACGCATGTTA
1 TGAGTTCTAAGCATGTTA
43504 T-AGTT
1 TGAGTT
43509 AGGTCCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGAGTTCTAAGCATGTTA
Found at i:47490 original size:16 final size:16
Alignment explanation
Indices: 47448--47490 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
47438 TGGATAATAG
*
47448 AAATTCATAATATTGT
1 AAATTTATAATATTGT
* *
47464 AATTTTTTAATATTGT
1 AAATTTATAATATTGT
47480 AAATTTATAAT
1 AAATTTATAAT
47491 TCTTTTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
AAATTTATAATATTGT
Found at i:48501 original size:13 final size:13
Alignment explanation
Indices: 48483--48515 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
48473 TTTTCCCTTT
*
48483 TTTTCCTTGTTTA
1 TTTTCCTTATTTA
48496 TTTTCCTTATTTA
1 TTTTCCTTATTTA
48509 TTTTCCT
1 TTTTCCT
48516 ACAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTCCTTATTTA
Found at i:49188 original size:18 final size:17
Alignment explanation
Indices: 49165--49198 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
49155 AATTAGTTAA
49165 TTTTATTAAAAATAATAG
1 TTTTATTAAAAA-AATAG
49183 TTTTATTAAAAAAATA
1 TTTTATTAAAAAAATA
49199 ACTAGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTTATTAAAAAAATAG
Found at i:49209 original size:21 final size:21
Alignment explanation
Indices: 49172--49219 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
49162 TAATTTTATT
** *
49172 AAAAATAATAGTTTTATTA-A
1 AAAAATAATAGAATTATAATA
49192 AAAAATAACTAGAATTATAATA
1 AAAAATAA-TAGAATTATAATA
49214 AAAAAT
1 AAAAAT
49220 TACAATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATAATAGAATTATAATA
Found at i:51348 original size:16 final size:17
Alignment explanation
Indices: 51327--51358 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
51317 AACTTAAAAC
51327 TTTAAAAATTT-AGAGG
1 TTTAAAAATTTGAGAGG
51343 TTTAAAAATTTGAGAG
1 TTTAAAAATTTGAGAG
51359 ACTTAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
TTTAAAAATTTGAGAGG
Found at i:53281 original size:27 final size:28
Alignment explanation
Indices: 53250--53304 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
53240 TCAAAGCTAT
**
53250 TAAATCAAATTATCAA-TAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
* *
53277 TAAATTATATTAGAAATTAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
53305 AGTAAAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAATCAAATTAGAAATTAAAAAACATC
Found at i:54057 original size:12 final size:12
Alignment explanation
Indices: 54040--54065 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54030 CAACAGTTGT
54040 GCAATCTGTTAG
1 GCAATCTGTTAG
54052 GCAATCTGTTAG
1 GCAATCTGTTAG
54064 GC
1 GC
54066 TTATGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (12 bp):
GCAATCTGTTAG
Found at i:55220 original size:36 final size:36
Alignment explanation
Indices: 55152--55220 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
55142 ATTAAAATGG
*
55152 TTTTCAAGTTTGGTAAATGTTTCTTTGAAAAATAGT
1 TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
* *
55188 TTTTCAAAGTTTGGTAGATGTTT-GTTGGAAAAT
1 TTTTC-AAGTTTGGTAAATGTTTCGTTGAAAAAT
55221 GATAATGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 13 0.45
37 16 0.55
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.46
Consensus pattern (36 bp):
TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
Found at i:59746 original size:36 final size:36
Alignment explanation
Indices: 59706--59774 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
59696 ATTAAAATGG
*
59706 TTTTC-AAGTTTGGTAAATGTTTCTTTGAAAAATAGT
1 TTTTCAAAGTTTGGTAAATGTTT-GTTGAAAAATAGT
*
59742 TTTTCAAAGTTTGGTAGATGTTTGTTGAAAAAT
1 TTTTCAAAGTTTGGTAAATGTTTGTTGAAAAAT
59775 GATAATGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (36 bp):
TTTTCAAAGTTTGGTAAATGTTTGTTGAAAAATAGT
Found at i:60889 original size:26 final size:28
Alignment explanation
Indices: 60821--60889 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
60811 ATGCTACTCA
60821 GGTAGGTCGCCATGCACTCCCAGCTACCT
1 GGTAGGTCGCCATGCACTCCCAGC-ACCT
* *
60850 GGATAGGTTGCCATGCACTCCCA-C-CGT
1 GG-TAGGTCGCCATGCACTCCCAGCACCT
60877 GGTAGGTCGCCAT
1 GGTAGGTCGCCAT
60890 ACATGCCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.28
27 4 0.11
29 3 0.08
30 19 0.53
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (28 bp):
GGTAGGTCGCCATGCACTCCCAGCACCT
Found at i:63475 original size:21 final size:22
Alignment explanation
Indices: 63451--63497 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
63441 ACACTAACAC
*
63451 TAAACTTGGTTCAACTAATTT-
1 TAAACTTGGTCCAACTAATTTA
*
63472 TAAATTTGGTCCAACTAATTTA
1 TAAACTTGGTCCAACTAATTTA
63494 TAAA
1 TAAA
63498 ATCTTTTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
TAAACTTGGTCCAACTAATTTA
Found at i:73586 original size:15 final size:15
Alignment explanation
Indices: 73568--73596 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73558 ATGCAGTAGA
73568 AGCTGCTACAGTTGT
1 AGCTGCTACAGTTGT
73583 AGCTGCTACAGTTG
1 AGCTGCTACAGTTG
73597 CAGTGGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (15 bp):
AGCTGCTACAGTTGT
Done.