Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005297.1 Hibiscus syriacus cultivar Beakdansim tig00011989_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: 60051
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:535 original size:12 final size:12
Alignment explanation
Indices: 518--542 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
508 TCAATTCATC
518 ATGTCACATGTA
1 ATGTCACATGTA
530 ATGTCACATGTA
1 ATGTCACATGTA
542 A
1 A
543 ACAATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTCACATGTA
Found at i:563 original size:3 final size:3
Alignment explanation
Indices: 548--599 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
538 TGTAAACAAT
*
548 ATA ATA TATA ATA ATA ATA ATA ATT A-A ATA ATA ATA AT- ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
592 ATA ATA AT
1 ATA ATA AT
600 GCAATTACCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:579 original size:17 final size:14
Alignment explanation
Indices: 548--599 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
538 TGTAAACAAT
548 ATAAT-ATATAATA
1 ATAATAATATAATA
561 ATAATAATAATTAAATA
1 ATAATAAT-A-T-AATA
578 ATAATAATATAATA
1 ATAATAATATAATA
592 ATAATAAT
1 ATAATAAT
600 GCAATTACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.14
14 14 0.40
15 2 0.06
16 2 0.06
17 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:594 original size:11 final size:11
Alignment explanation
Indices: 548--597 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
538 TGTAAACAAT
548 ATAATAT-ATA
1 ATAATATAATA
558 ATAATAATAATA
1 ATAAT-ATAATA
570 ATTAA-ATAATA
1 A-TAATATAATA
581 ATAATATAATA
1 ATAATATAATA
592 ATAATA
1 ATAATA
598 ATGCAATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.22
11 21 0.58
12 4 0.11
13 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAATA
Found at i:1057 original size:2 final size:2
Alignment explanation
Indices: 1050--1111 Score: 90
Period size: 2 Copynumber: 30.0 Consensus size: 2
1040 TGATTCTATC
1050 AT AT AT AT CAT CAT -T AT AT AT AT AT AT AT GAT AT AT AT AT AT
1 AT AT AT AT -AT -AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
1092 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1112 CTTATGTATC
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.02
2 49 0.86
3 7 0.12
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1069 original size:13 final size:12
Alignment explanation
Indices: 1047--1123 Score: 64
Period size: 10 Copynumber: 7.2 Consensus size: 12
1037 ATTTGATTCT
1047 ATCATATATATC
1 ATCATATATATC
1059 ATCAT-TATAT-
1 ATCATATATATC
*
1069 AT-ATATATATG
1 ATCATATATATC
1080 AT-ATATATAT-
1 ATCATATATATC
1090 AT-ATATATAT-
1 ATCATATATATC
1100 AT-ATATATAT-
1 ATCATATATATC
* *
1110 ATCTTATGTATC
1 ATCATATATATC
1122 AT
1 AT
1124 AATAATTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
9 2 0.03
10 29 0.49
11 21 0.36
12 7 0.12
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (12 bp):
ATCATATATATC
Found at i:7987 original size:22 final size:22
Alignment explanation
Indices: 7957--8001 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7947 GGTATATGAA
* *
7957 ATTTGTCCCGAAGGACCTCTGT
1 ATTTATCCCGAAGGACCTATGT
*
7979 ATTTATCCCGAATGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
8001 A
1 A
8002 CTGTATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTATCCCGAAGGACCTATGT
Found at i:8005 original size:27 final size:27
Alignment explanation
Indices: 7975--8049 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
7965 CGAAGGACCT
*
7975 CTGTATTTATCCCGAATGACCTATGTA
1 CTGTATTTATCCCGAAGGACCTATGTA
* * *
8002 CTGTATTTGTCTCGAAGGACTTATGTA
1 CTGTATTTATCCCGAAGGACCTATGTA
* * *
8029 TTGTATTTGTCTCGAAGGACC
1 CTGTATTTATCCCGAAGGACC
8050 ACTCCTTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (27 bp):
CTGTATTTATCCCGAAGGACCTATGTA
Found at i:8303 original size:13 final size:13
Alignment explanation
Indices: 8285--8322 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
8275 ATCGCTTATC
8285 TCATGTCATATTT
1 TCATGTCATATTT
*
8298 TCATGTCATATAT
1 TCATGTCATATTT
*
8311 T-ATATCATATTT
1 TCATGTCATATTT
8323 GTATTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (13 bp):
TCATGTCATATTT
Found at i:13901 original size:2 final size:2
Alignment explanation
Indices: 13894--13920 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13884 GTTCGTGTCT
13894 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13921 TTCTAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33645 original size:37 final size:36
Alignment explanation
Indices: 33592--33665 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
33582 ATTAAACTCT
* *
33592 TTTTATATTTTAAATTTTGTAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAGTATATAAA
* **
33628 TTTTATGAATTTAAATTTTTTAAAGGAAGTATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAGTATATAAA
33665 T
1 T
33666 ATTTTTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (36 bp):
TTTTATAATTTAAATTTTGTAAAAAAAGTATATAAA
Found at i:34697 original size:10 final size:9
Alignment explanation
Indices: 34678--34721 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
34668 ACTTTTTTAA
34678 AAAATAAAT
1 AAAATAAAT
34687 AAAATACAAT
1 AAAATA-AAT
*
34697 AAAATGAATT
1 AAAAT-AAAT
34707 AAAAATAAAT
1 -AAAATAAAT
34717 AAAAT
1 AAAAT
34722 TCAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 11 0.37
10 13 0.43
11 6 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAATAAAT
Found at i:34729 original size:20 final size:21
Alignment explanation
Indices: 34687--34733 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
34677 AAAAATAAAT
*
34687 AAAATACAATAAAATGAATTA
1 AAAATACAATAAAATCAATTA
34708 AAAATA-AATAAAATTCAA-TA
1 AAAATACAATAAAA-TCAATTA
34728 AAAATA
1 AAAATA
34734 TAATGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAATACAATAAAATCAATTA
Found at i:35632 original size:21 final size:21
Alignment explanation
Indices: 35607--35654 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
35597 TTCACATTAT
35607 ATTTTTATTG-AATTTTATTC
1 ATTTTTATTGTAATTTTATTC
* *
35627 ATTTTTATTGTATTTTTATTT
1 ATTTTTATTGTAATTTTATTC
35648 ATTTTTA
1 ATTTTTA
35655 AAAAAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
ATTTTTATTGTAATTTTATTC
Found at i:35650 original size:10 final size:10
Alignment explanation
Indices: 35606--35654 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
35596 CTTCACATTA
35606 TATTTTTATT
1 TATTTTTATT
* *
35616 GAATTTTATT
1 TATTTTTATT
*
35626 CATTTTTATT
1 TATTTTTATT
35636 GTATTTTTATT
1 -TATTTTTATT
35647 TATTTTTA
1 TATTTTTA
35655 AAAAAAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (10 bp):
TATTTTTATT
Found at i:39516 original size:44 final size:43
Alignment explanation
Indices: 39433--39551 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 43
39423 CCTATCAAAG
* * *
39433 TAAAATTAATTTTCATATTTTTCCTGTTGA-GGCCTCCAACAAAGGT
1 TAAAATTAA-TTTC-T-TTTTTCCTATCGAGGGTC-CCAACAAAGGT
*
39479 TAAAATTAATTT-TTCTGTTTCCTATCGAGGGTCCCAACCAAGGT
1 TAAAATTAATTTCTT-T-TTTCCTATCGAGGGTCCCAACAAAGGT
*
39523 TAAAATTAATTTCTTTTTTCCTGTCGAGG
1 TAAAATTAATTTCTTTTTTCCTATCGAGG
39552 CCCCAATCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 14 0.22
44 32 0.50
45 8 0.12
46 9 0.14
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (43 bp):
TAAAATTAATTTCTTTTTTCCTATCGAGGGTCCCAACAAAGGT
Found at i:51401 original size:21 final size:20
Alignment explanation
Indices: 51339--51407 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
51329 ATATGATAGG
*
51339 TCCTTCGGAACACAGATTACA
1 TCCTTCGGGACACAGA-TACA
* **
51360 TCCTTC-GGA-A-TGATAGG
1 TCCTTCGGGACACAGATACA
51377 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGAT-ACA
*
51398 TCCTTTGGGA
1 TCCTTCGGGA
51408 TGATAGGTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 8 0.22
18 5 0.14
19 2 0.06
20 5 0.14
21 16 0.44
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (20 bp):
TCCTTCGGGACACAGATACA
Found at i:51425 original size:38 final size:38
Alignment explanation
Indices: 51331--51426 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
51321 TACGAGACAT
* *
51331 ATGATAGGTCCTTCGGAACACAGATTACATCCTTCGGA
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGA
* *
51369 ATGATAGGTCCTTCGGGACACAGATGACATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGA
*
51407 ATGATAGGTCCTTTGGGACA
1 ATGATAGGTCCTTCGGGACA
51427 TAGTTTATAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGA
Found at i:53276 original size:20 final size:20
Alignment explanation
Indices: 53244--53281 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53234 ATCGGAAATC
53244 GTTCATGTGGTATTGATATT
1 GTTCATGTGGTATTGATATT
53264 GTTCA-GTGAGTATTGATA
1 GTTCATGTG-GTATTGATA
53282 CTCTGGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (20 bp):
GTTCATGTGGTATTGATATT
Found at i:58109 original size:22 final size:22
Alignment explanation
Indices: 58084--58131 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
58074 CAAAATTTAA
*
58084 CGAAACCGAAAGTAACCCGAAC
1 CGAAACCGAAAGAAACCCGAAC
*
58106 CGAAACCGAAAGAAACCTGAAC
1 CGAAACCGAAAGAAACCCGAAC
58128 CGAA
1 CGAA
58132 TTTTAATCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.29, G:0.19, T:0.04
Consensus pattern (22 bp):
CGAAACCGAAAGAAACCCGAAC
Found at i:58537 original size:20 final size:20
Alignment explanation
Indices: 58503--58542 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
58493 TATGTATTGT
58503 TTTTTAAAATTTAA-TAAAA
1 TTTTTAAAATTTAATTAAAA
*
58522 TTTTTAAATTTATAATTAAAA
1 TTTTTAAAATT-TAATTAAAA
58543 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTAAAATTTAATTAAAA
Done.