Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005224.1 Hibiscus syriacus cultivar Beakdansim tig00011827_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: 88977
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:10059 original size:16 final size:16
Alignment explanation
Indices: 10021--10059 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
10011 TATATTGAAT
*
10021 TCTCAACTTGTACATC
1 TCTCAAGTTGTACATC
10037 TCTCAAGTTGTACATC
1 TCTCAAGTTGTACATC
10053 TCTCAAG
1 TCTCAAG
10060 CTTCACCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (16 bp):
TCTCAAGTTGTACATC
Found at i:14655 original size:21 final size:21
Alignment explanation
Indices: 14631--14685 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
14621 CGATGAACAA
14631 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
14652 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
14673 TATCGATACTGAT
1 TATCGATACTGAT
14686 TGTGTATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:14705 original size:38 final size:39
Alignment explanation
Indices: 14651--14739 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 39
14641 GATGCAATTA
*
14651 GTATCGATACTGATGCAATTAGTATCGATACTGAT-TGT
1 GTATCGATACTAATGCAATTAGTATCGATACTGATGTGT
* * *
14689 GTATCGAAACTAATGCAATTGGTATCGATATTGATGTGT
1 GTATCGATACTAATGCAATTAGTATCGATACTGATGTGT
14728 GTATCGATACTA
1 GTATCGATACTA
14740 TAAGGAAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 31 0.69
39 14 0.31
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (39 bp):
GTATCGATACTAATGCAATTAGTATCGATACTGATGTGT
Found at i:20869 original size:7 final size:7
Alignment explanation
Indices: 20857--20913 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
20847 TATAATTTAA
20857 AAATAAT
1 AAATAAT
20864 AAATAAT
1 AAATAAT
20871 AAATAA-
1 AAATAAT
20877 AAATAA-
1 AAATAAT
**
20883 AAAGGGA-
1 AAA-TAAT
20890 AAATAAT
1 AAATAAT
20897 AAAATAAT
1 -AAATAAT
20905 AAATAAT
1 AAATAAT
20912 AA
1 AA
20914 TAGTAAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 10 0.23
7 26 0.60
8 7 0.16
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (7 bp):
AAATAAT
Found at i:20973 original size:18 final size:18
Alignment explanation
Indices: 20952--20994 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20942 GTTGTTTTTA
20952 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
*
20970 AAATAAAATAAAATAATT
1 AAATAAAAGAAAATAATT
20988 AAATAAA
1 AAATAAA
20995 TAATCTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:23747 original size:11 final size:11
Alignment explanation
Indices: 23731--23762 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
23721 AAAGTTCGCT
23731 GAAAATAAAAC
1 GAAAATAAAAC
*
23742 GAAAATAAAAT
1 GAAAATAAAAC
23753 GAAAATAAAA
1 GAAAATAAAA
23763 AAATATAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.12
Consensus pattern (11 bp):
GAAAATAAAAC
Found at i:26723 original size:8 final size:8
Alignment explanation
Indices: 26710--26750 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
26700 ATTATAATTT
26710 AAAAATAA
1 AAAAATAA
26718 AAAAATAA
1 AAAAATAA
26726 AAAAAT-A
1 AAAAATAA
26733 AAAAATAA
1 AAAAATAA
*
26741 TAATAATAA
1 -AAAAATAA
26750 A
1 A
26751 TAAGCAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 7 0.23
8 16 0.53
9 7 0.23
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:26731 original size:16 final size:17
Alignment explanation
Indices: 26709--26783 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
26699 AATTATAATT
26709 TAAAAATAAAAAAATAA
1 TAAAAATAAAAAAATAA
26726 -AAAAAT-AAAAAATAA
1 TAAAAATAAAAAAATAA
* * **
26741 TAATAATAAATAAGCAA
1 TAAAAATAAAAAAATAA
** *
26758 GGAAAATAATAAAATAA
1 TAAAAATAAAAAAATAA
26775 TAAATAATA
1 TAAA-AATA
26784 GTAGTAAAGA
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
15 9 0.21
16 11 0.26
17 18 0.43
18 4 0.10
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (17 bp):
TAAAAATAAAAAAATAA
Found at i:26773 original size:8 final size:8
Alignment explanation
Indices: 26711--26783 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
26701 TTATAATTTA
*
26711 AAAATAAA
1 AAAATAAT
*
26719 AAAATAAA
1 AAAATAAT
26727 AAAATAA-
1 AAAATAAT
26734 AAAATAAT
1 AAAATAAT
26742 AATAATAAAT
1 AA-AAT-AAT
* **
26752 AAGCA-AGG
1 AA-AATAAT
26760 AAAATAAT
1 AAAATAAT
26768 AAAATAAT
1 AAAATAAT
26776 -AAATAAT
1 AAAATAAT
26783 A
1 A
26784 GTAGTAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
7 15 0.28
8 29 0.55
9 3 0.06
10 6 0.11
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (8 bp):
AAAATAAT
Found at i:26843 original size:18 final size:18
Alignment explanation
Indices: 26822--26864 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
26812 GTTATTTTTA
26822 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
26840 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
26858 AAATAAA
1 AAATAAA
26865 TAATCTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:29557 original size:25 final size:25
Alignment explanation
Indices: 29523--29573 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29513 CCTCAAATAA
29523 TCATTCACTTCTCGAATTCTTTTGT
1 TCATTCACTTCTCGAATTCTTTTGT
29548 TCATTCACTTCTCGAATTCTTTTGT
1 TCATTCACTTCTCGAATTCTTTTGT
29573 T
1 T
29574 TTTCTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.53
Consensus pattern (25 bp):
TCATTCACTTCTCGAATTCTTTTGT
Found at i:29653 original size:16 final size:15
Alignment explanation
Indices: 29613--29653 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29603 TACTTTTCTC
*
29613 TTTTATCTTTTACTT
1 TTTTCTCTTTTACTT
*
29628 TTTTCGCTTTTACTT
1 TTTTCTCTTTTACTT
29643 ATTTTCTCTTT
1 -TTTTCTCTTT
29654 AAATGCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTCTCTTTTACTT
Found at i:32979 original size:18 final size:18
Alignment explanation
Indices: 32953--32991 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
32943 AGAAAAAAAA
**
32953 TTCTAATTCATGGTTAAT
1 TTCTAATTCAAAGTTAAT
*
32971 TTCTGATTCAAAGTTAAT
1 TTCTAATTCAAAGTTAAT
32989 TTC
1 TTC
32992 CTCGAATTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (18 bp):
TTCTAATTCAAAGTTAAT
Found at i:45198 original size:23 final size:22
Alignment explanation
Indices: 45172--45239 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
45162 AATCCTTTAC
45172 AATTATCTTTTGTAATTTTAGG
1 AATTATCTTTTGTAATTTTAGG
*
45194 AAATT-TCTTTT-CAATTTCTTAGG
1 -AATTATCTTTTGTAA-TT-TTAGG
* *
45217 AATTATCTCTTAGTATTTTTAGG
1 AATTATCT-TTTGTAATTTTAGG
45240 GTTTTGAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 2 0.06
22 12 0.33
23 17 0.47
24 4 0.11
25 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (22 bp):
AATTATCTTTTGTAATTTTAGG
Found at i:45377 original size:16 final size:14
Alignment explanation
Indices: 45336--45368 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45326 TATAAAAAAA
*
45336 TTAC-TTTTATCTT
1 TTACTTTTTCTCTT
45349 TTACTTTTTCTCTT
1 TTACTTTTTCTCTT
45363 TTACTT
1 TTACTT
45369 ATTTTCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (14 bp):
TTACTTTTTCTCTT
Found at i:45970 original size:16 final size:16
Alignment explanation
Indices: 45945--45978 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45935 AGAAGTTTGA
45945 TTCAACTTTACTTCCT
1 TTCAACTTTACTTCCT
* *
45961 TTCAATTTTACTTTCT
1 TTCAACTTTACTTCCT
45977 TT
1 TT
45979 AGTTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCAACTTTACTTCCT
Found at i:49126 original size:44 final size:43
Alignment explanation
Indices: 49049--49204 Score: 143
Period size: 44 Copynumber: 3.6 Consensus size: 43
49039 TTTTGTGTTC
* ** * *
49049 TTTAGCGGCATTTGTA-ACAAAAAACGCCGCTATATACCATACAT
1 TTTA-CGGCATTTGTATCCAAAAAATACCACTATATACCAGAC-T
* * * *
49093 TTTATGGCATTTGTATCCTAAAAATACCACTATATAACAGACC
1 TTTACGGCATTTGTATCCAAAAAATACCACTATATACCAGACT
* * *
49136 TTTAGCGGCGTTTGTATCCAAAAAATGCCGCTATATACCAGATCT
1 TTTA-CGGCATTTGTATCCAAAAAATACCACTATATACCAGA-CT
* *
49181 TTTGCGGCATTTGTATCCGAAAAA
1 TTTACGGCATTTGTATCCAAAAAA
49205 CACTGTGAAT
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
43 14 0.16
44 72 0.80
45 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (43 bp):
TTTACGGCATTTGTATCCAAAAAATACCACTATATACCAGACT
Found at i:57779 original size:13 final size:13
Alignment explanation
Indices: 57761--57802 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
57751 GTCATAAATC
*
57761 TATGACGCGTATT
1 TATGACGCGCATT
*
57774 TATGACACGCATT
1 TATGACGCGCATT
*
57787 TATGACGAGCATT
1 TATGACGCGCATT
57800 TAT
1 TAT
57803 CGTCATTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:67358 original size:26 final size:25
Alignment explanation
Indices: 67271--67360 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
67261 TACCTATACC
*
67271 AATGCCAGAAAATGATGCCAAATCT
1 AATGCCAGAAAAGGATGCCAAATCT
* *
67296 AATGCCAGAAAAGGATGGCAAATCC
1 AATGCCAGAAAAGGATGCCAAATCT
* ** *
67321 AACGTTGAAAAAAGGATGCCAAATCT
1 AATG-CCAGAAAAGGATGCCAAATCT
*
67347 AATGCTAGAAAAGG
1 AATGCCAGAAAAGG
67361 TACCATTTTC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 32 0.63
26 19 0.37
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (25 bp):
AATGCCAGAAAAGGATGCCAAATCT
Found at i:68708 original size:44 final size:44
Alignment explanation
Indices: 68616--68714 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
68606 TTCTATTAAT
* * * * *
68616 AAACGCCACAAAAAGTCAGGTTATTTAGCGGTGTTTGTATACTA
1 AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
* *
68660 AAACGCCGCTAAAGGTCAGGTTATATAGCGGCGTTT-TAGAATA
1 AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
68703 CAAACGCCGCAA
1 -AAACGCCGCAA
68715 CAGGTTCGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 5 0.11
44 41 0.89
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (44 bp):
AAACGCCGCAAAAAGTCAGGTTATATAGCGGCGTTTGTAGAATA
Found at i:68734 original size:43 final size:42
Alignment explanation
Indices: 68616--68739 Score: 108
Period size: 44 Copynumber: 2.9 Consensus size: 42
68606 TTCTATTAAT
* * * * * *
68616 AAACGCCACAAAAAGTCAGGTTATTTAGCGGTGTTTGTATACTA
1 AAACGCCGCTAAAGGTCA-GTTATTTAGCGGCGTTT-TAGAATA
*
68660 AAACGCCGCTAAAGGTCAGGTTATATAGCGGCGTTTTAGAATA
1 AAACGCCGCTAAAGGTCA-GTTATTTAGCGGCGTTTTAGAATA
*
68703 CAAACGCCGC-AACAGGTTC-GTTATTTAGCGGCATTTT
1 -AAACGCCGCTAA-AGG-TCAGTTATTTAGCGGCGTTTT
68740 TTGTCACAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
43 23 0.34
44 43 0.63
45 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCAGTTATTTAGCGGCGTTTTAGAATA
Found at i:70164 original size:16 final size:16
Alignment explanation
Indices: 70143--70177 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
70133 TATTACAATG
70143 AAATTATTACCTTAAT
1 AAATTATTACCTTAAT
70159 AAATTATTACCTTAAT
1 AAATTATTACCTTAAT
70175 AAA
1 AAA
70178 ATCCACATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTATTACCTTAAT
Found at i:70863 original size:20 final size:20
Alignment explanation
Indices: 70830--70868 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
70820 TAGTTTTATA
*
70830 AAGTTTTCTCTTTTCTTTTC
1 AAGTTTTCTCTTTTATTTTC
70850 AAGTTTTCAT-TTTTATTTT
1 AAGTTTTC-TCTTTTATTTT
70869 ATTTTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (20 bp):
AAGTTTTCTCTTTTATTTTC
Found at i:77444 original size:17 final size:18
Alignment explanation
Indices: 77411--77444 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
77401 TCTGCACTTA
77411 TTTTCAAAATGAAAATTG
1 TTTTCAAAATGAAAATTG
77429 TTTTCAAAAT-AAAATT
1 TTTTCAAAATGAAAATT
77445 TTGACTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTTCAAAATGAAAATTG
Found at i:84603 original size:24 final size:25
Alignment explanation
Indices: 84527--84616 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
84517 CCAGCACCAA
* * * *
84527 AAAATGATGTCAAATCCAACGCTAG
1 AAAAGGATGCCAAATCCAAAGCCAG
* *
84552 AAAAAGATGCCAAATCTAAAGCCAG
1 AAAAGGATGCCAAATCCAAAGCCAG
84577 AAAAGTG-TGCCAAATCCAAAGCC-G
1 AAAAG-GATGCCAAATCCAAAGCCAG
84601 AAAAGGATGCCAAATC
1 AAAAGGATGCCAAATC
84617 AAATACCGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
23 1 0.02
24 15 0.27
25 39 0.70
26 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (25 bp):
AAAAGGATGCCAAATCCAAAGCCAG
Found at i:86500 original size:21 final size:21
Alignment explanation
Indices: 86475--86515 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
86465 TTATACAAAA
86475 ATTGAGGAATTCATAAACAAG
1 ATTGAGGAATTCATAAACAAG
86496 ATTGAGGAATTCATAAACAA
1 ATTGAGGAATTCATAAACAA
86516 CGAGGCGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (21 bp):
ATTGAGGAATTCATAAACAAG
Done.