Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006051.1 Hibiscus syriacus cultivar Beakdansim tig00014313_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: 56337
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:14463 original size:30 final size:32
Alignment explanation
Indices: 14427--14507 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 32
14417 TATATTTTAT
14427 TTAAATATTTAAAGTATTTTTTTTA-T-AAAA
1 TTAAATATTTAAAGTATTTTTTTTAGTCAAAA
*
14457 TTAAATATTTAAAGT-TATCTTTTTAGTCAAAA
1 TTAAATATTTAAAGTAT-TTTTTTTAGTCAAAA
*
14489 -TAAATACTTAAAGTATTTT
1 TTAAATATTTAAAGTATTTT
14508 ATATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 22 0.50
31 16 0.36
32 5 0.11
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (32 bp):
TTAAATATTTAAAGTATTTTTTTTAGTCAAAA
Found at i:14493 original size:31 final size:28
Alignment explanation
Indices: 14428--14519 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 28
14418 ATATTTTATT
14428 TAAATATTTAAAGTATTTTTTTTAT-AAAA
1 TAAATATTTAAAGTA--TTTTTTATCAAAA
14457 TTAAATATTTAAAGTTATCTTTTTAGTCAAAA
1 -TAAATATTTAAAG-TAT-TTTTTA-TCAAAA
* *
14489 TAAATACTTAAAGTATTTTATATCAAAA
1 TAAATATTTAAAGTATTTTTTATCAAAA
14517 TAA
1 TAA
14520 GTACCTAAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.16
29 6 0.11
30 22 0.39
31 15 0.27
32 4 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
TAAATATTTAAAGTATTTTTTATCAAAA
Found at i:14516 original size:28 final size:28
Alignment explanation
Indices: 14428--14536 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 28
14418 ATATTTTATT
* *
14428 TAAATATTTAAAGTATTTTTTTTAT-AAAA
1 TAAATACTTAAAGTA--TTTTATATCAAAA
* *
14457 TTAAATATTTAAAGTTATCTTTTTAGTCAAAA
1 -TAAATACTTAAAG-TAT-TTTATA-TCAAAA
14489 TAAATACTTAAAGTATTTTATATCAAAA
1 TAAATACTTAAAGTATTTTATATCAAAA
* * *
14517 TAAGTACCTAAACTATTTTA
1 TAAATACTTAAAGTATTTTA
14537 ATATTTTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
28 23 0.33
29 6 0.09
30 22 0.31
31 15 0.21
32 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (28 bp):
TAAATACTTAAAGTATTTTATATCAAAA
Found at i:14667 original size:29 final size:28
Alignment explanation
Indices: 14634--14714 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 28
14624 ATGTACATAG
14634 TTTGATCAAAAAATACTTTAAGTATCTAT
1 TTTGATCAAAAAATACTTTAA-TATCTAT
* *
14663 TTTGATCAAAAAGATAATTTTCAATATTTAT
1 TTTGATCAAAAA-AT-ACTTT-AATATCTAT
*
14694 TTT-AACAAAAAAATACTTTAA
1 TTTGATC-AAAAAATACTTTAA
14715 ATATTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.05
29 16 0.36
30 6 0.14
31 18 0.41
32 2 0.05
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (28 bp):
TTTGATCAAAAAATACTTTAATATCTAT
Found at i:14704 original size:30 final size:30
Alignment explanation
Indices: 14641--14721 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
14631 TAGTTTGATC
* * *
14641 AAAAAATACTTTAAGTATCTATTTTGATCA
1 AAAAAATACTTTAAATATTTATTTTGAACA
* * *
14671 AAAAGATAATTTTCAATATTTATTTT-AACA
1 AAAAAAT-ACTTTAAATATTTATTTTGAACA
14701 AAAAAATACTTTAAATATTTA
1 AAAAAATACTTTAAATATTTA
14722 AAAATAATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 12 0.29
30 15 0.37
31 14 0.34
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (30 bp):
AAAAAATACTTTAAATATTTATTTTGAACA
Found at i:14909 original size:2 final size:2
Alignment explanation
Indices: 14902--14943 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14892 ATTTTGCTCA
14902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT
14944 TCATCATAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22842 original size:34 final size:34
Alignment explanation
Indices: 22799--22867 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
22789 GACTCAAAAT
22799 GTAAGAAACTAATAAAGTTTCAAACACTTATATC
1 GTAAGAAACTAATAAAGTTTCAAACACTTATATC
22833 GTAAGAAACTAATAAAGTTTCAAACACTTATATC
1 GTAAGAAACTAATAAAGTTTCAAACACTTATATC
22867 G
1 G
22868 AATGTATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (34 bp):
GTAAGAAACTAATAAAGTTTCAAACACTTATATC
Found at i:23071 original size:2 final size:2
Alignment explanation
Indices: 23064--23097 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
23054 GACAAAAACA
*
23064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23098 TCATGTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26190 original size:36 final size:34
Alignment explanation
Indices: 26139--26208 Score: 122
Period size: 36 Copynumber: 2.0 Consensus size: 34
26129 AACATCTACC
26139 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACA-TTTTCAAAG
26174 AAACATTTACCAAACTTTGAAAAACATTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTCAAAG
26209 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.38
36 21 0.62
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (34 bp):
AAACTTTACCAAACTTTGAAAAACATTTTCAAAG
Found at i:30766 original size:36 final size:35
Alignment explanation
Indices: 30710--30789 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 35
30700 ACCCATTTCT
*
30710 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
30744 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
30780 ATTTTCAAAG
1 ATTTTCAAAG
30790 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 14 0.34
36 26 0.63
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:33206 original size:31 final size:31
Alignment explanation
Indices: 33171--33230 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
33161 CCGAGACACT
*
33171 TAAAATAATAATGTTTGTAATGTTAGACATC
1 TAAAATAATAACGTTTGTAATGTTAGACATC
*
33202 TAAAATAGTAACGTTTGTAATGTTAGACA
1 TAAAATAATAACGTTTGTAATGTTAGACA
33231 CCTGGATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (31 bp):
TAAAATAATAACGTTTGTAATGTTAGACATC
Found at i:39252 original size:18 final size:21
Alignment explanation
Indices: 39215--39259 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
39205 TTTATTTAAT
39215 TATTTTGTTATTATTTTTATG
1 TATTTTGTTATTATTTTTATG
39236 TATTTT-TTA-TA-TTTTATG
1 TATTTTGTTATTATTTTTATG
*
39254 CATTTT
1 TATTTT
39260 CTTTTTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 2 0.09
20 3 0.13
21 6 0.26
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (21 bp):
TATTTTGTTATTATTTTTATG
Found at i:39315 original size:21 final size:21
Alignment explanation
Indices: 39263--39316 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
39253 GCATTTTCTT
*
39263 TTTTACTTTAGTATATATATAA
1 TTTTACATTA-TATATATATAA
*
39285 TTTTAGATTATATATATGATAA
1 TTTTACATTATATATAT-ATAA
39307 TTTT-CATTAT
1 TTTTACATTAT
39317 CTGTTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTACATTATATATATATAA
Found at i:43209 original size:60 final size:60
Alignment explanation
Indices: 43104--43229 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
43094 TTAAAGTATA
* * * *
43104 AAAATGGTCCATCAACTATAGGGTATTATTTTGTTAAGTCACTCGACTATTAAAAATTAT
1 AAAATGGTCCATCAACTATAGAGTATTACTTTATTAAGTCACTCGACTATTAAAAATTAC
* * * * *
43164 AAAATGGTCC-TCCAACTATAGAGTGTTGCTTTATTGAGTCTCTCGACTATTAAAAGTTAC
1 AAAATGGTCCAT-CAACTATAGAGTATTACTTTATTAAGTCACTCGACTATTAAAAATTAC
43224 AAAATG
1 AAAATG
43230 ATCACTCGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (60 bp):
AAAATGGTCCATCAACTATAGAGTATTACTTTATTAAGTCACTCGACTATTAAAAATTAC
Found at i:47212 original size:21 final size:22
Alignment explanation
Indices: 47178--47223 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
47168 ATGATTTTAA
*
47178 AAAAATTGAAAGTTTAGGTACT
1 AAAAATTGAAAGTTTAAGTACT
*
47200 AAAAA-TGATAGTTTAAGTACT
1 AAAAATTGAAAGTTTAAGTACT
47221 AAA
1 AAA
47224 TGTGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AAAAATTGAAAGTTTAAGTACT
Found at i:53854 original size:18 final size:19
Alignment explanation
Indices: 53828--53865 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53818 ATTTTTAACT
* *
53828 ATTATATTATTTTATTTTA
1 ATTATATTAATTAATTTTA
53847 ATTA-ATTAATTAATTTTA
1 ATTATATTAATTAATTTTA
53865 A
1 A
53866 ATGACTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATATTAATTAATTTTA
Found at i:53854 original size:23 final size:23
Alignment explanation
Indices: 53812--53864 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
53802 ATTAAAAATA
53812 AATTTTATTTTTAACTATTATATT
1 AATTTTATTTTTAACTATTA-ATT
*
53836 -ATTTTA-TTTTAATTAATTAATT
1 AATTTTATTTTTAACT-ATTAATT
53858 AATTTTA
1 AATTTTA
53865 AATGACTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTTTATTTTTAACTATTAATT
Done.