Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004127.1 Hibiscus syriacus cultivar Beakdansim tig00009028_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: 41686
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:7750 original size:21 final size:23
Alignment explanation
Indices: 7724--7766 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
7714 TTAATTATCA
7724 TAATTT-A-TACATGGACTAATG
1 TAATTTAACTACATGGACTAATG
7745 TAATTTAACTTACATGGACTAA
1 TAATTTAAC-TACATGGACTAA
7767 ATGTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
24 12 0.63
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (23 bp):
TAATTTAACTACATGGACTAATG
Found at i:7816 original size:24 final size:24
Alignment explanation
Indices: 7789--7848 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
7779 AAAGTTAATC
7789 ATTTAACTTACATGGACTAATGTA
1 ATTTAACTTACATGGACTAATGTA
7813 ATTTAACTTACATGGACTAATGTA
1 ATTTAACTTACATGGACTAATGTA
7837 ATTTAACTTACA
1 ATTTAACTTACA
7849 AATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (24 bp):
ATTTAACTTACATGGACTAATGTA
Found at i:10728 original size:14 final size:15
Alignment explanation
Indices: 10709--10741 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10699 TTAGATATCC
*
10709 TTTTTCTT-TTGATA
1 TTTTTCTTATTAATA
10723 TTTTTCTTATTAATA
1 TTTTTCTTATTAATA
10738 TTTT
1 TTTT
10742 CTTCTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTCTTATTAATA
Found at i:22490 original size:18 final size:18
Alignment explanation
Indices: 22456--22502 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
22446 TGGCTTCATT
*
22456 TGCAGGGACACAACAGAAG
1 TGCAGGG-CATAACAGAAG
22475 TGCAGGGCATAACAGAAG
1 TGCAGGGCATAACAGAAG
22493 TGCAGGGCAT
1 TGCAGGGCAT
22503 GCGACAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.36, C:0.19, G:0.34, T:0.11
Consensus pattern (18 bp):
TGCAGGGCATAACAGAAG
Found at i:27922 original size:22 final size:22
Alignment explanation
Indices: 27897--27940 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
27887 ATAGTTAATT
27897 TTTA-AAAAAATAATAATTATAA
1 TTTATAAAAAATAA-AATTATAA
**
27919 TTTATAATTAATAAAATTATAA
1 TTTATAAAAAATAAAATTATAA
27941 ATGACTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTATAAAAAATAAAATTATAA
Found at i:30907 original size:257 final size:257
Alignment explanation
Indices: 30377--30928 Score: 842
Period size: 255 Copynumber: 2.1 Consensus size: 257
30367 TCGGGTTGGG
* *
30377 TCGGGTCGGGTGAAACTTTATTTTGGTCGGATCGGGTCGATTTTTTTAAGTGTGATAATCGGGTT
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTC-GGT--ATTTTTTTAAGTGTGATAATCGGGTC
* * * *
30442 GGGTTGAGTTCGGGTTTAGGGTGAAAAATACCTGGCCCGACCCGAAAATATATATAAATTTACTT
63 GGGTCGAGTTCAGGTTTAGGGTGAAAAATACCCGACCCGACCCGAAAATATATATAAATTTACTT
* * * *
30507 TATATATTTAGGAATAATTATAATAATACATCTCTATATATATTTTTTCAATTAAGTTATTGTTT
128 TATATATTTAGAAATAATTACAATAATACACCTCTATATATATTTTTTCAATTAAGTTATTATTT
* *
30572 TTATTGAATAAAAATATTTTTTTATTATTTCGGGTCAAGTCAGTTCAGATTTCTAATTCATATAT
193 TTATTGAATAAAAATATTTTTTTATTATTTCGGGTCAAGTAAGTTCAAATTTCTAATTCATATAT
* *
30637 TCGGGTCGGGTG-AATTTTATTTTGGTCGGGTCGGT-TTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTATTTTTTTAAGTGTGATAATCGGGTCGGG
* * *
30700 TCGGGTTCAGGTTTAGGGTGAAAAATACCCGACCCGGCCCGAATATATATATAAATTTA-TCTTA
66 TCGAGTTCAGGTTTAGGGTGAAAAATACCCGACCCGACCCGAAAATATATATAAATTTACT-TTA
30764 TATATTTAGAAATAATTACAATAATATC-CCTCTATATATAATTTTTTTCAATTAAGTTATTATT
130 TATATTTAGAAATAATTACAATAATA-CACCTCTATATAT-A-TTTTTTCAATTAAGTTATTATT
*
30828 TTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCAGGTAAGTTCAAATTTCTAATTCATATA
192 TTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCAAGTAAGTTCAAATTTCTAATTCATATA
30893 T
257 T
*
30894 TCGGGTAGGGTGAAACTTTATTTTGGTCGGGTCGG
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
30929 GTCTCGAATA
Statistics
Matches: 267, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
254 1 0.00
255 115 0.43
256 2 0.01
257 95 0.36
258 24 0.09
259 18 0.07
260 12 0.04
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (257 bp):
TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTATTTTTTTAAGTGTGATAATCGGGTCGGG
TCGAGTTCAGGTTTAGGGTGAAAAATACCCGACCCGACCCGAAAATATATATAAATTTACTTTAT
ATATTTAGAAATAATTACAATAATACACCTCTATATATATTTTTTCAATTAAGTTATTATTTTTA
TTGAATAAAAATATTTTTTTATTATTTCGGGTCAAGTAAGTTCAAATTTCTAATTCATATAT
Found at i:31351 original size:14 final size:14
Alignment explanation
Indices: 31334--31365 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
31324 ACAAATTCTA
31334 ATTCCCTCATAAAC
1 ATTCCCTCATAAAC
31348 ATTCCCTCATAAAC
1 ATTCCCTCATAAAC
31362 ATTC
1 ATTC
31366 TAGCGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTCCCTCATAAAC
Found at i:37734 original size:58 final size:57
Alignment explanation
Indices: 37667--37784 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
37657 GAGTGACTAT
** *
37667 TTTATAATTTTTAATAGTTGTGA-ACTCAACAAAGCAACATCATATAGTCAAAT-GACCA
1 TTTATAATTTTT--TAGTCATGAGACTCAACAAAGCAACAACATATAGT-AAATGGACCA
* * *
37725 TTTATAATTTTTTAGTCATTAGACTCAACAGAGCAACAACATATAGTTAATGGACCA
1 TTTATAATTTTTTAGTCATGAGACTCAACAAAGCAACAACATATAGTAAATGGACCA
37782 TTT
1 TTT
37785 GTATACTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
56 9 0.17
57 31 0.60
58 12 0.23
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (57 bp):
TTTATAATTTTTTAGTCATGAGACTCAACAAAGCAACAACATATAGTAAATGGACCA
Found at i:39689 original size:48 final size:46
Alignment explanation
Indices: 39632--39726 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 46
39622 TTTTGAAACA
* *
39632 TATTCATGTAACATATAAATAGA-ATTTGATTATCGAAATAAAAAAGAT
1 TATTAATGTAA-AAATAAA-AGATATTTGATTATC-AAATAAAAAAGAT
*
39680 TATTAATGTAAAAATCAAAGATTATTTGATTATCAAATAAAAAAGAT
1 TATTAATGTAAAAATAAAAGA-TATTTGATTATCAAATAAAAAAGAT
39727 ATAATTCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 3 0.07
47 18 0.43
48 21 0.50
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (46 bp):
TATTAATGTAAAAATAAAAGATATTTGATTATCAAATAAAAAAGAT
Found at i:39855 original size:20 final size:20
Alignment explanation
Indices: 39826--39882 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
39816 AAATGACCAA
39826 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
* * * *
39846 CAATTTCGCAACACAAATTC
1 CAAATTCGCAACGCGAACTC
*
39866 CAAAATCGCAACGCGAA
1 CAAATTCGCAACGCGAA
39883 TAGATAAATC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:39891 original size:20 final size:20
Alignment explanation
Indices: 39868--39966 Score: 155
Period size: 20 Copynumber: 5.0 Consensus size: 20
39858 ACAAATTCCA
39868 AAATCGCAACGCGAATA-GAT
1 AAATCGCAACGCGAATATG-T
*
39888 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGCGAATATGT
39908 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
**
39928 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
39948 AAATCGCAACGCGAATATG
1 AAATCGCAACGCGAATATG
39967 AAAACCGCGT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 72 0.99
21 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:39895 original size:40 final size:40
Alignment explanation
Indices: 39851--39966 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 40
39841 AACTCCAATT
*
39851 TCGCAACACAAATTCCAAAATCGCAACGCGAATA-GATAAA
1 TCGCAACACAAATACCAAAATCGCAACGCGAATATG-TAAA
* * ***
39891 TCGCAACGCGAATAGGTAAATCGCAACGCGAATATGTAAA
1 TCGCAACACAAATACCAAAATCGCAACGCGAATATGTAAA
* ***
39931 TCGCAACGA-TAATATGTAAATCGCAACGCGAATATG
1 TCGCAAC-ACAAATACCAAAATCGCAACGCGAATATG
39967 AAAACCGCGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 64 0.98
41 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (40 bp):
TCGCAACACAAATACCAAAATCGCAACGCGAATATGTAAA
Found at i:39981 original size:20 final size:20
Alignment explanation
Indices: 39958--40001 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39948 AAATCGCAAC
*
39958 GCGAATATGAAAACCGCGTT
1 GCGAATATGAAAACCGCATT
* *
39978 GCGAATTTGAAAATCGCATT
1 GCGAATATGAAAACCGCATT
39998 GCGA
1 GCGA
40002 TAGTACTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
GCGAATATGAAAACCGCATT
Found at i:39982 original size:60 final size:60
Alignment explanation
Indices: 39867--39995 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
39857 CACAAATTCC
* * *
39867 AAAATCGCAACGCGAATAGATAAATCGCAACGCGAATAGGTAAATCGCAACGCGAATATG
1 AAAATCGCAACGAGAATAGATAAATCGCAACGCGAATAGGAAAACCGCAACGCGAATATG
* * * *** *
39927 TAAATCGCAACGATAATATG-TAAATCGCAACGCGAATATGAAAACCGCGTTGCGAATTTG
1 AAAATCGCAACGAGAATA-GATAAATCGCAACGCGAATAGGAAAACCGCAACGCGAATATG
39987 AAAATCGCA
1 AAAATCGCA
39996 TTGCGATAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (60 bp):
AAAATCGCAACGAGAATAGATAAATCGCAACGCGAATAGGAAAACCGCAACGCGAATATG
Found at i:39992 original size:40 final size:40
Alignment explanation
Indices: 39867--39995 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
39857 CACAAATTCC
*
39867 AAAATCGCAACGCGAATA-GATAAATCGCAACGCGAATAGG
1 AAAATCGCAACGCGAATATGA-AAATCGCAACGCGAATATG
* * **
39907 TAAATCGCAACGCGAATATGTAAATCGCAACGATAATATG
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
* * *** *
39947 TAAATCGCAACGCGAATATGAAAACCGCGTTGCGAATTTG
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
39987 AAAATCGCA
1 AAAATCGCA
39996 TTGCGATAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 73 0.99
41 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
Found at i:40054 original size:20 final size:20
Alignment explanation
Indices: 39994--40046 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
39984 TTGAAAATCG
*
39994 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTAATGTTTA
*
40014 CATTGCGAGAGTAATGTTTA
1 CATTGCGATAGTAATGTTTA
40034 CATTGCGATAGTA
1 CATTGCGATAGTA
40047 TTGCTTACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
CATTGCGATAGTAATGTTTA
Found at i:40098 original size:57 final size:57
Alignment explanation
Indices: 40036--40213 Score: 277
Period size: 57 Copynumber: 3.1 Consensus size: 57
40026 AATGTTTACA
* * * *
40036 TTGCGATAGTATTGCTTACTTATAACAGTAATTAGCGTTGCGAATTTGAAAATCGCG
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCG
* *
40093 TTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCA
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCG
*
40150 TTGCGATAGTATTGTTTACCTATATCGGTAATTA-CTGTTGCGAATTTGAAAATCACG
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGC-GTTGCGAATTTGAAAATCGCG
40207 TTGCGAT
1 TTGCGAT
40214 TTCCTAAACT
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
56 1 0.01
57 110 0.99
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (57 bp):
TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCG
Found at i:40242 original size:20 final size:20
Alignment explanation
Indices: 40219--40259 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40209 GCGATTTCCT
*
40219 AAACTGAGTTGCGAATTTGG
1 AAACTGAGTTGCGAAATTGG
*
40239 AAACTGTGTTGCGAAATTGG
1 AAACTGAGTTGCGAAATTGG
40259 A
1 A
40260 GTTCGCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAACTGAGTTGCGAAATTGG
Done.