Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000839.1 Hibiscus syriacus cultivar Beakdansim tig00001621_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: 60998
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:4899 original size:40 final size:39
Alignment explanation
Indices: 4849--4924 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
4839 TCTTTCATCA
*
4849 AAATATATTTTTTTTAA-TAGTAAAAAACTTAATAAAAAATT
1 AAATATA-TTTTTTTAATTAATAAAAAA--TAATAAAAAATT
4890 AAATA-ATTTTTTTAATTAATAAAAAATAATAAAAA
1 AAATATATTTTTTTAATTAATAAAAAATAATAAAAA
4925 TTTTACATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 9 0.27
39 9 0.27
40 10 0.30
41 5 0.15
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (39 bp):
AAATATATTTTTTTAATTAATAAAAAATAATAAAAAATT
Found at i:5409 original size:14 final size:14
Alignment explanation
Indices: 5389--5430 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5379 AATTTTAGAT
5389 ATTTAAAAAAATAA
1 ATTTAAAAAAATAA
*
5403 TTTTAAAAAAATAA
1 ATTTAAAAAAATAA
*
5417 AATTACAAAAAATA
1 ATTTA-AAAAAATA
5431 TATATATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTTAAAAAAATAA
Found at i:5745 original size:20 final size:20
Alignment explanation
Indices: 5720--5758 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5710 GAGTCCAAGA
5720 GACTTACATATAAATTTGGC
1 GACTTACATATAAATTTGGC
5740 GACTTACATATAAATTTGG
1 GACTTACATATAAATTTGG
5759 GGGAGACGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
GACTTACATATAAATTTGGC
Found at i:11741 original size:69 final size:70
Alignment explanation
Indices: 11608--11741 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 70
11598 TTCAAACTTA
* * **
11608 AATAAATATTATTTTAATTTGAAATATTCAAAAGTATATACTTATATTTAATATTCAAAGTTAAA
1 AATAAATATCATTTTAATTTGAAATATTCAAAAGTATAAACTTATAACTAATATTCAAAGTTAAA
11673 TGGAT
66 TGGAT
*
11678 AATAAATA-CATTTTAATTTGACATATTCAAAGAGTA-AAAC-TATCACACTAATATTCAAA-TT
1 AATAAATATCATTTTAATTTGAAATATTCAAA-AGTATAAACTTAT-A-ACTAATATTCAAAGTT
11739 AAA
63 AAA
11742 AATACATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
68 3 0.05
69 30 0.54
70 23 0.41
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (70 bp):
AATAAATATCATTTTAATTTGAAATATTCAAAAGTATAAACTTATAACTAATATTCAAAGTTAAA
TGGAT
Found at i:15776 original size:21 final size:21
Alignment explanation
Indices: 15752--15791 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15742 GAAATCAAGT
15752 TTTAA-AATTACTCCCCCTTAC
1 TTTAACAATT-CTCCCCCTTAC
*
15773 TTTAACACTTCTCCCCCTT
1 TTTAACAATTCTCCCCCTT
15792 TTTGTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAACAATTCTCCCCCTTAC
Found at i:18004 original size:25 final size:24
Alignment explanation
Indices: 17975--18024 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17965 TCGATTCCCT
17975 AAAGGGAAGAATCGATTCCCATTCA
1 AAAGGG-AGAATCGATTCCCATTCA
* * *
18000 AAAGGGGGAATCGGTTCCCCTTCA
1 AAAGGGAGAATCGATTCCCATTCA
18024 A
1 A
18025 GGGGGTATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
AAAGGGAGAATCGATTCCCATTCA
Found at i:18029 original size:22 final size:23
Alignment explanation
Indices: 17958--18039 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
17948 AGACCCCGTG
*
17958 GGGGGTATCGATTCCC--T-AAA
1 GGGGGAATCGATTCCCATTCAAA
*
17978 GGGAAGAATCGATTCCCATTCAAAA
1 GGG-GGAATCGATTCCCATTC-AAA
* *
18003 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
*
18025 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
18040 TCCTACACTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 3 0.06
21 11 0.22
22 15 0.30
23 1 0.02
24 14 0.28
25 6 0.12
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:20629 original size:20 final size:21
Alignment explanation
Indices: 20583--20643 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
20573 TTCCCCTGTG
20583 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
20606 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
20626 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
20644 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:24630 original size:19 final size:21
Alignment explanation
Indices: 24596--24635 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
24586 TAAATTCTTC
*
24596 TTCAAAATTTCATTTT-GTTT
1 TTCAAAATTCCATTTTAGTTT
24616 TTCAAAA-TCCATTTTAGTTT
1 TTCAAAATTCCATTTTAGTTT
24636 CTAGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (21 bp):
TTCAAAATTCCATTTTAGTTT
Found at i:26017 original size:20 final size:18
Alignment explanation
Indices: 25982--26023 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
25972 TGGAGCGTGG
25982 GGGGAATCGGTACCCCTAT
1 GGGGAATCGGTACCCCT-T
26001 GGGGAATCGGTACCCCCTT
1 GGGGAATCGGTA-CCCCTT
26020 GGGG
1 GGGG
26024 GGGAATCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.17, C:0.26, G:0.38, T:0.19
Consensus pattern (18 bp):
GGGGAATCGGTACCCCTT
Found at i:32136 original size:11 final size:11
Alignment explanation
Indices: 32090--32138 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
32080 GGTTTGGTCA
*
32090 GGTCTGGGTCG
1 GGTCTGGTTCG
*
32101 GGTCTGGTTTG
1 GGTCTGGTTCG
* *
32112 GGACCGGTTCG
1 GGTCTGGTTCG
*
32123 GGTCTGGTTTG
1 GGTCTGGTTCG
32134 GGTCT
1 GGTCT
32139 AATTTGGAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35
Consensus pattern (11 bp):
GGTCTGGTTCG
Found at i:32917 original size:59 final size:60
Alignment explanation
Indices: 32813--32956 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 60
32803 GGACTTTTGT
* * ** * *
32813 TGATTCGAAAATACCATGAATTGAGTAGTAGGAAATGTTAATCCCTCAAGTGGGGCGTTAC
1 TGATTC-AAAATACCGTGAATCGAGTAAAAGAAAATGTTAATCCCTCAAGTGAGGCGTTAC
* *
32874 TGATTCAAAATACCGTGAATCGAG-AAAAGAAAATGTTGATCCCTCAAGTGAGGCGTTGC
1 TGATTCAAAATACCGTGAATCGAGTAAAAGAAAATGTTAATCCCTCAAGTGAGGCGTTAC
*
32933 TGATTCAAAATGCCGTGAATCGAG
1 TGATTCAAAATACCGTGAATCGAG
32957 CAATAGGAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 52 0.70
60 16 0.22
61 6 0.08
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (60 bp):
TGATTCAAAATACCGTGAATCGAGTAAAAGAAAATGTTAATCCCTCAAGTGAGGCGTTAC
Found at i:33104 original size:42 final size:41
Alignment explanation
Indices: 32991--33104 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
32981 TCCCGAATGT
* *
32991 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAAA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAAA
** ** * * *
33032 CTTATAGATAACCTAAAGGATTTAAACATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAAA
*
33074 CTTACT-GATGGCCCGAATGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
33105 AGAAACCCTT
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
41 18 0.33
42 35 0.65
43 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAAA
Found at i:33311 original size:57 final size:58
Alignment explanation
Indices: 33159--33434 Score: 275
Period size: 57 Copynumber: 4.9 Consensus size: 58
33149 TACATTTATT
* * * * *
33159 ATCAAAAAACCCCTAAAAATTAGGCTTAGATTCTTTTTAAAATTCATTGGAAGTAATC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATC
* * *
33217 ATCAAGAAACCCCTGAAAATCATGCTTAGCTT-ATTTAAAAATTCATTGGAAATAATC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATC
* * * *
33274 AT-AAAAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAA-TCTTTAGAAATCATC
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATC
** * * *
33330 ATCAAGAAACTTCTGAAAATTAGTCTTAG--T-TTCTAAAAATCTCATTTG-AA-AA-C
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAAT-TCATTGGAAATAATC
* * * * *
33383 ATCAAGAAACCCCTAAAAATTAAGTTTAGCTTC-TTTCAAAATTCATTTGAAA
1 ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAA
33435 ACATCATATT
Statistics
Matches: 179, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
53 24 0.13
54 16 0.09
55 13 0.07
56 45 0.25
57 54 0.30
58 27 0.15
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (58 bp):
ATCAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATC
Found at i:34685 original size:28 final size:28
Alignment explanation
Indices: 34645--34699 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
34635 GCTTAGGCTG
34645 ACTTGGGAAGGTAATGTGTTTCAGGTTA
1 ACTTGGGAAGGTAATGTGTTTCAGGTTA
*
34673 ACTTGGGGAGGTAATGTGTTTCAGGTT
1 ACTTGGGAAGGTAATGTGTTTCAGGTT
34700 GTCTTCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.36
Consensus pattern (28 bp):
ACTTGGGAAGGTAATGTGTTTCAGGTTA
Found at i:35405 original size:29 final size:29
Alignment explanation
Indices: 35327--35421 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 29
35317 GATATGCCTT
* *
35327 CTTTC-TTTCTTTTTCCATTTTTCTTCTT-
1 CTTTCTTTTCTTTTTCTACTTTTCTT-TTG
* *
35355 -TTTCTCTTCTTTTACTACTTTTCTTTTG
1 CTTTCTTTTCTTTTTCTACTTTTCTTTTG
35383 CTTTCTTTTCTTTTCTCTA-TTTT-TTTGTG
1 CTTTCTTTTCTTTT-TCTACTTTTCTTT-TG
35412 CTTTTCTTTT
1 C-TTTCTTTT
35422 TCTTCTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
27 6 0.11
28 19 0.35
29 19 0.35
30 11 0.20
ACGTcount: A:0.04, C:0.21, G:0.03, T:0.72
Consensus pattern (29 bp):
CTTTCTTTTCTTTTTCTACTTTTCTTTTG
Found at i:35429 original size:14 final size:14
Alignment explanation
Indices: 35332--35430 Score: 64
Period size: 14 Copynumber: 7.2 Consensus size: 14
35322 GCCTTCTTTC
*
35332 TTTCTTTTTCCAT-T
1 TTTCTTTTT-CTTCT
35346 TTTCTTCTTT-TTCT
1 TTTCTT-TTTCTTCT
* * *
35360 CTTCTTTTACTACT
1 TTTCTTTTTCTTCT
*
35374 TTTCTTTTGCTTTCT
1 TTTCTTTTTC-TTCT
35389 TTTC-TTTTC-TCT
1 TTTCTTTTTCTTCT
* * *
35401 ATT-TTTTTGTGCT
1 TTTCTTTTTCTTCT
35414 TTTCTTTTTCTTCT
1 TTTCTTTTTCTTCT
35428 TTT
1 TTT
35431 TGCTATATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
12 9 0.14
13 7 0.11
14 38 0.59
15 10 0.16
ACGTcount: A:0.04, C:0.20, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTCTTTTTCTTCT
Found at i:35887 original size:2 final size:2
Alignment explanation
Indices: 35880--35955 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
35870 ATCCTATCAA
35880 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
35922 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
35956 CCGTTGTTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57071 original size:20 final size:21
Alignment explanation
Indices: 57036--57081 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
57026 CCACATTTGA
57036 AAAGATGATGTATTCTCTTTTC
1 AAAGATGA-GTATTCTCTTTTC
57058 AAAGATGA-TATTCTCTTTTC
1 AAAGATGAGTATTCTCTTTTC
57078 AAAG
1 AAAG
57082 GCAAAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 16 0.67
22 8 0.33
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (21 bp):
AAAGATGAGTATTCTCTTTTC
Done.