Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001248.1 Hibiscus syriacus cultivar Beakdansim tig00002450_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: 51833
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3947 original size:8 final size:8
Alignment explanation
Indices: 3934--3990 Score: 87
Period size: 8 Copynumber: 6.9 Consensus size: 8
3924 TCAATTATTT
3934 CTTTTTTC
1 CTTTTTTC
3942 CTTTTTTCC
1 CTTTTTT-C
*
3951 CTTTTTCC
1 CTTTTTTC
3959 CTTTTTTTC
1 C-TTTTTTC
3968 CTTTTTTC
1 CTTTTTTC
3976 CTTTTTTC
1 CTTTTTTC
3984 CTTTTTT
1 CTTTTTT
3991 TTTCAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 31 0.69
9 14 0.31
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (8 bp):
CTTTTTTC
Found at i:3968 original size:26 final size:26
Alignment explanation
Indices: 3935--3992 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
3925 CAATTATTTC
3935 TTTTTTCCTTTTTTCCCTTTTTCCCT
1 TTTTTTCCTTTTTTCCCTTTTTCCCT
* *
3961 TTTTTTCCTTTTTTCCTTTTTTCCTT
1 TTTTTTCCTTTTTTCCCTTTTTCCCT
3987 TTTTTT
1 TTTTTT
3993 TCAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTCCTTTTTTCCCTTTTTCCCT
Found at i:3991 original size:17 final size:17
Alignment explanation
Indices: 3934--3990 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
3924 TCAATTATTT
*
3934 CTTTTTTCCTTTTTTCC
1 CTTTTTTCCTTTTTTTC
*
3951 CTTTTTCCCTTTTTTTC
1 CTTTTTTCCTTTTTTTC
3968 CTTTTTTCC-TTTTTTC
1 CTTTTTTCCTTTTTTTC
3984 CTTTTTT
1 CTTTTTT
3991 TTTCAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
CTTTTTTCCTTTTTTTC
Found at i:6831 original size:8 final size:8
Alignment explanation
Indices: 6813--6850 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
6803 AAAAGTATAA
6813 ATGCAAA-
1 ATGCAAAG
6820 ATGCAAAG
1 ATGCAAAG
6828 ATGCAAAG
1 ATGCAAAG
6836 ATGCAAAG
1 ATGCAAAG
6844 ATGCAAA
1 ATGCAAA
6851 TGCATGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (8 bp):
ATGCAAAG
Found at i:14958 original size:20 final size:21
Alignment explanation
Indices: 14935--15015 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
14925 TTGGTGCAGA
*
14935 GGGAATCGATCCCCCCTTGA-
1 GGGAACCGATCCCCCCTTGAG
14955 GGGAACCGATCCCCCCTTTGAAG
1 GGGAACCGATCCCCCC-TTG-AG
* **
14978 GGGAACCGATTCCCCCTACAG
1 GGGAACCGATCCCCCCTTGAG
* *
14999 GGGAATCGATACCCCCT
1 GGGAACCGATCCCCCCT
15016 AGGGTTCTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
20 15 0.29
21 20 0.38
22 2 0.04
23 15 0.29
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATCCCCCCTTGAG
Found at i:14985 original size:23 final size:21
Alignment explanation
Indices: 14933--14994 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
14923 TTTTGGTGCA
*
14933 GAGGGAATCGATCCCCCC-TT
1 GAGGGAACCGATCCCCCCTTT
14953 GAGGGAACCGATCCCCCCTTT
1 GAGGGAACCGATCCCCCCTTT
*
14974 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATCCCCCCT
14995 ACAGGGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 17 0.46
21 3 0.08
22 1 0.03
23 16 0.43
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCTTT
Found at i:19930 original size:3 final size:3
Alignment explanation
Indices: 19924--19962 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
19914 TATTATTTTT
* *
19924 TAA TAA TAA TAT TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19963 AAAAAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:19944 original size:15 final size:15
Alignment explanation
Indices: 19924--19962 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
19914 TATTATTTTT
19924 TAATAATAATATTAA
1 TAATAATAATATTAA
19939 TAATAATAATATTAA
1 TAATAATAATATTAA
19954 TAATAATAA
1 TAATAATAA
19963 AAAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAATAATATTAA
Found at i:20525 original size:131 final size:131
Alignment explanation
Indices: 20291--20554 Score: 381
Period size: 131 Copynumber: 2.0 Consensus size: 131
20281 GTTGTCGAAT
*
20291 GTGTTGAGTCAATCGATCGGATGAAATAGCCAAGAGGGAGTGAATTGGCAATTAAAATTTTGGTG
1 GTGTTGAGTCAATCGATCGGACGAAATAGCCAAGAGGGAGTGAATTGGCAATTAAAATTTTGGTG
* *
20356 GAAGCTTGACAGAAAATAAAAAATATTTGCACAACGATTTAGAGTGGTTCGACTTTCTCAACCAA
66 GAAGCTTGACAGAAAATAAAAAATAATTGCACAACGATTTAGAGTGGTTCGACTTTATCAACCAA
20421 A
131 A
* * * *
20422 GTGTTGAGTTAATCGAT-TGACGGAATCAGCCAAGAGGGGGTGAATTGGCAATTAAAATTTT-GT
1 GTGTTGAGTCAATCGATCGGACGAAAT-AGCCAAGAGGGAGTGAATTGGCAATTAAAATTTTGGT
** * *
20485 GGAAGCTCTTG-CAGAAAATTGAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTATCAAC
65 GGAAG--CTTGACAGAAAATAAAAAATAATTGCACAACGATTTAGAGTGGTTCGACTTTATCAAC
20549 CAAA
128 CAAA
20553 GT
1 GT
20555 CTACGTCCAC
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
130 13 0.11
131 102 0.86
132 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (131 bp):
GTGTTGAGTCAATCGATCGGACGAAATAGCCAAGAGGGAGTGAATTGGCAATTAAAATTTTGGTG
GAAGCTTGACAGAAAATAAAAAATAATTGCACAACGATTTAGAGTGGTTCGACTTTATCAACCAA
A
Found at i:23830 original size:19 final size:18
Alignment explanation
Indices: 23802--23841 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
23792 AAAACCAGAA
*
23802 CCCCAGGGGGTATCGATT
1 CCCCAGGGGGAATCGATT
*
23820 CCCCTAGGGGGAATCGGTT
1 CCCC-AGGGGGAATCGATT
23839 CCC
1 CCC
23842 ATTCAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.20
Consensus pattern (18 bp):
CCCCAGGGGGAATCGATT
Found at i:23872 original size:22 final size:23
Alignment explanation
Indices: 23825--23875 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
23815 CGATTCCCCT
23825 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCATTCAA
*
23848 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCATTCAA
23870 AGGGGG
1 AGGGGG
23876 TATTGATTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.20
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCATTCAA
Found at i:30627 original size:44 final size:45
Alignment explanation
Indices: 30560--30660 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 45
30550 GCAACCCAAC
* * **
30560 AGTATCGATA-CTTCTCAAGGAGTATCGATACTACTATGTGTAGT
1 AGTATCGATATCGTCTCAAAGAGTATCGATACTACTATGTAAAGT
30604 AGTATCGATATCGTC-CAAAGAGTATCGATACTACTATGTAAAGT
1 AGTATCGATATCGTCTCAAAGAGTATCGATACTACTATGTAAAGT
30648 AGTATCGATATCG
1 AGTATCGATATCG
30661 GTCATTGTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 49 0.94
45 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (45 bp):
AGTATCGATATCGTCTCAAAGAGTATCGATACTACTATGTAAAGT
Found at i:30651 original size:24 final size:24
Alignment explanation
Indices: 30580--30657 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
30570 CTTCTCAAGG
**
30580 AGTATCGATACTACTATGTGTAGT
1 AGTATCGATACTACTATGTAAAGT
* **
30604 AGTATCGATA-T-C-GTCCAAAG-
1 AGTATCGATACTACTATGTAAAGT
30624 AGTATCGATACTACTATGTAAAGT
1 AGTATCGATACTACTATGTAAAGT
30648 AGTATCGATA
1 AGTATCGATA
30658 TCGGTCATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 10 0.24
21 4 0.10
22 2 0.05
23 6 0.14
24 20 0.48
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (24 bp):
AGTATCGATACTACTATGTAAAGT
Found at i:37702 original size:2 final size:2
Alignment explanation
Indices: 37695--37720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37685 TTATTTCTTT
37695 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
37721 ATACATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46371 original size:21 final size:19
Alignment explanation
Indices: 46300--46390 Score: 65
Period size: 21 Copynumber: 4.4 Consensus size: 19
46290 TATATATATA
* *
46300 TATATATATATATATATTAT
1 TATATATAAAT-TATTTTAT
* * *
46320 ATATATGTATAGTATTATTAT
1 -TATATATAAATTATT-TTAT
46341 TATATCATATATATTATTTTACT
1 TATAT-ATA-A-ATTATTTTA-T
46364 TATTATATAAATTATTTTAT
1 TA-TATATAAATTATTTTAT
46384 TATATAT
1 TATATAT
46391 TTTAAATATC
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.09
20 11 0.19
21 24 0.41
22 4 0.07
23 11 0.19
24 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATATATAAATTATTTTAT
Found at i:46372 original size:2 final size:2
Alignment explanation
Indices: 46275--46354 Score: 96
Period size: 2 Copynumber: 40.5 Consensus size: 2
46265 GAGACCATTT
46275 TA TA TA GTA TA TA TA 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 TA TA TA TA TA TA TA TA
*
46317 TA TA TA TA TG TA TA GTA T- TA T- TA T- TA TA TCA TA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA T
46355 TATTTTACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
1 4 0.06
2 59 0.86
3 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50127 original size:20 final size:20
Alignment explanation
Indices: 50099--50136 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50089 AAAAAGACCG
50099 AGCAAATAGATTAGAAAAAT
1 AGCAAATAGATTAGAAAAAT
*
50119 AGCAGATAGATTAGAAAA
1 AGCAAATAGATTAGAAAA
50137 GGAACAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.18
Consensus pattern (20 bp):
AGCAAATAGATTAGAAAAAT
Found at i:50144 original size:20 final size:20
Alignment explanation
Indices: 50104--50144 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
50094 GACCGAGCAA
* *
50104 ATAGATTAGAAAAATAGCAG
1 ATAGATTAGAAAAAGAACAG
*
50124 ATAGATTAGAAAAGGAACAG
1 ATAGATTAGAAAAAGAACAG
50144 A
1 A
50145 AGAAAGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (20 bp):
ATAGATTAGAAAAAGAACAG
Done.