Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002124.1 Hibiscus syriacus cultivar Beakdansim tig00004352_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: 54799
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1601 original size:2 final size:2
Alignment explanation
Indices: 1596--1651 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1586 TCGGAATTGA
1596 AT AT AT AT AT AT AT A- 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
1637 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1652 AGTTTGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6817 original size:22 final size:23
Alignment explanation
Indices: 6785--6833 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
6775 CCACATTCTG
*
6785 CAAATATTTACTA-AACTAACACC
1 CAAATATTTAC-ACAAATAACACC
6808 CAAAT-TTTACACAAATAACACC
1 CAAATATTTACACAAATAACACC
6830 CAAA
1 CAAA
6834 CATAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:19315 original size:23 final size:23
Alignment explanation
Indices: 19268--19315 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19258 AAATTATTAA
*
19268 TTAATATTGTACTATACATTGTT
1 TTAATATTGTACTATACATTATT
* **
19291 TTAATATTTTACTATTTATTATT
1 TTAATATTGTACTATACATTATT
19314 TT
1 TT
19316 GATGTTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAATATTGTACTATACATTATT
Found at i:25234 original size:22 final size:22
Alignment explanation
Indices: 25209--25251 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25199 AACTGAAATC
* *
25209 AACTGGAATCGAAATTAACCCG
1 AACTGAAAGCGAAATTAACCCG
*
25231 AACTGAAAGCGGAATTAACCC
1 AACTGAAAGCGAAATTAACCC
25252 AAACCAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (22 bp):
AACTGAAAGCGAAATTAACCCG
Found at i:25741 original size:19 final size:19
Alignment explanation
Indices: 25690--25743 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
25680 TTTTTAAAAA
*
25690 TTTAATAAAAATATTAACTT
1 TTTAATAAAAA-ATTAAATT
* ***
25710 TATAATTGGAAATTAAATT
1 TTTAATAAAAAATTAAATT
25729 TTTAATAAAAAATTA
1 TTTAATAAAAAATTA
25744 TTTCTTTATT
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (19 bp):
TTTAATAAAAAATTAAATT
Found at i:29665 original size:36 final size:36
Alignment explanation
Indices: 29620--29818 Score: 276
Period size: 36 Copynumber: 5.6 Consensus size: 36
29610 AAGACATACA
* *
29620 TCCTTCCGTTCAACTTGAATCAGAAGTGCCGATACT
1 TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCT
*
29656 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCT
**
29692 TCCTTCCGTTCGACTTGAATTGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCT
* *
29728 TCC-TCCGTTCGACTTGAATCAGAAGAGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCT
* *
29763 TCCCTCCGTTCGACTTGAATC-GAAAGTGACGATGCT
1 TCCTTCCGTTCGACTTGAATCAG-AAGTGCCGATGCT
* *
29799 TCCCTCCGTTCAACTTGAAT
1 TCCTTCCGTTCGACTTGAAT
29819 TGATGCAAAC
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
35 32 0.21
36 118 0.79
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCT
Found at i:29774 original size:71 final size:71
Alignment explanation
Indices: 29624--29818 Score: 273
Period size: 71 Copynumber: 2.7 Consensus size: 71
29614 CATACATCCT
* * * * *
29624 TCCGTTCAACTTGAATCAGAAGTGCCGATACTTCCTTCCGTTCGACTTGAATCGGAAGTGCCGAT
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCC-TCCGTTCGACTTGAATCAGAAGAGCCGAT
*
29689 GCTTCCT
65 GCTTCCC
* *
29696 TCCGTTCGACTTGAATTGGAAGTGCCGATGCTTCCTCCGTTCGACTTGAATCAGAAGAGTCGATG
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTCCGTTCGACTTGAATCAGAAGAGCCGATG
29761 CTTCCC
66 CTTCCC
* * *
29767 TCCGTTCGACTTGAATCGAAAGTGACGATGCTTCCCTCCGTTCAACTTGAAT
1 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTT-CCTCCGTTCGACTTGAAT
29819 TGATGCAAAC
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
71 62 0.56
72 48 0.44
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (71 bp):
TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTCCGTTCGACTTGAATCAGAAGAGCCGATG
CTTCCC
Found at i:29815 original size:107 final size:107
Alignment explanation
Indices: 29624--29820 Score: 313
Period size: 107 Copynumber: 1.8 Consensus size: 107
29614 CATACATCCT
* * * *
29624 TCCGTTCAACTTGAATCAGAAGTGCCGATACTTCCTTCCGTTCGACTTGAATCGGAAGTGCCGAT
1 TCCGTTCAACTTGAATCAGAAGAGCCGATACTTCCCTCCGTTCGACTTGAATCGAAAGTGACGAT
* *
29689 GCTTCCTTCCGTTCGACTTGAATTGGAAGTGCCGATGCTTCC
66 GCTTCCCTCCGTTCAACTTGAATTGGAAGTGCCGATGCTTCC
* * *
29731 TCCGTTCGACTTGAATCAGAAGAGTCGATGCTTCCCTCCGTTCGACTTGAATCGAAAGTGACGAT
1 TCCGTTCAACTTGAATCAGAAGAGCCGATACTTCCCTCCGTTCGACTTGAATCGAAAGTGACGAT
29796 GCTTCCCTCCGTTCAACTTGAATTG
66 GCTTCCCTCCGTTCAACTTGAATTG
29821 ATGCAAACTT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 81 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (107 bp):
TCCGTTCAACTTGAATCAGAAGAGCCGATACTTCCCTCCGTTCGACTTGAATCGAAAGTGACGAT
GCTTCCCTCCGTTCAACTTGAATTGGAAGTGCCGATGCTTCC
Found at i:32962 original size:10 final size:10
Alignment explanation
Indices: 32947--32973 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
32937 GAAAATGTAA
32947 AGAGGAACCG
1 AGAGGAACCG
32957 AGAGGAACCG
1 AGAGGAACCG
32967 AGAGGAA
1 AGAGGAA
32974 ACCTTTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.41, T:0.00
Consensus pattern (10 bp):
AGAGGAACCG
Found at i:51737 original size:23 final size:24
Alignment explanation
Indices: 51711--51758 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
51701 ATGCTTTGGA
51711 CAAGGACA-TTAGTTGACTAAGCT
1 CAAGGACATTTAGTTGACTAAGCT
51734 CAAGGACATTTAGTTGACTAAGCT
1 CAAGGACATTTAGTTGACTAAGCT
51758 C
1 C
51759 GGGAACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAGGACATTTAGTTGACTAAGCT
Found at i:54103 original size:26 final size:27
Alignment explanation
Indices: 54074--54130 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
54064 TTCACACCTA
54074 AATTAATTTGATGTCA-TGCTTACATC
1 AATTAATTTGATGTCATTGCTTACATC
**
54100 AATTGTTTTGATGTCATTGCTTACATC
1 AATTAATTTGATGTCATTGCTTACATC
54127 AATT
1 AATT
54131 TAGTTAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (27 bp):
AATTAATTTGATGTCATTGCTTACATC
Found at i:54128 original size:27 final size:26
Alignment explanation
Indices: 54080--54130 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
54070 CCTAAATTAA
54080 TTTGATGTCATGCTTACATCAATTGT
1 TTTGATGTCATGCTTACATCAATTGT
54106 TTTGATGTCATTGCTTACATCAATT
1 TTTGATGTCA-TGCTTACATCAATT
54131 TAGTTAGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (26 bp):
TTTGATGTCATGCTTACATCAATTGT
Done.