Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004471.1 Hibiscus syriacus cultivar Beakdansim tig00009858_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: 150280
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:130082 original size:12 final size:12
Alignment explanation
Indices: 130065--130130 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
130055 TTAGCATAAA
130065 CGGGTATTGGGC
1 CGGGTATTGGGC
*
130077 CGGGTATTGGGT
1 CGGGTATTGGGC
*
130089 CGGGTATTGGGT
1 CGGGTATTGGGC
130101 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
130112 CGGGAATCGGGC
1 CGGGTATTGGGC
130124 CGGGTAT
1 CGGGTAT
130131 ATATATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:130097 original size:24 final size:24
Alignment explanation
Indices: 130065--130130 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
130055 TTAGCATAAA
*
130065 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
130089 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* *
130112 CGGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
130131 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:130252 original size:13 final size:12
Alignment explanation
Indices: 130221--130257 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
130211 TTTTAATATT
*
130221 TATCGGGTCGGG
1 TATCGGGGCGGG
130233 TATCGGGGCGGG
1 TATCGGGGCGGG
130245 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
130258 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:132633 original size:11 final size:12
Alignment explanation
Indices: 132603--132656 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
132593 TTAGTATAAA
132603 CGGGTATTGGGC
1 CGGGTATTGGGC
*
132615 CGGGTATTGGGT
1 CGGGTATTGGGC
132627 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
132638 CGGGAATCGGGC
1 CGGGTATTGGGC
132650 CGGGTAT
1 CGGGTAT
132657 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:132690 original size:23 final size:23
Alignment explanation
Indices: 132654--132728 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
132644 TCGGGCCGGG
132654 TATATATATATATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
* *
132677 TATATATTTTTATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
* * *
132700 TTTAT-TA-ATA-TTATA-TATA
1 TATATATATATATTTAAATTAAA
132719 TATATATATA
1 TATATATATA
132729 AATTATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 7 0.17
20 6 0.14
21 3 0.07
22 1 0.02
23 25 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATATATATATTTAAATTAAA
Found at i:132731 original size:36 final size:33
Alignment explanation
Indices: 132676--132744 Score: 84
Period size: 36 Copynumber: 2.0 Consensus size: 33
132666 TTTAAATTAA
* * *
132676 ATATATATTTTTATTTAAATTAAATTTATTAATATT
1 ATATATATATATATATAAATT--ATTT-TTAATATT
132712 ATATATATATATATATAAATTATTTTTAATATT
1 ATATATATATATATATAAATTATTTTTAATATT
132745 TATCGGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 8 0.27
34 4 0.13
36 18 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATATATATATATATATAAATTATTTTTAATATT
Found at i:132762 original size:12 final size:12
Alignment explanation
Indices: 132745--132783 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
132735 TTTTAATATT
*
132745 TATCGGGTCGGG
1 TATCGGGGCGGG
132757 TATCGGGGCGGG
1 TATCGGGGCGGG
*
132769 TAATCGGGGTGGG
1 T-ATCGGGGCGGG
132782 TA
1 TA
132784 ATCAGGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.13, C:0.13, G:0.51, T:0.23
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:132776 original size:13 final size:13
Alignment explanation
Indices: 132746--132786 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
132736 TTTAATATTT
*
132746 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
132758 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
132771 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
132784 ATC
1 ATC
132787 AGGTAATCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.22
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:133587 original size:14 final size:14
Alignment explanation
Indices: 133569--133627 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
133559 TAAAGGGCTC
*
133569 GTTCGTTCATTTAC
1 GTTCGTTCATTTAT
133583 GTTCG---ATTATAT
1 GTTCGTTCATT-TAT
133595 GTTCGTTCATTTAT
1 GTTCGTTCATTTAT
* *
133609 GATCGTTTATTTAT
1 GTTCGTTCATTTAT
133623 GTTCG
1 GTTCG
133628 AACAGAGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
14 24 0.65
15 3 0.08
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (14 bp):
GTTCGTTCATTTAT
Found at i:133618 original size:26 final size:27
Alignment explanation
Indices: 133569--133627 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
133559 TAAAGGGCTC
*
133569 GTTCGTTCATTTACGTTCGATTA-TAT
1 GTTCGTTCATTTACGATCGATTATTAT
* *
133595 GTTCGTTCATTTATGATCGTTTATTTAT
1 GTTCGTTCATTTACGATCGATTA-TTAT
133623 GTTCG
1 GTTCG
133628 AACAGAGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.71
28 8 0.29
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (27 bp):
GTTCGTTCATTTACGATCGATTATTAT
Found at i:133864 original size:10 final size:10
Alignment explanation
Indices: 133849--133889 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
133839 GTGTTTGTGT
133849 TGTTCGTTTA
1 TGTTCGTTTA
133859 TGTTCGTTTA
1 TGTTCGTTTA
133869 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
133882 TGTTCGTT
1 TGTTCGTT
133890 CATTCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:133875 original size:23 final size:24
Alignment explanation
Indices: 133849--133906 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
133839 GTGTTTGTGT
*
133849 TGTTCGTTTATGTTCGTTTATT-G
1 TGTTCGTTTATGTTCGTTCATTCG
133872 TGTTCGTTTATGTTCGTTCATTCG
1 TGTTCGTTTATGTTCGTTCATTCG
*
133896 TGTTTGTTTAT
1 TGTTCGTTTAT
133907 TTATTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.09, C:0.10, G:0.21, T:0.60
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCATTCG
Found at i:138184 original size:15 final size:15
Alignment explanation
Indices: 138144--138178 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
138134 ACTTCTCTTT
138144 ACAACCC-AAACCCA
1 ACAACCCAAAACCCA
*
138158 ACAACCCAAAACCTA
1 ACAACCCAAAACCCA
138173 ACAACC
1 ACAACC
138179 ATAAACGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (15 bp):
ACAACCCAAAACCCA
Found at i:139940 original size:29 final size:30
Alignment explanation
Indices: 139878--139945 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
139868 TTATATGAAT
* *
139878 TATGGGATAAAGGTATGGAAATGAAATGTT
1 TATGCGATAAAGGTATGGAAATGAAATGTC
* **
139908 TATGTGATAAAGGTATGG-AATGTTATGTC
1 TATGCGATAAAGGTATGGAAATGAAATGTC
139937 TATGCGATA
1 TATGCGATA
139946 TAAATTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGCGATAAAGGTATGGAAATGAAATGTC
Found at i:140843 original size:23 final size:23
Alignment explanation
Indices: 140791--140861 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
140781 GAACATGTTT
*
140791 ATGAACACGTTCATGAACATATAA
1 ATGAACACGTTCGTGAACAT-TAA
*
140815 CA--AACACGTTCGCGAACATTAA
1 -ATGAACACGTTCGTGAACATTAA
** *
140837 ATGAACATATTCGTGAACAATAA
1 ATGAACACGTTCGTGAACATTAA
140860 AT
1 AT
140862 AAACGAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 3 0.08
23 33 0.87
25 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (23 bp):
ATGAACACGTTCGTGAACATTAA
Found at i:142653 original size:1 final size:1
Alignment explanation
Indices: 142649--142674 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
142639 GTAGTGCTAC
142649 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
142675 CCTCAGCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:149070 original size:27 final size:27
Alignment explanation
Indices: 149032--149083 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
149022 AGCTAGAGTG
149032 TGATAATACAGCAAGCAAAAAGAAGGA
1 TGATAATACAGCAAGCAAAAAGAAGGA
*
149059 TGATAATTCAGCAAGCAAAAAGAAG
1 TGATAATACAGCAAGCAAAAAGAAG
149084 TTAAAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.13
Consensus pattern (27 bp):
TGATAATACAGCAAGCAAAAAGAAGGA
Done.