Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001029.1 Hibiscus syriacus cultivar Beakdansim tig00002049_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: 50412
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9129 original size:173 final size:175
Alignment explanation
Indices: 8563--9184 Score: 690
Period size: 177 Copynumber: 3.5 Consensus size: 175
8553 CACTATTGTC
* * * * * * *
8563 GTTTATCTGTCCACCTTCAGTATCCAACTGCTTCTCATCCTTCTTAGACTCGTCCAATTTACTCT
1 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCATCCAACTTACTCT
* * * *
8628 CTTCAGTGAT---CTTGTTTTCTTGTGTATTTAAGTTGCCAGTGCCATCATCTTTAGCTAGACTC
66 CTTCAGTGTTCCCCTTGTTTTCTTGTG---TGAAGTTGCCAGTGCCACCATCTTTAGC-ACACTC
* * *
8690 ACATTTGAGTCCCCTTTCCTGTCTTCCTTGGATAAATTCTC-GC-CACTGTT
127 ACATTTGAGTCCCCTATCCT-TCATCC-TGG-TAAATTCTCACCACACTGTT
* * *
8740 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCTTTCTTGGACTCATCCGACTTACTCC
1 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCATCCAACTTACTCT
* *
8805 CTTCAGTGTTCCCCTTGTTTTCTTGTGTGTTTGAGTTGTCAGTGCCACCATC-TTAGTCACACTC
66 CTTCAGTGTTCCCCTTGTTTTCTTGTGTG---AAGTTGCCAGTGCCACCATCTTTAG-CACACTC
* * * * *
8869 ACGTTCGAATCCCCTATCCTTGCATCCTTGAGTAAATTCTCATCACCATTGTT
127 ACATTTGAGTCCCCTATCCTT-CATCC-TG-GTAAATTCTCACCA-CACTGTT
* *
8922 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCTTTC-TGGACTCATCCGACTTACTCT
1 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCATCCAACTTACTCT
* * *
8986 CTTCAGTGTTTCCCTTGTTTTCTTGTGTGAAGTTGCCAGTGCCACCATCTTTAGCCCTATTCACA
66 CTTCAGTGTTCCCCTTGTTTTCTTGTGTGAAGTTGCCAGTGCCACCATCTTTAGCAC-ACTCACA
9051 TTTGAGTCCCCTATCC-TC-T-C-GGCTAAATTCTCACCATCACTGTT
130 TTTGAGTCCCCTATCCTTCATCCTGG-TAAATTCTCACCA-CACTGTT
* * * *
9095 GTTTGTCTGTCCAGCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCAACCAACTGACTGT
1 GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCATCCAACTTACTCT
* *
9160 CTTCAGTATTCCCCCTGTTTTCTTG
66 CTTCAGTGTTCCCCTTGTTTTCTTG
9185 CGTACTTAAG
Statistics
Matches: 385, Mismatches: 44, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
172 1 0.00
173 60 0.16
174 39 0.10
175 1 0.00
176 1 0.00
177 66 0.17
178 22 0.06
179 64 0.17
180 34 0.09
181 48 0.12
182 49 0.13
ACGTcount: A:0.17, C:0.29, G:0.14, T:0.40
Consensus pattern (175 bp):
GTTTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTGGACTCATCCAACTTACTCT
CTTCAGTGTTCCCCTTGTTTTCTTGTGTGAAGTTGCCAGTGCCACCATCTTTAGCACACTCACAT
TTGAGTCCCCTATCCTTCATCCTGGTAAATTCTCACCACACTGTT
Found at i:15111 original size:2 final size:2
Alignment explanation
Indices: 15104--15203 Score: 168
Period size: 2 Copynumber: 50.5 Consensus size: 2
15094 AGCATCACCG
15104 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
15145 TA GTA TA TA TA TC 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
15187 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
15204 CTTTTGATAT
Statistics
Matches: 93, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
1 2 0.02
2 89 0.96
3 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18040 original size:50 final size:50
Alignment explanation
Indices: 17971--18096 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
17961 TTAGCAAGAA
* * * *
17971 AGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCTCCACGTGGATAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGACGCCACGTGGATAT
* ** * * *
18021 AGCGTGCCCCCTGCCCCGCGATATACGGTGATCTGACGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGACGCCACGTGGATAT
* *
18071 AGCGCCCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
18097 CTGGATATCT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.17, C:0.37, G:0.26, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGACGCCACGTGGATAT
Found at i:18506 original size:111 final size:111
Alignment explanation
Indices: 18365--18592 Score: 402
Period size: 111 Copynumber: 2.1 Consensus size: 111
18355 CTCGGATGGA
* * * *
18365 AATTATATATCTCTACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTAT
1 AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
* *
18430 TAGTAATATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAG
66 TAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAG
18476 AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
1 AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
18541 TAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAG
66 TAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAG
18587 AATTAA
1 AATTAA
18593 TTTTTATAAT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
AATTAAATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAT
TAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAG
Found at i:22712 original size:40 final size:41
Alignment explanation
Indices: 22627--22727 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 41
22617 GCCCCTGATT
* * *
22627 CGCGCTATACCACAATGTGGCGTATAGCGCGTATCAGGGGG
1 CGCGCTATACCACCACGTGGCGTATAACGCGTATCAGGGGG
22668 -GCGCTATACC-CCACGTGGCGTATAACGCGGT-TCAGGGGG
1 CGCGCTATACCACCACGTGGCGTATAACGC-GTATCAGGGGG
* *
22707 CGCGCT-TTCCTCCACGTGGCG
1 CGCGCTATACCACCACGTGGCG
22728 CCAAATCAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
39 26 0.49
40 27 0.51
ACGTcount: A:0.17, C:0.30, G:0.34, T:0.20
Consensus pattern (41 bp):
CGCGCTATACCACCACGTGGCGTATAACGCGTATCAGGGGG
Found at i:28869 original size:32 final size:31
Alignment explanation
Indices: 28794--28869 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 31
28784 ATTGAAGTTT
*
28794 AATTT-TTTTAATTTAATTACTTAACTTTCA
1 AATTTATTTTAATTTAATCACTTAACTTTCA
** * *
28824 AA-TTACTCCTAATTTAATCATTCTATCTTTCA
1 AATTTA-TTTTAATTTAATCACT-TAACTTTCA
28856 AATTTATTTTAATT
1 AATTTATTTTAATT
28870 ATATATTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 12 0.34
32 16 0.46
33 3 0.09
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTTATTTTAATTTAATCACTTAACTTTCA
Found at i:29192 original size:40 final size:39
Alignment explanation
Indices: 29137--29216 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 39
29127 ACGAAATAAA
*
29137 ACCGATACTTTAGGTACTAAATGTGTAGTTTACCCTTCTT
1 ACCGATACTTTAGGTACTAAATGT-TAGTCTACCCTTCTT
*
29177 ACCGATATTTTAGGTACTAAATGTTAGTCTACCCTTCTT
1 ACCGATACTTTAGGTACTAAATGTTAGTCTACCCTTCTT
29216 A
1 A
29217 TATTTAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (39 bp):
ACCGATACTTTAGGTACTAAATGTTAGTCTACCCTTCTT
Found at i:29757 original size:29 final size:30
Alignment explanation
Indices: 29723--29781 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29713 GTACCAAAAA
*
29723 TATAATTTT-AT-TTTTATTTTTTATATACT
1 TATAATTTTAATATTTT-TTGTTTATATACT
29752 TATAATTTTAATATTTTTTGTTTATATACT
1 TATAATTTTAATATTTTTTGTTTATATACT
29782 AAAATTTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.33
30 14 0.52
31 4 0.15
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (30 bp):
TATAATTTTAATATTTTTTGTTTATATACT
Found at i:29787 original size:29 final size:29
Alignment explanation
Indices: 29726--29788 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29716 CCAAAAATAT
* *
29726 AATTTTATTTTTATTTTTTATATACTTAT
1 AATTTTATTTTTATTGTTTATATACTTAA
29755 AATTTTAATATTTT-TTGTTTATATAC-TAA
1 AATTTT-AT-TTTTATTGTTTATATACTTAA
29784 AATTT
1 AATTT
29789 GTCAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.43
30 13 0.43
31 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (29 bp):
AATTTTATTTTTATTGTTTATATACTTAA
Found at i:30966 original size:58 final size:59
Alignment explanation
Indices: 30898--31057 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 59
30888 AATTTAAATC
* * *
30898 CTAAATTAATCTTTAAACTTTTGAATATTTTAATTTTATCCCCAACCTATGA-CTCATTT
1 CTAAATTAATCTTTAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACCTC-TTT
* * * * * *
30957 -TAAATTAATCCTTAAATTTTTTAACATTCTAATTTCATCCCTAAACTATGACCCTCTTT
1 CTAAATTAATCTTTAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGA-CCTCTTT
* * *
31016 CTAAACTAAT-TCTCAAACTTTTAAATATTTCAATTTCATCCC
1 CTAAATTAATCT-TTAAACTTTTAAATATTTTAATTTCATCCC
31058 AAATTAATCC
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 43 0.53
59 3 0.04
60 35 0.43
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (59 bp):
CTAAATTAATCTTTAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACCTCTTT
Found at i:31055 original size:60 final size:58
Alignment explanation
Indices: 30912--31057 Score: 143
Period size: 60 Copynumber: 2.5 Consensus size: 58
30902 ATTAATCTTT
* * * * * *
30912 AAACTTTTGAATATTTTAATTTTATCCCCAACCTATGACTCATTTTAAATTAATCCTT
1 AAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTCATTTTAAACTAATCCTC
* * * * *
30970 AAATTTTTTAACA-TTCTAATTTCATCCCTAAACTATGACCCTC-TTTCTAAACTAATTCTC
1 AAACTTTTAAATATTTC-AATTTCATCCCCAAACTATGA--CTCATTT-TAAACTAATCCTC
31030 AAACTTTTAAATATTTCAATTTCATCCC
1 AAACTTTTAAATATTTCAATTTCATCCC
31058 AAATTAATCC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
57 2 0.03
58 28 0.40
59 3 0.04
60 34 0.49
61 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (58 bp):
AAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTCATTTTAAACTAATCCTC
Found at i:38380 original size:2 final size:2
Alignment explanation
Indices: 38375--38412 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
38365 TTCATTTGTG
38375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
38413 GAGTCGAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42199 original size:21 final size:21
Alignment explanation
Indices: 42173--42214 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42163 ATTTGAATAT
42173 TATGAAGGGGTA-TCGATTCCC
1 TATGAAGGGGTACT-GATTCCC
42194 TATGAAGGGGTACTGATTCCC
1 TATGAAGGGGTACTGATTCCC
42215 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACTGATTCCC
Found at i:49370 original size:29 final size:29
Alignment explanation
Indices: 49336--49394 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
49326 CCTAAATTAA
49336 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
49365 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
49394 T
1 T
49395 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Done.