Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 9 of 9
Found at i:1495961 original size:30 final size:30
Alignment explanation
Indices: 1495925--1495988 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1495915 GAAGGACCTG
* *
1495925 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1495955 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1495985 TCCA
1 TCCA
1495989 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1496840 original size:64 final size:63
Alignment explanation
Indices: 1496650--1496887 Score: 266
Period size: 64 Copynumber: 3.7 Consensus size: 63
1496640 GCCAATTTCC
* * *
1496650 TCTTTTAATGAAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT
1 TCTTTTAA--AAGG-ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTT
1496715 T
63 T
* * * *
1496716 CCTTATT-AATGAGATGCATCGATGCACT-CCTATGCATCGATGCATTGATTGCATTCGATGTTA
1 TCTT-TTAAAAG-GATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTT-
1496779 T
63 T
* * * * *
1496780 TATTTTAAAAGGATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCT
1 TCTTTTAAAAGGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTT-T
*
1496844 TCTTTTAAAA-GAGTGCATCGATGCACTACCAATGCATCGATGCA
1 TCTTTTAAAAGGA-TGCATCGATGCACTACCTATGCATCGATGCA
1496888 CATTCAAACA
Statistics
Matches: 145, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
63 48 0.33
64 90 0.62
65 1 0.01
66 4 0.03
67 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
TCTTTTAAAAGGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTT
Found at i:1498048 original size:38 final size:38
Alignment explanation
Indices: 1497997--1498092 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
1497987 CTCGTATAAA
* *
1497997 TGTCCCGAAGGACCTATTATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
* *
1498035 TGTCCCGAAGGACCTGTCATCTCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
1498073 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
1498093 ATGTCTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:1498647 original size:35 final size:35
Alignment explanation
Indices: 1498601--1498668 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1498591 TCATTTAGGG
1498601 GGAATCGATACCCCCCAGGGGGAATCTGTTCCCGA
1 GGAATCGATACCCCCCAGGGGGAATCTGTTCCCGA
1498636 GGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1498669 CTGCACATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.18
Consensus pattern (35 bp):
GGAATCGATACCCCCCAGGGGGAATCTGTTCCCGA
Found at i:1498669 original size:20 final size:20
Alignment explanation
Indices: 1498597--1498661 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1498587 TTTTTCATTT
1498597 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
*
1498617 AGGGGGAATCTG-T---TCCC
1 AGGGGGAATC-GATACCCCCC
*
1498634 --GAGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
1498652 AGGGGGAATC
1 AGGGGGAATC
1498662 TGTTCCCCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
14 1 0.03
15 8 0.24
17 3 0.09
18 3 0.09
20 18 0.53
21 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.32, T:0.14
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:1504422 original size:38 final size:38
Alignment explanation
Indices: 1504371--1504466 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
1504361 CTCGTATAAA
* *
1504371 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
* *
1504409 TGTCCCGAAGGACCTGTCATCCCGAATGATGTAATATG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
* *
1504447 TGTCCCGTATGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
1504467 ATGACTTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
Found at i:1504433 original size:17 final size:17
Alignment explanation
Indices: 1504373--1504434 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
1504363 CGTATAAATG
*
1504373 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTGTCA
*
1504390 TCCCGAAGGATGTCATCTGT-G
1 TCCCGAAGGA---C--CTGTCA
1504411 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
1504428 TCCCGAA
1 TCCCGAA
1504435 TGATGTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
16 4 0.11
17 17 0.47
18 1 0.03
20 1 0.03
21 10 0.28
22 3 0.08
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (17 bp):
TCCCGAAGGACCTGTCA
Found at i:1505027 original size:35 final size:36
Alignment explanation
Indices: 1504981--1505051 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
1504971 TTTCATTTAG
*
1504981 GGGGAATCGATACCCCCGA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1505016 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1505052 CCTGCACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.20, C:0.30, G:0.34, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:1509276 original size:20 final size:19
Alignment explanation
Indices: 1509251--1509301 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1509241 ACCTCTACTG
1509251 GAGTATCAATACTCTACCCTT
1 GAGTATCAATAC-CT-CCCTT
*
1509272 G-GTATCGATA-CTCCCTT
1 GAGTATCAATACCTCCCTT
1509289 GAGTATCAATACC
1 GAGTATCAATACC
1509302 AAAAATGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.23
18 10 0.38
19 1 0.04
20 8 0.31
21 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (19 bp):
GAGTATCAATACCTCCCTT
Found at i:1511866 original size:2 final size:2
Alignment explanation
Indices: 1511861--1511894 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1511851 AAAAATTATC
*
1511861 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511895 TACACTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1514077 original size:26 final size:26
Alignment explanation
Indices: 1514048--1514099 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1514038 CGATCGAGAT
*
1514048 TACAAGTCGTCACAAAGGGAGAGTTG
1 TACAAATCGTCACAAAGGGAGAGTTG
*
1514074 TACAAATCGTTACAAAGGGAGAGTTG
1 TACAAATCGTCACAAAGGGAGAGTTG
1514100 CTCAAGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (26 bp):
TACAAATCGTCACAAAGGGAGAGTTG
Found at i:1519092 original size:28 final size:29
Alignment explanation
Indices: 1519035--1519093 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
1519025 ATCACCTTTA
*
1519035 ATCTTAATAGTATTTTTATTCAAAAAATT
1 ATCTTAATAGTATTTTGATTCAAAAAATT
* * *
1519064 ATCTTAATATTA-TTTGATTCGAATAATT
1 ATCTTAATAGTATTTTGATTCAAAAAATT
1519092 AT
1 AT
1519094 AAATCAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (29 bp):
ATCTTAATAGTATTTTGATTCAAAAAATT
Found at i:1520600 original size:20 final size:19
Alignment explanation
Indices: 1520575--1520642 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
1520565 TGACCCTAGG
*
1520575 GTATCGATACTGCAAGTATA
1 GTATCGATACTGTAAGTA-A
*
1520595 GTATCGATACTGTAAGTAG
1 GTATCGATACTGTAAGTAA
*
1520614 GTATCAATACTGTAAGTAAA
1 GTATCGATACTGTAAGT-AA
1520634 GTATCGATA
1 GTATCGATA
1520643 GTTGACCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (19 bp):
GTATCGATACTGTAAGTAA
Found at i:1522738 original size:45 final size:46
Alignment explanation
Indices: 1522611--1522879 Score: 332
Period size: 45 Copynumber: 6.0 Consensus size: 46
1522601 CCATAAGTGG
* * * *
1522611 CACCTTTTATGTCAATAATGCATCGTTATGTATTTTTCATTTATGA
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
* * *
1522657 CACATTTTATGCCAATAATGCACCATTATACA-TTTTCATTTATGG
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
* *
1522702 CACC-TTTATGCCAATAATGTACCGTTATGCATTTTTCATTTATGA
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
* * * *
1522747 CACATTTTCTACCAATAATGCACCGTTATGCA-TTTTCATTTATGA
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
* * * * *
1522792 CACCTTTTTTGCCAATAATGCATCATTTTGTATTTTT-ATTTATGG
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
*
1522837 CACCTTTTATGCTAATAATGCACCATTATGCATTTTT-ATTTAT
1 CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTAT
1522880 TTCAATAACA
Statistics
Matches: 191, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
44 24 0.13
45 113 0.59
46 54 0.28
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.45
Consensus pattern (46 bp):
CACCTTTTATGCCAATAATGCACCATTATGCATTTTTCATTTATGA
Found at i:1522769 original size:90 final size:91
Alignment explanation
Indices: 1522608--1522879 Score: 386
Period size: 90 Copynumber: 3.0 Consensus size: 91
1522598 ATACCATAAG
*
1522608 TGGCACCTTTTATGTCAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAAT
1 TGGCACCTTTTATGCCAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAAT
*
1522673 AATGCACCATTATACATTTTCATTTA
66 AATGCACCATTATGCATTTTCATTTA
* * * * *
1522699 TGGCACC-TTTATGCCAATAATGTACCGTTATGCATTTTTCATTTATGACACATTTTCTACCAAT
1 TGGCACCTTTTATGCCAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAAT
*
1522763 AATGCACCGTTATGCATTTTCATTTA
66 AATGCACCATTATGCATTTTCATTTA
* * * * * * *
1522789 TGACACCTTTTTTGCCAATAATGCATCATTTTGTATTTTT-ATTTATGGCACCTTTTATGCTAAT
1 TGGCACCTTTTATGCCAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAAT
*
1522853 AATGCACCATTATGCATTTTTATTTA
66 AATGCACCATTATGCATTTTCATTTA
1522879 T
1 T
1522880 TTCAATAACA
Statistics
Matches: 158, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
90 125 0.79
91 33 0.21
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (91 bp):
TGGCACCTTTTATGCCAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAAT
AATGCACCATTATGCATTTTCATTTA
Found at i:1522806 original size:135 final size:136
Alignment explanation
Indices: 1522623--1522879 Score: 383
Period size: 135 Copynumber: 1.9 Consensus size: 136
1522613 CCTTTTATGT
* *
1522623 CAATAATGCATCGTTATGTATTTTTCATTTATGACACATTTTATGCCAATAATGCACCATTATAC
1 CAATAATGCACCGTTATGCATTTTTCATTTATGACACATTTTATGCCAATAATGCACCATTATAC
* *
1522688 ATTTTCATTTATGGCACC-TTTATGCCAATAATGTACCGTTATGCATTTTTCATTTATGACACAT
66 ATTTTCATTTATGGCACCTTTTATGCCAATAATGCACCATTATGCATTTTT-ATTTATGACACAT
1522752 TTTCTAC
130 TTTCTAC
* * * * **
1522759 CAATAATGCACCGTTATGCA-TTTTCATTTATGACACCTTTTTTGCCAATAATGCATCATTTTGT
1 CAATAATGCACCGTTATGCATTTTTCATTTATGACACATTTTATGCCAATAATGCACCATTATAC
* *
1522823 ATTTTTATTTATGGCACCTTTTATGCTAATAATGCACCATTATGCATTTTTATTTAT
66 ATTTTCATTTATGGCACCTTTTATGCCAATAATGCACCATTATGCATTTTTATTTAT
1522880 TTCAATAACA
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
135 61 0.56
136 47 0.44
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (136 bp):
CAATAATGCACCGTTATGCATTTTTCATTTATGACACATTTTATGCCAATAATGCACCATTATAC
ATTTTCATTTATGGCACCTTTTATGCCAATAATGCACCATTATGCATTTTTATTTATGACACATT
TTCTAC
Done.