Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009064.1 Hibiscus syriacus cultivar Beakdansim tig00112487_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: 748991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 4
Found at i:728637 original size:14 final size:14
Alignment explanation
Indices: 728618--728707 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
728608 GTTGAAATGA
728618 AATCGCAACGAGAG
1 AATCGCAACGAGAG
728632 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
728649 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
728665 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
728684 AATCGCAACGAGAG
1 AATCGCAACGAGAG
728698 AATCGCAACG
1 AATCGCAACG
728708 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:728655 original size:33 final size:33
Alignment explanation
Indices: 728611--728724 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
728601 TCTTTTGGTT
728611 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
728643 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
728676 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
728709 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
728725 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 5 0.06
33 72 0.94
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:728656 original size:19 final size:18
Alignment explanation
Indices: 728614--728729 Score: 94
Period size: 19 Copynumber: 6.9 Consensus size: 18
728604 TTTGGTTGAA
728614 ATGAAATCGCAA--CGAG
1 ATGAAATCGCAACGCGAG
728630 A-G-AATCGCAACGCGAG
1 ATGAAATCGCAACGCGAG
728646 ATGACAATCGCAA--CGAG
1 ATGA-AATCGCAACGCGAG
*
728663 A-G-AATCGCAACGCGAA
1 ATGAAATCGCAACGCGAG
728679 ATGAAAATCGCAA--CGAG
1 ATG-AAATCGCAACGCGAG
*
728696 A-G-AATCGCAACGCGAA
1 ATGAAATCGCAACGCGAG
*
728712 ATGAAAATCGCAATGCGA
1 ATG-AAATCGCAACGCGA
728730 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 27
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 16 0.20
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
ATGAAATCGCAACGCGAG
Found at i:728760 original size:14 final size:14
Alignment explanation
Indices: 728741--728795 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
728731 TTTGGTTTCG
728741 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
728755 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
728774 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
728788 CGTTGCGA
1 CGTTGCGA
728796 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:728773 original size:33 final size:33
Alignment explanation
Indices: 728725--728795 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
728715 AAAATCGCAA
**
728725 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
728758 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
728791 TGCGA
1 TGCGA
728796 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:728803 original size:33 final size:33
Alignment explanation
Indices: 728736--728817 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
728726 GCGATTTTGG
***
728736 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
728769 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
728802 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
728818 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:728822 original size:20 final size:20
Alignment explanation
Indices: 728748--728836 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
728738 TCGCGTTGCG
728748 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
728768 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
728781 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
728801 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
728821 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
728837 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:728954 original size:31 final size:32
Alignment explanation
Indices: 728916--728984 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
728906 AATACTAACT
728916 TGAAAATCGCAACG-AGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAAGAATAGCAACGCGAAA
* *
728947 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGA-AGAATAGCAACGCGAAA
728980 TGAAA
1 TGAAA
728985 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 14 0.41
33 20 0.59
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.12
Consensus pattern (32 bp):
TGAAAATCGCAACGAAGAATAGCAACGCGAAA
Found at i:729217 original size:22 final size:22
Alignment explanation
Indices: 729165--729219 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
729155 TGGTTGTGAG
**
729165 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
729187 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
729209 GGATTTCTTCG
1 GGATTTCTTCG
729220 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:729388 original size:20 final size:20
Alignment explanation
Indices: 729363--729536 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
729353 CTTTAAATAT
729363 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
729383 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
729405 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
729424 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
729444 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
729464 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
729484 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
729504 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
729524 CGCGTTGCGATTT
1 CGCGTTGCGATTT
729537 TCATATTCAC
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:729528 original size:60 final size:60
Alignment explanation
Indices: 729365--729555 Score: 247
Period size: 60 Copynumber: 3.2 Consensus size: 60
729355 TTAAATATCG
** *
729365 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
729426 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
* * ** *
729486 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
729546 CGTTGCGATT
1 CGTTGCGATT
729556 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 84 0.76
61 26 0.24
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:729636 original size:20 final size:20
Alignment explanation
Indices: 729611--729662 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
729601 AAGAATCGCG
*
729611 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
729631 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
729651 TTGCGATTCTGG
1 TTGCGATTCTGG
729663 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:734536 original size:14 final size:14
Alignment explanation
Indices: 734517--734579 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
734507 AAAAAAAATA
734517 ATATTTCTGATAAT
1 ATATTTCTGATAAT
734531 ATATTTCCT--TAACT
1 ATATTT-CTGATAA-T
* * *
734545 ATATAT-TAAAAAT
1 ATATTTCTGATAAT
734558 AATATTTCTGATAAT
1 -ATATTTCTGATAAT
734573 ATATTTC
1 ATATTTC
734580 CTTAACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 26 0.68
15 7 0.18
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (14 bp):
ATATTTCTGATAAT
Found at i:734563 original size:42 final size:42
Alignment explanation
Indices: 734510--734596 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
734500 AAATGTTAAA
734510 AAAAATAATATTTCTGATAATATATTTCCTTAACTATATATT
1 AAAAATAATATTTCTGATAATATATTTCCTTAACTATATATT
734552 AAAAATAATATTTCTGATAATATATTTCCTTAACTATATATT
1 AAAAATAATATTTCTGATAATATATTTCCTTAACTATATATT
734594 AAA
1 AAA
734597 CTGTTATATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (42 bp):
AAAAATAATATTTCTGATAATATATTTCCTTAACTATATATT
Found at i:734952 original size:21 final size:19
Alignment explanation
Indices: 734905--734942 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
734895 ATCTATGTCC
734905 AAAGATCTTAGACAATAGT
1 AAAGATCTTAGACAATAGT
734924 AAAGATCTTAGACAATAGT
1 AAAGATCTTAGACAATAGT
734943 GTAATTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
AAAGATCTTAGACAATAGT
Found at i:743392 original size:13 final size:13
Alignment explanation
Indices: 743374--743400 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
743364 AAATTTTGAA
743374 CAGTCTTCATATG
1 CAGTCTTCATATG
743387 CAGTCTTCATATG
1 CAGTCTTCATATG
743400 C
1 C
743401 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Done.