Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008633.1 Hibiscus syriacus cultivar Beakdansim tig00111605_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: 14934
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6919 original size:62 final size:61
Alignment explanation
Indices: 6853--6985 Score: 144
Period size: 62 Copynumber: 2.2 Consensus size: 61
6843 AACGCAAACT
* *
6853 TCCAAATTCGCAATGCGA-ACTCCGACTATCGCATTGCGA-TTTACATATTCGCATTGCGATAG
1 TCCAAATTCGCAATGCGATACTCCAACT-TCGCATTGCGATTTTACAAATTCG--TTGCGATAG
* * * * * *
6915 TCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAG
1 TCCAAATTCGCAATGCGATACTCCAACTTCGCATTGCGATTTTACAAATTCGTTGCGATAG
*
6976 TCGAAATTCG
1 TCCAAATTCG
6986 TGTTGCGATA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
61 17 0.29
62 26 0.44
63 16 0.27
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (61 bp):
TCCAAATTCGCAATGCGATACTCCAACTTCGCATTGCGATTTTACAAATTCGTTGCGATAG
Found at i:6926 original size:21 final size:21
Alignment explanation
Indices: 6853--7008 Score: 122
Period size: 21 Copynumber: 7.6 Consensus size: 21
6843 AACGCAAACT
* *
6853 TCCAAATTCGCAATGCGA-AC
1 TCCAAATTCGCATTGCGATAG
* * *
6873 TCCGACTATCGCATTGCGAT-T
1 TCCAAAT-TCGCATTGCGATAG
* *
6894 TACATATTCGCATTGCGATAG
1 TCCAAATTCGCATTGCGATAG
*
6915 TCCAAGTTCGCATTGCGATAG
1 TCCAAATTCGCATTGCGATAG
* * **
6936 TCCAAGTTCGCGTTGCGATTT
1 TCCAAATTCGCATTGCGATAG
*
6957 TTCAAATTCG--TTGCGATAG
1 TCCAAATTCGCATTGCGATAG
* **
6976 TCGAAATTCGTGTTGCGATAG
1 TCCAAATTCGCATTGCGATAG
*
6997 TCCAAAATCGCA
1 TCCAAATTCGCA
7009 ACGACTGGTG
Statistics
Matches: 106, Mismatches: 25, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.14
20 17 0.16
21 74 0.70
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
TCCAAATTCGCATTGCGATAG
Found at i:7720 original size:26 final size:26
Alignment explanation
Indices: 7684--7735 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
7674 GATTTTGGAC
*
7684 TATCGCAACGAATTTGGAATAAATCG
1 TATCGCAACGAACTTGGAATAAATCG
7710 TATCGCAACGAACTTGGAATAAATCG
1 TATCGCAACGAACTTGGAATAAATCG
7736 CAACGCGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (26 bp):
TATCGCAACGAACTTGGAATAAATCG
Found at i:7737 original size:21 final size:21
Alignment explanation
Indices: 7711--7845 Score: 152
Period size: 21 Copynumber: 6.4 Consensus size: 21
7701 AATAAATCGT
7711 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
7732 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
7753 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
7774 ATTGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
7795 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
7816 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
7837 ATCGCAACG
1 ATCGCAACG
7846 CGAACTTCGA
Statistics
Matches: 97, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.21
21 56 0.58
23 21 0.22
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:7757 original size:42 final size:42
Alignment explanation
Indices: 7710--7824 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
7700 GAATAAATCG
7710 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
* *
7752 TATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTGGAC
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
*
7794 TATCGCAACGAATTTGGAATAAATCGCAACG
1 TATCGCAACGAACTTGGAATAAATCGCAACG
7825 AATTTGGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
Found at i:7841 original size:42 final size:41
Alignment explanation
Indices: 7710--7845 Score: 175
Period size: 42 Copynumber: 3.2 Consensus size: 41
7700 GAATAAATCG
* *
7710 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTGGAA
* *
7752 TATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTGGAC
1 TATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTGGAA
* *
7794 TATCGCAACGAATTTGGAATAAATCGCAA-CGAATTTGGAA
1 TATCGCAACGAACTTGGAATAAATCGCAACCGAACTTGGAA
7834 TAAATCGCAACG
1 T--ATCGCAACG
7846 CGAACTTCGA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 10 0.12
42 76 0.88
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
TATCGCAACGAACTTGGAATAAATCGCAACCGAACTTGGAA
Found at i:7861 original size:21 final size:21
Alignment explanation
Indices: 7711--7870 Score: 127
Period size: 21 Copynumber: 7.6 Consensus size: 21
7701 AATAAATCGT
7711 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
7732 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
7753 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
7774 ATTGCAACGCGAACTTGGACT-
1 ATCGCAA-GCGAACTTGGAATA
*
7795 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
*
7816 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
7837 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
7858 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
7871 TATGTAAATC
Statistics
Matches: 116, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
19 20 0.17
21 66 0.57
23 30 0.26
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAAGCGAACTTGGAATA
Found at i:14140 original size:92 final size:91
Alignment explanation
Indices: 13981--14150 Score: 236
Period size: 92 Copynumber: 1.8 Consensus size: 91
13971 TATTTTTTTT
* * * *
13981 TTTGTAATTTTTTTGATTTTTTTAAATTCAAGTAGATTAAATTGTAATATAGATAAAAATACATT
1 TTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAG---AAATTGCAAGATAAATAAAAATACATT
14046 GAAATTAGATAAATAAACATACTAATTTC
63 GAAATTAGATAAATAAACATACTAATTTC
14075 TTTGTAATTTTTCTGATTTTTTATTTAAATTCAAGTAG-AATTGCAAGATAAAT-AAAATACATT
1 TTTGTAATTTTTCTGA--TTTT-TTTAAATTCAAGTAGAAATTGCAAGATAAATAAAAATACATT
14138 GAAATTAGATAAA
63 GAAATTAGATAAA
14151 CAAATATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
92 23 0.33
93 12 0.17
94 15 0.22
96 4 0.06
97 15 0.22
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (91 bp):
TTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGAAATTGCAAGATAAATAAAAATACATTGAA
ATTAGATAAATAAACATACTAATTTC
Done.