Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008430.1 Hibiscus syriacus cultivar Beakdansim tig00111220_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: 1186098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1161548 original size:2 final size:2
Alignment explanation
Indices: 1161543--1161580 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1161533 GGATAAATTA
1161543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1161581 GTATGTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1168299 original size:22 final size:22
Alignment explanation
Indices: 1168258--1168324 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1168248 CTCGTATAAA
1168258 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1168281 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1168303 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1168325 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1170024 original size:21 final size:21
Alignment explanation
Indices: 1170000--1170044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1169990 TCTTGTTCGT
* *
1170000 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1170021 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1170042 TTG
1 TTG
1170045 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1173209 original size:22 final size:22
Alignment explanation
Indices: 1173168--1173234 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1173158 CTCGTATAAA
1173168 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1173191 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1173213 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1173235 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1174930 original size:21 final size:21
Alignment explanation
Indices: 1174906--1174950 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1174896 TCTTGTTCGT
* *
1174906 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1174927 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1174948 TTG
1 TTG
1174951 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1178408 original size:18 final size:18
Alignment explanation
Indices: 1178385--1178423 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1178375 GGAGCAGCAC
*
1178385 GAGGAACAAGCTCCTCCA
1 GAGGAACAACCTCCTCCA
*
1178403 GAGGAACAACCTCGTCCA
1 GAGGAACAACCTCCTCCA
1178421 GAG
1 GAG
1178424 TATCAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (18 bp):
GAGGAACAACCTCCTCCA
Found at i:1178716 original size:17 final size:16
Alignment explanation
Indices: 1178687--1178752 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1178677 CATTTTAGAT
*
1178687 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
1178703 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
1178719 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
1178736 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
1178752 A
1 A
1178753 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:1179023 original size:25 final size:25
Alignment explanation
Indices: 1178992--1179072 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
1178982 TTAACAAAAG
1178992 GGGGAGAAATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
* *
1179017 GGGGAGAAGTGTT--AGAG--T-AA
1 GGGGAGAAATGTTAAAGTGTTTAAA
1179037 GGGG-G--ATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
*
1179059 GGGGAGAAGTGTTA
1 GGGGAGAAATGTTA
1179073 GAGTAAGGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
17 4 0.09
19 4 0.09
20 6 0.14
21 2 0.05
22 6 0.14
23 4 0.09
25 17 0.40
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.26
Consensus pattern (25 bp):
GGGGAGAAATGTTAAAGTGTTTAAA
Found at i:1179026 original size:17 final size:17
Alignment explanation
Indices: 1179006--1179071 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 17
1178996 AGAAATGTTA
1179006 AAGTGTTTAAAGGGGAG
1 AAGTGTTTAAAGGGGAG
*
1179023 AAGTGTTAGAGTAAGGGGGATG
1 AAGTGTT----TAAAGGGGA-G
1179045 TTAAAGTGTTTAAAGGGGAG
1 ---AAGTGTTTAAAGGGGAG
1179065 AAGTGTT
1 AAGTGTT
1179072 AGAGTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
17 14 0.36
20 1 0.03
21 16 0.41
22 1 0.03
25 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (17 bp):
AAGTGTTTAAAGGGGAG
Found at i:1179052 original size:42 final size:42
Alignment explanation
Indices: 1179000--1179084 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1178990 AGGGGGAGAA
1179000 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1179042 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1179084 A
1 A
1179085 GTAATTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (42 bp):
ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
Found at i:1179062 original size:21 final size:21
Alignment explanation
Indices: 1179000--1179063 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
1178990 AGGGGGAGAA
1179000 ATGTTAAAGTGTTTAAAGGGG
1 ATGTTAAAGTGTTTAAAGGGG
*
1179021 A-G---AAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTT----TAAAGGGG
1179042 ATGTTAAAGTGTTTAAAGGGG
1 ATGTTAAAGTGTTTAAAGGGG
1179063 A
1 A
1179064 GAAGTGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
17 7 0.21
20 1 0.03
21 17 0.52
22 1 0.03
25 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGTTAAAGTGTTTAAAGGGG
Found at i:1179083 original size:21 final size:21
Alignment explanation
Indices: 1179017--1179085 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
1179007 AGTGTTTAAA
1179017 GGGGAGAAGTGTTAGAGTAAG
1 GGGGAGAAGTGTTAGAGTAAG
*
1179038 GGGGATGTTAAAGTGTT----TAAA
1 GGGGA-G---AAGTGTTAGAGTAAG
1179059 GGGGAGAAGTGTTAGAGTAAG
1 GGGGAGAAGTGTTAGAGTAAG
1179080 GGGGAG
1 GGGGAG
1179086 TAATTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
17 7 0.18
20 1 0.03
21 22 0.58
22 1 0.03
25 7 0.18
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (21 bp):
GGGGAGAAGTGTTAGAGTAAG
Found at i:1182931 original size:6 final size:6
Alignment explanation
Indices: 1182890--1182968 Score: 79
Period size: 6 Copynumber: 13.2 Consensus size: 6
1182880 TCCTCTTTAT
* * * * * *
1182890 TTATTT TTATTA ATATTA ATATTA GTA-TA TATATTA TCATTA TTATCA
1 TTATTA TTATTA TTATTA TTATTA TTATTA T-TATTA TTATTA TTATTA
*
1182938 TTATTA TCATTA TTATTA TTATTA TTATTA T
1 TTATTA TTATTA TTATTA TTATTA TTATTA T
1182969 GGTTTTGTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
5 2 0.03
6 56 0.92
7 3 0.05
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (6 bp):
TTATTA
Found at i:1182935 original size:9 final size:9
Alignment explanation
Indices: 1182921--1182968 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
1182911 TTAGTATATA
1182921 TATTATCAT
1 TATTATCAT
1182930 TATTATCAT
1 TATTATCAT
1182939 TATTATCAT
1 TATTATCAT
*
1182948 TATTATTAT
1 TATTATCAT
*
1182957 TATTATTAT
1 TATTATCAT
1182966 TAT
1 TAT
1182969 GGTTTTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATCAT
Done.