Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003954.1 Hibiscus syriacus cultivar Beakdansim tig00008550_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: 59106
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1080 original size:23 final size:23
Alignment explanation
Indices: 1050--1116 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1040 CTACAGAGGG
1050 AATCGGTTCCCCTTCAAAGGGGA
1 AATCGGTTCCCCTTCAAAGGGGA
*
1073 AATCGGTTCCCCTTC-AAGGGGG
1 AATCGGTTCCCCTTCAAAGGGGA
* * *
1095 TATCGATTCCCCTTCAAGGGGG
1 AATCGGTTCCCCTTCAAAGGGG
1117 TATCGATTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.24
Consensus pattern (23 bp):
AATCGGTTCCCCTTCAAAGGGGA
Found at i:1116 original size:22 final size:22
Alignment explanation
Indices: 1025--1127 Score: 127
Period size: 22 Copynumber: 4.7 Consensus size: 22
1015 CAAAACCTCA
*
1025 GGGGTATCGATTCCCCTAC-AG
1 GGGGTATCGATTCCCCTTCAAG
* * *
1046 AGGGAATCGGTTCCCCTTCAAAG
1 GGGGTATCGATTCCCCTTC-AAG
** *
1069 GGGAAATCGGTTCCCCTTCAAG
1 GGGGTATCGATTCCCCTTCAAG
1091 GGGGTATCGATTCCCCTTCAAG
1 GGGGTATCGATTCCCCTTCAAG
1113 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
1128 TCTACACCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.21
22 37 0.52
23 19 0.27
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.24
Consensus pattern (22 bp):
GGGGTATCGATTCCCCTTCAAG
Found at i:1176 original size:29 final size:27
Alignment explanation
Indices: 1131--1184 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 27
1121 GATTCCCTCT
1131 ACACCAAAACTGATAAAATCTGATTTTAA
1 ACACCAAAACTGAT-AAAT-TGATTTTAA
*
1160 ACACTCAAAA-TGCTAAATTGATTTT
1 ACAC-CAAAACTGATAAATTGATTTT
1185 CTCTAGTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
29 7 0.30
30 5 0.22
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (27 bp):
ACACCAAAACTGATAAATTGATTTTAA
Found at i:4974 original size:22 final size:21
Alignment explanation
Indices: 4934--4973 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4924 GAGTTTATTT
4934 TCATTTTTCAATTTTAAAATA
1 TCATTTTTCAATTTTAAAATA
4955 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4974 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:7059 original size:23 final size:23
Alignment explanation
Indices: 7021--7065 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
7011 TTTTTGGCTT
7021 TAAAATGGTTTGAAA-TATTTTG
1 TAAAATGGTTTGAAATTATTTTG
*
7043 TAAAATTGTTTTGAAATTATTTT
1 TAAAA-TGGTTTGAAATTATTTT
7066 AAGTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (23 bp):
TAAAATGGTTTGAAATTATTTTG
Found at i:13203 original size:20 final size:20
Alignment explanation
Indices: 13163--13201 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
13153 CATTGCAGTA
13163 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
13183 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
13202 GACCTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:30178 original size:27 final size:27
Alignment explanation
Indices: 30096--30178 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
30086 GAAGGTGGAT
30096 AATACTGCGGCTCAGG-TTGCGGAGGAGGAA
1 AATACTGCGGCTC-GGATTGC-GA--AGGAA
* *
30126 AATACTGCGGCTCGGATTGCGGAGGAT
1 AATACTGCGGCTCGGATTGCGAAGGAA
* * * *
30153 AATACTGTGGCTTGGGTTTCGAAGGA
1 AATACTGCGGCTCGGATTGCGAAGGA
30179 GGATAATATC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 25 0.56
29 3 0.07
30 17 0.38
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (27 bp):
AATACTGCGGCTCGGATTGCGAAGGAA
Found at i:30180 original size:30 final size:30
Alignment explanation
Indices: 30086--30186 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 30
30076 ACGATCTTGT
* * *
30086 GAAGGTGGATAATACTGCGGCTCAGGTTGC
1 GAAGGAGGATAATACTGCGGCTTAGGTTTC
* * * *
30116 GGAGGAGGAAAATACTGCGGC-TCGGATT-
1 GAAGGAGGATAATACTGCGGCTTAGGTTTC
* * *
30144 G-CGGAGGATAATACTGTGGCTTGGGTTTC
1 GAAGGAGGATAATACTGCGGCTTAGGTTTC
30173 GAAGGAGGATAATA
1 GAAGGAGGATAATA
30187 TCGTGGGGAT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 16 0.29
28 6 0.11
29 4 0.07
30 29 0.53
ACGTcount: A:0.27, C:0.13, G:0.38, T:0.23
Consensus pattern (30 bp):
GAAGGAGGATAATACTGCGGCTTAGGTTTC
Found at i:32807 original size:18 final size:19
Alignment explanation
Indices: 32765--32808 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
32755 TTTGATTCAC
*
32765 GGAATGAAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
32785 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
32803 GGAATA
1 GGAATA
32809 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:33876 original size:18 final size:19
Alignment explanation
Indices: 33834--33877 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
33824 TTTGATTCAC
*
33834 GGAATGAAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
33854 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
33872 GGAATA
1 GGAATA
33878 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:34945 original size:18 final size:19
Alignment explanation
Indices: 34903--34946 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
34893 TTTGATTCAC
*
34903 GGAATGAAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
34923 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
34941 GGAATA
1 GGAATA
34947 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:45565 original size:27 final size:26
Alignment explanation
Indices: 45500--45586 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 26
45490 TTGTGAAGGT
45500 GGATAATACTGCGGCTCAGGTTGCGGAGGA
1 GGATAATACTGCGGCTC-GGTTGC---GGA
*
45530 GGAAAATACTGCGGCTCGGATTGCGGA
1 GGATAATACTGCGGCTCGG-TTGCGGA
* * *
45557 GGATAATACTGTGGCTTGGGTTGCGAA
1 GGATAATACTGCGGC-TCGGTTGCGGA
45584 GGA
1 GGA
45587 GGATAATATC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 25 0.50
28 3 0.06
29 2 0.04
30 20 0.40
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (26 bp):
GGATAATACTGCGGCTCGGTTGCGGA
Found at i:45588 original size:30 final size:30
Alignment explanation
Indices: 45494--45594 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
45484 ACGATCTTGT
* *
45494 GAAGGTGGATAATACTGCGGCTCAGGTTGC
1 GAAGGAGGATAATACTGCGGCTCGGGTTGC
* * *
45524 GGAGGAGGAAAATACTGCGGCTCGGATTGC
1 GAAGGAGGATAATACTGCGGCTCGGGTTGC
* *
45554 ---GGAGGATAATACTGTGGCTTGGGTTGC
1 GAAGGAGGATAATACTGCGGCTCGGGTTGC
45581 GAAGGAGGATAATA
1 GAAGGAGGATAATA
45595 TCGTGGGGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 23 0.39
30 36 0.61
ACGTcount: A:0.27, C:0.13, G:0.39, T:0.22
Consensus pattern (30 bp):
GAAGGAGGATAATACTGCGGCTCGGGTTGC
Found at i:48202 original size:18 final size:19
Alignment explanation
Indices: 48160--48203 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
48150 TTTGATTCAC
*
48160 GGAATGAAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
48180 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
48198 GGAATA
1 GGAATA
48204 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:57825 original size:21 final size:23
Alignment explanation
Indices: 57780--57838 Score: 86
Period size: 21 Copynumber: 2.6 Consensus size: 23
57770 ACTATACATT
*
57780 GTACCGATACTACTTTAAGTAGTA
1 GTACCGATACTAC-TGAAGTAGTA
57804 GTACCGATACTA-TGAAGT-GTA
1 GTACCGATACTACTGAAGTAGTA
57825 GTACCGATACTACT
1 GTACCGATACTACT
57839 CCTTCAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 15 0.45
22 6 0.18
24 12 0.36
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (23 bp):
GTACCGATACTACTGAAGTAGTA
Done.