Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004858.1 Hibiscus syriacus cultivar Beakdansim tig00010956_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: 42528
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2171 original size:20 final size:20
Alignment explanation
Indices: 2146--2199 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2136 TGTGGCAGGC
2146 AGACATCTAAAACTCATGTT
1 AGACATCTAAAACTCATGTT
2166 AGACATCTAAAACTCATGTT
1 AGACATCTAAAACTCATGTT
* *
2186 AGATATTTAAAACT
1 AGACATCTAAAACT
2200 AATGCTCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (20 bp):
AGACATCTAAAACTCATGTT
Found at i:2759 original size:26 final size:27
Alignment explanation
Indices: 2726--2782 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
2716 GTTATGAACA
2726 ATAAATGTTATGAATATTATTGAT-TC
1 ATAAATGTTATGAATATTATTGATGTC
2752 ATAAATGTTATGAATATTATTGATGTC
1 ATAAATGTTATGAATATTATTGATGTC
2779 ATAA
1 ATAA
2783 TCTTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (27 bp):
ATAAATGTTATGAATATTATTGATGTC
Found at i:6721 original size:18 final size:18
Alignment explanation
Indices: 6698--6732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6688 AGGAAAAGGC
*
6698 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
6716 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
6733 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:6917 original size:20 final size:20
Alignment explanation
Indices: 6892--7002 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
6882 TTACACATTC
*
6892 ATTTGAATATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
*
6912 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
6931 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
6946 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
6966 ACTTGATTATCGCAACGGGA
1 ATTTGAATATCGCAACGCGA
*
6986 ATTT-AACTATCACAACG
1 ATTTGAA-TATCGCAACG
7003 AGAAAATTGC
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.14
15 3 0.04
19 4 0.05
20 57 0.77
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:6947 original size:34 final size:34
Alignment explanation
Indices: 6900--7035 Score: 121
Period size: 34 Copynumber: 3.8 Consensus size: 34
6890 TCATTTGAAT
*
6900 ATCGCAACACGAATTTGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
*
6934 ATCGCAACGCGAATTTGACTATCGCAACGCGAACTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
* * *
6974 ATCGCAACGGGAATTTAACTATCACAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
* * * *
7008 ATTGCAAAGCGTATTAGACTATCGCAAC
1 ATCGCAACGCGAATTTGACTATCGCAAC
7036 ACGAATTGAC
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
34 50 0.61
35 3 0.04
38 1 0.01
39 2 0.02
40 26 0.32
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:7028 original size:74 final size:73
Alignment explanation
Indices: 6894--7044 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 73
6884 ACACATTCAT
* * * *
6894 TTGAATATCGCAACACGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATCGC
1 TTGAATATCGCAACACGAATTTAACTATCACAACGCAAAAATCGCAAAGCGAATTAGACTATCGC
*
6959 AACGCGAA
66 AACACGAA
* ** * *
6967 CTTGATTATCGCAACGGGAATTTAACTATCACAACG-AGAAAATTGCAAAGCGTATTAGACTATC
1 -TTGAATATCGCAACACGAATTTAACTATCACAACGCA-AAAATCGCAAAGCGAATTAGACTATC
7031 GCAACACGAA
64 GCAACACGAA
7041 TTGA
1 TTGA
7045 CTTTCGCTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
73 5 0.08
74 61 0.92
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (73 bp):
TTGAATATCGCAACACGAATTTAACTATCACAACGCAAAAATCGCAAAGCGAATTAGACTATCGC
AACACGAA
Found at i:7070 original size:20 final size:20
Alignment explanation
Indices: 7045--7083 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7035 CACGAATTGA
*
7045 CTTTCGCTTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
7065 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
7084 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.23, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:7096 original size:20 final size:20
Alignment explanation
Indices: 7053--7098 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
7043 GACTTTCGCT
*
7053 TTGCGATTTTGGCTTTCGCA
1 TTGCGATTTTGGCTTTAGCA
*
7073 TTGCGATTTTGAG-TTTAGCG
1 TTGCGATTTTG-GCTTTAGCA
7093 TTGCGA
1 TTGCGA
7099 AAGTTTACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTGGCTTTAGCA
Found at i:8969 original size:13 final size:13
Alignment explanation
Indices: 8951--8984 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
8941 TCTCTTCGTT
8951 TCTTTTTCCCTTC
1 TCTTTTTCCCTTC
8964 TC-TTTTCCCTTC
1 TCTTTTTCCCTTC
8976 TCTTTTTCC
1 TCTTTTTCC
8985 TTCACCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTTTTTCCCTTC
Found at i:8971 original size:12 final size:12
Alignment explanation
Indices: 8950--8987 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
8940 TTCTCTTCGT
8950 TTCT-TTTTCCC
1 TTCTCTTTTCCC
8961 TTCTCTTTTCCC
1 TTCTCTTTTCCC
*
8973 TTCTCTTTTTCC
1 TTCTCTTTTCCC
8985 TTC
1 TTC
8988 ACCCTCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTCTTTTCCC
Found at i:11343 original size:19 final size:20
Alignment explanation
Indices: 11319--11366 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
11309 AACAATTTTC
*
11319 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* * *
11338 TTTTGACAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
11358 TTTTGAAAA
1 TTTTGAAAA
11367 AGGATTTAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:12163 original size:20 final size:20
Alignment explanation
Indices: 12140--12177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12130 ATATGTACTT
*
12140 AATTTTAACAATTAGTATCA
1 AATTTAAACAATTAGTATCA
*
12160 AATTTAAACAATTGGTAT
1 AATTTAAACAATTAGTAT
12178 TGCATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTTAAACAATTAGTATCA
Found at i:12546 original size:21 final size:18
Alignment explanation
Indices: 12503--12560 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
12493 CAACAATTGG
12503 TAACAATTGATATATTTT
1 TAACAATTGATATATTTT
*
12521 TAACAATTGATGTCATTTTGT
1 TAACAATTGATAT-A-TTT-T
* *
12542 TAACAATCGATATCTTTT
1 TAACAATTGATATATTTT
12560 T
1 T
12561 CATTAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 14 0.42
19 4 0.12
20 3 0.09
21 12 0.36
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (18 bp):
TAACAATTGATATATTTT
Found at i:25751 original size:17 final size:17
Alignment explanation
Indices: 25726--25760 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25716 TGATACGTTG
25726 TCTGAATTCTGTTCTGA
1 TCTGAATTCTGTTCTGA
*
25743 TCTGGATTCTGTTCTGA
1 TCTGAATTCTGTTCTGA
25760 T
1 T
25761 ATCTGATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (17 bp):
TCTGAATTCTGTTCTGA
Found at i:25765 original size:24 final size:24
Alignment explanation
Indices: 25738--25793 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
25728 TGAATTCTGT
* *
25738 TCTGATCTGGATTCTGTTCTGATA
1 TCTGATATGAATTCTGTTCTGATA
* *
25762 TCTGATATGAATTCTGTTTTGATT
1 TCTGATATGAATTCTGTTCTGATA
25786 TCTGATAT
1 TCTGATAT
25794 CTCCATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (24 bp):
TCTGATATGAATTCTGTTCTGATA
Found at i:40491 original size:2 final size:2
Alignment explanation
Indices: 40484--40519 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40474 TACGTAATGT
*
40484 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40520 TAGAAGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42406 original size:9 final size:8
Alignment explanation
Indices: 42392--42461 Score: 58
Period size: 9 Copynumber: 8.8 Consensus size: 8
42382 CCAAAGATGT
42392 CAACTTTG
1 CAACTTTG
42400 CCAACTTT-
1 -CAACTTTG
*
42408 CAATTTTG
1 CAACTTTG
42416 CCAACTTT-
1 -CAACTTTG
42424 CAACTTTG
1 CAACTTTG
42432 TCAACTTT-
1 -CAACTTTG
*
42440 CAATTTTG
1 CAACTTTG
42448 CCAACTTT-
1 -CAACTTTG
42456 CAACTT
1 CAACTT
42462 GCTAATATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
7 25 0.49
9 26 0.51
ACGTcount: A:0.26, C:0.27, G:0.06, T:0.41
Consensus pattern (8 bp):
CAACTTTG
Found at i:42415 original size:16 final size:16
Alignment explanation
Indices: 42391--42461 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
42381 ACCAAAGATG
42391 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
42407 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
42423 TCAACTTTGTCAACTT
1 TCAACTTTGCCAACTT
*
42439 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
42455 TCAACTT
1 TCAACTT
42462 GCTAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:42437 original size:32 final size:32
Alignment explanation
Indices: 42391--42461 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
42381 ACCAAAGATG
42391 TCAACTTTGCCAACTTTCAATTTTGCCAACTT
1 TCAACTTTGCCAACTTTCAATTTTGCCAACTT
*
42423 TCAACTTTGTCAACTTTCAATTTTGCCAACTT
1 TCAACTTTGCCAACTTTCAATTTTGCCAACTT
42455 TCAACTT
1 TCAACTT
42462 GCTAATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (32 bp):
TCAACTTTGCCAACTTTCAATTTTGCCAACTT
Done.