Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000958.1 Hibiscus syriacus cultivar Beakdansim tig00001914_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: 36597
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:130 original size:15 final size:15
Alignment explanation
Indices: 110--167 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
100 CGTTCGTGAA
110 CGTTCGATTATGTTT
1 CGTTCGATTATGTTT
*
125 CGTTCGGTTATGTTT
1 CGTTCGATTATGTTT
*
140 -G-T---TTATGGTT
1 CGTTCGATTATGTTT
150 CGTTCGATTATG-TT
1 CGTTCGATTATGTTT
164 CGTT
1 CGTT
168 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 7 0.19
11 1 0.03
12 1 0.03
13 1 0.03
14 7 0.19
15 19 0.53
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.53
Consensus pattern (15 bp):
CGTTCGATTATGTTT
Found at i:145 original size:25 final size:25
Alignment explanation
Indices: 111--186 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
101 GTTCGTGAAC
* *
111 GTTCGATTATGTTTCGTTCGGTTAT
1 GTTCGTTTATGTTTCGTTCGATTAT
* *
136 GTTTGTTTATGGTTCGTTCGATTAT
1 GTTCGTTTATGTTTCGTTCGATTAT
*
161 GTTCGTTTATG-TTCATTC-ATTAT
1 GTTCGTTTATGTTTCGTTCGATTAT
184 GTT
1 GTT
187 TAACTCATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.18
24 6 0.13
25 31 0.69
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (25 bp):
GTTCGTTTATGTTTCGTTCGATTAT
Found at i:908 original size:10 final size:10
Alignment explanation
Indices: 893--967 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
883 GGGTCTCCAA
893 CGTTTATGTT
1 CGTTTATGTT
903 CGTTTATGTT
1 CGTTTATGTT
913 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
924 ATGTTCGTGTT
1 -CGTTTATGTT
935 CGTTTATGTT
1 CGTTTATGTT
945 CG----TGTT
1 CGTTTATGTT
951 CGTTTATGTT
1 CGTTTATGTT
961 CGTTTAT
1 CGTTTAT
968 TTTTTAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:924 original size:16 final size:16
Alignment explanation
Indices: 899--963 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
889 CCAACGTTTA
899 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
915 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
931 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
947 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
963 T
1 T
964 TTATTTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4247 original size:20 final size:21
Alignment explanation
Indices: 4222--4262 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
4212 TAATTCTGGG
4222 TGTGCATCGATGCACT-TCAA
1 TGTGCATCGATGCACTCTCAA
4242 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
4263 ATAAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:4909 original size:32 final size:32
Alignment explanation
Indices: 4868--4933 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
4858 TATAGGTATA
4868 GTTGGCATGCCAAGAGTCGAGGGTTCTACGTG
1 GTTGGCATGCCAAGAGTCGAGGGTTCTACGTG
4900 GTTGGCATGCCAAGAGTCGAGGGTTCTACGTG
1 GTTGGCATGCCAAGAGTCGAGGGTTCTACGTG
4932 GT
1 GT
4934 CCTTCGGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.38, T:0.26
Consensus pattern (32 bp):
GTTGGCATGCCAAGAGTCGAGGGTTCTACGTG
Found at i:5726 original size:31 final size:31
Alignment explanation
Indices: 5688--5841 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
5678 CCCGAAGGAC
* *
5688 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
5719 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
5750 CAGTCCATATGTTCCGAAAAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5781 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5812 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
5842 CCCTCGACCT
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:6718 original size:20 final size:21
Alignment explanation
Indices: 6689--6732 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
6679 TCTTGTTCGT
*
6689 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6709 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6730 TTG
1 TTG
6733 CCAGAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9715 original size:31 final size:31
Alignment explanation
Indices: 9677--9830 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
9667 TCCCGAGGAC
* *
9677 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
9708 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
9739 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
9770 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
9801 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
9831 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:10711 original size:21 final size:21
Alignment explanation
Indices: 10687--10731 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10677 TTCTGTTCGT
* *
10687 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
10708 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
10729 TTG
1 TTG
10732 CCCAAATCAT
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:14197 original size:68 final size:67
Alignment explanation
Indices: 14070--14198 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 67
14060 TAGAGGTCCA
* * * *** *
14070 ATTTTTTAATATTTGTTATTATGACATACTCTTAAAATTTATTTTTAAATTTTTTTTATTAGGAC
1 ATTTTTCAATACTTGTTATTATGACATACCCTTAAAATTTATTTTTAAACAATTGTTATTAGGAC
14135 TC
66 TC
*
14137 ATTTTTCAATACTTGTTATTATGGA-ACTACCCTTAAAATTTATTTTTCAACAATTGTTATTA
1 ATTTTTCAATACTTGTTATTAT-GACA-TACCCTTAAAATTTATTTTTAAACAATTGTTATTA
14199 CGAACAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
67 21 0.40
68 31 0.60
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTTTCAATACTTGTTATTATGACATACCCTTAAAATTTATTTTTAAACAATTGTTATTAGGAC
TC
Found at i:16514 original size:64 final size:60
Alignment explanation
Indices: 16405--16588 Score: 219
Period size: 62 Copynumber: 2.9 Consensus size: 60
16395 CAAACGTTAC
*
16405 TTCGAATTTTCTTAGTTATATATATATTTACTTGATCTCGAATTATATGATTACGAGTATAT
1 TTCGAATTTTCTTAGTTATATATATATTTACTTGATCTC-AAAT-TATGATTACGAGTATAT
*
16467 TTCGACTTTTCTTAGTTATATGTATATATTTACTTGATCTCAAATTATGATTACGAGATACGGTT
1 TTCGAATTTTCTTAGTTATA--TATATATTTACTTGATCTCAAATTATGATTACGAG-TA----T
16532 AT
59 AT
* *
16534 ATAT-TAATTTTCTTAGTTATATATATATTTACTCGATCTC-AATTATGATTACGAG
1 -T-TCGAATTTTCTTAGTTATATATATATTTACTTGATCTCAAATTATGATTACGAG
16589 ATCGGGTATA
Statistics
Matches: 108, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
62 31 0.29
63 5 0.05
64 19 0.18
65 15 0.14
66 18 0.17
67 3 0.03
68 16 0.15
69 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (60 bp):
TTCGAATTTTCTTAGTTATATATATATTTACTTGATCTCAAATTATGATTACGAGTATAT
Found at i:16618 original size:64 final size:65
Alignment explanation
Indices: 16364--16625 Score: 272
Period size: 64 Copynumber: 4.0 Consensus size: 65
16354 ATTGTGTATG
** *
16364 TTACTCGATCTCGAATTATGATTACGAGATACAAACGT-TACTTCGAATTTTCTTAGTTATATAT
1 TTACTCGATCTCGAATTATGATTACGAGATAC--GGGTATA-TTCG-ACTTTCTTAGTTATATAT
16428 ATAT
62 ATAT
*
16432 TTACTTGATCTCGAATTATATGATTACGAG-TA----TAT-TTCGACTTTTCTTAGTTATATGTA
1 TTACTCGATCTCGAA-T-TATGATTACGAGATACGGGTATATTCGAC-TTTCTTAGTTATA--TA
16491 TATAT
61 TATAT
* * * ** *
16496 TTACTTGATCTCAAATTATGATTACGAGATACGGTTATATATTAATTTTCTTAGTTATATATATA
1 TTACTCGATCTCGAATTATGATTACGAGATACGGGTATAT-TCGACTTTCTTAGTTATATATATA
16561 T
65 T
16562 TTACTCGATCTC-AATTATGATTACGAGAT-CGGGTATAGTTCGACTTTCTTAGTTATATATATA
1 TTACTCGATCTCGAATTATGATTACGAGATACGGGTATA-TTCGACTTTCTTAGTTATATATATA
16625 T
65 T
16626 ATAAAGAATC
Statistics
Matches: 169, Mismatches: 11, Indels: 32
0.80 0.05 0.15
Matches are distributed among these distances:
61 1 0.01
62 29 0.17
63 4 0.02
64 51 0.30
65 18 0.11
66 18 0.11
67 3 0.02
68 28 0.17
69 5 0.03
70 12 0.07
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
TTACTCGATCTCGAATTATGATTACGAGATACGGGTATATTCGACTTTCTTAGTTATATATATAT
Found at i:19107 original size:63 final size:63
Alignment explanation
Indices: 18981--19109 Score: 145
Period size: 63 Copynumber: 2.0 Consensus size: 63
18971 TAGTGCATGC
* * ** * *
18981 CACATAATCATTTTAGGTGACATGACATTTATCATGTCATCATTTTAACAACGTGGTACATGT
1 CACATAATCATTTTAGATGACATGACATGTATCACATCATCATTTTAACAACGTGGAAAATGT
* * *
19044 CACATTATCATTTTAGATGACATGACATGTGTTACATCATCA-TTTAA-ATACGTGTGAAAATGT
1 CACATAATCATTTTAGATGACATGACATGTATCACATCATCATTTTAACA-ACGTG-GAAAATGT
19107 CAC
1 CAC
19110 GTCAACAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 1 0.02
62 10 0.18
63 44 0.80
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (63 bp):
CACATAATCATTTTAGATGACATGACATGTATCACATCATCATTTTAACAACGTGGAAAATGT
Found at i:31240 original size:24 final size:24
Alignment explanation
Indices: 31213--31259 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31203 TGATCACTTT
31213 CCAACCCAACATTAACATCACAAC
1 CCAACCCAACATTAACATCACAAC
*
31237 CCAACCCAACATTTACATCACAA
1 CCAACCCAACATTAACATCACAA
31260 TCCTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.40, G:0.00, T:0.15
Consensus pattern (24 bp):
CCAACCCAACATTAACATCACAAC
Done.