Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008099.1 Hibiscus syriacus cultivar Beakdansim tig00110627_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: 767286
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 5 of 5
Found at i:756052 original size:36 final size:36
Alignment explanation
Indices: 756007--756078 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 36
755997 AAATCTACCA
*
756007 AAATTTTACCAAACTTTG-AAAAACATTTTTCAAAG
1 AAATTTTACCAAACTTTGAAAAAACATTTTCCAAAG
756042 AAATATTTACCAAACTTTGAAAAAACATTTTCCAAAG
1 AAAT-TTTACCAAACTTTGAAAAAACATTTTCCAAAG
756079 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 4 0.12
36 14 0.41
37 16 0.47
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (36 bp):
AAATTTTACCAAACTTTGAAAAAACATTTTCCAAAG
Found at i:756097 original size:35 final size:36
Alignment explanation
Indices: 756012--756098 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
756002 TACCAAAATT
* *
756012 TTACCAAACTTTG-AAAAACATTTTTCAAAGAAATAT
1 TTACCAAACTTTGAAAAAACATTTTCCAAAG-AATAG
* *
756048 TTACCAAACTTTGAAAAAACATTTTCCAAAG-TTGG
1 TTACCAAACTTTGAAAAAACATTTTCCAAAGAATAG
*
756083 TTGCCAAACTTTGAAA
1 TTACCAAACTTTGAAA
756099 CTTTTAACAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.36
36 13 0.29
37 16 0.36
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (36 bp):
TTACCAAACTTTGAAAAAACATTTTCCAAAGAATAG
Found at i:758653 original size:2 final size:2
Alignment explanation
Indices: 758646--758700 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
758636 TATTGTGTTC
758646 AT AT 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 AT AT
758688 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
758701 GGTTATAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:759342 original size:35 final size:31
Alignment explanation
Indices: 759294--759391 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 31
759284 GTGAAAAATA
** * *
759294 TTTTTTTGGTCAAAATAAGTACCTAAACTTAT
1 TTTTTTTTATCAAAATAGGTACCTAAA-GTAT
**
759326 CCTTTTTATTTATCAAAATAGGTATTTAAAGTAT
1 --TTTTT-TTTATCAAAATAGGTACCTAAAGTAT
*
759360 TTTTTTTTATCAAAATAGGTGCCTAAAGTAT
1 TTTTTTTTATCAAAATAGGTACCTAAAGTAT
759391 T
1 T
759392 CAATATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
31 24 0.44
32 5 0.09
34 8 0.15
35 17 0.31
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
TTTTTTTTATCAAAATAGGTACCTAAAGTAT
Found at i:762078 original size:7 final size:7
Alignment explanation
Indices: 762063--762170 Score: 65
Period size: 7 Copynumber: 15.4 Consensus size: 7
762053 TATGATATGA
*
762063 TTTAAGG
1 TTTAGGG
762070 TTTAGGG
1 TTTAGGG
**
762077 TTTATAG
1 TTTAGGG
*
762084 TTTAGAG
1 TTTAGGG
*
762091 TTTA-TG
1 TTTAGGG
* *
762097 TAATAGGA
1 T-TTAGGG
*
762105 TTTAAGG
1 TTTAGGG
**
762112 TTTAGAA
1 TTTAGGG
*
762119 TTTAGTG
1 TTTAGGG
*
762126 TTTATGG
1 TTTAGGG
**
762133 TTTAAAG
1 TTTAGGG
*
762140 TTTAGGA
1 TTTAGGG
762147 TTTAGGG
1 TTTAGGG
762154 TTTAGGG
1 TTTAGGG
762161 TTTAGGG
1 TTTAGGG
762168 TTT
1 TTT
762171 TAGAGTTTAT
Statistics
Matches: 75, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
6 2 0.03
7 72 0.96
8 1 0.01
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:762092 original size:42 final size:41
Alignment explanation
Indices: 762041--762200 Score: 144
Period size: 42 Copynumber: 3.8 Consensus size: 41
762031 AAGGTTTAGG
* *
762041 GTTTAGAGTTGATATGATATGATTTAAGGTTTAGGGTTTAT
1 GTTTAGAGTTTATATGATAGGATTTAAGGTTTAGGGTTTAT
* * **
762082 AGTTTAGAGTTTATGTAATAGGATTTAAGGTTTAGAATTTAGT
1 -GTTTAGAGTTTATATGATAGGATTTAAGGTTTAGGGTTTA-T
* * * *
762125 GTTTATG-GTTTA-AAGTTTAGGATTTAGGGTTTAGGGTTTAGG
1 GTTTA-GAGTTTATATG-ATAGGATTTAAGGTTTAGGGTTTA-T
* *
762167 GTTTTAGAGTTTATGTGATATGATTTAAGGTTTA
1 G-TTTAGAGTTTATATGATAGGATTTAAGGTTTA
762201 TAGTTTAGGG
Statistics
Matches: 93, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 67 0.72
43 25 0.27
44 1 0.01
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (41 bp):
GTTTAGAGTTTATATGATAGGATTTAAGGTTTAGGGTTTAT
Found at i:762094 original size:28 final size:27
Alignment explanation
Indices: 762063--762179 Score: 78
Period size: 28 Copynumber: 4.1 Consensus size: 27
762053 TATGATATGA
762063 TTTAAGGTTTAGGGTTTATAGTTTAGAG
1 TTTAAGGTTTAGGGTTTA-AGTTTAGAG
* * * *
762091 TTT-ATGTAATAGGATTTAAGGTTTAGAA
1 TTTAAGGT-TTAGGGTTTAA-GTTTAGAG
*
762119 TTT-AGTGTTTATGGTTTAAAGTTTAG-G
1 TTTAAG-GTTTAGGGTTT-AAGTTTAGAG
* *
762146 ATTTAGGGTTTAGGGTTTAGGGTTTTAGAG
1 -TTTAAGGTTTAGGGTTTA-AG-TTTAGAG
762176 TTTA
1 TTTA
762180 TGTGATATGA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
27 5 0.07
28 48 0.71
29 14 0.21
30 1 0.01
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (27 bp):
TTTAAGGTTTAGGGTTTAAGTTTAGAG
Found at i:762178 original size:15 final size:14
Alignment explanation
Indices: 762105--762214 Score: 57
Period size: 14 Copynumber: 7.8 Consensus size: 14
762095 TGTAATAGGA
* *
762105 TTTAAGGTTTAGAA
1 TTTAGGGTTTAGAG
*
762119 TTTAGTGTTTATG-G
1 TTTAGGGTTTA-GAG
**
762133 TTTAAAGTTTAG-G
1 TTTAGGGTTTAGAG
*
762146 ATTTAGGGTTTAGGG
1 -TTTAGGGTTTAGAG
762161 TTTAGGGTTTTAGAG
1 TTTAGGG-TTTAGAG
* *
762176 TTTA-TGTGATATGA-
1 TTTAGGGT-TTA-GAG
* *
762190 TTTAAGGTTTATAG
1 TTTAGGGTTTAGAG
762204 TTTAGGGTTTA
1 TTTAGGGTTTA
762215 TTGTTCAAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
13 4 0.05
14 54 0.73
15 16 0.22
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:762193 original size:29 final size:29
Alignment explanation
Indices: 762084--762256 Score: 101
Period size: 28 Copynumber: 6.1 Consensus size: 29
762074 GGGTTTATAG
* *
762084 TTTAGAGTTTATGTAATAGGATTTAAGG-
1 TTTAGAGTTTATGTGATATGATTTAAGGT
* * * *
762112 TTTAGAATTTA-GTGTTTATGGTTTAAAG-
1 TTTAGAGTTTATGTG-ATATGATTTAAGGT
* * * * *
762140 TTTAG-GATTTA-GGGTTTAGGGTTTAGGGT
1 TTTAGAG-TTTATGTG-ATATGATTTAAGGT
762169 TTTAGAGTTTATGTGATATGATTTAAGG-
1 TTTAGAGTTTATGTGATATGATTTAAGGT
* * * * *
762197 TTTATAGTTTA-GGGTTTATTG-TTCAAAGT
1 TTTAGAGTTTATGTG-ATA-TGATTTAAGGT
762226 TTTAGAGTTTATGTGATATGATTTAAGGT
1 TTTAGAGTTTATGTGATATGATTTAAGGT
762255 TT
1 TT
762257 ATATGTTAAG
Statistics
Matches: 109, Mismatches: 26, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
27 4 0.04
28 60 0.55
29 40 0.37
30 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (29 bp):
TTTAGAGTTTATGTGATATGATTTAAGGT
Found at i:762200 original size:57 final size:56
Alignment explanation
Indices: 762128--762284 Score: 190
Period size: 57 Copynumber: 2.8 Consensus size: 56
762118 ATTTAGTGTT
* * *
762128 TATGGTTTAAAGTTTAGGATTTAGGGTTTAGGGTTTAGGGTTTTAGAGTTTATGTGA
1 TATGATTTAAGGTTTA-TATTTAGGGTTTAGGGTTTAGGGTTTTAGAGTTTATGTGA
** * **
762185 TATGATTTAAGGTTTATAGTTTAGGGTTTATTGTTCAAAGTTTTAGAGTTTATGTGA
1 TATGATTTAAGGTTTATA-TTTAGGGTTTAGGGTTTAGGGTTTTAGAGTTTATGTGA
*
762242 TATGATTTAAGGTTTATATGTTAAGGG-TTAGGGGTTAGGGTTT
1 TATGATTTAAGGTTTATAT-TT-AGGGTTTAGGGTTTAGGGTTT
762285 AAGTTATAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
56 2 0.02
57 77 0.93
58 4 0.05
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (56 bp):
TATGATTTAAGGTTTATATTTAGGGTTTAGGGTTTAGGGTTTTAGAGTTTATGTGA
Found at i:762214 original size:21 final size:21
Alignment explanation
Indices: 762100--762214 Score: 81
Period size: 21 Copynumber: 5.4 Consensus size: 21
762090 GTTTATGTAA
*
762100 TAGGATTTAAGGTTTAGAATT
1 TAGGATTTAAGGTTTAGAGTT
* *
762121 TAGTG-TTTATGGTTTAAAGTT
1 TAG-GATTTAAGGTTTAGAGTT
* *
762142 TAGGATTTAGGGTTTAGGGTT
1 TAGGATTTAAGGTTTAGAGTT
* * * *
762163 TAGGGTTTTAGAGTTTA-TGTGA
1 TAGGATTTAAG-GTTTAGAGT-T
* *
762185 TATGATTTAAGGTTTATAGTT
1 TAGGATTTAAGGTTTAGAGTT
*
762206 TAGGGTTTA
1 TAGGATTTA
762215 TTGTTCAAAG
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
20 1 0.01
21 54 0.76
22 16 0.23
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
TAGGATTTAAGGTTTAGAGTT
Found at i:764201 original size:12 final size:12
Alignment explanation
Indices: 764184--764216 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
764174 GTCGAGCTTG
764184 AATCGAGCTCAC
1 AATCGAGCTCAC
764196 AATCGAGCTCAC
1 AATCGAGCTCAC
*
764208 AATTGAGCT
1 AATCGAGCT
764217 TCAATTGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (12 bp):
AATCGAGCTCAC
Found at i:764334 original size:29 final size:29
Alignment explanation
Indices: 764276--764335 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
764266 AGTTCGAACC
* *
764276 TTTTCGAGTTCGAGTCGAGTTTCAATATT
1 TTTTCGAGTTCGAGTCGAGCTTCAAAATT
*
764305 TTTTCGAGTTCGAGTCGAGCTTGAAAATT
1 TTTTCGAGTTCGAGTCGAGCTTCAAAATT
764334 TT
1 TT
764336 AGGCTCGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (29 bp):
TTTTCGAGTTCGAGTCGAGCTTCAAAATT
Found at i:765388 original size:20 final size:20
Alignment explanation
Indices: 765294--765655 Score: 448
Period size: 20 Copynumber: 18.2 Consensus size: 20
765284 GATTTTCCAT
* ** *
765294 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
765314 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
765334 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765354 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
765374 AATCGCAACGCGTATGGGT-
1 AATCGCAACGCGTATCCGTA
*
765393 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765413 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
765433 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765453 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
765473 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765493 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
765513 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765533 AATCGCAACG-ATATCCGTA
1 AATCGCAACGCGTATCCGTA
765552 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
765572 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
765592 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
765612 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
765632 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
765652 AATC
1 AATC
765656 ACACACTTAA
Statistics
Matches: 299, Mismatches: 33, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 37 0.12
20 259 0.87
21 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:765424 original size:99 final size:100
Alignment explanation
Indices: 765313--765655 Score: 464
Period size: 99 Copynumber: 3.5 Consensus size: 100
765303 GCGAATATGA
* *
765313 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
1 AAATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
**
765377 CGCAACGCGTATGGGT-AATCGCAATGCGTATCCGT
65 CGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
*
765412 ATATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAA-CTGCAACGTGTATCCGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATC-GCAACGTGTATCCGTAAAT
765476 CGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
65 CGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
* *
765512 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATATCCGTAAATCGCAACGCGTATCCGTAAATC
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATC
* * * * *
765576 GCAACG-ATAATCCGTAAATCGCAACGAGAATCTGT
66 GCAACGCGT-ATCCGTAAATCGCAATGCGTATCCGT
* * * *
765611 AAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATC
1 AAATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTAAATC
765656 ACACACTTAA
Statistics
Matches: 220, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
98 3 0.01
99 155 0.70
100 62 0.28
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (100 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATC
GCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
Found at i:765488 original size:139 final size:139
Alignment explanation
Indices: 765313--765655 Score: 455
Period size: 139 Copynumber: 2.5 Consensus size: 139
765303 GCGAATATGA
* * *
765313 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAAT
** *
765377 CGCAACGCGTATGGGT-AATCGCAATGCG-TATCCGTATATCGCAACGCGTATCCGTAAATCGCA
65 CGCAACGCGTATCCGTAAATCGCAA--CGATATCCGTAAATCGCAACGCGTATCCGTAAATCGCA
*
765440 ACGCGT-ATCCGT
128 ACG-ATAATCCGT
* * * *
765452 AAA-CTGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAAT
1 AAATC-GCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAAT
765516 CGCAACGCGTATCCGTAAATCGCAACGATATCCGTAAATCGCAACGCGTATCCGTAAATCGCAAC
65 CGCAACGCGTATCCGTAAATCGCAACGATATCCGTAAATCGCAACGCGTATCCGTAAATCGCAAC
765581 GATAATCCGT
130 GATAATCCGT
* * * *
765591 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGTATCCGTAAAT
765655 C
65 C
765656 ACACACTTAA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
138 5 0.03
139 165 0.92
140 10 0.06
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (139 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGTAAATC
GCAACGCGTATCCGTAAATCGCAACGATATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG
ATAATCCGT
Done.