Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009099.1 Hibiscus syriacus cultivar Beakdansim tig00112553_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: 322120
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:299286 original size:22 final size:21
Alignment explanation
Indices: 299244--299283 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
299234 GAGTTTGTTT
*
299244 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
299265 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
299284 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:301278 original size:64 final size:63
Alignment explanation
Indices: 301210--301390 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
301200 TTGGAATACT
* ***
301210 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
301274 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
301338 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
301391 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:301362 original size:19 final size:19
Alignment explanation
Indices: 301338--301388 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
301328 GAAAATATTC
301338 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
301357 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
301376 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
301389 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:301364 original size:65 final size:65
Alignment explanation
Indices: 301231--301390 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
301221 TGCACCAAGT
* ***
301231 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
301295 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
301359 A
65 A
* *
301360 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
301391 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:301430 original size:65 final size:64
Alignment explanation
Indices: 301232--301435 Score: 179
Period size: 65 Copynumber: 3.2 Consensus size: 64
301222 GCACCAAGTG
* * * * * *
301232 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGCCTGATGCATCGATGCATGGCTTG
1 TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATAT-TCATGATGCATCGATGCATGAC-TG
301296 -
64 A
* *
301296 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGGTGCATCAAATGCATTCGATG-TTTCAAAATATTCATGA-TGCATCGATGCAT-GACT
301358 GA
63 GA
** *
301360 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATTGATGCATCGATGCATGTAC
1 -TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA-TGATGCATCGATGCATG-AC
301423 TGA
62 TGA
301426 TGCATCGGTG
1 TGCATCGGTG
301436 TATGCCTTTG
Statistics
Matches: 119, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
62 3 0.03
63 9 0.08
64 43 0.36
65 59 0.50
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (64 bp):
TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATATTCATGATGCATCGATGCATGACTGA
Found at i:301630 original size:20 final size:21
Alignment explanation
Indices: 301607--301646 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
301597 GAATCGAATA
301607 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
301627 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
301647 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:302819 original size:19 final size:21
Alignment explanation
Indices: 302782--302824 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
302772 TAACTTTTTC
*
302782 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
302802 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
302822 TTT
1 TTT
302825 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:306029 original size:24 final size:24
Alignment explanation
Indices: 306002--306051 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
305992 TGGTGGTTGA
*
306002 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
306026 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
306050 TT
1 TT
306052 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:311888 original size:428 final size:429
Alignment explanation
Indices: 310895--312185 Score: 2185
Period size: 428 Copynumber: 3.0 Consensus size: 429
310885 GTTGATTATG
* * *
310895 ATGAAA-TTTTTTCTTCTGTGGTCAGGTACACTTCAATCCGAGCAGTACTTGCATTGGTGGCTAG
1 ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTTCATTGGTGGCTAG
* * *
310959 TTGGGATTTGCATTTAGAGCAGATAGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAGC
66 TTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAAC
* * * *
311024 ATATCTACATGCAGCAGTCTGAAGGTTTCACTCAACCTGAAAACGAGCATTTAGTTTGCAGATTG
131 AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATTG
*
311089 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCGAGACAGTGGTATAAACGATTTGACTCCTATAT
196 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
*
311154 GATCACGATTGGCTACAATCGATGTGAG-ATTGATTGTTGTGTCTATGTTAAGAGCCTTGATGAT
261 GATCACGATTGGCTACAACCGATGTGAGTA-TGATTGTTGTGTCTATGTTAAGAGCCTTGATGAT
* * *
311218 GGTTCTTTTATTTTCCTGTTACTGTATGTTAATGATATGTTGATTACTGTGAAGAACATGGATGA
325 GGTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGA
*
311283 TGTTATCGATTTGAAAACCTTATTGAGTCAGGAATTTGAT
390 TGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
* * * *
311323 ATGAATTTTTTTTCTCTTGTGGTCAAGCACACTTCAATCTGAGCAGTACTTGT-ATTGGTGGCTA
1 ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGTACTT-TCATTGGTGGCTA
* *
311387 GTTGAGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAT
65 GTTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAA
*
311452 CAGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAATGAGCATTTAGTTTGCAGATT
130 CAGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATT
*
311517 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCTAGACAGTGGTATAAACGATTTGACTCCTATA
195 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATA
* *
311582 TGATCACAATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGTCTTGATGAT
260 TGATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGAT
* * *
311647 GGTTC-TTTATTTTTCTGTTACTATATGTTGATGATATGTTGATTACTACGAATAACATGGATGA
325 GGTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGA
311711 TGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
390 TGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
*
311751 ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGAACTTTCATTGGTGGCTAG
1 ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTTCATTGGTGGCTAG
* * **
311816 TTGGGATTTGTATTTAGAGTAGATGGATGTTAAAACTGCTTTTTCCCATGGTGATTTAGAGGAAC
66 TTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAAC
* * *
311881 AGATCTACATGCGACAGCCTGAAGGTTGCACTCAACCTGGAAACGAGCATTTAGTTTACAGATTG
131 AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATTG
311946 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
196 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
*
312011 GATCACGATTGGCTAAAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGATG
261 GATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGATG
*
312076 GTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTCGATTACTGCGAAGAACATGGATGAT
326 GTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGAT
312141 GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
391 GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
312180 ATGAAA
1 ATGAAA
312186 GATTTAGGTG
Statistics
Matches: 808, Mismatches: 50, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
427 1 0.00
428 405 0.50
429 401 0.50
430 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (429 bp):
ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTTCATTGGTGGCTAG
TTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAAC
AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATTG
AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
GATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGATG
GTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGAT
GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
Done.