Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008693.1 Hibiscus syriacus cultivar Beakdansim tig00111721_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: 2243253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2193408 original size:28 final size:28
Alignment explanation
Indices: 2193373--2193441 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
2193363 ACTTATTAAG
2193373 ACTA-AGGGTATTTTGGTAATTTTAACC
1 ACTAGAGGGTATTTTGGTAATTTTAACC
2193400 ACTAGAGGGTATTTTGGTAATTTTAACC
1 ACTAGAGGGTATTTTGGTAATTTTAACC
*
2193428 ACTAGAGGGAATTT
1 ACTAGAGGGTATTT
2193442 CGGTTTTCAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 4 0.10
28 36 0.90
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (28 bp):
ACTAGAGGGTATTTTGGTAATTTTAACC
Found at i:2194143 original size:29 final size:30
Alignment explanation
Indices: 2194086--2194154 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
2194076 AAAACCGAAT
*
2194086 TAAACGGGGACGGGAAAAAATTATTTATGC
1 TAAACGGGGACGGGAAAAAACTATTTATGC
*
2194116 TAAACGGGGACGGG-AAAAACTGTTTATGC
1 TAAACGGGGACGGGAAAAAACTATTTATGC
2194145 TAAACGGGGA
1 TAAACGGGGA
2194155 TGGGGATGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAAACTATTTATGC
Found at i:2194167 original size:36 final size:36
Alignment explanation
Indices: 2194119--2194229 Score: 154
Period size: 35 Copynumber: 3.1 Consensus size: 36
2194109 TTTATGCTAA
*
2194119 ACGGGGA-CGGGAAAAACTGTTTATGCTAAACGGGG
1 ACGGGGATAGGGAAAAACTGTTTATGCTAAACGGGG
* * *
2194154 ATGGGGATGGGGAAAATC-GTTTATGCTAAACGGGG
1 ACGGGGATAGGGAAAAACTGTTTATGCTAAACGGGG
* *
2194189 ACGGGGATAGGGAAAAACTGTTTATGTTAAATGGGG
1 ACGGGGATAGGGAAAAACTGTTTATGCTAAACGGGG
2194225 ACGGG
1 ACGGG
2194230 TTTAGTAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 38 0.58
36 28 0.42
ACGTcount: A:0.31, C:0.10, G:0.39, T:0.21
Consensus pattern (36 bp):
ACGGGGATAGGGAAAAACTGTTTATGCTAAACGGGG
Found at i:2194309 original size:2 final size:2
Alignment explanation
Indices: 2194302--2194374 Score: 96
Period size: 2 Copynumber: 37.5 Consensus size: 2
2194292 ATTAAAAATA
2194302 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
* * * *
2194344 A- AT AT TT AT AT AT TT A- AT TT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2194375 CTCGACCCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2202067 original size:2 final size:2
Alignment explanation
Indices: 2202060--2202101 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2202050 TAAATGGTAC
2202060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2202102 AAAGACTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2202261 original size:17 final size:18
Alignment explanation
Indices: 2202220--2202258 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2202210 ACTAAAATAC
*
2202220 TAAAGATGGAGACTAAAA
1 TAAATATGGAGACTAAAA
2202238 TAAATATGGAG-CTAAACA
1 TAAATATGGAGACTAAA-A
2202256 TAA
1 TAA
2202259 TATTCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.21
Consensus pattern (18 bp):
TAAATATGGAGACTAAAA
Found at i:2203527 original size:17 final size:17
Alignment explanation
Indices: 2203505--2203537 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2203495 AGTGTTTTTT
*
2203505 TTCTTGATTTTTCTTTG
1 TTCTTGATTTTCCTTTG
2203522 TTCTTGATTTTCCTTT
1 TTCTTGATTTTCCTTT
2203538 CCCTTTGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.70
Consensus pattern (17 bp):
TTCTTGATTTTCCTTTG
Found at i:2205839 original size:21 final size:21
Alignment explanation
Indices: 2205791--2205842 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2205781 GCGTTGACAT
*
2205791 ATTCTAAAGCTCTGAAAGAAC
1 ATTCTAGAGCTCTGAAAGAAC
2205812 ATTCTAGAGCTCTGAAAGAAC
1 ATTCTAGAGCTCTGAAAGAAC
2205833 ATTCTAGAGC
1 ATTCTAGAGC
2205843 ATTCTCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (21 bp):
ATTCTAGAGCTCTGAAAGAAC
Found at i:2212880 original size:19 final size:19
Alignment explanation
Indices: 2212843--2212880 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2212833 TAAATATAAC
* *
2212843 ATTAAAATATGATTCATTT
1 ATTAAAATATAATTAATTT
2212862 ATTAAAATATAATTAATTT
1 ATTAAAATATAATTAATTT
2212881 GCTTCGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTAAAATATAATTAATTT
Found at i:2219438 original size:17 final size:16
Alignment explanation
Indices: 2219408--2219448 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
2219398 CTGATGAGTG
2219408 TTTTT-TTTTTCTTGA
1 TTTTTCTTTTTCTTGA
2219423 TTTTTCTTTGTTCTTGA
1 TTTTTCTTT-TTCTTGA
*
2219440 TTTTCCTTT
1 TTTTTCTTT
2219449 CCCTTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 3 0.13
17 15 0.65
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTTCTTGA
Found at i:2219993 original size:3 final size:3
Alignment explanation
Indices: 2219985--2220010 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2219975 ATAAATAAAT
2219985 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2220011 TATTTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2223243 original size:337 final size:331
Alignment explanation
Indices: 2222584--2223249 Score: 892
Period size: 333 Copynumber: 2.0 Consensus size: 331
2222574 ATAAATATAT
**
2222584 TATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATTTTACCGTC
1 TATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATTTTACCACC
* ** * * *
2222649 AACCATGGCTCCTAAACCCACCACTGGGAGTGCAGCAGCAGCTGGGGAGCAATGCCGTGTAGCAG
66 AACCATGACTCCTAAACCCACCACAAGGAATGCAGCAACAGCTGGGGAGCAATGCCGTGTACCAG
* * * ** * * *
2222714 CGGTGACTGATCGGGATTCAATCGTGTTTTGTAGCTCTTTACTTGAGAAGGGAGATACTATTTGA
131 CGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAGAAGGAAGATACTATTTGA
2222779 TACGATTGGATGTTTAAATTTATTGCTATTGGATTTGAACACAAGATGTTTGATGAAATGCTTTT
196 TACGATTGGATGTTTAAATTTATTGCTATTGGATTTGAACACAAGATGTTTGATGAAATGCTTTT
*
2222844 CAATTTGATTTTGCTTTTATTATTGTTATGTTGCTGGATTTTTTGGAAACCATTTTTAGAAATTA
261 CAATTTGATTTTGCTTTTATTATGGTTATGTTGCTGGATTTTTTGGAAACCATTTTTAGAAA-TA
2222909 AAATAAA
325 AAATAAA
* * * ** *
2222916 TATTTTCTTCATTTCTTGGAACCTTAATTTTCTGTATTCTCCTTTTATTTTTCTATTTTACCACC
1 TATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATTTTACCACC
* * * * *
2222981 GACCATGAC-CGCTAAACCCACCGTCAATGAATGCAGCAACATCTGGGGAGCAATGTCGTGTACC
66 AACCATGACTC-CTAAACCCACC-ACAAGGAATGCAGCAACAGCTGGGGAGCAATGCCGTGTACC
* *
2223045 AGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGTTCCTTACTTGAGAAATGAAGATACTATT
129 AGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAG-AAGGAAGATACTATT
* *
2223110 TGATACGATTGGAT-TTTGAATTTATTATTGCTATTTGGATTTGAACACAATATGTTTGATGAAA
193 TGATACGATTGGATGTTT-AA-AT-TTATTGCTA-TTGGATTTGAACACAAGATGTTTGATGAAA
* *
2223174 TGC-TTTC-ATTTGATTTTGCTTTTATGATATGGTTATGTTTCTAGGATTTTTTGGAAACTA-TT
254 TGCTTTTCAATTTGATTTTGCTTTTAT--TATGGTTATGTTGCT-GGATTTTTTGGAAACCATTT
2223236 TTAGAAATAAAATA
316 TTAGAAATAAAATA
2223250 GTATTTTGCA
Statistics
Matches: 290, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
331 1 0.00
332 75 0.26
333 76 0.26
334 29 0.10
335 19 0.07
336 20 0.07
337 54 0.19
338 16 0.06
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (331 bp):
TATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATTTTACCACC
AACCATGACTCCTAAACCCACCACAAGGAATGCAGCAACAGCTGGGGAGCAATGCCGTGTACCAG
CGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAGAAGGAAGATACTATTTGA
TACGATTGGATGTTTAAATTTATTGCTATTGGATTTGAACACAAGATGTTTGATGAAATGCTTTT
CAATTTGATTTTGCTTTTATTATGGTTATGTTGCTGGATTTTTTGGAAACCATTTTTAGAAATAA
AATAAA
Found at i:2227467 original size:12 final size:12
Alignment explanation
Indices: 2227450--2227487 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2227440 TGTTTCTTAC
2227450 TCTTGTTGTGTT
1 TCTTGTTGTGTT
2227462 TCTTGTTGTG--
1 TCTTGTTGTGTT
*
2227472 TCTTGTTATGTT
1 TCTTGTTGTGTT
2227484 TCTT
1 TCTT
2227488 TCTGTGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.03, C:0.11, G:0.21, T:0.66
Consensus pattern (12 bp):
TCTTGTTGTGTT
Found at i:2227478 original size:22 final size:22
Alignment explanation
Indices: 2227450--2227513 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
2227440 TGTTTCTTAC
2227450 TCTTGTTGTGTTTCTTGT-TGTG
1 TCTTGTTGTGTTTCTT-TCTGTG
*
2227472 TCTTGTTATGTTTCTTTCTGTG
1 TCTTGTTGTGTTTCTTTCTGTG
* *
2227494 TCTTGCTGCTGTTTTTTTCT
1 TCTTGTTG-TGTTTCTTTCT
2227514 TTGCAGTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.03
22 25 0.69
23 10 0.28
ACGTcount: A:0.02, C:0.14, G:0.20, T:0.64
Consensus pattern (22 bp):
TCTTGTTGTGTTTCTTTCTGTG
Found at i:2228017 original size:13 final size:13
Alignment explanation
Indices: 2227999--2228043 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2227989 GGGCTTGTAA
2227999 ATATAATATTAAT
1 ATATAATATTAAT
*
2228012 ATATAATATTATT
1 ATATAATATTAAT
*
2228025 ATATATATAATAAT
1 ATATA-ATATTAAT
*
2228039 GTATA
1 ATATA
2228044 TATAATAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
ATATAATATTAAT
Found at i:2228032 original size:17 final size:16
Alignment explanation
Indices: 2228005--2228036 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2227995 GTAAATATAA
2228005 TATTAATATATAATAT
1 TATTAATATATAATAT
2228021 TATTATATATATAATA
1 TATTA-ATATATAATA
2228037 ATGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAATATATAATAT
Found at i:2228043 original size:16 final size:15
Alignment explanation
Indices: 2227999--2228051 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
2227989 GGGCTTGTAA
2227999 ATATAAT-ATTA-AT
1 ATATAATAATTATAT
2228012 ATATAATATTATTATAT
1 ATATAATA--ATTATAT
*
2228029 ATATAATAA-TGTAT
1 ATATAATAATTATAT
2228043 ATATAATAA
1 ATATAATAA
2228052 CGTCCCTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 7 0.20
14 13 0.37
15 1 0.03
16 4 0.11
17 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATAATAATTATAT
Found at i:2228730 original size:20 final size:20
Alignment explanation
Indices: 2228707--2228751 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2228697 ACCCAAAAGA
2228707 TTTACAAATTACCCGAAGGC
1 TTTACAAATTACCCGAAGGC
*
2228727 TTTACAAATTACCCGGAGGC
1 TTTACAAATTACCCGAAGGC
2228747 TTTAC
1 TTTAC
2228752 TTTTCTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
TTTACAAATTACCCGAAGGC
Found at i:2232493 original size:18 final size:18
Alignment explanation
Indices: 2232451--2232493 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2232441 TTGTTTACTA
*
2232451 TTGCTTCCCTAAAAATGT
1 TTGCTTTCCTAAAAATGT
2232469 TTGCTTTCCTAAAAATGT
1 TTGCTTTCCTAAAAATGT
2232487 TTGCTTT
1 TTGCTTT
2232494 GAATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (18 bp):
TTGCTTTCCTAAAAATGT
Found at i:2236281 original size:12 final size:12
Alignment explanation
Indices: 2236264--2236310 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
2236254 TGTTTCTTGC
2236264 TCTTGCTGTGTT
1 TCTTGCTGTGTT
2236276 TCTTGCTGTG--
1 TCTTGCTGTGTT
*
2236286 TCTTGTTGTGTT
1 TCTTGCTGTGTT
*
2236298 TCTCGCTGTGTT
1 TCTTGCTGTGTT
2236310 T
1 T
2236311 TGCTATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 9 0.30
12 21 0.70
ACGTcount: A:0.00, C:0.17, G:0.26, T:0.57
Consensus pattern (12 bp):
TCTTGCTGTGTT
Found at i:2236295 original size:22 final size:22
Alignment explanation
Indices: 2236264--2236320 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2236254 TGTTTCTTGC
*
2236264 TCTTGCTGTGTTTCTTGCTGTG
1 TCTTGCTGTGTTTCTCGCTGTG
*
2236286 TCTTGTTGTGTTTCTCGCTGTG
1 TCTTGCTGTGTTTCTCGCTGTG
* *
2236308 TTTTGCTATGTTT
1 TCTTGCTGTGTTT
2236321 TTTTTTACAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.02, C:0.16, G:0.25, T:0.58
Consensus pattern (22 bp):
TCTTGCTGTGTTTCTCGCTGTG
Found at i:2236830 original size:18 final size:17
Alignment explanation
Indices: 2236784--2236832 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 17
2236774 GGTTTTGTAA
2236784 ATAATAATTA-ATAT-T
1 ATAATAATTATATATAT
2236799 ATAAT-ATTAT-TATAT
1 ATAATAATTATATATAT
2236814 ATAATAATGTATATATAT
1 ATAATAAT-TATATATAT
2236832 A
1 A
2236833 AACGTCACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.24
15 11 0.38
16 2 0.07
17 3 0.10
18 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATAATAATTATATATAT
Done.