Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000955.1 Hibiscus syriacus cultivar Beakdansim tig00001911_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: 58251
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:315 original size:90 final size:90
Alignment explanation
Indices: 120--326 Score: 290
Period size: 90 Copynumber: 2.3 Consensus size: 90
110 AGGCACATGG
* * * * **
120 GGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGAGAACTCTTTATCTTGGTGCC
1 GGGGCTGGTCATATGCAAAACACATGGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTAGCACC
* * *
185 TAAATGATCCTCATGCAAGGCACAG
66 TAAATGATCCACATGCAAGGAACAA
*
210 GGGGCTGGTCATATGCAAAACACATGGCTTGGTCGAATAGGGAGAGAACTCTTCATCTTAGCACC
1 GGGGCTGGTCATATGCAAAACACATGGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTAGCACC
275 TAAATGATCCACATGCAAGGAACATA
66 TAAATGATCCACATGCAAGGAACA-A
**
301 GGGGCTGGTC-TATGCAAGGCACATGG
1 GGGGCTGGTCATATGCAAAACACATGG
327 GTGTTCTAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 94 0.90
91 10 0.10
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (90 bp):
GGGGCTGGTCATATGCAAAACACATGGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTAGCACC
TAAATGATCCACATGCAAGGAACAA
Found at i:11329 original size:41 final size:41
Alignment explanation
Indices: 11272--11430 Score: 273
Period size: 41 Copynumber: 3.9 Consensus size: 41
11262 GGATAGCTTG
*
11272 GTGGAGCATTTGGAAGACATATACAGTTCACAAACAACTTA
1 GTGGAGCATTTGGAAGACATATACAGCTCACAAACAACTTA
* * * *
11313 GTGGAGTATTTAGAAGACATATACAACTCACAAACAGCTTA
1 GTGGAGCATTTGGAAGACATATACAGCTCACAAACAACTTA
11354 GTGGAGCATTTGGAAGACATATACAGCTCACAAACAACTTA
1 GTGGAGCATTTGGAAGACATATACAGCTCACAAACAACTTA
11395 GTGGAGCATTTGGAAGACATATACAGCTCACAAACA
1 GTGGAGCATTTGGAAGACATATACAGCTCACAAACA
11431 TATGACACAC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (41 bp):
GTGGAGCATTTGGAAGACATATACAGCTCACAAACAACTTA
Found at i:18759 original size:19 final size:20
Alignment explanation
Indices: 18735--18777 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
18725 AGCATTTATC
*
18735 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
18754 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
18774 TTCA
1 TTCA
18778 AAGAGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:19317 original size:15 final size:15
Alignment explanation
Indices: 19297--19332 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19287 TTTGATAACA
*
19297 TTTCTTTCCATTTCC
1 TTTCTTACCATTTCC
19312 TTTCTTACCATTTCC
1 TTTCTTACCATTTCC
19327 TTTCTT
1 TTTCTT
19333 CTTAATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTACCATTTCC
Found at i:23364 original size:30 final size:31
Alignment explanation
Indices: 23325--23384 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
23315 ACATGCTGCC
**
23325 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
23356 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
23385 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:27618 original size:15 final size:15
Alignment explanation
Indices: 27598--27637 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
27588 AAGAAATTAT
*
27598 GAAAGAAATG-AATT
1 GAAAGAAATGAAATG
27612 GATAAGAAATGAAATG
1 GA-AAGAAATGAAATG
27628 GAAAGAAATG
1 GAAAGAAATG
27638 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:30934 original size:15 final size:15
Alignment explanation
Indices: 30914--30953 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
30904 AAGAAATTAT
*
30914 GAAAGAAAT-AAATT
1 GAAAGAAATGAAATG
30928 GATAAGAAATGAAATG
1 GA-AAGAAATGAAATG
30944 GAAAGAAATG
1 GAAAGAAATG
30954 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 15 0.65
16 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:33040 original size:27 final size:27
Alignment explanation
Indices: 33010--33072 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
33000 TTTATGATAA
*
33010 ATGCAAATGCAAAAGGTGTTATTGATG
1 ATGCAAATGCAAAAAGTGTTATTGATG
33037 ATGCAAATGCAAAAAGTGTTATTGATG
1 ATGCAAATGCAAAAAGTGTTATTGATG
33064 ATGCCAAAT
1 ATG-CAAAT
33073 AATAGAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (27 bp):
ATGCAAATGCAAAAAGTGTTATTGATG
Found at i:33093 original size:14 final size:16
Alignment explanation
Indices: 33069--33100 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33059 TGATGATGCC
33069 AAATAATAGAAA-ACA
1 AAATAATAGAAACACA
33084 AAATAA-AGAAACACA
1 AAATAATAGAAACACA
33099 AA
1 AA
33101 GAAAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (16 bp):
AAATAATAGAAACACA
Found at i:35139 original size:49 final size:53
Alignment explanation
Indices: 35044--35147 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 53
35034 CCTATAATCA
35044 CTATTTTTCTCCTCCTTCCTCTTCTTTCTCTCTCTTTTCGCTTTTTCTCTGTCC
1 CTATTTTTCTCCTCCTTCCTCTTC-TTCTCTCTCTTTTCGCTTTTTCTCTGTCC
*
35098 CTATTTTTCTCCTCC-TCCTCTTC-TCTCTCTC-TTT-GTTTTTTCTCTGTCC
1 CTATTTTTCTCCTCCTTCCTCTTCTTCTCTCTCTTTTCGCTTTTTCTCTGTCC
35147 C
1 C
35148 CTAAAGGGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
49 15 0.31
50 3 0.06
51 8 0.16
53 8 0.16
54 15 0.31
ACGTcount: A:0.02, C:0.38, G:0.04, T:0.57
Consensus pattern (53 bp):
CTATTTTTCTCCTCCTTCCTCTTCTTCTCTCTCTTTTCGCTTTTTCTCTGTCC
Found at i:36340 original size:13 final size:13
Alignment explanation
Indices: 36309--36348 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
36299 TAATTCAATA
36309 TAATTTAAT-AAT
1 TAATTTAATAAAT
36321 T-ATTTAATAAAT
1 TAATTTAATAAAT
*
36333 TAATTTAATAACT
1 TAATTTAATAAAT
36346 TAA
1 TAA
36349 ACAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 5 0.20
13 13 0.52
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATTTAATAAAT
Found at i:41467 original size:2 final size:2
Alignment explanation
Indices: 41460--41526 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
41450 ATTTTCCTAT
41460 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
41502 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41527 TATTTTTATC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.