Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004730.1 Hibiscus syriacus cultivar Beakdansim tig00010670_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: 78763
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4167 original size:18 final size:18
Alignment explanation
Indices: 4144--4187 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4134 AATCAGGGTT
*
4144 AGCGGGTTCTTCTGCTTC
1 AGCGGGCTCTTCTGCTTC
4162 AGCGGGCTCTTCTGCTTC
1 AGCGGGCTCTTCTGCTTC
*
4180 AGTGGGCT
1 AGCGGGCT
4188 GAGGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.27, G:0.32, T:0.34
Consensus pattern (18 bp):
AGCGGGCTCTTCTGCTTC
Found at i:14487 original size:16 final size:17
Alignment explanation
Indices: 14455--14489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14445 AATGTGAATG
14455 AATGATATAATTAAAGT
1 AATGATATAATTAAAGT
*
14472 AATGATGTAA-TAAAGT
1 AATGATATAATTAAAGT
14488 AA
1 AA
14490 GAAAGACTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
AATGATATAATTAAAGT
Found at i:23741 original size:17 final size:17
Alignment explanation
Indices: 23719--23790 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
23709 AATTAAGAGT
23719 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
23736 TAGTTTTATGAATGGAC
1 TAGTTTAATAAATGAAC
* * * *
23753 CAGTTTAATTAATAAAA
1 TAGTTTAATAAATGAAC
* *
23770 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
23788 TAG
1 TAG
23791 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 16, Indels: 2
0.68 0.29 0.04
Matches are distributed among these distances:
17 26 0.68
18 12 0.32
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:30071 original size:16 final size:17
Alignment explanation
Indices: 30039--30073 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30029 AATGTGAATG
30039 AATGATATAATTAAAGT
1 AATGATATAATTAAAGT
*
30056 AATGATGTAA-TAAAGT
1 AATGATATAATTAAAGT
30072 AA
1 AA
30074 GAAAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
AATGATATAATTAAAGT
Found at i:32580 original size:16 final size:16
Alignment explanation
Indices: 32559--32589 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32549 AGGAGAGGTA
*
32559 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCATTTCT
32575 TTTCTTTTTCATTTC
1 TTTCTTTTTCATTTC
32590 ACGAAAGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTCATTTCT
Found at i:39879 original size:12 final size:12
Alignment explanation
Indices: 39862--39886 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39852 GTATAAATAC
39862 AGGATAGGAATT
1 AGGATAGGAATT
39874 AGGATAGGAATT
1 AGGATAGGAATT
39886 A
1 A
39887 TATATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
AGGATAGGAATT
Found at i:62239 original size:3 final size:3
Alignment explanation
Indices: 62151--62226 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
62141 ATAGGGTCTT
62151 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62198 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62227 TTTTTCTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63486 original size:2 final size:2
Alignment explanation
Indices: 63479--63507 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63469 TCAATTCTTC
63479 TA TA 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 TA TA T
63508 TACTTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63689 original size:26 final size:26
Alignment explanation
Indices: 63653--63704 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
63643 ACCTTGCACC
63653 TCAGTCTATCCCTTAATATAATTCTT
1 TCAGTCTATCCCTTAATATAATTCTT
63679 TCAGTCTATCCCTTAATATAATTCTT
1 TCAGTCTATCCCTTAATATAATTCTT
63705 ATTCCAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (26 bp):
TCAGTCTATCCCTTAATATAATTCTT
Found at i:69487 original size:16 final size:15
Alignment explanation
Indices: 69452--69506 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 15
69442 AAGAAAAATA
69452 ATATATATATTATTTCTT
1 ATATATATA-TA-TT-TT
69470 ATATATATATATATTT
1 ATATATATATAT-TTT
69486 ATA-ATA-ATATTTT
1 ATATATATATATTTT
*
69499 AAATATAT
1 ATATATAT
69507 TGATAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 5 0.15
14 7 0.21
15 3 0.09
16 6 0.18
17 3 0.09
18 9 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATATATATTTT
Found at i:69524 original size:23 final size:23
Alignment explanation
Indices: 69472--69524 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
69462 TATTTCTTAT
* *
69472 ATATATATATATTTATAATAATA
1 ATATAAATATATTGATAATAATA
* *
69495 TTTTAAATATATTGATAATAA-A
1 ATATAAATATATTGATAATAATA
69517 CATATAAA
1 -ATATAAA
69525 ATTAAAACCA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATAAATATATTGATAATAATA
Found at i:70767 original size:3 final size:3
Alignment explanation
Indices: 70761--70809 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
70751 TAATATTTAT
* * * *
70761 TAA TAA TAA -AA CAA AAA TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
70808 TA
1 TA
70810 TTCAAATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:70787 original size:27 final size:27
Alignment explanation
Indices: 70749--70809 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
70739 TTGGGCATGT
*
70749 AATAATATTTATTAATAATAA-AACAAA
1 AATAATAATTA-TAATAATAATAACAAA
* * *
70776 AATAATAATTATAATTATAATAATAAT
1 AATAATAATTATAATAATAATAACAAA
70803 AATAATA
1 AATAATA
70810 TTCAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAATAATTATAATAATAATAACAAA
Found at i:73680 original size:10 final size:10
Alignment explanation
Indices: 73665--73698 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
73655 ATAATTTATA
73665 TTTCTTTTTT
1 TTTCTTTTTT
73675 TTTCTTTTTT
1 TTTCTTTTTT
73685 TTTCCTTTTTT
1 TTT-CTTTTTT
73696 TTT
1 TTT
73699 ATGCGGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:73685 original size:11 final size:11
Alignment explanation
Indices: 73665--73698 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
73655 ATAATTTATA
73665 TTTC-TTTTTT
1 TTTCTTTTTTT
73675 TTTCTTTTTTT
1 TTTCTTTTTTT
*
73686 TTCCTTTTTTT
1 TTTCTTTTTTT
73697 TT
1 TT
73699 ATGCGGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Done.