Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001155.1 Hibiscus syriacus cultivar Beakdansim tig00002302_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: 33662
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1671 original size:117 final size:117
Alignment explanation
Indices: 1451--1671 Score: 268
Period size: 117 Copynumber: 1.9 Consensus size: 117
1441 CTTTCAAATC
* *
1451 AAAATTTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAAGATTT
1 AAAAATTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
* * *
1516 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTAATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
1568 AAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTC-TTTTCTCAACAT
1 AAAAATTTCTTTTTCAATACTTTT-AAATTTCATTTTTGAAAGCTCTAAATCATTCT-TCAACAT
* * **
1631 TTCATTTTAATTTTCCAAGTCTGTTTTAGCTTT-TAAAAGAA
64 TTCATTTTAATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
1672 TATCATTTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
116 8 0.09
117 76 0.87
118 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (117 bp):
AAAAATTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
CATTTTAATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:2999 original size:19 final size:19
Alignment explanation
Indices: 2975--3018 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
2965 GGACCCTTAC
2975 GCATCGGTGCACTAAGAGT
1 GCATCGGTGCACTAAGAGT
2994 GCATCGGTGCACTAAGAGT
1 GCATCGGTGCACTAAGAGT
3013 GCATCG
1 GCATCG
3019 ATGTTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (19 bp):
GCATCGGTGCACTAAGAGT
Found at i:3463 original size:27 final size:27
Alignment explanation
Indices: 3421--3488 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
3411 TTGTAGGAAT
3421 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
3446 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
3473 TATAGAGATATGATTT
1 TATAGAGATATGATTT
3489 TGTAAATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:7227 original size:27 final size:27
Alignment explanation
Indices: 7185--7252 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
7175 GTGTAGGAAT
*
7185 TATAGAG--ATGATTTGTTGCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
7210 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
7237 TATAGAGATATGATTT
1 TATAGAGATATGATTT
7253 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:16835 original size:2 final size:2
Alignment explanation
Indices: 16828--16891 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
16818 ACCATATACA
16828 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
16870 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
16892 CTTCATATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17900 original size:19 final size:20
Alignment explanation
Indices: 17878--17919 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17868 TTAAACTGAT
*
17878 TTAAATAATTTAATAAA-TA
1 TTAAATAATTTAAAAAATTA
*
17897 TTAAATATTTTAAAAAATTA
1 TTAAATAATTTAAAAAATTA
17917 TTA
1 TTA
17920 TTAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAATTTAAAAAATTA
Found at i:18383 original size:16 final size:18
Alignment explanation
Indices: 18347--18384 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
18337 TCAAAGATTC
*
18347 AAATTATATAACTAGAAA
1 AAATTATATAAATAGAAA
18365 AAATTAT-TAAATA-AAA
1 AAATTATATAAATAGAAA
18381 AAAT
1 AAAT
18385 AAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTATATAAATAGAAA
Found at i:19320 original size:39 final size:39
Alignment explanation
Indices: 19215--19335 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 39
19205 AAATATATTA
*
19215 ATATTTTAAAATAATTAAAATAATATATTTTATAATAATAT
1 ATATTTT-TAATAATT-AAATAATATATTTTATAATAATAT
* ** ** *
19256 ATTATATTTAATCTGTTAAATTAATATATTTTATAATTTTTT
1 A-TATTTTTAAT-AATTAAA-TAATATATTTTATAATAATAT
19298 ATATTTTTAATAATTAAATAATATATTTTA-AA-AATAT
1 ATATTTTTAATAATTAAATAATATATTTTATAATAATAT
19335 A
1 A
19336 AAAAAATATT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
37 3 0.05
38 2 0.03
39 12 0.19
40 5 0.08
41 16 0.25
42 26 0.41
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (39 bp):
ATATTTTTAATAATTAAATAATATATTTTATAATAATAT
Found at i:19337 original size:22 final size:20
Alignment explanation
Indices: 19297--19358 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
19287 TATAATTTTT
*
19297 TATATTTTTAATAATTAAATAA
1 TATA-TTTTAAAAATTAAA-AA
19319 TATATTTTAAAAATATAAAAA
1 TATATTTTAAAAAT-TAAAAA
*
19340 AATATTCTTAAAATATTAA
1 TATATT-TTAAAA-ATTAA
19359 TTATAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 16 0.46
22 17 0.49
23 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATTTTAAAAATTAAAAA
Found at i:19352 original size:21 final size:21
Alignment explanation
Indices: 19302--19355 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
19292 TTTTTTATAT
*
19302 TTTTAATAAT-TAAATAATATA
1 TTTTAA-AATATAAATAAAATA
19323 TTTTAAAAATATAAA-AAAATA
1 TTTT-AAAATATAAATAAAATA
19344 TTCTTAAAATAT
1 TT-TTAAAATAT
19356 TAATTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAATATAAATAAAATA
Found at i:19641 original size:2 final size:2
Alignment explanation
Indices: 19634--19673 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19624 TCATTTAATT
19634 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
19674 AATTATACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32509 original size:3 final size:3
Alignment explanation
Indices: 32501--32528 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32491 ACAAATGCAA
32501 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
32529 GTTGTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:32533 original size:3 final size:3
Alignment explanation
Indices: 32527--32616 Score: 164
Period size: 3 Copynumber: 30.3 Consensus size: 3
32517 ATTATTATTA
*
32527 TTG TTG TTG TTG TTG TTG CTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
32575 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG -TG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
32617 GGTGGTGGTG
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 82 0.98
ACGTcount: A:0.00, C:0.01, G:0.33, T:0.66
Consensus pattern (3 bp):
TTG
Done.