Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006625.1 Hibiscus syriacus cultivar Beakdansim tig00016281_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: 63077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:8240 original size:27 final size:27
Alignment explanation
Indices: 8210--8282 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 27
8200 TGAAAATAAA
8210 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
8237 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
8262 -ATAAAAATATTTTTAAGTTAA
1 AAT-AAAATATTTTTAAATTAA
8283 TATATATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.05
25 19 0.47
26 3 0.08
27 16 0.40
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:8262 original size:25 final size:25
Alignment explanation
Indices: 8210--8284 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 25
8200 TGAAAATAAA
*
8210 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
8237 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
*
8262 -ATAAAA-ATATTT-TTAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
8284 A
1 A
8285 TATATAGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.20
23 6 0.13
24 6 0.13
25 9 0.20
26 2 0.04
27 13 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:8285 original size:22 final size:24
Alignment explanation
Indices: 8211--8286 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 24
8201 GAAAATAAAA
*
8211 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATATTT--ATTAAGTTAAT
*
8237 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTATTAAGTTAAT
8262 ATAAAA-ATATTT-TTAAGTTAAT
1 ATAAAATATATTTATTAAGTTAAT
8284 ATA
1 ATA
8287 TATAGTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 12 0.26
23 6 0.13
24 6 0.13
25 10 0.22
27 12 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTATTAAGTTAAT
Found at i:22658 original size:16 final size:16
Alignment explanation
Indices: 22637--22694 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
22627 AGATAAGAGC
22637 GAGAGTTTGATACTTT
1 GAGAGTTTGATACTTT
*
22653 GAGAGTTT-ATGAGTTT
1 GAGAGTTTGAT-ACTTT
* *
22669 CAGAGTCTGATACTTT
1 GAGAGTTTGATACTTT
22685 -AGGAGTTTGA
1 GA-GAGTTTGA
22695 AGAATTTAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.40
Consensus pattern (16 bp):
GAGAGTTTGATACTTT
Found at i:25947 original size:23 final size:24
Alignment explanation
Indices: 25921--25968 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25911 AATACAATTG
25921 AATTT-AAAATT-CAATTAATGAAA
1 AATTTCAAAATTACAATTAAT-AAA
*
25944 AATTTCAAAATTACCATTAATAAA
1 AATTTCAAAATTACAATTAATAAA
25968 A
1 A
25969 CTTGATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AATTTCAAAATTACAATTAATAAA
Found at i:27397 original size:173 final size:171
Alignment explanation
Indices: 27051--27557 Score: 583
Period size: 173 Copynumber: 3.0 Consensus size: 171
27041 AACACCCCTA
* * *
27051 ATTATCTCTGCATATTTTAGTCAATTATGTGAAGCATA--ATGTTCCCGGTGGGGGAACTATTTC
1 ATTATCTATGCATATTTTAGTCAATTATATGAAGCATATGATGTT-CCGGTGGGGGAACTATTCC
* * * * * * * *
27114 TGTAAATCCAATATTCTGTTTGATGAGAT-TGACA-CTGACATGTTAGATATTCTCTAAAAAAGG
65 CGTTAACCCAATATTCTGTTTGATGAGATGAGACATATGACATGTAAGAGATTCTCTGAAAAAGG
* * *
27177 TGAAAGCACTTTTTGTGGGACGAGCCTTTCCTTTTCTGTCAG
130 TGAAAGCACTTATTCTGGGACGAGCCTTTCCTTTTCTATCAG
* *
27219 ATTATCTATGCATATTTTAGTCAATTATATGAAGCATATGATGTTCCTAGCGGGGGAACTATTCC
1 ATTATCTATGCATATTTTAGTCAATTATATGAAGCATATGATGTTCC-GGTGGGGGAACTATTCC
* * * * *
27284 CATTAACCCAATCTCCTGTTTGATGAGATGAGACATTATGACATATAAGAGATTCTATGAAAAAG
65 CGTTAACCCAATATTCTGTTTGATGAGATGAGACA-TATGACATGTAAGAGATTCTCTGAAAAAG
* * * *
27349 GTGAAATCGCTTATTCTGGGATGAGCCTTTTCTTTTCTATCAG
129 GTGAAAGCACTTATTCTGGGACGAGCCTTTCCTTTTCTATCAG
* * *
27392 ATTATCTATACATATTTTAGTCAATTATATGAAGCATGTGATGTTCGCGGTGGAGGAACTATTCC
1 ATTATCTATGCATATTTTAGTCAATTATATGAAGCATATGATGTTC-CGGTGGGGGAACTATTCC
* * * * * *
27457 CGTTAACCCAATGTTCTATTTGATGAGAAGAGACACTATGACATGTCAGAGGTTCTCTGGAAAAG
65 CGTTAACCCAATATTCTGTTTGATGAGATGAGACA-TATGACATGTAAGAGATTCTCTGAAAAAG
* * * *
27522 GAGAAAG-ATCTTCTTATGGGACAAGCCTTTCCTTTT
129 GTGAAAGCA-CTTATTCTGGGACGAGCCTTTCCTTTT
27558 TTTTATATCA
Statistics
Matches: 282, Mismatches: 49, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
168 36 0.13
169 2 0.01
170 42 0.15
171 4 0.01
173 197 0.70
174 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (171 bp):
ATTATCTATGCATATTTTAGTCAATTATATGAAGCATATGATGTTCCGGTGGGGGAACTATTCCC
GTTAACCCAATATTCTGTTTGATGAGATGAGACATATGACATGTAAGAGATTCTCTGAAAAAGGT
GAAAGCACTTATTCTGGGACGAGCCTTTCCTTTTCTATCAG
Found at i:34042 original size:18 final size:18
Alignment explanation
Indices: 34019--34060 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
34009 GAAAAGTTGT
34019 TAGCTGCACTTGTGCTCA
1 TAGCTGCACTTGTGCTCA
*
34037 TAGCTGTACTTGTGCTCA
1 TAGCTGCACTTGTGCTCA
34055 TAGCTG
1 TAGCTG
34061 GATTGAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (18 bp):
TAGCTGCACTTGTGCTCA
Found at i:34569 original size:20 final size:20
Alignment explanation
Indices: 34532--34571 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34522 CAACCTAAGG
* *
34532 CATAATTCTCCATTAAAAGT
1 CATAAATCTCCATCAAAAGT
*
34552 CATAAATCTTCATCAAAAGT
1 CATAAATCTCCATCAAAAGT
34572 ATGCATTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (20 bp):
CATAAATCTCCATCAAAAGT
Found at i:43758 original size:20 final size:19
Alignment explanation
Indices: 43733--43791 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 19
43723 TTCAAATTCA
43733 AGTTTTATAGACTTTGAATT
1 AGTTTTA-AGACTTTGAATT
43753 AGTTTTGAAGACTTTGAATT
1 AGTTTT-AAGACTTTGAATT
*
43773 AGTTTTAAAAACTTTGAAT
1 AGTTTT-AAGACTTTGAAT
43792 AAATTCAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (19 bp):
AGTTTTAAGACTTTGAATT
Found at i:62325 original size:18 final size:18
Alignment explanation
Indices: 62302--62337 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62292 AGAAGAATAA
62302 CTCTCAGCTCTTGAAAAC
1 CTCTCAGCTCTTGAAAAC
62320 CTCTCAGCTCTTGAAAAC
1 CTCTCAGCTCTTGAAAAC
62338 ACAAAACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (18 bp):
CTCTCAGCTCTTGAAAAC
Done.