Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007994.1 Hibiscus syriacus cultivar Beakdansim tig00110444_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: 788627
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 4 of 4
Found at i:758655 original size:107 final size:105
Alignment explanation
Indices: 758536--758758 Score: 385
Period size: 107 Copynumber: 2.1 Consensus size: 105
758526 AGTTACTGTT
*
758536 AAACTATTATTATACCAAGAAAATAATGTAATA-TTTTATGAAGAACAAGCAATTTAGGAGAAAA
1 AAACTATTATTATACCAAGAAAATAATGTAATATTTTTA-GAAGAACAAGAAATTTAGGAGAAAA
*
758600 CCAAAGACTAAAATGATAAAAAAAATATAAGCTTTGACGAC
65 ACAAAGACTAAAATGATAAAAAAAATATAAGCTTTGACGAC
758641 TAAAACTATTATTATACCAAGAAAATAATGTAATATTTTTAGAAGAACAAGAAATTTAGGAGAAA
1 --AAACTATTATTATACCAAGAAAATAATGTAATATTTTTAGAAGAACAAGAAATTTAGGAGAAA
*
758706 AACAAAGACTAAAATGATAAAAAAATTATAAGCTTTGACGAC
64 AACAAAGACTAAAATGATAAAAAAAATATAAGCTTTGACGAC
758748 AAACTATTATT
1 AAACTATTATT
758759 GTATAAGGCA
Statistics
Matches: 112, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
105 11 0.10
107 96 0.86
108 5 0.04
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.26
Consensus pattern (105 bp):
AAACTATTATTATACCAAGAAAATAATGTAATATTTTTAGAAGAACAAGAAATTTAGGAGAAAAA
CAAAGACTAAAATGATAAAAAAAATATAAGCTTTGACGAC
Found at i:759624 original size:37 final size:37
Alignment explanation
Indices: 759551--759626 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 37
759541 AAGGACTGTA
* *
759551 ACATCAGGACAAGATTTCCCACAATGCGTCTTCGATC
1 ACATCAGGACAAGATTTCCCACAATGCATCTACGATC
* * * * *
759588 ACATGAGGATAAGCTTTCCCGCAATGTATCTACGATC
1 ACATCAGGACAAGATTTCCCACAATGCATCTACGATC
759625 AC
1 AC
759627 CGGGATATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (37 bp):
ACATCAGGACAAGATTTCCCACAATGCATCTACGATC
Found at i:769384 original size:22 final size:20
Alignment explanation
Indices: 769359--769398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
769349 GGTCAACGCC
769359 GGTCAAAGTTCTGGTCAACAGT
1 GGTCAAAG-TC-GGTCAACAGT
*
769381 GGTCAACGTCGGTCAACA
1 GGTCAAAGTCGGTCAACA
769399 ATCAACGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.23
Consensus pattern (20 bp):
GGTCAAAGTCGGTCAACAGT
Found at i:773589 original size:17 final size:18
Alignment explanation
Indices: 773567--773603 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
773557 TCTTATGCAC
773567 ATCAATA-G-CTTTATCAG
1 ATCAATATGTCTTT-TCAG
773584 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
773602 AT
1 AT
773604 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:785296 original size:285 final size:285
Alignment explanation
Indices: 784936--785476 Score: 922
Period size: 285 Copynumber: 1.9 Consensus size: 285
784926 GAAAAAAAAG
*
784936 ATATTTTAAATTTAGATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
1 ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
* *
785001 TGAATACAAAAGGACACGCCAAATGACAAAAATTCTTATAACTAATTAATAAATATATAGCAAAA
66 TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAAC-AAA
* *
785066 ATAAC-AACAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATC
130 ATAACAAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATA
* * *
785130 ATTTCTAGAGAAATTATATTTTCGATAATTGATGGAATTGTACCTGAAATGTAAAATTAAATTTG
195 ATTTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATGTAAAATTAAATTTG
785195 AAAAATAATTTGACAAAAACAATAAT
260 AAAAATAATTTGACAAAAACAATAAT
* * * *
785221 ATATTTTAAATTTAAATCATTTTAGAGTGGATTTATCTGAGTTTAATATTTAAATGATTTATGTT
1 ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
* *
785286 TGAATACAAAAGGACACGTCAAATGACAACAATCCTTATAACTAATTAATAAATATATAACAAAA
66 TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
*
785351 TAACAAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAGAAATCAATAA
131 TAACAAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATAA
*
785416 TTTCTAGAGAAATTATATTTCCGATAACTGATGGGATTATACCTGAAATGTAAAATTAAAT
196 TTTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATGTAAAATTAAAT
785477 AATCAGTCCA
Statistics
Matches: 239, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
284 8 0.03
285 231 0.97
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (285 bp):
ATATTTTAAATTTAAATAAATTTAGAATGGATTTATCTGAGTTTAATATTTAAATGATTTATATT
TGAATACAAAAGGACACGCCAAATGACAAAAATCCTTATAACTAATTAATAAATATATAACAAAA
TAACAAAAAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTTGTTATTCGAAAAATCAATAA
TTTCTAGAGAAATTATATTTCCGATAACTGATGGAATTATACCTGAAATGTAAAATTAAATTTGA
AAAATAATTTGACAAAAACAATAAT
Found at i:785688 original size:21 final size:21
Alignment explanation
Indices: 785664--785703 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
785654 ACGAAAATTG
*
785664 AATTTGAAT-ATTTTATTATAT
1 AATTTAAATAATTTT-TTATAT
785685 AATTTAAATAATTTTTTAT
1 AATTTAAATAATTTTTTAT
785704 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTAAATAATTTTTTATAT
Found at i:788469 original size:74 final size:74
Alignment explanation
Indices: 788348--788497 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
788338 TAGTTGTTGG
788348 TCACCGATTTAGGTTGGTTCGAACGGTGACCGCGCCCTTTTGGAGCTCTCGGTCTAGTGAATAGA
1 TCACCGATTTAGGTTGGTTCGAACGGTGACCGCGCCCTTTTGGAGCTCTCGGTCTAGTGAATAGA
788413 AAAAGGGGT
66 AAAAGGGGT
*
788422 TCACCGGTTTAGGTTGGTTCGAACGGTGACCGCGCCCTTTTGGAGCTCTCGGTCTAGTGAATAGA
1 TCACCGATTTAGGTTGGTTCGAACGGTGACCGCGCCCTTTTGGAGCTCTCGGTCTAGTGAATAGA
788487 AAAAGGGGT
66 AAAAGGGGT
788496 TC
1 TC
788498 TTTATTTTGG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (74 bp):
TCACCGATTTAGGTTGGTTCGAACGGTGACCGCGCCCTTTTGGAGCTCTCGGTCTAGTGAATAGA
AAAAGGGGT
Done.