Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004589.1 Hibiscus syriacus cultivar Beakdansim tig00010249_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: 59856
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:27683 original size:28 final size:29
Alignment explanation
Indices: 27627--27696 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
27617 GCTGCTGGAA
*
27627 ACCGGTTTGACCGGTTTTCAATCGATTTTG
1 ACCGGTTTGACCGG-TTTCAACCGATTTTG
27657 ACCGGTTTGACCGG-TTCAAACCG-TTTTG
1 ACCGGTTTGACCGGTTTC-AACCGATTTTG
*
27685 ACCGGTCTGACC
1 ACCGGTTTGACC
27697 CGACCCGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 19 0.51
29 4 0.11
30 14 0.38
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGATTTTG
Found at i:27720 original size:17 final size:17
Alignment explanation
Indices: 27698--27735 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
27688 GGTCTGACCC
27698 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
27715 GACCCGACCCGACTGTT
1 GACCCGACCCGACCGTT
27732 GACC
1 GACC
27736 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:27735 original size:24 final size:22
Alignment explanation
Indices: 27682--27742 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
27672 TCAAACCGTT
27682 TTGACCGGTCTGACCCGACCCGAC
1 TTGACC-GT-TGACCCGACCCGAC
**
27706 CCGACCGTTGACCCGACCCGAC
1 TTGACCGTTGACCCGACCCGAC
27728 TGTTGACCGTTGACC
1 --TTGACCGTTGACC
27743 GTTGACTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.45
23 2 0.06
24 15 0.48
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (22 bp):
TTGACCGTTGACCCGACCCGAC
Found at i:31905 original size:30 final size:30
Alignment explanation
Indices: 31854--31963 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 30
31844 TTAAGATAAT
* * *
31854 AATAAAAT-TGATCTTTTAAGTTAATAAAAG
1 AATAAAATAT-ATATTTGAAGTTAATAAAAA
* * *
31884 AATAAAATATATATTTGAAGTTAAGATAAT
1 AATAAAATATATATTTGAAGTTAATAAAAA
* * *
31914 AACAAAATATA-ATTTTAAAATTAATAAAAA
1 AATAAAATATATA-TTTGAAGTTAATAAAAA
31944 AATAAAATATATTATTTGAA
1 AATAAAATATA-TATTTGAA
31964 CATAAATTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 1 0.02
30 55 0.87
31 6 0.10
32 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (30 bp):
AATAAAATATATATTTGAAGTTAATAAAAA
Found at i:31913 original size:60 final size:61
Alignment explanation
Indices: 31844--31995 Score: 184
Period size: 60 Copynumber: 2.5 Consensus size: 61
31834 TTTTATTAAC
* * * * *
31844 TTAAGATAATAATAAAAT-TGATCTTTTAAGTTAATAAAAGAATAAAATATA-TATTTGAAG
1 TTAAGATAATAACAAAATATAAT-TTTAAAATTAATAAAAAAATAAAATATATTATTTGAAG
*
31904 TTAAGATAATAACAAAATATAATTTTAAAATTAATAAAAAAATAAAATATATTATTTGAAC
1 TTAAGATAATAACAAAATATAATTTTAAAATTAATAAAAAAATAAAATATATTATTTGAAG
* * *
31965 ATAA-ATTAATAACAAAATATATTTTTTAAAT
1 TTAAGA-TAATAACAAAATATAATTTTAAAAT
31996 ATATTTTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 43 0.54
61 37 0.46
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (61 bp):
TTAAGATAATAACAAAATATAATTTTAAAATTAATAAAAAAATAAAATATATTATTTGAAG
Found at i:33771 original size:19 final size:19
Alignment explanation
Indices: 33747--33784 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
33737 AAATGGTGAG
33747 GAAAAT-AAATAAAAATAAA
1 GAAAATAAAAT-AAAATAAA
33766 GAAAATAAAATAAAATAAA
1 GAAAATAAAATAAAATAAA
33785 ATAAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
GAAAATAAAATAAAATAAA
Found at i:33777 original size:5 final size:5
Alignment explanation
Indices: 33748--33789 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
33738 AATGGTGAGG
*
33748 AAAAT -AAAT AAAA- ATAAAG AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAA
33790 GAAGGAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 5 0.15
5 27 0.82
6 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:36316 original size:147 final size:145
Alignment explanation
Indices: 36027--36319 Score: 426
Period size: 148 Copynumber: 2.0 Consensus size: 145
36017 CATTATAGAA
* *
36027 TTTCCTTGTTGCACACAAAAATATCATTTTGGAAATTATAAAAAAGTATTTTTACTATTAAAAAA
1 TTTCCTTATTGCACACAAAAAAATCATTTTGGAAATTATAAAAAAGTATTTTTACTATTAAAAAA
* * *
36092 TAATTTTAGCTTCAAAATTAAAAAAAAACGACTAAAATGAATGAAGTAAAAATTAATTTTTGAGT
66 TAATTTTAGCTTCAAAATTAAAAAAAAACGACTAAAAAGAATGAACTAAAAAATAATTTTTGAGT
*
36157 AAATTATGCGTTTAG
131 AAATTATACGTTTAG
36172 TTTCCTTATTGCACACCAAAAAAAATTCATTTTGGAAATTATAAAAAAGTATTTTTACTATTAAA
1 TTTCCTTATTGCACA-C-AAAAAAA-TCATTTTGGAAATTATAAAAAAGTATTTTTACTATTAAA
* * * *** * *
36237 AAATATTTTTAGCTTCCAAATT-TAAAAATGTGACTAAAAAGATTTAACTAAAAAATAATTTTTG
63 AAATAATTTTAGCTTCAAAATTAAAAAAAAACGACTAAAAAGAATGAACTAAAAAATAATTTTTG
36301 AGTAAATTATACGTTTAG
128 AGTAAATTATACGTTTAG
36319 T
1 T
36320 ATTTAAATAA
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
145 14 0.11
146 1 0.01
147 57 0.44
148 59 0.45
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (145 bp):
TTTCCTTATTGCACACAAAAAAATCATTTTGGAAATTATAAAAAAGTATTTTTACTATTAAAAAA
TAATTTTAGCTTCAAAATTAAAAAAAAACGACTAAAAAGAATGAACTAAAAAATAATTTTTGAGT
AAATTATACGTTTAG
Found at i:41018 original size:143 final size:143
Alignment explanation
Indices: 40755--41040 Score: 518
Period size: 143 Copynumber: 2.0 Consensus size: 143
40745 TTTATTATCA
*
40755 AATATAGTTTCATTGGACCTTCCCACTTGACCTTCAAGTATTCAAAGATAATTTTCAGCCATAAT
1 AATACAGTTTCATTGGACCTTCCCACTTGACCTTCAAGTATTCAAAGATAATTTTCAGCCATAAT
40820 AACTCACAAATCCCAAGTGCCATTACCCTAAACTCAACTTCTGTACTTGATCTAGCCACAACATT
66 AACTCACAAATCCCAAGTGCCATTACCCTAAACTCAACTTCTGTACTTGATCTAGCCACAACATT
* *
40885 TTGTTTTTTGCTC
131 CTATTTTTTGCTC
*
40898 AATACAGTTTCATTGGACCTTCCCACTTGACCTTCAAGTCTTCAAAGATAATTTTCAGCCATAAT
1 AATACAGTTTCATTGGACCTTCCCACTTGACCTTCAAGTATTCAAAGATAATTTTCAGCCATAAT
* *
40963 AACTCACAAATCCCAAGTGCCATTACCCTAAACTCAACTTTTGTACTTGATCTAGCCACAACGTT
66 AACTCACAAATCCCAAGTGCCATTACCCTAAACTCAACTTCTGTACTTGATCTAGCCACAACATT
41028 CTATTTTTTGCTC
131 CTATTTTTTGCTC
41041 CTCCAAATCA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 137 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (143 bp):
AATACAGTTTCATTGGACCTTCCCACTTGACCTTCAAGTATTCAAAGATAATTTTCAGCCATAAT
AACTCACAAATCCCAAGTGCCATTACCCTAAACTCAACTTCTGTACTTGATCTAGCCACAACATT
CTATTTTTTGCTC
Found at i:45630 original size:2 final size:2
Alignment explanation
Indices: 45625--45666 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
45615 TAGGTGACTG
45625 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
45667 TCCCTTCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52118 original size:91 final size:90
Alignment explanation
Indices: 51972--52137 Score: 305
Period size: 91 Copynumber: 1.8 Consensus size: 90
51962 TTTTATAGCC
51972 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
1 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
* *
52037 GAATTTAATAATCCCTCTTATATCT
66 AAATTAAATAATCCCTCTTATATCT
52062 AAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 AAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
52127 GAAATTAAATA
65 GAAATTAAATA
52138 TTTGGGATTA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 23 0.32
91 50 0.68
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (90 bp):
AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
AAATTAAATAATCCCTCTTATATCT
Found at i:53186 original size:43 final size:43
Alignment explanation
Indices: 53139--53223 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
53129 GCATACTCTA
53139 ATACTACTAGTATGTTTATATGTATAATATTCATGATTCATAC
1 ATACTACTAGTATGTTTATATGTATAATATTCATGATTCATAC
53182 ATACTACTAGTATGTTTATATGTATAATATTCATGATTCATA
1 ATACTACTAGTATGTTTATATGTATAATATTCATGATTCATA
53224 TAGTATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (43 bp):
ATACTACTAGTATGTTTATATGTATAATATTCATGATTCATAC
Done.