Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004778.1 Hibiscus syriacus cultivar Beakdansim tig00010774_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: 52940
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3573 original size:13 final size:14
Alignment explanation
Indices: 3538--3574 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3528 TGTATTTATT
3538 TATTCTTTTGATTTG
1 TATTC-TTTGATTTG
3553 TATTCTTTGATTTG
1 TATTCTTTGATTTG
3567 T-TTCTTTG
1 TATTCTTTG
3575 GCTTCCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.68
Consensus pattern (14 bp):
TATTCTTTGATTTG
Found at i:15987 original size:21 final size:21
Alignment explanation
Indices: 15923--15994 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
15913 TTAATTAGGG
*
15923 TTTAGGGTTTAAGGTTTTAGAA
1 TTTAAGGTTT-AGGTTTTAGAA
*
15945 TGTAAGGTTTAGG-TTTAGAA
1 TTTAAGGTTTAGGTTTTAGAA
*
15965 TTTAAGGTTTGGGTTTTAGAA
1 TTTAAGGTTTAGGTTTTAGAA
*
15986 TTTAGGGTT
1 TTTAAGGTT
15995 CAAATAGGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 18 0.41
21 18 0.41
22 8 0.18
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTAGGTTTTAGAA
Found at i:28388 original size:32 final size:31
Alignment explanation
Indices: 28347--28440 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
28337 AAAAAAAGCC
** *
28347 ATATCAATTTGGATTAAAAAAATTAAATTTAA
1 ATATCAATTTCAATT-AAAAAATTAAACTTAA
*
28379 ATATTAATTTCAATTAAAAAATTAAACTTAA
1 ATATCAATTTCAATTAAAAAATTAAACTTAA
* * * * * *
28410 ACATCAATATAAATTAACAAATCAAATTTAA
1 ATATCAATTTCAATTAAAAAATTAAACTTAA
28441 GTATATCATT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 39 0.76
32 12 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.35
Consensus pattern (31 bp):
ATATCAATTTCAATTAAAAAATTAAACTTAA
Found at i:28401 original size:31 final size:31
Alignment explanation
Indices: 28363--28440 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
28353 ATTTGGATTA
* * * *
28363 AAAAAATTAAATTTAAATATTAATTTCAATT
1 AAAAAATTAAATTTAAACATCAATATAAATT
*
28394 AAAAAATTAAACTTAAACATCAATATAAATT
1 AAAAAATTAAATTTAAACATCAATATAAATT
* *
28425 AACAAATCAAATTTAA
1 AAAAAATTAAATTTAA
28441 GTATATCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAAATTAAATTTAAACATCAATATAAATT
Found at i:29029 original size:60 final size:60
Alignment explanation
Indices: 28875--29030 Score: 149
Period size: 61 Copynumber: 2.6 Consensus size: 60
28865 GGAATGTTCA
** * *
28875 AAAAGTTATAG-GACCAATTTAGAATGCAG-GTCATAGTTTGGAGATGGAATTGAAAACGTTC
1 AAAAGTT-TAGAGA-CAATTTAGAATG-AGAGTCATAGTTTACAGATGAAATTGAAAACATTC
* * * *
28936 AAAAGTTT-GAGGAAAAGTTTAGAATGATAGTCATAGTTTACAGATGAAATTG-GAACATTT
1 AAAAGTTTAGA-GACAA-TTTAGAATGAGAGTCATAGTTTACAGATGAAATTGAAAACATTC
*
28996 AAAAGTTTAGAGATCAATTTAAAATGAGAGTCATA
1 AAAAGTTTAGAGA-CAATTTAGAATGAGAGTCATA
29031 CTGTGAGGAC
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
59 1 0.01
60 35 0.45
61 42 0.54
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (60 bp):
AAAAGTTTAGAGACAATTTAGAATGAGAGTCATAGTTTACAGATGAAATTGAAAACATTC
Found at i:33748 original size:21 final size:20
Alignment explanation
Indices: 33715--33753 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
33705 GAATGTGTCT
*
33715 GCAGAGGACAAAACCACCGG
1 GCAGAAGACAAAACCACCGG
*
33735 GCAGAAGAGCAAAATCACC
1 GCAGAAGA-CAAAACCACC
33754 ATTACAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.28, G:0.26, T:0.03
Consensus pattern (20 bp):
GCAGAAGACAAAACCACCGG
Found at i:34754 original size:22 final size:20
Alignment explanation
Indices: 34720--34762 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
34710 ATATTTATTT
* *
34720 AAAATATTTTTTATCAAATAA
1 AAAATATGTTTTA-AAAATAA
34741 AAAATTATGTTTTAAAAATAA
1 AAAA-TATGTTTTAAAAATAA
34762 A
1 A
34763 TATTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAATATGTTTTAAAAATAA
Found at i:44205 original size:13 final size:13
Alignment explanation
Indices: 44187--44212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44177 TGACCTAAAG
44187 AAATATGAGCAAC
1 AAATATGAGCAAC
44200 AAATATGAGCAAC
1 AAATATGAGCAAC
44213 TTAACCGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AAATATGAGCAAC
Found at i:44802 original size:7 final size:7
Alignment explanation
Indices: 44790--44815 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44780 TAACAATGTA
44790 TTAAATT
1 TTAAATT
44797 TTAAATT
1 TTAAATT
44804 TTAAATT
1 TTAAATT
44811 TTAAA
1 TTAAA
44816 AAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:48384 original size:23 final size:22
Alignment explanation
Indices: 48355--48422 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
48345 AAAAAGTTTA
48355 AAAATTTTAAGATTTTTTATTTT
1 AAAATTTTAA-ATTTTTTATTTT
* *
48378 AAAATTTTAATATAATGTTATTTT
1 AAAATTTTAA-AT-TTTTTATTTT
*
48402 AAATATTTTTAATTTTTTATT
1 AAA-ATTTTAAATTTTTTATT
48423 ACTTTCAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 18 0.49
24 13 0.35
25 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
AAAATTTTAAATTTTTTATTTT
Found at i:48737 original size:2 final size:2
Alignment explanation
Indices: 48730--48754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48720 TACAAAAATA
48730 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
48755 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.