Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006133.1 Hibiscus syriacus cultivar Beakdansim tig00014543_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: 44537
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:798 original size:17 final size:17
Alignment explanation
Indices: 776--815 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
766 TTCAAACATC
* *
776 ATAAAGATGTCTTATTG
1 ATAAAGATGCCTTAATG
793 ATAAAGATGCCTTAATG
1 ATAAAGATGCCTTAATG
810 ATAAAG
1 ATAAAG
816 CTAGAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (17 bp):
ATAAAGATGCCTTAATG
Found at i:4455 original size:21 final size:24
Alignment explanation
Indices: 4422--4465 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 24
4412 TGATTTGGTC
4422 TTATCTCAATTAAA-T-GAATATT
1 TTATCTCAATTAAAGTGGAATATT
*
4444 TTAT-TCATTTAAAGTGGAATAT
1 TTATCTCAATTAAAGTGGAATAT
4466 AATGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (24 bp):
TTATCTCAATTAAAGTGGAATATT
Found at i:6150 original size:45 final size:45
Alignment explanation
Indices: 6063--6193 Score: 210
Period size: 45 Copynumber: 2.9 Consensus size: 45
6053 GTAATCATGC
*
6063 AAATAAGCTTACAAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
6107 AATTAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
6152 AAATAAGCTTACAAGATTGTGGGATAAATGGTAAGTATATTG
1 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTG
6194 ATAAGAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 22 0.28
45 57 0.72
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:10849 original size:13 final size:13
Alignment explanation
Indices: 10831--10869 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
10821 ATGGGCGTGA
*
10831 ATGGTGATGGAGG
1 ATGGTGATGGAAG
*
10844 ATGGTGATTGAAAG
1 ATGGTGA-TGGAAG
10858 ATGGTGATGGAA
1 ATGGTGATGGAA
10870 ATAGATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:10862 original size:14 final size:14
Alignment explanation
Indices: 10831--10870 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
10821 ATGGGCGTGA
*
10831 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
*
10844 ATGGTGATTGAAAG
1 ATGGTGATGGAAAG
10858 ATGGTGATGGAAA
1 ATGGTGATGGAAA
10871 TAGATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:14874 original size:18 final size:18
Alignment explanation
Indices: 14853--14902 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
14843 TGTAGGAGTC
*
14853 TTTTCTTTTCTCTTTTGT
1 TTTTCTTTTCTCTTTTCT
14871 TTTTCTTCTT-TC-TTTCT
1 TTTTCTT-TTCTCTTTTCT
*
14888 TTCT-TTTTCTCTTTT
1 TTTTCTTTTCTCTTTT
14903 TGTTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.07
16 4 0.15
17 10 0.37
18 9 0.33
19 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTCTCTTTTCT
Found at i:14881 original size:21 final size:22
Alignment explanation
Indices: 14855--14902 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
14845 TAGGAGTCTT
*
14855 TTCTTTTCTCT-TTTGTTTTTC
1 TTCTTTTCTCTCTTTCTTTTTC
*
14876 TTC-TTTCTTTCTTTCTTTTTC
1 TTCTTTTCTCTCTTTCTTTTTC
14897 -TCTTTT
1 TTCTTTT
14903 TGTTGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (22 bp):
TTCTTTTCTCTCTTTCTTTTTC
Found at i:19170 original size:61 final size:61
Alignment explanation
Indices: 19074--19189 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
19064 GTGTTAAACC
19074 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
1 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
* * * * * * *
19135 TACACTAGGTTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCC
1 TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCC
19190 TCCACCTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (61 bp):
TACACTAAGCTTACACTATAGTGCTAATCCAGATATGAAACACAAGGTCGTGCCCACCATG
Found at i:25787 original size:17 final size:18
Alignment explanation
Indices: 25755--25790 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
25745 ATCGGTGCTC
25755 AACAATGGCTATAACATT
1 AACAATGGCTATAACATT
*
25773 AACAATGTC-ATAACATT
1 AACAATGGCTATAACATT
25790 A
1 A
25791 GTATATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (18 bp):
AACAATGGCTATAACATT
Found at i:27107 original size:19 final size:19
Alignment explanation
Indices: 27083--27124 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
27073 CAACACAAAC
*
27083 AAAAAAGATAA-AAGAAATG
1 AAAAAA-ATAAGAAAAAATG
27102 AAAAAAATAAGAAAAAATG
1 AAAAAAATAAGAAAAAATG
27121 AAAA
1 AAAA
27125 CTAAGCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAGAAAAAATG
Found at i:34834 original size:22 final size:23
Alignment explanation
Indices: 34807--34850 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34797 CAAGAAGTTT
*
34807 TCTTCTCTTGA-AAAATATTTTC
1 TCTTCTCTTCATAAAATATTTTC
*
34829 TCTTCTTTTCATAAAATATTTT
1 TCTTCTCTTCATAAAATATTTT
34851 TTCTCCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (23 bp):
TCTTCTCTTCATAAAATATTTTC
Found at i:36756 original size:21 final size:21
Alignment explanation
Indices: 36726--36773 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
36716 TAGAATAAGT
*
36726 GATTTGGCATAACCAAAATTA
1 GATTTTGCATAACCAAAATTA
36747 GATTTTGCATAACCAAAATTA
1 GATTTTGCATAACCAAAATTA
36768 GATTTT
1 GATTTT
36774 AGTTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
GATTTTGCATAACCAAAATTA
Found at i:38136 original size:21 final size:21
Alignment explanation
Indices: 38096--38136 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38086 AATGATTTAC
*
38096 GACTCGATCAACAGTTAACAT
1 GACTCGATCAACAGTCAACAT
*
38117 GACTCGATCAACGGTCAACA
1 GACTCGATCAACAGTCAACA
38137 CGGGCTCAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (21 bp):
GACTCGATCAACAGTCAACAT
Found at i:40737 original size:2 final size:2
Alignment explanation
Indices: 40730--40766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40720 CAAAATGAGC
*
40730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40767 ATGGATGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.