Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001467.1 Hibiscus syriacus cultivar Beakdansim tig00002842_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: 63200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:6575 original size:30 final size:30
Alignment explanation
Indices: 6539--6595 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
6529 TGAGCAGGAA
6539 TGATAAAGGGAAAGGGAAAATGGTTGATAC
1 TGATAAAGGGAAAGGGAAAATGGTTGATAC
*
6569 TGATAAAGGTAAAGGGAAAATGGTTGA
1 TGATAAAGGGAAAGGGAAAATGGTTGA
6596 CACCGTACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.33, T:0.21
Consensus pattern (30 bp):
TGATAAAGGGAAAGGGAAAATGGTTGATAC
Found at i:9293 original size:60 final size:60
Alignment explanation
Indices: 9199--9321 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
9189 ATAGTTTGCG
* * ** * *
9199 ATGAAAGTCATAGTTTGGGGATGGAATTGAAATGTTCACAAGTTTA-AGGACTAATTTAGA
1 ATGAAAGCCATAGCTTAAGGATGAAATTGAAATGTTCAAAAGTTTAGA-GACTAATTTAGA
* *
9259 ATGAAAGCCATAGCTTAAGGATGAAATTGGAATGTTTAAAAGTTTAGAGACTAATTTAGA
1 ATGAAAGCCATAGCTTAAGGATGAAATTGAAATGTTCAAAAGTTTAGAGACTAATTTAGA
9319 ATG
1 ATG
9322 GGAAACAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (60 bp):
ATGAAAGCCATAGCTTAAGGATGAAATTGAAATGTTCAAAAGTTTAGAGACTAATTTAGA
Found at i:18246 original size:20 final size:20
Alignment explanation
Indices: 18221--18266 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18211 CTGTTGGTAC
**
18221 CGATACTGAACTTTCAGTAT
1 CGATACTGAACCCTCAGTAT
*
18241 CGATACTGAACCCTGAGTAT
1 CGATACTGAACCCTCAGTAT
18261 CGATAC
1 CGATAC
18267 CCACTTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (20 bp):
CGATACTGAACCCTCAGTAT
Found at i:25715 original size:21 final size:21
Alignment explanation
Indices: 25689--25728 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25679 ATTGAATTTG
*
25689 GATCCGGATATTT-GGATATCC
1 GATCC-GAAATTTCGGATATCC
25710 GATCCGAAATTTCGGATAT
1 GATCCGAAATTTCGGATAT
25729 TCGGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GATCCGAAATTTCGGATATCC
Found at i:32935 original size:2 final size:2
Alignment explanation
Indices: 32928--32973 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
32918 TTGAATTGAC
32928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32970 TA TA
1 TA TA
32974 AAAGCTTAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35303 original size:31 final size:32
Alignment explanation
Indices: 35268--35329 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
35258 ATTAAAACAC
**
35268 TAAAACAGA-CAAAAACTGATAATTTAAGTAT
1 TAAAACAGACCAAAAACAAATAATTTAAGTAT
* *
35299 TAAAATATACCAAAAACAAATAATTTAAGTA
1 TAAAACAGACCAAAAACAAATAATTTAAGTA
35330 CTACCCGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (32 bp):
TAAAACAGACCAAAAACAAATAATTTAAGTAT
Found at i:41558 original size:35 final size:34
Alignment explanation
Indices: 41519--41596 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
41509 AGTTCAGTCC
*
41519 TCAATTTCATTCTAAACTCTAAATTTCAAAATAAT
1 TCAATTT-ATTCTAAACCCTAAATTTCAAAATAAT
* * *
41554 TCAATTATATTTTAAACCCTAAATTTTAAAATACT
1 TCAATT-TATTCTAAACCCTAAATTTCAAAATAAT
41589 TCAATTTA
1 TCAATTTA
41597 GGGTTTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 35 0.92
36 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (34 bp):
TCAATTTATTCTAAACCCTAAATTTCAAAATAAT
Found at i:41630 original size:35 final size:35
Alignment explanation
Indices: 41591--41665 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
41581 AAAATACTTC
*
41591 AATTTAGGGTTTAGAAT-ATAATTAAAGTATTTTGG
1 AATTTAGGGCTTAGAATGA-AATTAAAGTATTTTGG
* *
41626 AATTTAGGGCTTAGAATGAAATTGAAGTGTTTTGG
1 AATTTAGGGCTTAGAATGAAATTAAAGTATTTTGG
41661 AATTT
1 AATTT
41666 TGAACATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AATTTAGGGCTTAGAATGAAATTAAAGTATTTTGG
Found at i:51393 original size:31 final size:32
Alignment explanation
Indices: 51355--51415 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
51345 AGATTCATAA
* *
51355 GTTAAATTGATA-TTTTATCTAAATTTCAAAG
1 GTTAAATTAATATTTTTATCTAAAGTTCAAAG
*
51386 GTTAAATTAATATTTTTATCTGAAGTTCAA
1 GTTAAATTAATATTTTTATCTAAAGTTCAA
51416 GGATAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (32 bp):
GTTAAATTAATATTTTTATCTAAAGTTCAAAG
Found at i:51425 original size:32 final size:31
Alignment explanation
Indices: 51358--51427 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
51348 TTCATAAGTT
* * *
51358 AAATTGATATTTTATCTAAATTTCAAAGGTT
1 AAATTAATATTTTATCTAAAGTTCAAAGGTA
*
51389 AAATTAATATTTTTATCTGAAGTTC-AAGGATA
1 AAATTAATA-TTTTATCTAAAGTTCAAAGG-TA
51421 AAATTAA
1 AAATTAA
51428 AAAATTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (31 bp):
AAATTAATATTTTATCTAAAGTTCAAAGGTA
Found at i:52349 original size:24 final size:24
Alignment explanation
Indices: 52321--52367 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52311 GATTTAATAG
*
52321 AATGTAACGTTAAATTCTTTAAGT
1 AATGTAACATTAAATTCTTTAAGT
52345 AATGTAACATTAAATTCTTTAAG
1 AATGTAACATTAAATTCTTTAAG
52368 ATCGTCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (24 bp):
AATGTAACATTAAATTCTTTAAGT
Found at i:55233 original size:85 final size:84
Alignment explanation
Indices: 55091--55261 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 84
55081 CTTCACAGAA
*
55091 AAAAAAAAATTAACTCGACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
1 AAAAAAAAATTAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
55156 ACACTTGTATTGTCGTTGT
66 ACACTTGTATTGTCGTTGT
* * *
55175 AAAAAAAATTCTAACTCAACTTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACATTTGC
1 AAAAAAAAAT-TAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGC
55240 CACACTTGTATTGTCGTTGT
65 CACACTTGTATTGTCGTTGT
55260 AA
1 AA
55262 CACTCCAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 9 0.11
85 73 0.89
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (84 bp):
AAAAAAAAATTAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
ACACTTGTATTGTCGTTGT
Found at i:57059 original size:2 final size:2
Alignment explanation
Indices: 57052--57099 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57042 CCGATTTTCA
57052 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
57094 AT AT AT
1 AT AT AT
57100 GCATATGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.