Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001898.1 Hibiscus syriacus cultivar Beakdansim tig00003847_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: 74097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1178 original size:33 final size:33
Alignment explanation
Indices: 1111--1265 Score: 205
Period size: 33 Copynumber: 4.8 Consensus size: 33
1101 AAAGATAAAA
* *
1111 AATAAGTTGGCCA-CATACCAA-A-GAATTTTCC
1 AATAAATTGGCCACCA-ACCAAGATGAATTTTTC
*
1142 AATAAATTAGCCACCAACCAAGATGAATTTTTC
1 AATAAATTGGCCACCAACCAAGATGAATTTTTC
1175 AATAAATTGGCCACCAACCAA-A-GAA-TTTTC
1 AATAAATTGGCCACCAACCAAGATGAATTTTTC
*
1205 TAATAAATTGGCCACCAACCAAGATGAGTTTTTC
1 -AATAAATTGGCCACCAACCAAGATGAATTTTTC
*
1239 AATAAATTGACCACCAACCAAGATGAA
1 AATAAATTGGCCACCAACCAAGATGAA
1266 ATTTCTAACT
Statistics
Matches: 110, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
30 5 0.05
31 40 0.36
32 5 0.05
33 55 0.50
34 5 0.05
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (33 bp):
AATAAATTGGCCACCAACCAAGATGAATTTTTC
Found at i:1179 original size:64 final size:63
Alignment explanation
Indices: 1111--1259 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 63
1101 AAAGATAAAA
*
1111 AATAAGTTGGCCACATACCAAAGAATTTTCCAATAAATTAGCCACCAACCAAGATGAATTTTTC
1 AATAAATTGGCCACA-ACCAAAGAATTTTCCAATAAATTAGCCACCAACCAAGATGAATTTTTC
* * *
1175 AATAAATTGGCCACCAACCAAAGAATTTTCTAATAAATTGGCCACCAACCAAGATGAGTTTTTC
1 AATAAATTGGCCA-CAACCAAAGAATTTTCCAATAAATTAGCCACCAACCAAGATGAATTTTTC
*
1239 AATAAATTGACCACCAACCAA
1 AATAAATTGGCCA-CAACCAA
1260 GATGAAATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 77 0.97
65 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (63 bp):
AATAAATTGGCCACAACCAAAGAATTTTCCAATAAATTAGCCACCAACCAAGATGAATTTTTC
Found at i:3367 original size:57 final size:57
Alignment explanation
Indices: 3277--3388 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
3267 TGGAGCATGG
*
3277 TGAGTCTAGCCGATTGCCTAAACAGCTACGCTTGCAAGATCCGGAAGATCAGGCTGT
1 TGAGTCTAGCAGATTGCCTAAACAGCTACGCTTGCAAGATCCGGAAGATCAGGCTGT
* *
3334 TGAGTCTAGCAGATTGCCTAAAC-GTTTATGCTTGCAAGATCCGGAAGATCAGGCT
1 TGAGTCTAGCAGATTGCCTAAACAG-CTACGCTTGCAAGATCCGGAAGATCAGGCT
3389 TCATCTACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
56 1 0.02
57 50 0.98
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (57 bp):
TGAGTCTAGCAGATTGCCTAAACAGCTACGCTTGCAAGATCCGGAAGATCAGGCTGT
Found at i:14612 original size:21 final size:23
Alignment explanation
Indices: 14573--14614 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
14563 AAAATTGTAT
14573 TTAACGCTAAAGTCTAAAAAAAA
1 TTAACGCTAAAGTCTAAAAAAAA
*
14596 TTAA-GCTAAGGT-TAAAAAA
1 TTAACGCTAAAGTCTAAAAAA
14615 CGATGGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (23 bp):
TTAACGCTAAAGTCTAAAAAAAA
Found at i:15264 original size:22 final size:21
Alignment explanation
Indices: 15239--15279 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15229 ATTTAAATTT
15239 TAAAACTTAAAATCTTAAACGA
1 TAAAACTTAAAATC-TAAACGA
* *
15261 TAAAATTTAAACTCTAAAC
1 TAAAACTTAAAATCTAAAC
15280 TCTAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAACTTAAAATCTAAACGA
Found at i:30297 original size:18 final size:18
Alignment explanation
Indices: 30274--30308 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30264 TTCCATCCGG
*
30274 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
30292 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
30309 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:41432 original size:31 final size:31
Alignment explanation
Indices: 41397--41467 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
41387 TTATCATCAT
* *
41397 TTTAAATATGTAGTAAATGTCACGTTAACAC
1 TTTAAATATGTAATAAATGTCACATTAACAC
* * * * *
41428 TTTAAACATGTAATATATGTTATATTATCAC
1 TTTAAATATGTAATAAATGTCACATTAACAC
41459 TTTAAATAT
1 TTTAAATAT
41468 ATAACACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTAAATATGTAATAAATGTCACATTAACAC
Found at i:45186 original size:24 final size:24
Alignment explanation
Indices: 45159--45208 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45149 TGGTAGTTGG
45159 TTTAATGG-ATGTTTAAACTTTATT
1 TTTAATGGTATGTTT-AACTTTATT
*
45183 TTTAATGGTATGTTTAAGTTTATT
1 TTTAATGGTATGTTTAACTTTATT
45207 TT
1 TT
45209 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGTATGTTTAACTTTATT
Found at i:48450 original size:15 final size:15
Alignment explanation
Indices: 48426--48468 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
48416 TGAGTGTTTG
48426 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
48440 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
48454 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
48469 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:50832 original size:24 final size:24
Alignment explanation
Indices: 50787--50836 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
50777 TGGTGGTTGG
50787 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
* *
50811 TTTAGTGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
50835 TT
1 TT
50837 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:63440 original size:2 final size:2
Alignment explanation
Indices: 63433--63479 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
63423 AATTAGTCTA
63433 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
63475 AT AT A
1 AT AT A
63480 ACATTCTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67980 original size:29 final size:30
Alignment explanation
Indices: 67912--67980 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
67902 ATTTTAATTC
*
67912 AAACTCCGAAATATTGAAAATTAATATTAT
1 AAACTCCAAAATATTGAAAATTAATATTAT
**
67942 AAACTCCAAAATATTGAAAA-TGGTATTAT
1 AAACTCCAAAATATTGAAAATTAATATTAT
*
67971 AAACTTCAAA
1 AAACTCCAAA
67981 GTTAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (30 bp):
AAACTCCAAAATATTGAAAATTAATATTAT
Found at i:68697 original size:21 final size:21
Alignment explanation
Indices: 68672--68733 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
68662 TATGAAGTAC
68672 AATTAAATTATTTTTGATATT
1 AATTAAATTATTTTTGATATT
** **
68693 AATTAAAAAAAAATTTG-TATT
1 AATT-AAATTATTTTTGATATT
*
68714 AATTAAATTTTTTTTGATAT
1 AATTAAATTATTTTTGATAT
68734 ATAAGTATTT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 7 0.23
21 15 0.50
22 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
AATTAAATTATTTTTGATATT
Found at i:71810 original size:43 final size:43
Alignment explanation
Indices: 71749--71831 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
71739 GGAAGATATA
71749 TACTTTTCAGGTCAGATCGAGTGAATGATATAAAATTTTCAGG
1 TACTTTTCAGGTCAGATCGAGTGAATGATATAAAATTTTCAGG
* *
71792 TACTTTTCAGGTCGGATCGGGTGAATGATATAAAATTTTC
1 TACTTTTCAGGTCAGATCGAGTGAATGATATAAAATTTTC
71832 GGTTCGGTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (43 bp):
TACTTTTCAGGTCAGATCGAGTGAATGATATAAAATTTTCAGG
Done.