Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009002.1 Hibiscus syriacus cultivar Beakdansim tig00112384_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: 64674
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4486 original size:18 final size:18
Alignment explanation
Indices: 4463--4506 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4453 AACTTTGACT
*
4463 AAAAAGTCAACCT-TTTCG
1 AAAAAGGCAA-CTGTTTCG
4481 AAAAAGGCAACTGTTTCG
1 AAAAAGGCAACTGTTTCG
*
4499 AAGAAGGC
1 AAAAAGGC
4507 CTATTTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (18 bp):
AAAAAGGCAACTGTTTCG
Found at i:7442 original size:59 final size:60
Alignment explanation
Indices: 7365--7541 Score: 209
Period size: 60 Copynumber: 3.0 Consensus size: 60
7355 TCGTATGTTC
7365 TCAAACT-ATGATCCTCATTTTAAATTAGTCCCTAAA-TTTTGAATATTCTAATTTCATCA
1 TCAAACTAAT-ATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCATCA
* * * * *
7424 TCAAACTAATATACTCATTTTAAACTAGTCCTTAAACTTTTGAACATTCTAATTTCATCC
1 TCAAACTAATATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCATCA
* * * * *
7484 TCAAACTACA-ACCCTTATTCTAAATTGGTCCCTAAACTTTTAAATATT-TCAATTTCAT
1 TCAAACTA-ATATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCT-AATTTCAT
7542 TCTCAAATTT
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
59 31 0.31
60 68 0.68
61 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
TCAAACTAATATCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCATCA
Found at i:13606 original size:2 final size:2
Alignment explanation
Indices: 13599--13630 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13589 AGGCTTCGTG
13599 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
13631 GTAATTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19182 original size:94 final size:94
Alignment explanation
Indices: 19056--19233 Score: 311
Period size: 94 Copynumber: 1.9 Consensus size: 94
19046 ATTTTGATTA
* * *
19056 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAATTCACTCTTCTTCTTATTCTTTTAATCGTT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
*
19121 AGAGTTCCTTTATTGGGTGTTTCAGACTC
66 AGAGTTCATTTATTGGGTGTTTCAGACTC
19150 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
1 TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
*
19215 AGGGTTCATTTATTGGGTG
66 AGAGTTCATTTATTGGGTG
19234 CTTCTCGTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 79 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (94 bp):
TGTTCATCACAAAACGATGCTTCTAGTTCTAGGAACTCACTCCTCTTCTTATTCTTTTAATCATT
AGAGTTCATTTATTGGGTGTTTCAGACTC
Found at i:21537 original size:16 final size:16
Alignment explanation
Indices: 21497--21530 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21487 TTTTAAGTGT
21497 TTAACA-TTTTTTTCG
1 TTAACATTTTTTTTCG
21512 TTAACATTTTTTTTCG
1 TTAACATTTTTTTTCG
21528 TTA
1 TTA
21531 CTATTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAACATTTTTTTTCG
Found at i:22151 original size:21 final size:21
Alignment explanation
Indices: 22127--22232 Score: 83
Period size: 20 Copynumber: 5.2 Consensus size: 21
22117 ACGTTGCATT
*
22127 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** ** **
22148 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
22168 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
22189 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
22209 TCGCGTTGCGATAGTTG-AAA
1 TCGCGTTGCGATAGTTGAAAA
22229 TCGC
1 TCGC
22233 AACGCGATCT
Statistics
Matches: 61, Mismatches: 22, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:22168 original size:41 final size:41
Alignment explanation
Indices: 22123--22232 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
22113 ATTCACGTTG
* *
22123 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22164 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22205 CATTTCGCGTTGCGATAGTTG-AAATCGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGC
22233 AACGCGATCT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 7 0.10
41 60 0.90
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:22676 original size:41 final size:41
Alignment explanation
Indices: 22411--22659 Score: 392
Period size: 41 Copynumber: 6.0 Consensus size: 41
22401 ACAACGAATT
* *
22411 TGGAAAATCGCAACGACGACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
*
22453 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
22494 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* * *
22535 TGGAAAATCGTAACACGGTTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
22576 TGGAAAATCGCAATGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
22617 TGCAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
22658 TG
1 TG
22660 CAATGCGAAT
Statistics
Matches: 194, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
41 178 0.92
42 16 0.08
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Found at i:23913 original size:20 final size:20
Alignment explanation
Indices: 23890--23938 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
23880 AATTTATCTA
*
23890 ATTTAAGATTCA-ATTATTTT
1 ATTTAAAATTCAGA-TATTTT
*
23910 ATTTAAAATTTAGATATTTT
1 ATTTAAAATTCAGATATTTT
23930 ATTTAAAAT
1 ATTTAAAAT
23939 GTATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTTAAAATTCAGATATTTT
Found at i:23984 original size:29 final size:28
Alignment explanation
Indices: 23952--24007 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
23942 TAATTTAAGT
23952 TTTAAATTTTAGA-ATTTAGAAATTAAAAA
1 TTTAAATTTTA-ATATTTA-AAATTAAAAA
*
23981 TTTAGATTTTAATATTTAAAATTAAAA
1 TTTAAATTTTAATATTTAAAATTAAAA
24008 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTAAATTTTAATATTTAAAATTAAAAA
Found at i:24001 original size:21 final size:21
Alignment explanation
Indices: 23909--24003 Score: 88
Period size: 21 Copynumber: 4.5 Consensus size: 21
23899 TCAATTATTT
23909 TATTTAAAATTTAGATATTT--
1 TATTTAAAATTTAGA-ATTTAA
* *
23929 TATTTAAAATGTATAATTTAA
1 TATTTAAAATTTAGAATTTAA
*
23950 GT-TTTAAATTTTAGAATTTAGA
1 -TATTTAAAATTTAGAATTTA-A
* * *
23972 AATTAAAAATTTAGATTTTAA
1 TATTTAAAATTTAGAATTTAA
23993 TATTTAAAATT
1 TATTTAAAATT
24004 AAAATAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 13 0.22
21 25 0.42
22 17 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
TATTTAAAATTTAGAATTTAA
Found at i:25417 original size:15 final size:16
Alignment explanation
Indices: 25399--25428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25389 ATTTAATAGT
25399 TAAATTA-ATAAAATA
1 TAAATTATATAAAATA
25414 TAAATTATATAAAAT
1 TAAATTATATAAAAT
25429 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTATATAAAATA
Found at i:28504 original size:3 final size:3
Alignment explanation
Indices: 28485--28545 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
28475 TAAAAGATTA
*
28485 TTC TTT TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28532 TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TT
28546 GTTTTCTGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:32948 original size:16 final size:16
Alignment explanation
Indices: 32927--32958 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32917 ACTATTCACA
*
32927 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
32943 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
32959 ATCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:37866 original size:215 final size:218
Alignment explanation
Indices: 37443--37883 Score: 537
Period size: 215 Copynumber: 2.0 Consensus size: 218
37433 AACAAGTCTC
* * * * * *
37443 TAATAAGATTTGGTTCGTGATCTCGCAAGTTGTGCAATTGTGCGCTAATCGTATCGTTGTTGTAT
1 TAATAA-ATTTGGTTCGTGATATCGCAAGTTATGCAACTGTACACTAATCGTATCGTTATTGTAT
* * * ** * * * *
37508 CTTGGGAAACATACGGCCAAGATATCTCGAGCACCAAAGAGTGACTGAAAATTTGTCTTAAGGAA
65 CCTGAGAAACAGACAACCAAGATATCTCAAACACCAAAGAGTGACTGAAAATATGTCTTAAGAAA
* * * *
37573 ATTGCGTAATTGCAGGCATCAACCATATTCAAGTTCGATTTCATCTTATTATTCAAGTTCTTTAT
130 ACTGCGTAATTACAGGCATCAACCAAATTCAAGTACGATTTCATCTTATTATTCAAGTTCTTTAT
37638 TCTAATATGTTCCTCCTCATTCAT
195 TCTAATATGTTCCTCCTCATTCAT
* * * *
37662 TAATAAATTTGGTTTGTGATATCGCAAGTTATGCTACTGTACATTGATCGTATCGTTATTGTATC
1 TAATAAATTTGGTTCGTGATATCGCAAGTTATGCAACTGTACACTAATCGTATCGTTATTGTATC
* * * *
37727 CTGAGAGACAGACAACCAAGATATCTTAAACACCAAGGAGTGGCT-AAAA-ATGTCTTAA-AAAA
66 CTGAGAAACAGACAACCAAGATATCTCAAACACCAAAGAGTGACTGAAAATATGTCTTAAGAAAA
* * * * * **
37789 CTGCGTAGTTACAGGCCTCAACCAAATTCAGGTACGATTTCTTGTTATTATTCGGGTTCTTTATT
131 CTGCGTAATTACAGGCATCAACCAAATTCAAGTACGATTTCATCTTATTATTCAAGTTCTTTATT
*
37854 CTAATATGTTCCTCCTCATTTAT
196 CTAATATGTTCCTCCTCATTCAT
37877 TAATAAA
1 TAATAAA
37884 GTTCGATATT
Statistics
Matches: 187, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
215 86 0.46
216 8 0.04
217 4 0.02
218 83 0.44
219 6 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (218 bp):
TAATAAATTTGGTTCGTGATATCGCAAGTTATGCAACTGTACACTAATCGTATCGTTATTGTATC
CTGAGAAACAGACAACCAAGATATCTCAAACACCAAAGAGTGACTGAAAATATGTCTTAAGAAAA
CTGCGTAATTACAGGCATCAACCAAATTCAAGTACGATTTCATCTTATTATTCAAGTTCTTTATT
CTAATATGTTCCTCCTCATTCAT
Found at i:40759 original size:21 final size:22
Alignment explanation
Indices: 40726--40766 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40716 TTAAAAATTA
*
40726 TAAAGGTAGTACCGATACTCAT
1 TAAAGGTAGTACCAATACTCAT
40748 TAAAGG-AGTACCAATACTC
1 TAAAGGTAGTACCAATACTC
40767 CCTGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TAAAGGTAGTACCAATACTCAT
Found at i:41973 original size:20 final size:20
Alignment explanation
Indices: 41932--41979 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
41922 AATGATTTTC
* *
41932 TTTTGAAAGCAAAATTGGAT
1 TTTTAAAAGCAAAATTGAAT
41952 TTTTAAAAGCAAAA-TGAAAT
1 TTTTAAAAGCAAAATTG-AAT
*
41972 TTTGAAAA
1 TTTTAAAA
41980 TGATTTTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTAAAAGCAAAATTGAAT
Found at i:52848 original size:26 final size:26
Alignment explanation
Indices: 52819--52871 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52809 AGAGTAACTT
52819 GTAATGCGATGGCATGGCTCATCTTA
1 GTAATGCGATGGCATGGCTCATCTTA
52845 GTAATGCGATGGCATGGCTCATCTTA
1 GTAATGCGATGGCATGGCTCATCTTA
52871 G
1 G
52872 GAGAGCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (26 bp):
GTAATGCGATGGCATGGCTCATCTTA
Found at i:58463 original size:23 final size:23
Alignment explanation
Indices: 58433--58482 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
58423 CGAACCTACA
58433 TTACTTGGACTTAGGTATGAGTT
1 TTACTTGGACTTAGGTATGAGTT
58456 TTACTTGGACTTAGGTATGAGTT
1 TTACTTGGACTTAGGTATGAGTT
58479 TTAC
1 TTAC
58483 ATATACAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (23 bp):
TTACTTGGACTTAGGTATGAGTT
Found at i:59497 original size:29 final size:29
Alignment explanation
Indices: 59441--59502 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
59431 AAAATGGGTT
59441 AAAATCTGAAACTTGAAAAGGGAATAAAA
1 AAAATCTGAAACTTGAAAAGGGAATAAAA
*
59470 AAAAT-TGAAACTTGAAAAGGGAATTAAA
1 AAAATCTGAAACTTGAAAAGGGAATAAAA
59498 AAAAT
1 AAAAT
59503 GTACCTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (29 bp):
AAAATCTGAAACTTGAAAAGGGAATAAAA
Found at i:61636 original size:32 final size:32
Alignment explanation
Indices: 61593--61654 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
61583 ATAACTTGGT
*
61593 TTTTTCATGTTGTCAAAGAGTTGAATAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
61625 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
61655 AAAATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Done.