Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009362.1 Hibiscus syriacus cultivar Beakdansim tig00113186_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: 85733
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:610 original size:24 final size:25
Alignment explanation
Indices: 575--629 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
565 ACTTGGAGCC
*
575 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
599 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
623 TCAAGTG
1 TCAAGTG
630 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:4234 original size:17 final size:17
Alignment explanation
Indices: 4212--4246 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4202 AAATAAAATA
4212 AGGTAAGACTCCCTTAG
1 AGGTAAGACTCCCTTAG
4229 AGGTAAGACTCCCTTAG
1 AGGTAAGACTCCCTTAG
4246 A
1 A
4247 ATCAACAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (17 bp):
AGGTAAGACTCCCTTAG
Found at i:7068 original size:22 final size:20
Alignment explanation
Indices: 7043--7082 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7033 CATGTTTGTT
7043 ATGGTAATGTGAGCTAAGTATG
1 ATGGTAAT-T-AGCTAAGTATG
*
7065 ATGGTCATTAGCTAAGTA
1 ATGGTAATTAGCTAAGTA
7083 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (20 bp):
ATGGTAATTAGCTAAGTATG
Found at i:12147 original size:20 final size:20
Alignment explanation
Indices: 12122--12163 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12112 GCTATTTTTT
*
12122 AAAAAAAACAAAAATGCCAA
1 AAAAAAAACAAAAAAGCCAA
12142 AAAAAAAACAAAAAAGCCAA
1 AAAAAAAACAAAAAAGCCAA
12162 AA
1 AA
12164 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAACAAAAAAGCCAA
Found at i:17598 original size:14 final size:13
Alignment explanation
Indices: 17581--17630 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
17571 GTGCAAAAAG
17581 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
17595 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
17608 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
17619 AAAGAAAAAGAA
1 AAAGAAAAAGAA
17631 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:17627 original size:19 final size:18
Alignment explanation
Indices: 17575--17630 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
17565 ATTGGAGTGC
17575 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
17592 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
17611 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
17630 A
1 A
17631 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:17628 original size:11 final size:11
Alignment explanation
Indices: 17575--17630 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
17565 ATTGGAGTGC
17575 AAAAAG-AAAG
1 AAAAAGAAAAG
17585 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
17599 AAGAAGAAAAG
1 AAAAAGAAAAG
17610 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
17623 AAAAAGAA
1 AAAAAGAA
17631 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:20084 original size:17 final size:17
Alignment explanation
Indices: 20062--20094 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20052 ACCTATAGTT
*
20062 CACATCTTTATAATATG
1 CACATCATTATAATATG
20079 CACATCATTATAATAT
1 CACATCATTATAATAT
20095 ACTACATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:24672 original size:30 final size:31
Alignment explanation
Indices: 24620--24679 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
24610 CTTAGCTTTA
**
24620 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
24650 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
24680 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:29840 original size:27 final size:27
Alignment explanation
Indices: 29810--29875 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
29800 CTACTCTTTC
*
29810 ATGAATGTGCATGACTATTCGGTTGAA
1 ATGAAGGTGCATGACTATTCGGTTGAA
29837 ATGAAGGTGCATGACTATTCGGTTGAA
1 ATGAAGGTGCATGACTATTCGGTTGAA
29864 ATGAAGGTGCAT
1 ATGAAGGTGCAT
29876 CTCCCTTGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (27 bp):
ATGAAGGTGCATGACTATTCGGTTGAA
Found at i:30641 original size:15 final size:14
Alignment explanation
Indices: 30621--30650 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
30611 CCATCATAGC
30621 TATAGATGTAATATA
1 TATAGATG-AATATA
30636 TATAGATGAATATA
1 TATAGATGAATATA
30650 T
1 T
30651 CTATGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (14 bp):
TATAGATGAATATA
Found at i:38252 original size:14 final size:14
Alignment explanation
Indices: 38235--38273 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
38225 TTGCTTTTGA
38235 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
38249 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
38263 TTTTCTTCTTT
1 TTTTCTTCTTT
38274 CTTGTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:38271 original size:28 final size:29
Alignment explanation
Indices: 38217--38291 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
38207 ACTTGCTTCA
38217 CTTTTCTTTTGCTTTTGATTTTCTTCTTT-TT
1 CTTTTC-TTT-CTTTTG-TTTTCTTCTTTCTT
38248 CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
1 CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
* *
38277 -GTTTCTTTTTTTTGT
1 CTTTTCTTTCTTTTGT
38292 AGCACTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
28 24 0.59
29 8 0.20
30 3 0.07
31 6 0.15
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.76
Consensus pattern (29 bp):
CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
Found at i:38984 original size:16 final size:16
Alignment explanation
Indices: 38965--38996 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38955 TAGTTAACTC
38965 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
38981 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
38997 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:47911 original size:13 final size:13
Alignment explanation
Indices: 47889--47918 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47879 ACTAAACACC
47889 TTTC-ACATACCT
1 TTTCAACATACCT
47901 TTTCAACATACCT
1 TTTCAACATACCT
47914 TTTCA
1 TTTCA
47919 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:63708 original size:18 final size:18
Alignment explanation
Indices: 63682--63725 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
63672 GTGAAGTATG
* *
63682 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGGCGTGGCA
*
63700 AATGTTGTTGGCGTGGTA
1 AATGTTGTTGGCGTGGCA
*
63718 AGTGTTGT
1 AATGTTGT
63726 AATATTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.39, T:0.39
Consensus pattern (18 bp):
AATGTTGTTGGCGTGGCA
Found at i:68340 original size:14 final size:14
Alignment explanation
Indices: 68321--68350 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
68311 GGTGATGAAC
68321 TATGGTAATGGAAA
1 TATGGTAATGGAAA
*
68335 TATGGTGATGGAAA
1 TATGGTAATGGAAA
68349 TA
1 TA
68351 GTATCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
TATGGTAATGGAAA
Found at i:76922 original size:19 final size:21
Alignment explanation
Indices: 76879--76930 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
76869 GAAACCCCTT
76879 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
76900 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
76919 TGAAGATACATG
1 TGAAAATACATG
76931 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:85455 original size:15 final size:16
Alignment explanation
Indices: 85437--85474 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
85427 AGAAAAGATA
*
85437 AAATAAA-AGGAAATG
1 AAATAAAGAGAAAATG
85452 AAATAAAGAGAAAATG
1 AAATAAAGAGAAAATG
85468 AAGATAA
1 AA-ATAA
85475 CTTACAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.13
Consensus pattern (16 bp):
AAATAAAGAGAAAATG
Done.