Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003415.1 Hibiscus syriacus cultivar Beakdansim tig00007193_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: 63554
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3924 original size:51 final size:51
Alignment explanation
Indices: 3832--4075 Score: 297
Period size: 51 Copynumber: 4.9 Consensus size: 51
3822 CATAATTCAT
***
3832 AATACAAAAA-TGTAGCACTTAACACATACTTACATATGTGTAAGTGAATAA
1 AATA-AAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
*
3883 AATAAATAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
1 AATAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
* *
3934 CAACAAAAAAGTGTAGCACTTAACACATTC-TACACCGGTGTAAGTGAAT-A
1 -AATAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
* * * * *
3984 AATAAAAAAGTGTAGCACTTAACACATATTTACAACAGTGCAAGTAAATAA
1 AATAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
*
4035 AAT-AAAAA--GTAGCAGC-TAACACATAC-TACACCGATGTAAGT
1 AATAAAAAAGTGTAGCA-CTTAACACATACTTACACCGGTGTAAGT
4076 TACATCTCCC
Statistics
Matches: 169, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
47 11 0.07
48 15 0.09
49 27 0.16
50 25 0.15
51 65 0.38
52 26 0.15
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (51 bp):
AATAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAA
Found at i:4010 original size:101 final size:99
Alignment explanation
Indices: 3837--4075 Score: 304
Period size: 101 Copynumber: 2.4 Consensus size: 99
3827 TTCATAATAC
*** *
3837 AAAAATGTAGCACTTAACACATACTTACATATGTGTAAGTGAATAAAATAAATAAGTGTAGCACT
1 AAAAATGTAGCACTTAACACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
* * * *
3902 TAACACATACTTACACCGGTGTAAGTGAATAACAACA
65 TAACACATACTTACAACAGTGCAAGTAAATAA-AA-A
*
3939 AAAAAGTGTAGCACTTAACACATTCTACACCGGTGTAAGTGAAT-AAATAAAAAAGTGTAGCACT
1 AAAAA-TGTAGCACTTAACACATACTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
* *
4003 TAACACATATTTACAACAGTGCAAGTAAATAAAAT
65 TAACACATACTTACAACAGTGCAAGTAAATAAAAA
*
4038 AAAAA-GTAGCAGC-TAACACATACTACACCGATGTAAGT
1 AAAAATGTAGCA-CTTAACACATACTACACCGGTGTAAGT
4076 TACATCTCCC
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
97 29 0.24
98 1 0.01
99 5 0.04
100 2 0.02
101 46 0.38
102 21 0.17
103 18 0.15
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (99 bp):
AAAAATGTAGCACTTAACACATACTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTT
AACACATACTTACAACAGTGCAAGTAAATAAAAA
Found at i:7318 original size:42 final size:42
Alignment explanation
Indices: 7259--7343 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
7249 TATTGGATTA
7259 AGACACTAGATCCCTTCAATAAGGTCAGTAGTTCGAATCTCG
1 AGACACTAGATCCCTTCAATAAGGTCAGTAGTTCGAATCTCG
*
7301 AGACACTAGATCCCTTCAATAAGGTTAGTAGTTCGAATCTCG
1 AGACACTAGATCCCTTCAATAAGGTCAGTAGTTCGAATCTCG
7343 A
1 A
7344 CTTTTATTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
AGACACTAGATCCCTTCAATAAGGTCAGTAGTTCGAATCTCG
Found at i:11886 original size:50 final size:50
Alignment explanation
Indices: 11811--11912 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
11801 TCTGGGATAG
* *
11811 TACTATAATGTATTTTTAGTTGTGTTCCCCGATTATGAAGAGTTACTAAA
1 TACTATAATGTATTTTTAGTTGTGTTCCCCAATTATGAAAAGTTACTAAA
*
11861 TACTATAATGTATTTTTAGTTGTGTTCCCCAATTATGAAAATTTACTAAA
1 TACTATAATGTATTTTTAGTTGTGTTCCCCAATTATGAAAAGTTACTAAA
11911 TA
1 TA
11913 GTAATACAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (50 bp):
TACTATAATGTATTTTTAGTTGTGTTCCCCAATTATGAAAAGTTACTAAA
Found at i:27331 original size:34 final size:34
Alignment explanation
Indices: 27286--27352 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
27276 AATAGGAATT
*
27286 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
27321 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
27353 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:28391 original size:23 final size:23
Alignment explanation
Indices: 28365--28409 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28355 CACCACAGCT
*
28365 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
28388 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
28410 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:28647 original size:149 final size:149
Alignment explanation
Indices: 28388--28691 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
28378 CGAAGTGCCC
*
28388 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
28453 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28518 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
28537 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
28602 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28667 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
28686 CGTAGA
1 CGTAGA
28692 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:29539 original size:18 final size:18
Alignment explanation
Indices: 29518--29552 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29508 TCCCATCTAG
29518 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
29536 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
29553 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:30161 original size:21 final size:21
Alignment explanation
Indices: 30137--30181 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30127 TCTTGTTCGT
*
30137 TTGAAGGGGTA-TCGGTTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
30158 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
30179 TTG
1 TTG
30182 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:38284 original size:4 final size:4
Alignment explanation
Indices: 38275--38371 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
38265 TTTCCTCACC
* * * *
38275 TTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T TTCT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * **
38319 TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
38368 TTAT
1 TTAT
38372 GTATATTGTC
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
3 9 0.13
4 55 0.81
5 2 0.03
6 2 0.03
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:38313 original size:10 final size:10
Alignment explanation
Indices: 38298--38322 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38288 TATCTATTTA
38298 TTTATTTTTC
1 TTTATTTTTC
38308 TTTATTTTTC
1 TTTATTTTTC
38318 TTTAT
1 TTTAT
38323 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:48797 original size:1 final size:1
Alignment explanation
Indices: 48791--48818 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
48781 TCCTAAGTTG
48791 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
48819 CGTTTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50178 original size:105 final size:105
Alignment explanation
Indices: 49605--50170 Score: 997
Period size: 105 Copynumber: 5.4 Consensus size: 105
49595 AGGTTTTACC
49605 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49670 ACGAAGGGACCGCTGGTTGTCAACAAACATTTTTTAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTTCTCAATTT
* * *
49711 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
49776 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
49816 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
49881 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
49921 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
49986 ACGAAGGGACCACTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
** *
50026 CAGAGCCAATTTCTGCTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
50091 ACGAAGGGACCGCTGGTTGTCGACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
50131 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
50171 GAAACAACAC
Statistics
Matches: 439, Mismatches: 21, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 348 0.79
106 91 0.21
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:52227 original size:10 final size:10
Alignment explanation
Indices: 52212--52236 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52202 TATCTATTTA
52212 TTTATTTTTC
1 TTTATTTTTC
52222 TTTATTTTTC
1 TTTATTTTTC
52232 TTTAT
1 TTTAT
52237 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:62502 original size:2 final size:2
Alignment explanation
Indices: 62495--62520 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62485 TATTTGCGTG
62495 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
62521 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.