Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004566.1 Hibiscus syriacus cultivar Beakdansim tig00010148_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: 49988
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3282 original size:29 final size:29
Alignment explanation
Indices: 3239--3294 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3229 TAACATATGA
* * * *
3239 ATGTGTTCTATGTGAAAGTGCTTTATGTG
1 ATGTGTTATACGTGAAAATGCTCTATGTG
3268 ATGTGTTATACGTGAAAATGCTCTATG
1 ATGTGTTATACGTGAAAATGCTCTATG
3295 CAAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (29 bp):
ATGTGTTATACGTGAAAATGCTCTATGTG
Found at i:3454 original size:22 final size:23
Alignment explanation
Indices: 3429--3473 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3419 TACGCTATTC
*
3429 TTCGGG-ATATTCTACGTGGTCT
1 TTCGGGAAAATTCTACGTGGTCT
3451 TTCGGGACAAATTCTACGTGGTC
1 TTCGGGA-AAATTCTACGTGGTC
3474 ATTCTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
24 14 0.70
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (23 bp):
TTCGGGAAAATTCTACGTGGTCT
Found at i:3522 original size:24 final size:24
Alignment explanation
Indices: 3437--3554 Score: 97
Period size: 24 Copynumber: 5.0 Consensus size: 24
3427 TCTTCGGGAT
*
3437 ATTCTACGTGGTC-TTTCGG-GACAA
1 ATTCTACGTGG-CACTTCGGTG-CAA
3461 ATTCTACGTGGTCA-TTC--TG-AA
1 ATTCTACGTGG-CACTTCGGTGCAA
* *
3482 TATATCTAC-TGGCACTTTGGTGTAA
1 -AT-TCTACGTGGCACTTCGGTGCAA
*
3507 ATTCTACGTGACACTTCGGTGCAA
1 ATTCTACGTGGCACTTCGGTGCAA
*
3531 ATTCTAAGTGGCACTTCGGTGCAA
1 ATTCTACGTGGCACTTCGGTGCAA
3555 TTTTTTGAGC
Statistics
Matches: 79, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.05
22 7 0.09
23 11 0.14
24 55 0.70
25 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (24 bp):
ATTCTACGTGGCACTTCGGTGCAA
Found at i:6234 original size:17 final size:18
Alignment explanation
Indices: 6212--6253 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
6202 GTACCATAGT
6212 ATGGTA-GTATCGATACC
1 ATGGTAGGTATCGATACC
6229 ATGGTAAGGGTATCGATACC
1 ATGGT-A-GGTATCGATACC
6249 A-GGTA
1 ATGGTA
6254 ACATCGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 3 0.14
20 12 0.55
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGGTAGGTATCGATACC
Found at i:6335 original size:95 final size:92
Alignment explanation
Indices: 6123--6342 Score: 307
Period size: 95 Copynumber: 2.4 Consensus size: 92
6113 TATCGACGAG
* * * *
6123 GTAGTATCAATACTATGGTAAGGGTATCAATACCAGCAACATCAAATCTGAAATTGGTATCGATA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGCAACATCAAATCTAAAATTGGTATCGATA
* *
6188 CCAAGGAGGAATCAGTACCATAGTATG
66 CCAAGGAGGAATCAGTACCATAATATA
* *
6215 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAATCTAAAATTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCA-GCAACATCAAATCTAAAATTGGTATCGAT
*
6280 ACCAGAAGG-GGACATCGGTACCATAATATA
65 ACC--AAGGAGGA-ATCAGTACCATAATATA
*
6310 GTAGTATCGATACCATGGTAGGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
6343 TGAAGAGCCA
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
92 32 0.28
93 29 0.25
94 3 0.03
95 50 0.44
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (92 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAGCAACATCAAATCTAAAATTGGTATCGATA
CCAAGGAGGAATCAGTACCATAATATA
Found at i:6858 original size:57 final size:58
Alignment explanation
Indices: 6672--6947 Score: 420
Period size: 57 Copynumber: 4.8 Consensus size: 58
6662 ATGGCACTAA
*
6672 GTGTACAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
6730 GTGTGTAAAAATGTTAAGAAATTCATACTAA--GTATGAA-TTCCGCATTGGGCACTTT
1 GTGTG-CAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
6786 GTGTGCAAAAATGTTAAGAAATTCAT-CTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
6844 GTGTGCAAAATGTTAAG-AATTCATACTAAGTATATGAATTTCCGTATTGGGAACTTT
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
6901 ATGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTT-CGTAT
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
6948 GGGAATATAT
Statistics
Matches: 200, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
55 4 0.02
56 48 0.24
57 74 0.37
58 50 0.25
59 24 0.12
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:9089 original size:31 final size:31
Alignment explanation
Indices: 9046--9111 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
9036 ACTAAGGAAG
9046 GTTGATCTGTTGACGGTGGGAAAGCACTGCA
1 GTTGATCTGTTGACGGTGGGAAAGCACTGCA
*
9077 GTTGGTCTGTTGACGGTGGGAAAGCACTGCA
1 GTTGATCTGTTGACGGTGGGAAAGCACTGCA
9108 GTTG
1 GTTG
9112 CTTGCTCACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.38, T:0.27
Consensus pattern (31 bp):
GTTGATCTGTTGACGGTGGGAAAGCACTGCA
Found at i:10724 original size:47 final size:47
Alignment explanation
Indices: 10671--10774 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 47
10661 TTCTTAAGGA
* * * * *
10671 ATTTCTATGTGGTCCTT-ATGGACAAATTTTATATGGCACTTTGGTGC
1 ATTTCTACGCGGTCCTTCA-GGACAAATTCTACATGGCACTTCGGTGC
*
10718 ATTTCTACGCGGTCCTTCAGGACAAATTCTACGTGGCACTTCGGTGC
1 ATTTCTACGCGGTCCTTCAGGACAAATTCTACATGGCACTTCGGTGC
*
10765 AATTTATACG
1 -ATTTCTACG
10775 AGCTGTAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 39 0.81
48 9 0.19
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (47 bp):
ATTTCTACGCGGTCCTTCAGGACAAATTCTACATGGCACTTCGGTGC
Found at i:11614 original size:40 final size:40
Alignment explanation
Indices: 11570--11649 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
11560 GCATAAACCA
11570 GAGTCTAGAGTGTTTTTAAATTGAATACATGCCAACATAT
1 GAGTCTAGAGTGTTTTTAAATTGAATACATGCCAACATAT
11610 GAGTCTAGAGTGTTTTTAAATTGAATACATGCCAACATAT
1 GAGTCTAGAGTGTTTTTAAATTGAATACATGCCAACATAT
11650 AGTGAGAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (40 bp):
GAGTCTAGAGTGTTTTTAAATTGAATACATGCCAACATAT
Found at i:13097 original size:19 final size:20
Alignment explanation
Indices: 13052--13101 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
13042 AGTGCTCGGG
*
13052 TACTATTTATACAGTATCAA
1 TACTATTCATACAGTATCAA
13072 TACTATTCATACAGTAT-AA
1 TACTATTCATACAGTATCAA
*
13091 TATTATTCATA
1 TACTATTCATA
13102 AAAATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:18593 original size:81 final size:79
Alignment explanation
Indices: 18456--18607 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 79
18446 ATTAATAAAT
* *
18456 AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TT
1 AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTT
18520 TAATGTTTATTTAA
66 TAATGTTTATTTAA
* * * * *
18534 AAAAT-TTATTTAATTATTTCGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACATT
1 AAAATATTATTTAATTAATTC-AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAAT
18598 CTTTTAATGT
62 CTTTTAATGT
18608 CTACTTACTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
77 14 0.23
78 15 0.24
79 1 0.02
80 3 0.05
81 21 0.34
82 8 0.13
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (79 bp):
AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTT
TAATGTTTATTTAA
Found at i:24452 original size:17 final size:17
Alignment explanation
Indices: 24430--24478 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
24420 GTACCATAAT
24430 ATGGTAGTATCGATACC
1 ATGGTAGTATCGATACC
24447 ATGGTAAGGGTATCGATACC
1 ATGGT-A--GTATCGATACC
*
24467 A-GGTAGCATCGA
1 ATGGTAGTATCGA
24479 ATCTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 5 0.18
18 2 0.07
19 3 0.11
20 12 0.43
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (17 bp):
ATGGTAGTATCGATACC
Found at i:24468 original size:95 final size:95
Alignment explanation
Indices: 24337--24559 Score: 365
Period size: 95 Copynumber: 2.3 Consensus size: 95
24327 ATACCGAAGA
*
24337 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAATCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAATCTAAAATTAGTATCGA
** * *
24402 TACTGGAAGGGGGTATCGGTACCATAATAT
66 TACCAGAAGGGGGTATCAGCACCATAATAT
*
24432 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAGCATCGAATCTAAAATTAGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAATCTAAAATTAGTATCGA
*
24497 TACCAGAAGGGGGTATCAGCACCATAGTAT
66 TACCAGAAGGGGGTATCAGCACCATAATAT
* *
24527 AGTAGTATCGATACCATGGTAGGGGTATCGATA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATA
24560 TTGAAGAGCC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 119 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAATCTAAAATTAGTATCGA
TACCAGAAGGGGGTATCAGCACCATAATAT
Found at i:24894 original size:59 final size:59
Alignment explanation
Indices: 24823--25236 Score: 618
Period size: 59 Copynumber: 7.1 Consensus size: 59
24813 TAGTCACAAT
* * * *
24823 TATTGGGAACTTTGTGTGCAAAAATGTTAAGAAATTCATACAAATTGTATGAATTTCCA
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
* * * *
24882 CATTGGGCACTTTGTGTGCAAAACTATTAAGAAATTCATATTAAGTGTATGAATTTCCG
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
*
24941 TATTGGACACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
25000 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
** * *
25059 TACGGGGCAC-TTGATGTGCAAAAA-GATAAGAAATTCATACTAAGTGTATGAATTTTCG
1 TATTGGGCACTTTG-TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
*
25117 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCG
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
* * * * * *
25176 CATTGGGCACTTTATGTG-AAAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCTG
1 TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
25234 TAT
1 TAT
25237 GAGAAATATA
Statistics
Matches: 323, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
58 90 0.28
59 233 0.72
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (59 bp):
TATTGGGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
Found at i:25140 original size:117 final size:118
Alignment explanation
Indices: 24823--25236 Score: 602
Period size: 117 Copynumber: 3.5 Consensus size: 118
24813 TAGTCACAAT
* * * * **
24823 TATTGGGAACTTTG-TGTGCAAAAATGTTAAGAAATTCATACAAATTGTATGAATTTCCACATTG
1 TATTGGGCAC-TTGATGTGCAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
24887 GGCACTTTGTGTGCAAAACTATTAAGAAATTCATATTAAGTGTATGAATTTCCG
65 GGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
* *
24941 TATTGGACACTTTG-TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 TATTGGGCAC-TTGATGTGCAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
25005 GGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
65 GGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
** *
25059 TACGGGGCACTTGATGTGCAAAAA-GATAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGG
1 TATTGGGCACTTGATGTGCAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGG
*
25123 GCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCG
66 GCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
* * * * *
25176 CATTGGGCACTTTATGTG-AAAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCTGTAT
1 TATTGGGCACTTGATGTGCAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
25237 GAGAAATATA
Statistics
Matches: 272, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
116 5 0.02
117 141 0.52
118 126 0.46
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (118 bp):
TATTGGGCACTTGATGTGCAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGG
GCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCG
Found at i:30829 original size:23 final size:24
Alignment explanation
Indices: 30803--30857 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
30793 GGTTCTACGC
30803 GGTCCTTCGAGAC-AATTCTACAT
1 GGTCCTTCGAGACAAATTCTACAT
* * *
30826 GGTCATTCGGGACAAATTCTACGT
1 GGTCCTTCGAGACAAATTCTACAT
*
30850 GGCCCTTC
1 GGTCCTTC
30858 ATGACATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (24 bp):
GGTCCTTCGAGACAAATTCTACAT
Found at i:42939 original size:20 final size:19
Alignment explanation
Indices: 42914--42959 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
42904 TCAAAATAAT
* *
42914 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATATAATTTTG
*
42933 CTTTTCAATATATAATTTTG
1 -TTTTCAAAATATAATTTTG
42953 TTTTCAA
1 TTTTCAA
42960 GAGAATCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTCAAAATATAATTTTG
Found at i:47503 original size:20 final size:20
Alignment explanation
Indices: 47458--47507 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
47448 AGATGAAAAA
47458 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
*
47479 TATCGATACTGATGTGGAG-G
1 TATCGATACTGAT-TGAAGAG
47499 TATCGATAC
1 TATCGATAC
47508 CATAATTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:48167 original size:23 final size:24
Alignment explanation
Indices: 48141--48195 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
48131 GGTTCTACGC
*
48141 GGTCCTTCGAGAC-TATTCTACAT
1 GGTCCTTCGAGACAAATTCTACAT
* * *
48164 GGTCATTCGGGACAAATTCTACGT
1 GGTCCTTCGAGACAAATTCTACAT
*
48188 GGCCCTTC
1 GGTCCTTC
48196 ATGACATATC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (24 bp):
GGTCCTTCGAGACAAATTCTACAT
Done.