Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007122.1 Hibiscus syriacus cultivar Beakdansim tig00018609_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: 63946
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1573 original size:57 final size:57
Alignment explanation
Indices: 1463--1602 Score: 176
Period size: 56 Copynumber: 2.4 Consensus size: 57
1453 TTTTTTGGGT
* * **
1463 AAGTACAAAATGGTCCACGACTATAGGGTTTACTTTGTTGAGTCTATTGACTA-TAA
1 AAGTACAAAATGGTCCACGACTATAGGATTTACTTTGTTGAGTCCATCAACTATTAA
* *
1519 AAGTACAAAATGGTCC-CTGACTTTAGGATGTTGCTTTGTTGAGTCCATCAACTATTAA
1 AAGTACAAAATGGTCCAC-GACTATAGGAT-TTACTTTGTTGAGTCCATCAACTATTAA
1577 AAGTTACAAAATGGTCACACGACTAT
1 AAG-TACAAAATGGTC-CACGACTAT
1603 CCATTATGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
55 1 0.01
56 25 0.35
57 20 0.28
58 6 0.08
59 12 0.17
60 6 0.08
61 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (57 bp):
AAGTACAAAATGGTCCACGACTATAGGATTTACTTTGTTGAGTCCATCAACTATTAA
Found at i:5875 original size:38 final size:37
Alignment explanation
Indices: 5833--5953 Score: 126
Period size: 38 Copynumber: 3.3 Consensus size: 37
5823 ATTTGGAAAA
5833 TTCATCTTTGGTAGGTGGTCAACTTTGCACATGGGAAT
1 TTCATCTTTGGTAGGTGG-CAACTTTGCACATGGGAAT
* * * * *
5871 TTCATC-TTGTTTGGTGGCCAAC-TT--A-TTGGAAAA
1 TTCATCTTTGGTAGGTGG-CAACTTTGCACATGGGAAT
*
5904 TTCATCTTTGGTAAGTGGCAAACTTTGCACATGGGAAT
1 TTCATCTTTGGTAGGTGGC-AACTTTGCACATGGGAAT
5942 TTCATCTTTGGT
1 TTCATCTTTGGT
5954 CCCTAAAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
33 12 0.18
34 12 0.18
35 2 0.03
36 2 0.03
37 14 0.22
38 23 0.35
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (37 bp):
TTCATCTTTGGTAGGTGGCAACTTTGCACATGGGAAT
Found at i:8648 original size:21 final size:22
Alignment explanation
Indices: 8619--8663 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
8609 TATCCAGACA
**
8619 AGCAGTACTCCGCAACAGGTGG
1 AGCAGTACTCCAAAACAGGTGG
8641 AGCA-TACTCCAAAACAGGTGG
1 AGCAGTACTCCAAAACAGGTGG
8662 AG
1 AG
8664 TTTCAACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.13
Consensus pattern (22 bp):
AGCAGTACTCCAAAACAGGTGG
Found at i:10194 original size:31 final size:32
Alignment explanation
Indices: 10087--10214 Score: 154
Period size: 32 Copynumber: 4.0 Consensus size: 32
10077 CCCGAAGGAC
*
10087 CACTATCCATATGTTCCGAA-GAACATAGGTAA
1 CACTATCCATATGTCCCGAATG-ACATAGGTAA
* * *
10119 CACTGTCCATATGTCCCAAATAACATAGGTAA
1 CACTATCCATATGTCCCGAATGACATAGGTAA
*
10151 TC-CTGTCCATATGTCCCGAATGACATAGGTAA
1 -CACTATCCATATGTCCCGAATGACATAGGTAA
* *
10183 -ACTATCCATATGTCTCGAAAGACATAGGTAA
1 CACTATCCATATGTCCCGAATGACATAGGTAA
10214 C
1 C
10215 CCTCGACTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
31 27 0.33
32 55 0.66
33 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (32 bp):
CACTATCCATATGTCCCGAATGACATAGGTAA
Found at i:14447 original size:20 final size:20
Alignment explanation
Indices: 14396--14451 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
14386 ATGTGAAATT
*
14396 TGTCCCGAATGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
* *
14416 TACGTTCCGAAGGACCTCTGTA
1 T--GTCCCGAAGGACCTATGTA
14438 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
14452 ACTATCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:14509 original size:32 final size:32
Alignment explanation
Indices: 14451--14578 Score: 122
Period size: 32 Copynumber: 4.0 Consensus size: 32
14441 CCCGAAGGAC
* * *
14451 CACTATCCATATGTTCC-AAAGAACATAGGTAA
1 CACTGTCCATATG-TCCTGAAGGACATAGGTAA
*
14483 CACTGTCCATGTGTCCTGAAGGACATAGGTAA
1 CACTGTCCATATGTCCTGAAGGACATAGGTAA
*
14515 TC-CTGTCCATATGTTCC-GAAGGACATATGTAA
1 -CACTGTCCATATG-TCCTGAAGGACATAGGTAA
* *
14547 -ACTATCCATATGT-CTCGAAAGACATAGGTAA
1 CACTGTCCATATGTCCT-GAAGGACATAGGTAA
14578 C
1 C
14579 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 26 0.32
32 48 0.60
33 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (32 bp):
CACTGTCCATATGTCCTGAAGGACATAGGTAA
Found at i:17737 original size:71 final size:71
Alignment explanation
Indices: 17588--17782 Score: 320
Period size: 71 Copynumber: 2.8 Consensus size: 71
17578 ATTTGGCAAG
* * *
17588 TTGGAAAATTTATCTTTGGTAGGTGGCCAACTTTGCACATGAGAAATT-ATCTTGGTTGGTGGCC
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCC
17652 AACTTA
66 AACTTA
*
17658 TTGAAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCC
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCC
17723 AACTTA
66 AACTTA
* **
17729 TTGGAAAATTCATCTTTGGTGGGTGGAAAACTTTGCACATGGGAATTTCATCTT
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAATTTCATCTT
17783 TGGTCCCTAA
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.38
71 72 0.62
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (71 bp):
TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCC
AACTTA
Found at i:17784 original size:38 final size:38
Alignment explanation
Indices: 17594--17786 Score: 176
Period size: 34 Copynumber: 5.4 Consensus size: 38
17584 CAAGTTGGAA
*
17594 AATTT-ATCTTTGGTAGGTGGCCAACTTTGCACATGAG
1 AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
* * * **
17631 AAATT-ATC-TTGGTTGGTGGCCAAC-TT--A-TTGAA
1 AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
*
17663 AAATTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
1 AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
* * *
17701 AATTTCATC-TTGGTTGGTGGCCAAC-TT--A-TTGGA
1 AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
* * **
17734 AAATTCATCTTTGGTGGGTGGAAAACTTTGCACATGGG
1 AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
17772 AATTTCATCTTTGGT
1 AATTTCATCTTTGGT
17787 CCCTAAAATA
Statistics
Matches: 126, Mismatches: 19, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
32 8 0.06
33 15 0.12
34 29 0.23
35 6 0.05
36 17 0.13
37 24 0.19
38 27 0.21
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (38 bp):
AATTTCATCTTTGGTAGGTGGCCAACTTTGCACATGGG
Found at i:20806 original size:48 final size:48
Alignment explanation
Indices: 20750--20847 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
20740 AGTGGCAGAC
20750 TTATTGGGCATGGATGAAACCTTCAAAGATAAGGATTTGGCCTTGATA
1 TTATTGGGCATGGATGAAACCTTCAAAGATAAGGATTTGGCCTTGATA
*
20798 TTATTGGGCATGGATGAAACCTTCAAAGATGAGGATTTGGCCTTGATA
1 TTATTGGGCATGGATGAAACCTTCAAAGATAAGGATTTGGCCTTGATA
20846 TT
1 TT
20848 GTTGTCATCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (48 bp):
TTATTGGGCATGGATGAAACCTTCAAAGATAAGGATTTGGCCTTGATA
Found at i:25665 original size:12 final size:12
Alignment explanation
Indices: 25648--25673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25638 CATAAAGATA
25648 TTAATGTAAGAG
1 TTAATGTAAGAG
25660 TTAATGTAAGAG
1 TTAATGTAAGAG
25672 TT
1 TT
25674 TTTCTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (12 bp):
TTAATGTAAGAG
Found at i:52606 original size:30 final size:30
Alignment explanation
Indices: 52530--52634 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 30
52520 TCTATGTAAC
*
52530 TTAATAAAAATATTTAATAT-ATTATTTATAT
1 TTAA-AAAAATATTTAATATGA-TATTTGTAT
** * *
52561 TT-TTAAAATAGTTAATCTGATATTTGTAT
1 TTAAAAAAATATTTAATATGATATTTGTAT
* * *
52590 TTAAAAAAATATTTAATGTGATGTTCGTATT
1 TTAAAAAAATATTTAATATGATATTTGTA-T
*
52621 TTAAGAAAATATTT
1 TTAAAAAAATATTT
52635 GATTTGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 22 0.37
30 21 0.36
31 16 0.27
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (30 bp):
TTAAAAAAATATTTAATATGATATTTGTAT
Found at i:52630 original size:31 final size:30
Alignment explanation
Indices: 52565--52634 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
52555 TTATATTTTT
* *
52565 AAAATAGTTAATCTGATATTTGTATTTAAA
1 AAAATATTTAATCTGATATTCGTATTTAAA
* * *
52595 AAAATATTTAATGTGATGTTCGTATTTTAAG
1 AAAATATTTAATCTGATATTCGTA-TTTAAA
52626 AAAATATTT
1 AAAATATTT
52635 GATTTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (30 bp):
AAAATATTTAATCTGATATTCGTATTTAAA
Found at i:52866 original size:28 final size:29
Alignment explanation
Indices: 52834--52924 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
52824 GGTTATTATA
* * * *
52834 TTAAAA-TACATGTATCACACTAGACAAT
1 TTAAAACTACATGTATTAAATTAGACATT
* * * *
52862 TTAAAATTATATGCATTATATTAGACATT
1 TTAAAACTACATGTATTAAATTAGACATT
52891 TTAAAACTACATGTATTAAATTAGACATT
1 TTAAAACTACATGTATTAAATTAGACATT
52920 TTAAA
1 TTAAA
52925 GATATAAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 6 0.12
29 46 0.88
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAAAACTACATGTATTAAATTAGACATT
Found at i:52936 original size:29 final size:29
Alignment explanation
Indices: 52876--52937 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
52866 AATTATATGC
* **
52876 ATTATATTAGACATTTTAAAACTACATGT
1 ATTAAATTAGACATTTTAAAACTACAAAT
*
52905 ATTAAATTAGACATTTTAAAGA-TATAAAT
1 ATTAAATTAGACATTTTAAA-ACTACAAAT
52934 ATTA
1 ATTA
52938 CATTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (29 bp):
ATTAAATTAGACATTTTAAAACTACAAAT
Found at i:56446 original size:17 final size:18
Alignment explanation
Indices: 56426--56459 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56416 TAACTTACAT
56426 TTAACTTT-AACTCAATA
1 TTAACTTTAAACTCAATA
*
56443 TTAATTTTAAACTCAAT
1 TTAACTTTAAACTCAAT
56460 CTATTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAACTTTAAACTCAATA
Found at i:56623 original size:29 final size:28
Alignment explanation
Indices: 56555--56646 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 28
56545 AATATATATA
*
56555 ATTTAAGAAAATAATTAATAT-ATTATTTAT
1 ATTTAA-AAAAT-ATTAATATGA-TATTTGT
*
56585 ATATT-TAAAATAGTTAATATGATATTTGT
1 AT-TTAAAAAATA-TTAATATGATATTTGT
* * *
56614 ATTTAAAAAAATATTAATGTGATGTTCGT
1 ATTT-AAAAAATATTAATATGATATTTGT
56643 ATTT
1 ATTT
56647 GAGAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.06
29 37 0.73
30 9 0.18
31 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (28 bp):
ATTTAAAAAATATTAATATGATATTTGT
Found at i:56886 original size:29 final size:29
Alignment explanation
Indices: 56854--56927 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
56844 ACATGTATCG
* * * *
56854 TATTGGACAATTTAAAATTATATGCATTA
1 TATTAGACATTTTAAAAGTACATGCATTA
*
56883 TATTAGACATTTTAAAAGTACATGTATTA
1 TATTAGACATTTTAAAAGTACATGCATTA
*
56912 AATTAGACATTTTAAA
1 TATTAGACATTTTAAA
56928 GATATAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (29 bp):
TATTAGACATTTTAAAAGTACATGCATTA
Found at i:61977 original size:74 final size:74
Alignment explanation
Indices: 61856--61998 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 74
61846 GGATGAATTT
61856 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGTTGCTATA
1 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGTTGCTATA
61921 ACAATTTTC
66 ACAATTTTC
* * * *
61930 ATCAGCATAAAATAGATATTAACGCTGGAATTGCAGCAGACACAACTGTATTACCAGTTGCTGTA
1 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGTTGCTATA
61995 ACAA
66 ACAA
61999 CTAAAAATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (74 bp):
ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGTTGCTATA
ACAATTTTC
Found at i:63286 original size:20 final size:21
Alignment explanation
Indices: 63261--63309 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
63251 CTGCGATGGT
63261 CGCAATAGTGTCCGC-ACGGC
1 CGCAATAGTGTCCGCGACGGC
*
63281 CGCAATAGTGTCCGCGACGGG
1 CGCAATAGTGTCCGCGACGGC
*
63302 CGCTATAG
1 CGCAATAG
63310 CGCCGCGCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (21 bp):
CGCAATAGTGTCCGCGACGGC
Done.