Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006070.1 Hibiscus syriacus cultivar Beakdansim tig00014355_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: 60152
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6990 original size:21 final size:21
Alignment explanation
Indices: 6947--6990 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6937 AATATAAATT
*
6947 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTACTACA
*
6968 GTGTATCGATGCACTACTGCA
1 GTGTATCGATGCACTACTACA
6989 GT
1 GT
6991 AACTTCGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCACTACTACA
Found at i:13171 original size:15 final size:16
Alignment explanation
Indices: 13153--13184 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
13143 CCCTTGCAAA
13153 AATTAAAATGA-AAAT
1 AATTAAAATGAGAAAT
13168 AATTAAAATGAGAAAT
1 AATTAAAATGAGAAAT
13184 A
1 A
13185 TGAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (16 bp):
AATTAAAATGAGAAAT
Found at i:19077 original size:31 final size:31
Alignment explanation
Indices: 19039--19111 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
19029 GAGTCGATGG
*
19039 TTACCTATGTCTTTCGAGACATATGAATA-T
1 TTACCTATGTCTTTCAAGACATATGAATAGT
*
19069 ATTACCTATGTCTTTCAAGACATATGGATAGT
1 -TTACCTATGTCTTTCAAGACATATGAATAGT
19101 TTACCTATGTC
1 TTACCTATGTC
19112 CTTAGGGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (31 bp):
TTACCTATGTCTTTCAAGACATATGAATAGT
Found at i:19155 original size:30 final size:30
Alignment explanation
Indices: 19069--19157 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
19059 ATATGAATAT
* * *
19069 ATTACCTATGTCTTTCAAG-ACATATGGATA
1 ATTACCTATGTCCTT-AGGAACATATGGACA
* * *
19099 GTTTACCTATGTCCTTAGGGATATATGGACA
1 -ATTACCTATGTCCTTAGGAACATATGGACA
* *
19130 ATTACCTATGTTCTTCGGAACATATGGA
1 ATTACCTATGTCCTTAGGAACATATGGA
19158 TAGGGGTCCT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (30 bp):
ATTACCTATGTCCTTAGGAACATATGGACA
Found at i:19486 original size:18 final size:19
Alignment explanation
Indices: 19463--19498 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19453 AAATGACTTA
*
19463 TATTATGATATA-AGAATC
1 TATTATGAGATATAGAATC
19481 TATTATGAGATATAGAAT
1 TATTATGAGATATAGAAT
19499 ATGAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (19 bp):
TATTATGAGATATAGAATC
Found at i:21567 original size:9 final size:9
Alignment explanation
Indices: 21550--21594 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
21540 AAGACATATG
21550 AATGATAAT
1 AATGATAAT
*
21559 AATGTTAAT
1 AATGATAAT
*
21568 AATGATAAG
1 AATGATAAT
*
21577 AATAATAAT
1 AATGATAAT
21586 AATGATAAT
1 AATGATAAT
21595 GATAATGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
AATGATAAT
Found at i:21573 original size:18 final size:18
Alignment explanation
Indices: 21550--21600 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
21540 AAGACATATG
**
21550 AATGATAATAATGTTAAT
1 AATGATAATAATAATAAT
*
21568 AATGATAAGAATAATAAT
1 AATGATAATAATAATAAT
*
21586 AATGATAATGATAAT
1 AATGATAATAATAAT
21601 GAAATGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (18 bp):
AATGATAATAATAATAAT
Found at i:21575 original size:6 final size:6
Alignment explanation
Indices: 21566--21608 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
21556 AATAATGTTA
*
21566 ATAATG ATAA-G AATAATA ATAATG ATAATG ATAATG A-AATG AT
1 ATAATG ATAATG -ATAATG ATAATG ATAATG ATAATG ATAATG AT
21609 TTGTATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 6 0.19
6 26 0.81
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (6 bp):
ATAATG
Found at i:28357 original size:54 final size:54
Alignment explanation
Indices: 28253--28440 Score: 243
Period size: 54 Copynumber: 3.5 Consensus size: 54
28243 TACGTTGTAT
* * * *
28253 TTACCGTATCGACACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAA
1 TTACTGTATCGGCACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAA
* * * *
28307 TTACTGTATTGGCACTCTGTGTGCAACAC-ACGCAATTCATAAAGAATTTGTGAA
1 TTACTGTATCGGCACTATGTGTGCAAC-CTACGCAATTCATAATGAGTTTGTGAA
* * * *
28361 TTACTGTATCAGCACTATGCGTGCAACCTACGTAATTCACAATGAGTTTGTGAA
1 TTACTGTATCGGCACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAA
*
28415 TTACCGTATCGGCACTATGTGTGCAA
1 TTACTGTATCGGCACTATGTGTGCAA
28441 AACTAAGAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 111 0.98
55 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
TTACTGTATCGGCACTATGTGTGCAACCTACGCAATTCATAATGAGTTTGTGAA
Found at i:36743 original size:2 final size:2
Alignment explanation
Indices: 36736--36761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36726 TTTAGAATGA
36736 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
36762 GAAACTAATT
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
Found at i:39904 original size:2 final size:2
Alignment explanation
Indices: 39897--39952 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
39887 AATTCAACAA
39897 AT AT AT AT AT 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 AT AT AT AT AT
39939 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
39953 CAAATTGACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42516 original size:21 final size:21
Alignment explanation
Indices: 42492--42536 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
42482 CATATCAAGC
*
42492 ATAAATGTTCTTGATCATTTT
1 ATAAATGTTCTTAATCATTTT
*
42513 ATAAATGTTTTTAATCATTTT
1 ATAAATGTTCTTAATCATTTT
42534 ATA
1 ATA
42537 TATGATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
ATAAATGTTCTTAATCATTTT
Found at i:42605 original size:51 final size:50
Alignment explanation
Indices: 42533--42648 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 50
42523 TTAATCATTT
*
42533 TATATATGATACATATCAAGAATAAATGTTCTTTAATCAAATATATATATA
1 TATATATGATACATATCAAGAATAAATGTAC-TTAATCAAATATATATATA
42584 TATATATGATACATATCAAGAATAAATGTACTTAATCAAATATATATATA
1 TATATATGATACATATCAAGAATAAATGTACTTAATCAAATATATATATA
*
42634 TATATAT-ATATATAT
1 TATATATGATACATAT
42649 ATATGATATA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 7 0.11
50 26 0.41
51 30 0.48
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (50 bp):
TATATATGATACATATCAAGAATAAATGTACTTAATCAAATATATATATA
Found at i:42674 original size:2 final size:2
Alignment explanation
Indices: 42623--42661 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
42613 ACTTAATCAA
42623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
42662 GGATGGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45681 original size:25 final size:25
Alignment explanation
Indices: 45643--45766 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
45633 AGTTAGGGGA
*
45643 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
45667 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
45692 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
45717 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
45742 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
45767 GGGTTGGTTC
Statistics
Matches: 97, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
24 9 0.09
25 88 0.91
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:45893 original size:3 final size:3
Alignment explanation
Indices: 45885--45948 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
45875 GCAAAAATTG
* **
45885 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45929 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
45949 CGGACAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:45940 original size:32 final size:32
Alignment explanation
Indices: 45887--45950 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
45877 AAAAATTGTA
*
45887 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
45919 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
45951 GACAAAACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:46312 original size:87 final size:91
Alignment explanation
Indices: 46153--46362 Score: 293
Period size: 89 Copynumber: 2.4 Consensus size: 91
46143 CGTCTAAGGG
* * * ** * * *
46153 TGACACGGCTCCTACGTGATGAGGAGATTTGGTTATCTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
46218 AATGAGGACGACTGGTTATC-A-GGT
66 AATGAGGACGACTGGTTATCTATGGT
*
46242 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TAAAGG-TGATAACACGGTTCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
* *
46305 GATGAGGACGGCTGGTTATCTATGGT
66 AATGAGGACGACTGGTTATCTATGGT
46331 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
46363 TCCGGGGGAT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
87 37 0.34
88 5 0.05
89 66 0.61
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (91 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
AATGAGGACGACTGGTTATCTATGGT
Found at i:46363 original size:43 final size:43
Alignment explanation
Indices: 46128--46363 Score: 165
Period size: 43 Copynumber: 5.3 Consensus size: 43
46118 CTCATACGCA
* ** *
46128 ATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTG
1 ATGAAGAGATCTGGTTATCTAAGGTTGACACGGCTCCTACGTG
* * * * * * *
46171 ATGAGGAGATTTGGTTATCTTTAGGGATGATAACTCGGTTCCTACGTA
1 ATGAAGAGATCTGGTTATC--TAAGG-T--TGACACGGCTCCTACGTG
* *
46219 ATGAGGACGA-CTGGTTATC--AGGTTGACACGGCTCTTACGTG
1 ATGAAGA-GATCTGGTTATCTAAGGTTGACACGGCTCCTACGTG
** * *
46260 ATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAAGAGATCTGGTTATCT-AAGGT--TGACACGGCTCCTACGTG
* * * *
46306 ATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCATACGTG
1 ATGAAGA-GATCTGGTTATCTAAGGTTGACACGGCTCCTACGTG
46349 ATGAAGAGATCTGGT
1 ATGAAGAGATCTGGT
46364 CCGGGGGATG
Statistics
Matches: 145, Mismatches: 34, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
40 2 0.01
41 26 0.18
42 1 0.01
43 41 0.28
44 6 0.04
45 8 0.06
46 29 0.20
47 1 0.01
48 29 0.20
49 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (43 bp):
ATGAAGAGATCTGGTTATCTAAGGTTGACACGGCTCCTACGTG
Found at i:46404 original size:130 final size:134
Alignment explanation
Indices: 46242--46488 Score: 353
Period size: 135 Copynumber: 1.9 Consensus size: 134
46232 GTTATCAGGT
* * *
46242 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
*
46304 TGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCG
66 TGATGAGGACGACTGGTTATCCTAAT-GTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCG
46367 GGGGA
130 GGGGA
* *
46372 TGACACGGTTCATACATGATGAA-AAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCT
1 TGACACGGCTCATACATGATGAAGAAA-TCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCT
*
46436 ACGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCCTACGTGATGA
63 ACGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGA
46489 GGAAGTCCGG
Statistics
Matches: 102, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
129 2 0.02
130 30 0.29
132 2 0.02
134 2 0.02
135 39 0.38
136 25 0.25
137 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (134 bp):
TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCGG
GGGA
Found at i:47458 original size:13 final size:13
Alignment explanation
Indices: 47450--47474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47440 TTTTTTCTTT
47450 TTTCATTTTTTCA
1 TTTCATTTTTTCA
47463 TTTCATTTTTTC
1 TTTCATTTTTTC
47475 CATCATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:48744 original size:17 final size:17
Alignment explanation
Indices: 48722--48757 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
48712 ATACTCATCC
48722 GAATAGGCATCATTCGA
1 GAATAGGCATCATTCGA
48739 GAATAGGCATCATTCGA
1 GAATAGGCATCATTCGA
48756 GA
1 GA
48758 TTGATCATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (17 bp):
GAATAGGCATCATTCGA
Done.