Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000527.1 Hibiscus syriacus cultivar Beakdansim tig00001009_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: 83769
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:51 original size:11 final size:11
Alignment explanation
Indices: 31--60 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21 ACAGGAGGTT
31 GAGAACTAGGC
1 GAGAACTAGGC
*
42 GAGAATTAGGC
1 GAGAACTAGGC
53 GAGAACTA
1 GAGAACTA
61 TGGTTGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (11 bp):
GAGAACTAGGC
Found at i:5990 original size:30 final size:29
Alignment explanation
Indices: 5923--6006 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
5913 AATCATTTCG
5923 ATTTAAAGGACCAAAATAGCAAAAATAGA
1 ATTTAAAGGACCAAAATAGCAAAAATAGA
* * *
5952 ACTTAAAGGACTAAAATATCAAAAATAGAA
1 ATTTAAAGGACCAAAATAGCAAAAATAG-A
*
5982 ATTTAAAGGACCATAATAGCAAAAA
1 ATTTAAAGGACCAAAATAGCAAAAA
6007 AACTCAGAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 25 0.53
30 22 0.47
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.19
Consensus pattern (29 bp):
ATTTAAAGGACCAAAATAGCAAAAATAGA
Found at i:7327 original size:3 final size:3
Alignment explanation
Indices: 7319--7366 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
7309 ACAAAATGTA
7319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
7365 AA
1 AA
7367 ATTATAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7925 original size:36 final size:37
Alignment explanation
Indices: 7877--8010 Score: 155
Period size: 36 Copynumber: 3.6 Consensus size: 37
7867 TTTCTCAAAG
* * *
7877 GAAAAATGTCTCAAGCGAGACGAATTTTGTTTTGAGA
1 GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
* * * *
7914 G-AAATTGTCTCAAACGAGACCAAATTTATTTTTAGC
1 GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
* *
7950 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTTA-A
1 GAAAATTGTCTCAAGCGAGACGAAATTTG-TTTTTAGA
7987 GAAAACTTGTCTCAAGCGAGACGA
1 GAAAA-TTGTCTCAAGCGAGACGA
8011 CCCTTTGTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 29 0.36
37 29 0.36
38 22 0.28
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (37 bp):
GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
Found at i:7960 original size:37 final size:37
Alignment explanation
Indices: 7877--8008 Score: 142
Period size: 37 Copynumber: 3.6 Consensus size: 37
7867 TTTCTCAAAG
* * * * *
7877 GAAAAATGTCTCAAGCGAGACGAATTTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
* * * *
7914 G-AAATTGTCTCAAACGAGACCAAATTTATTTTTAGC
1 GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
*
7950 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTTA-A
1 GAAAACTGTCTCAAGCGAGACAAAATTT-ATTTTTAGA
7987 GAAAACTTGTCTCAAGCGAGAC
1 GAAAAC-TGTCTCAAGCGAGAC
8009 GACCCTTTGT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
36 29 0.36
37 30 0.38
38 21 0.26
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
Found at i:14367 original size:32 final size:32
Alignment explanation
Indices: 14317--14391 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
14307 TGGTCGTACA
* * *
14317 AGCCTACTCAAGGGAGTACATTAGGGCCTAAG
1 AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
* * *
14349 AGCCTACCCAAAGAAGTACCTTGGGGCCTTAG
1 AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
14381 AGCCTACCCAA
1 AGCCTACCCAA
14392 GGCAACCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (32 bp):
AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
Found at i:16050 original size:20 final size:21
Alignment explanation
Indices: 16025--16070 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16015 TTTGTGGTCG
16025 TTTCTAGCCG-CTGGGGATGA
1 TTTCTAGCCGTCTGGGGATGA
* * *
16045 TTTCTAGTCGTTTGGGGATGC
1 TTTCTAGCCGTCTGGGGATGA
16066 TTTCT
1 TTTCT
16071 CTGCAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.11, C:0.17, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTCTAGCCGTCTGGGGATGA
Found at i:19831 original size:30 final size:29
Alignment explanation
Indices: 19786--19862 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
19776 TTACAAATAT
*
19786 TTTTTTCTAACATTTGTAACTAAGGGCCCAA
1 TTTTTTC-AATATTTGTAAC-AAGGGCCCAA
* * ** *
19817 TTTTTTCAATATTTGATATCAATGGCTTAT
1 TTTTTTCAATATTTG-TAACAAGGGCCCAA
19847 TTTTTTCAATATTTGT
1 TTTTTTCAATATTTGT
19863 TATTAGGTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 28 0.72
31 10 0.26
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTTTTCAATATTTGTAACAAGGGCCCAA
Found at i:22609 original size:14 final size:14
Alignment explanation
Indices: 22590--22632 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
22580 CATTTGTTAT
*
22590 TATTATTTAATTAA
1 TATTATTAAATTAA
*
22604 TATTATTAAAATAA
1 TATTATTAAATTAA
22618 TATTAATTAAATTAA
1 TATT-ATTAAATTAA
22633 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTATTAAATTAA
Found at i:22663 original size:20 final size:20
Alignment explanation
Indices: 22640--22685 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
22630 TAAAATTTCA
22640 AAATTGTATTTAAATAGTCC
1 AAATTGTATTTAAATAGTCC
*
22660 AAATTTTATTTAAATAGTCC
1 AAATTGTATTTAAATAGTCC
22680 AAATTG
1 AAATTG
22686 CCTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
AAATTGTATTTAAATAGTCC
Found at i:22691 original size:20 final size:20
Alignment explanation
Indices: 22640--22691 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
22630 TAAAATTTCA
*
22640 AAATTGTATTTAAATAGTCC
1 AAATTGCATTTAAATAGTCC
**
22660 AAATTTTATTTAAATAGTCC
1 AAATTGCATTTAAATAGTCC
*
22680 AAATTGCCTTTA
1 AAATTGCATTTA
22692 TTTTCCCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (20 bp):
AAATTGCATTTAAATAGTCC
Found at i:34353 original size:29 final size:28
Alignment explanation
Indices: 34312--34369 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 28
34302 ATTTTCACCT
34312 AACTAATTGATGTAAGCAATGACATCAA
1 AACTAATTGATGTAAGCAATGACATCAA
34340 AACTAAATTGATGTAAGCAATGACATCAA
1 AACT-AATTGATGTAAGCAATGACATCAA
34369 A
1 A
34370 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (28 bp):
AACTAATTGATGTAAGCAATGACATCAA
Found at i:39044 original size:29 final size:29
Alignment explanation
Indices: 38999--39057 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
38989 ATTTTCACCT
38999 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
*
39028 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
39057 A
1 A
39058 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAAGCAATGACATCAA
Found at i:55304 original size:39 final size:39
Alignment explanation
Indices: 55247--55325 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
55237 GTTTTAAGTT
*
55247 GAGAACACCTAATATATTCTTTGGCATGTTTACCCTATA
1 GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
*
55286 GAGAACACCAAATGTATTCTTTGGCATGTTTACCCTATA
1 GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
55325 G
1 G
55326 GTCGTATACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (39 bp):
GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
Found at i:56431 original size:47 final size:47
Alignment explanation
Indices: 56352--56443 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 47
56342 TTCTCTTTCA
* ** * *
56352 TTTTTTTAATATTTAATTTATCGATCGATTAATCTAAATCAAATACT
1 TTTTTTTAACATTTAACCTATCAATCGATTAATCTAAATAAAATACT
* * *
56399 TTTTTTTAACATTTAACCTATTAATCGTTTAATCTGAATAAAATA
1 TTTTTTTAACATTTAACCTATCAATCGATTAATCTAAATAAAATA
56444 TTATAGAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (47 bp):
TTTTTTTAACATTTAACCTATCAATCGATTAATCTAAATAAAATACT
Found at i:57048 original size:12 final size:12
Alignment explanation
Indices: 57031--57055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57021 CGAGTTGTAT
57031 TTTAAAATTTTC
1 TTTAAAATTTTC
57043 TTTAAAATTTTC
1 TTTAAAATTTTC
57055 T
1 T
57056 CAACCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAAATTTTC
Found at i:57638 original size:12 final size:12
Alignment explanation
Indices: 57621--57647 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57611 GCATATTGCA
57621 TGACCTTGTCGT
1 TGACCTTGTCGT
57633 TGACCTTGTCGT
1 TGACCTTGTCGT
57645 TGA
1 TGA
57648 TCATGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.22, G:0.26, T:0.41
Consensus pattern (12 bp):
TGACCTTGTCGT
Found at i:60701 original size:3 final size:3
Alignment explanation
Indices: 60688--60735 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
60678 GTGTTAGCTG
*
60688 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60736 AAGTTTAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:65361 original size:84 final size:83
Alignment explanation
Indices: 65179--65348 Score: 288
Period size: 84 Copynumber: 2.0 Consensus size: 83
65169 AAACTCATGT
*
65179 TTTAGGATATTATTTT-ATATATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
1 TTTAGGATATTATTTTAATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
*
65243 TAAGTGTTTTAATTAGGA
66 TAAGTATTTTAATTAGGA
* *
65261 TTTAGGATATTATTTTAAATATATTTTATCTTATCTTTGTTTTATGTATTTTAGTTTAAATAGTT
1 TTTAGGATATTATTTT-AATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTT
65326 TTAAGTATTTTAATTAGGA
65 TTAAGTATTTTAATTAGGA
65345 TTTA
1 TTTA
65349 TTTCTTTATT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 16 0.20
84 66 0.80
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (83 bp):
TTTAGGATATTATTTTAATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
TAAGTATTTTAATTAGGA
Found at i:74397 original size:17 final size:17
Alignment explanation
Indices: 74371--74412 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
74361 AAACTTGAAG
*
74371 CCTCTTTTTTTATTTTT
1 CCTCTCTTTTTATTTTT
74388 CCTCTC-TTTTATTTTT
1 CCTCTCTTTTTATTTTT
74404 CCTCTCTTT
1 CCTCTCTTT
74413 CACACCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTCTCTTTTTATTTTT
Found at i:74410 original size:18 final size:16
Alignment explanation
Indices: 74378--74412 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
74368 AAGCCTCTTT
74378 TTTTATTTTTCCTCTC
1 TTTTATTTTTCCTCTC
74394 TTTTATTTTTCCTCTC
1 TTTTATTTTTCCTCTC
74410 TTT
1 TTT
74413 CACACCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTTCCTCTC
Found at i:74537 original size:41 final size:42
Alignment explanation
Indices: 74458--74537 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
74448 CTTTTTCCAT
* * **
74458 GAAGAAAAAAATTGTTCATTGTTTGGAACAGTAGAAAAAAAA
1 GAAGAAAAAAATTGTTCACTGTTTCGAACAACAGAAAAAAAA
*
74500 GAAGAAAAAAATTG-TCACTGTTTCGAACAACATAAAAA
1 GAAGAAAAAAATTGTTCACTGTTTCGAACAACAGAAAAA
74538 TGTTCACTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.23
Consensus pattern (42 bp):
GAAGAAAAAAATTGTTCACTGTTTCGAACAACAGAAAAAAAA
Found at i:83552 original size:31 final size:31
Alignment explanation
Indices: 83517--83577 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
83507 TAGCATAGGA
83517 AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
1 AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
* *
83548 AGGCATTTGCTCGATGGCTTCAAGAAAGGG
1 AGGCATTTGCTCGATAGCTTCAAAAAAGGG
83578 TATATTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (31 bp):
AGGCATTTGCTCGATAGCTTCAAAAAAGGGC
Done.