Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008468.1 Hibiscus syriacus cultivar Beakdansim tig00111287_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: 67573
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15098 original size:30 final size:30
Alignment explanation
Indices: 15055--15125 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
15045 AAGCCTTAGA
*
15055 AAAAGTT-TGGGACC-ATTTTGT-ATTTTG
1 AAAAGTTATGGGACCTATTTGGTAATTTTG
15082 TCAAAAGTTATGGGACCTATTTGGTAATTTTG
1 --AAAAGTTATGGGACCTATTTGGTAATTTTG
15114 AAAAGTTATGGG
1 AAAAGTTATGGG
15126 GTAAATGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
29 7 0.18
30 19 0.50
31 6 0.16
32 6 0.16
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (30 bp):
AAAAGTTATGGGACCTATTTGGTAATTTTG
Found at i:27709 original size:16 final size:16
Alignment explanation
Indices: 27658--27711 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
27648 ATAACCATTT
27658 AAATTCAAACATCCAAAAC
1 AAATTCAAACATCC---AC
* *
27677 AAATTCCACCATCCAC
1 AAATTCAAACATCCAC
*
27693 AAATTCAAACATTCAC
1 AAATTCAAACATCCAC
27709 AAA
1 AAA
27712 CATCTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 18 0.60
19 12 0.40
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATTCAAACATCCAC
Found at i:33605 original size:22 final size:21
Alignment explanation
Indices: 33570--33610 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
33560 AAGCCTATTT
33570 TCATTTTTCAATTTTTGAAATA
1 TCATTTTTCAA-TTTTGAAATA
**
33592 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
33611 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:35390 original size:7 final size:7
Alignment explanation
Indices: 35374--35413 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
35364 GTCAAAGAAA
*
35374 GTCAATG
1 GTCAACG
35381 GTCAACG
1 GTCAACG
35388 GTC-ACG
1 GTCAACG
35394 GTCAACG
1 GTCAACG
*
35401 ATCAACG
1 GTCAACG
35408 GTCAAC
1 GTCAAC
35414 AGTCGGGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:35408 original size:14 final size:14
Alignment explanation
Indices: 35375--35413 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
35365 TCAAAGAAAG
* *
35375 TCAATGGTCAACGG
1 TCAACGGTCAACGA
35389 TC-ACGGTCAACGA
1 TCAACGGTCAACGA
35402 TCAACGGTCAAC
1 TCAACGGTCAAC
35414 AGTCGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:35429 original size:17 final size:17
Alignment explanation
Indices: 35407--35447 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
35397 AACGATCAAC
*
35407 GGTCAACAGTCGGGTCG
1 GGTCAACAGCCGGGTCG
35424 GGTCAACAGCCGGGTCG
1 GGTCAACAGCCGGGTCG
35441 GGTCAAC
1 GGTCAAC
35448 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.15
Consensus pattern (17 bp):
GGTCAACAGCCGGGTCG
Found at i:35465 original size:19 final size:19
Alignment explanation
Indices: 35441--35530 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
35431 AGCCGGGTCG
*
35441 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
35460 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
35479 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * * *
35498 GATCAAACCGGTTTAAAACT
1 GGTCAAACCGG-TTCAGACC
35518 GGTCAAACCGGTT
1 GGTCAAACCGGTT
35531 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.02
19 47 0.76
20 14 0.23
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:35479 original size:10 final size:10
Alignment explanation
Indices: 35443--35530 Score: 76
Period size: 9 Copynumber: 9.1 Consensus size: 10
35433 CCGGGTCGGG
*
35443 TCAACCCGGT
1 TCAAACCGGT
*
35453 TCAGACCGG-
1 TCAAACCGGT
35462 TCAAACCGGT
1 TCAAACCGGT
*
35472 TCAGACCGG-
1 TCAAACCGGT
35481 TCAAACCGGT
1 TCAAACCGGT
* *
35491 TCGAACC-GA
1 TCAAACCGGT
35500 TCAAACCGGTT
1 TCAAACCGG-T
* *
35511 TAAAACTGG-
1 TCAAACCGGT
35520 TCAAACCGGT
1 TCAAACCGGT
35530 T
1 T
35531 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 30 0.50
10 23 0.38
11 7 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:42703 original size:7 final size:7
Alignment explanation
Indices: 42691--42737 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
42681 GTCAAAGAAA
42691 GTCAACG
1 GTCAACG
42698 GTCAACG
1 GTCAACG
42705 GTC-ACG
1 GTCAACG
42711 GTCAACG
1 GTCAACG
42718 GTCAACG
1 GTCAACG
*
42725 ATCAACG
1 GTCAACG
*
42732 ATCAAC
1 GTCAAC
42738 AGTCGGGTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:42781 original size:15 final size:17
Alignment explanation
Indices: 42733--42770 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
42723 CGATCAACGA
*
42733 TCAACAGTCGGGTCGGG
1 TCAACAGCCGGGTCGGG
42750 TCAACAGCCGGGTCGGG
1 TCAACAGCCGGGTCGGG
42767 TCAA
1 TCAA
42771 ACCGGTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (17 bp):
TCAACAGCCGGGTCGGG
Found at i:42789 original size:19 final size:19
Alignment explanation
Indices: 42765--42835 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
42755 AGCCGGGTCG
* *
42765 GGTCAAACCGGTTCGGGCC
1 GGTCAAACCGGTTCAGACC
42784 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
42803 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
42823 GGTCAAACCGGTT
1 GGTCAAACCGGTT
42836 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 31 0.66
20 16 0.34
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:42803 original size:10 final size:10
Alignment explanation
Indices: 42767--42835 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
42757 CCGGGTCGGG
42767 TCAAACCGGT
1 TCAAACCGGT
***
42777 TCGGGCCGG-
1 TCAAACCGGT
42786 TCAAACCGGT
1 TCAAACCGGT
*
42796 TCAGACCGG-
1 TCAAACCGGT
42805 TCAAACCGGT
1 TCAAACCGGT
*
42815 TCAAAACTGG-
1 TC-AAACCGGT
42825 TCAAACCGGT
1 TCAAACCGGT
42835 T
1 T
42836 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
9 20 0.44
10 19 0.42
11 6 0.13
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:45191 original size:78 final size:78
Alignment explanation
Indices: 45097--45250 Score: 299
Period size: 78 Copynumber: 2.0 Consensus size: 78
45087 ATATTGCTTG
45097 ATCTTGATTTCAATTATAATCTAAATGAACACCATTTACAAAACATATACATTTCAAACCACATG
1 ATCTTGATTTCAATTATAATCTAAATGAACACCATTTACAAAACATATACATTTCAAACCACATG
45162 TTAGAATTTTATT
66 TTAGAATTTTATT
*
45175 ATCTTGATTTCAATTATAATCTAAATGAACATCATTTACAAAACATATACATTTCAAACCACATG
1 ATCTTGATTTCAATTATAATCTAAATGAACACCATTTACAAAACATATACATTTCAAACCACATG
45240 TTAGAATTTTA
66 TTAGAATTTTA
45251 CTAACATTGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (78 bp):
ATCTTGATTTCAATTATAATCTAAATGAACACCATTTACAAAACATATACATTTCAAACCACATG
TTAGAATTTTATT
Found at i:46414 original size:57 final size:57
Alignment explanation
Indices: 46236--46572 Score: 445
Period size: 57 Copynumber: 6.0 Consensus size: 57
46226 CCCTCTACCA
* * * * *
46236 ATACGGAAATTCACCTACA--TATTATGAATTTCTT-A-TGTTTACACATATAGTTCCC
1 ATACGGAAATTCA--TACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
** * *
46291 ATACAAAAATTCATACACTTAGTATGAATTTCTT-A-TTTTTGCACCCATAGCGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
* * *
46346 ATACGGAAATTCATACACTTAGCATGAATTTCTTAACTTTTTGAACACATAATGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
46403 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
* * *
46460 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACATATAGTGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
* *
46517 ATATGGAAATTCATACACTTTGTATGAATTTCTTAACTTTTTGCACAC-TCAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAT-AGTGCC
46573 ATTTGGAAAT
Statistics
Matches: 250, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
53 4 0.02
55 71 0.28
56 2 0.01
57 173 0.69
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (57 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACATAGTGCCC
Found at i:47011 original size:20 final size:20
Alignment explanation
Indices: 46986--47054 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
46976 GTTATCAATG
46986 GTATCGATACCTTCCTTATA
1 GTATCGATACCTTCCTTATA
*
47006 GTATCGATACATTCCTTATA
1 GTATCGATACCTTCCTTATA
* * *
47026 GTATCGATACC-CCCTTTTG
1 GTATCGATACCTTCCTTATA
47045 GTATCGATAC
1 GTATCGATAC
47055 TGCTTGCATC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 15 0.34
20 29 0.66
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCGATACCTTCCTTATA
Found at i:49983 original size:15 final size:14
Alignment explanation
Indices: 49959--49988 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
49949 ATTCATGCTT
49959 TTCAGTAAAAATTA
1 TTCAGTAAAAATTA
49973 TTCATGTAAAAATTA
1 TTCA-GTAAAAATTA
49988 T
1 T
49989 GTCTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (14 bp):
TTCAGTAAAAATTA
Found at i:50106 original size:83 final size:82
Alignment explanation
Indices: 49968--50122 Score: 256
Period size: 83 Copynumber: 1.9 Consensus size: 82
49958 TTTCAGTAAA
* *
49968 AATTATTCATGTAAAAATTATGTCTTTTTTATCCATTGAAAGACTGATTCACCCGCTAAATACCC
1 AATTATTCATGTAAAAATTATGTCTTTTTTATCCACTGAAAGACTGATTCACCCGCTAAATACCA
50033 AATTTTTATCCAATAAT
66 AATTTTTATCCAATAAT
** *
50050 AATTATTCATGTAAATTTTATGTCATTTTTTATCCACTGAAAGACTGATTCACCCGCTAAATATC
1 AATTATTCATGTAAAAATTATGTC-TTTTTTATCCACTGAAAGACTGATTCACCCGCTAAATACC
50115 AAATTTTT
65 AAATTTTT
50123 TCCCGAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 22 0.33
83 45 0.67
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (82 bp):
AATTATTCATGTAAAAATTATGTCTTTTTTATCCACTGAAAGACTGATTCACCCGCTAAATACCA
AATTTTTATCCAATAAT
Found at i:53301 original size:26 final size:25
Alignment explanation
Indices: 53272--53324 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
53262 ATTATTGTTA
*
53272 TCGTATGTTAAATGTACTCGTGGATC
1 TCGTATGTTAAAGGTACTCG-GGATC
53298 TCGTATGTTAAAGGTACTCGGGATC
1 TCGTATGTTAAAGGTACTCGGGATC
53323 TC
1 TC
53325 CTGACCGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (25 bp):
TCGTATGTTAAAGGTACTCGGGATC
Found at i:55917 original size:32 final size:31
Alignment explanation
Indices: 55876--55960 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
55866 CGAGATGTTC
* * * *
55876 CCTTAGGTAGGCTCTCAAGCTCCAATGTACT
1 CCTTGGGTAGGCTCTAAAGCCCCAAGGTACT
* *
55907 CCTTTGGGTAGGATCTAAAGCCCCAAGGTATT
1 CC-TTGGGTAGGCTCTAAAGCCCCAAGGTACT
* *
55939 CCTTGGGTAGGCTTTAAGGCCC
1 CCTTGGGTAGGCTCTAAAGCCC
55961 AAATTGACTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAAGCCCCAAGGTACT
Found at i:65573 original size:77 final size:78
Alignment explanation
Indices: 65457--65705 Score: 286
Period size: 78 Copynumber: 3.2 Consensus size: 78
65447 GCATCCTATC
*
65457 ATGCCAATAATGCACCCATATGCATTATTCTTTTATGTTGATAATGCA-CCATATATATTTCAAC
1 ATGCCAATAATGCACCCATATGCATTATTC-TTTATGTTGATAATGCACCCATATACATTTCAAC
*
65521 CATGGCAACTTTTA
65 CATGGCAACCTTTA
* * **
65535 ATGCCAATAA-GCACCCATATGCATAATTCGTTTATGTTGATAATGCACCCATATACATTTTAGT
1 ATGCCAATAATGCACCCATATGCATTATTC-TTTATGTTGATAATGCACCCATATACATTTCAAC
* * *
65599 TATGGCATCCTTTC
65 CATGGCAACCTTTA
* ** * * * *
65613 ATGCAAATAATGCACTGATATGCATTATTCTTTATGCTGATAATGCACCCATATGCATTTCATCT
1 ATGCCAATAATGCACCCATATGCATTATTCTTTATGTTGATAATGCACCCATATACATTTCAACC
* *
65678 ATGGCATCCTTTC
66 ATGGCAACCTTTA
**
65691 ATGATAATAATGCAC
1 ATGCCAATAATGCAC
65706 ACAGTGCCCA
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
77 35 0.24
78 97 0.66
79 16 0.11
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (78 bp):
ATGCCAATAATGCACCCATATGCATTATTCTTTATGTTGATAATGCACCCATATACATTTCAACC
ATGGCAACCTTTA
Found at i:66141 original size:20 final size:20
Alignment explanation
Indices: 66116--66187 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
66106 GATTCTTCAA
66116 TATCGATACCCCTATCATGG
1 TATCGATACCCCTATCATGG
** *
66136 TATCGAATACTACTATAATATGG
1 TATCG-ATACCCCTAT--CATGG
* *
66159 TACCGATACCCCTACCATGG
1 TATCGATACCCCTATCATGG
66179 TATCGATAC
1 TATCGATAC
66188 TACTATAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 17 0.43
21 8 0.20
22 7 0.17
23 8 0.20
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (20 bp):
TATCGATACCCCTATCATGG
Found at i:66201 original size:42 final size:41
Alignment explanation
Indices: 66119--66227 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 41
66109 TCTTCAATAT
*
66119 CGATACCCCTATCATGGTATCGAATACTACTATAATATGGTA
1 CGATACCCCTACCATGGTATCG-ATACTACTATAATATGGTA
66161 CCGATACCCCTACCATGGTATCGATACTACTATAATATGGTA
1 -CGATACCCCTACCATGGTATCGATACTACTATAATATGGTA
*
66203 CGATACCCC--CCTTCGGTATCGATAC
1 CGATACCCCTACCAT-GGTATCGATAC
66228 CAATTTAGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
39 3 0.05
40 11 0.17
41 9 0.14
42 19 0.30
43 21 0.33
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (41 bp):
CGATACCCCTACCATGGTATCGATACTACTATAATATGGTA
Done.