Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006794.1 Hibiscus syriacus cultivar Beakdansim tig00017223_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: 67858
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5634 original size:25 final size:26
Alignment explanation
Indices: 5600--5661 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
5590 TTTAACACGG
5600 AGGTGAATTTTTTGCAAGGG-AAAGA
1 AGGTGAATTTTTTGCAAGGGAAAAGA
5625 AGGTGAATTTTTTTGCAAGGGAAAAGA
1 AGGTGAA-TTTTTTGCAAGGGAAAAGA
*
5652 AGTTGAATTT
1 AGGTGAATTT
5662 ATATGTATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 7 0.21
26 16 0.47
27 11 0.32
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (26 bp):
AGGTGAATTTTTTGCAAGGGAAAAGA
Found at i:5643 original size:26 final size:27
Alignment explanation
Indices: 5600--5661 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
5590 TTTAACACGG
5600 AGGTGAA-TTTTTTGCAAGGG-AAAGA
1 AGGTGAATTTTTTTGCAAGGGAAAAGA
5625 AGGTGAATTTTTTTGCAAGGGAAAAGA
1 AGGTGAATTTTTTTGCAAGGGAAAAGA
*
5652 AGTTGAATTT
1 AGGTGAATTT
5662 ATATGTATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 7 0.21
26 13 0.38
27 14 0.41
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (27 bp):
AGGTGAATTTTTTTGCAAGGGAAAAGA
Found at i:9917 original size:60 final size:59
Alignment explanation
Indices: 9835--9990 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 59
9825 ATCGGTCCCT
9835 AAACTTTT-AA-ATGTTCTAATTTCATCCCTAAACTATGA-TTATAATTCTAAATTAGTCCTC
1 AAACTTTTGAACAT-TTC-AATTTCATCCC-AAACTATGACTT-TAATTCTAAATTAGTCCTC
** * * *
9895 AAACTTTTGAACATTTCAATTTCATCTCCAAGTTATGACTTTCATTCTAAATTGGTTCTC
1 AAACTTTTGAACATTTCAATTTCATC-CCAAACTATGACTTTAATTCTAAATTAGTCCTC
9955 AAACTTTTTGAAC-TTTCCAATTTCATCCCAAACTAT
1 AAAC-TTTTGAACATTT-CAATTTCATCCCAAACTAT
9991 AAGCATATAC
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
60 54 0.65
61 27 0.33
62 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (59 bp):
AAACTTTTGAACATTTCAATTTCATCCCAAACTATGACTTTAATTCTAAATTAGTCCTC
Found at i:15703 original size:24 final size:23
Alignment explanation
Indices: 15671--15724 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
15661 TAGTTTAAAA
* *
15671 TAAAAAT-AATTATATTTATATTT
1 TAAAAATAAATAATAATT-TATTT
15694 TATAAAATAAATAATAATTTATTT
1 TA-AAAATAAATAATAATTTATTT
15718 TAAAAAT
1 TAAAAAT
15725 TTAATTCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 12 0.44
25 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAATAAATAATAATTTATTT
Found at i:15927 original size:12 final size:12
Alignment explanation
Indices: 15910--15935 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15900 ACTTATTTAA
15910 TAATTAAAAATT
1 TAATTAAAAATT
15922 TAATTAAAAATT
1 TAATTAAAAATT
15934 TA
1 TA
15936 TAATTTGTAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATTAAAAATT
Found at i:16384 original size:23 final size:21
Alignment explanation
Indices: 16345--16393 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
16335 TTGGTTGAAT
*
16345 AAAATTAATTAAATAATAATTTA
1 AAAATTAATGAAATAAT--TTTA
16368 AAAATTAA-GAAACTAATTTTA
1 AAAATTAATGAAA-TAATTTTA
16389 AAAAT
1 AAAAT
16394 GTCACGTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTAATGAAATAATTTTA
Found at i:16726 original size:19 final size:19
Alignment explanation
Indices: 16702--16751 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
16692 GTATCATGAT
16702 GATCGAAAGAGTGGGTTGG
1 GATCGAAAGAGTGGGTTGG
16721 GATCGAAAGAGTGGGTTGG
1 GATCGAAAGAGTGGGTTGG
*
16740 AATCGAAAGAGT
1 GATCGAAAGAGT
16752 TTAAGTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.20
Consensus pattern (19 bp):
GATCGAAAGAGTGGGTTGG
Found at i:19784 original size:29 final size:29
Alignment explanation
Indices: 19752--19815 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
19742 TTTCCAAAAA
19752 GTCACCTTTTTCAAAATAATTCCCAGAAT
1 GTCACCTTTTTCAAAATAATTCCCAGAAT
* *
19781 GTCACATTTTTCAAAATATTTCCCAGAAT
1 GTCACCTTTTTCAAAATAATTCCCAGAAT
19810 GTCACC
1 GTCACC
19816 GTTTCGGACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (29 bp):
GTCACCTTTTTCAAAATAATTCCCAGAAT
Found at i:25230 original size:9 final size:9
Alignment explanation
Indices: 25194--25255 Score: 61
Period size: 10 Copynumber: 6.4 Consensus size: 9
25184 GCTACTGGAA
25194 ACCGGTTTCG
1 ACCGGTTT-G
25204 ACCGGTTTTG
1 ACCGG-TTTG
*
25214 ACCAGTTTG
1 ACCGGTTTG
*
25223 AACCGTTTTG
1 -ACCGGTTTG
*
25233 ACCGGTCTG
1 ACCGGTTTG
25242 AACCGGTTTG
1 -ACCGGTTTG
25252 ACCG
1 ACCG
25256 TCTGACCCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 15 0.35
10 25 0.58
11 3 0.07
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:25232 original size:19 final size:19
Alignment explanation
Indices: 25208--25260 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
25198 GTTTCGACCG
*
25208 GTTTTGACCAGTTTGAACC
1 GTTTTGACCAGTCTGAACC
*
25227 GTTTTGACCGGTCTGAACC
1 GTTTTGACCAGTCTGAACC
*
25246 GGTTTGACC-GTCTGA
1 GTTTTGACCAGTCTGA
25261 CCCGACTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (19 bp):
GTTTTGACCAGTCTGAACC
Found at i:25308 original size:22 final size:22
Alignment explanation
Indices: 25277--25319 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25267 TCGACCCGAC
* *
25277 CGACCCGACCCGATCGTTGACT
1 CGACCAGACCCGACCGTTGACT
25299 CGACCAGACCCGACCGTTGAC
1 CGACCAGACCCGACCGTTGAC
25320 CGTTGACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.23, T:0.14
Consensus pattern (22 bp):
CGACCAGACCCGACCGTTGACT
Found at i:32579 original size:10 final size:9
Alignment explanation
Indices: 32556--32634 Score: 59
Period size: 9 Copynumber: 8.3 Consensus size: 9
32546 GCTGCTGAAA
32556 ACCGGTTTG
1 ACCGGTTTG
32565 ACCGGTTTCG
1 ACCGGTTT-G
32575 ACCGGTTTTG
1 ACCGG-TTTG
* *
32585 ATCGGTTCG
1 ACCGGTTTG
* *
32594 AATCGTTTTG
1 -ACCGGTTTG
* *
32604 ACCGATCTG
1 ACCGGTTTG
32613 AACCGGTTTG
1 -ACCGGTTTG
*
32623 ACCGGTCTG
1 ACCGGTTTG
32632 ACC
1 ACC
32635 CGACCCGACC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
9 28 0.50
10 25 0.45
11 3 0.05
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:32632 original size:19 final size:20
Alignment explanation
Indices: 32555--32630 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 20
32545 TGCTGCTGAA
*
32555 AACCGGTTTGACCGGTTTCG
1 AACCGGTTTGACCGGTCTCG
*
32575 -ACCGGTTTTGATCGGT-TCG
1 AACCGG-TTTGACCGGTCTCG
* * *
32594 AATCGTTTTGACCGATCT-G
1 AACCGGTTTGACCGGTCTCG
32613 AACCGGTTTGACCGGTCT
1 AACCGGTTTGACCGGTCT
32631 GACCCGACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
19 32 0.71
20 13 0.29
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.33
Consensus pattern (20 bp):
AACCGGTTTGACCGGTCTCG
Found at i:35946 original size:32 final size:31
Alignment explanation
Indices: 35908--35984 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
35898 CGGGGCTGTG
*
35908 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
35940 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
35971 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
35985 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:35977 original size:63 final size:63
Alignment explanation
Indices: 35861--35984 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
35851 CCCTAAGGGA
* * * * *
35861 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCTGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
* *
35924 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAGA
35985 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:36902 original size:29 final size:29
Alignment explanation
Indices: 36860--36962 Score: 152
Period size: 29 Copynumber: 3.6 Consensus size: 29
36850 CATTCGAAAC
* *
36860 TTCCTAAAATGTCACCTTTTTTAAAATAA
1 TTCCTAGAATGTCACCTTTTTTAAAATAT
*
36889 TTCCTAGAATGTCACCTTTTTCAAAATAT
1 TTCCTAGAATGTCACCTTTTTTAAAATAT
*
36918 TTCCTAGATTGTCACCTTTTTTAAAATAT
1 TTCCTAGAATGTCACCTTTTTTAAAATAT
* *
36947 TTCCCAGAATATCACC
1 TTCCTAGAATGTCACC
36963 CAGTCAGGTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (29 bp):
TTCCTAGAATGTCACCTTTTTTAAAATAT
Found at i:42031 original size:47 final size:47
Alignment explanation
Indices: 41980--42288 Score: 507
Period size: 47 Copynumber: 6.6 Consensus size: 47
41970 TGTATTAACA
41980 CATCCATTT-ATGCATTTT-AATTTATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCAA-TTATGGCATCCTTTCATGCCTTAATG
* *
42027 CATCCTTTCATGTATTTTCAATTATGGCATCCTTTCATGTCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
42074 CATCCTTTCATGCATTTTCAATTATTGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
42121 CATCCTTTCATGCATTTTCAATTACGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
42168 CATCCTTTCATGCATTTTCAATTACGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
42215 CATCCTTTCATGCATTGTCAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
42262 CATCCTTTCATGCATTTT-AATTTATGG
1 CATCCTTTCATGCATTTTCAA-TTATGG
42289 ATTCGATTTG
Statistics
Matches: 247, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
46 5 0.02
47 240 0.97
48 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
Found at i:45524 original size:2 final size:2
Alignment explanation
Indices: 45517--45572 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
45507 TACATACATG
* *
45517 AT AT AT AT AT AC AC 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
45559 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
45573 TGTCAGAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:47944 original size:30 final size:30
Alignment explanation
Indices: 47910--47967 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
47900 TGAACACAAT
*
47910 TAAAAT-TCGTATATAATATTAAATATTTGA
1 TAAAATGTCATATATAAT-TTAAATATTTGA
* *
47940 TAAAATGTCATGTATAATTTTAATATTT
1 TAAAATGTCATATATAATTTAAATATTT
47968 CTTATGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (30 bp):
TAAAATGTCATATATAATTTAAATATTTGA
Found at i:49968 original size:24 final size:24
Alignment explanation
Indices: 49939--49984 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
49929 TTATCCTTGA
49939 ATGAAATGTTGGATTCCTTGCTGC
1 ATGAAATGTTGGATTCCTTGCTGC
49963 ATGAAATGTTGGATTCCTTGCT
1 ATGAAATGTTGGATTCCTTGCT
49985 AGATGCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (24 bp):
ATGAAATGTTGGATTCCTTGCTGC
Found at i:54178 original size:6 final size:6
Alignment explanation
Indices: 54164--54214 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
54154 GATGTCTCAG
* ** * *
54164 AGAGAA AGAGGA AGAGGA AGAGGA AGAGTT TGAGGA AGAGGT AGAGGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA
54212 AGA
1 AGA
54215 AATCAACTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.08
Consensus pattern (6 bp):
AGAGGA
Found at i:59205 original size:19 final size:19
Alignment explanation
Indices: 59153--59207 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
59143 ACATATGTAA
*
59153 TCCTTTGGAACATATGCGG
1 TCCTTTGGAATATATGCGG
* **
59172 TTCTTTAGGACATATATTTGG
1 TCCTTT-GGA-ATATATGCGG
59193 TCCTTTGGAATATAT
1 TCCTTTGGAATATAT
59208 ATATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (19 bp):
TCCTTTGGAATATATGCGG
Found at i:62508 original size:16 final size:17
Alignment explanation
Indices: 62477--62509 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62467 GCCACCATAG
*
62477 TCTCGAATATAAATTAA
1 TCTCAAATATAAATTAA
62494 TCTCAAATA-AAATTAA
1 TCTCAAATATAAATTAA
62510 GAGAACCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
TCTCAAATATAAATTAA
Found at i:65500 original size:20 final size:21
Alignment explanation
Indices: 65470--65510 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
65460 TCAATCTTGC
65470 GGGATAAACGAATAGGGTTGT
1 GGGATAAACGAATAGGGTTGT
65491 GGGA-AAACGAATAGGGTTGT
1 GGGATAAACGAATAGGGTTGT
65511 CAAGTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.22
Consensus pattern (21 bp):
GGGATAAACGAATAGGGTTGT
Done.