Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001789.1 Hibiscus syriacus cultivar Beakdansim tig00003610_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: 37630
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6901 original size:26 final size:28
Alignment explanation
Indices: 6866--6919 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
6856 CCCGAACCTG
6866 AAAATATTATATA-TATAATTA-ATATA
1 AAAATATTATATATTATAATTATATATA
*
6892 AAAATATTATATATTATATTTATATATA
1 AAAATATTATATATTATAATTATATATA
6920 TATATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.52
27 7 0.28
28 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATATTATATATTATAATTATATATA
Found at i:8157 original size:19 final size:19
Alignment explanation
Indices: 8133--8176 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
8123 AAATCGTTAA
8133 CCATGCCAATAACGACTAT
1 CCATGCCAATAACGACTAT
***
8152 CCATGCTTCTAACGACTAT
1 CCATGCCAATAACGACTAT
8171 CCATGC
1 CCATGC
8177 TTTGAAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (19 bp):
CCATGCCAATAACGACTAT
Found at i:8177 original size:19 final size:19
Alignment explanation
Indices: 8142--8178 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8132 ACCATGCCAA
8142 TAACGACTATCCATGCTTC
1 TAACGACTATCCATGCTTC
8161 TAACGACTATCCATGCTT
1 TAACGACTATCCATGCTT
8179 TGAAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (19 bp):
TAACGACTATCCATGCTTC
Found at i:9786 original size:27 final size:27
Alignment explanation
Indices: 9735--9799 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
9725 ATTGTTATAC
9735 AATATTTTTT-ATGATTATAATATTAAT
1 AATATTTTTTAATGATTATAATATT-AT
*
9762 TATATTTTTTAAT-ATATATAA-ATTAT
1 AATATTTTTTAATGAT-TATAATATTAT
9788 AATATTATTTTA
1 AATATT-TTTTA
9800 TAAAATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.21
27 19 0.58
28 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
AATATTTTTTAATGATTATAATATTAT
Found at i:10439 original size:16 final size:16
Alignment explanation
Indices: 10418--10449 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10408 TTTATAATAT
*
10418 ATACAATATAAAAAAA
1 ATACAAAATAAAAAAA
10434 ATACAAAATAAAAAAA
1 ATACAAAATAAAAAAA
10450 CTAGATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (16 bp):
ATACAAAATAAAAAAA
Found at i:11905 original size:3 final size:3
Alignment explanation
Indices: 11897--11941 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
11887 TTGGGTTTGT
11897 TAA 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
11942 CATGGGTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15035 original size:20 final size:20
Alignment explanation
Indices: 15010--15088 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
15000 CAATGTGTTT
15010 TAAAGTTTCGAAACTCTGTC
1 TAAAGTTTCGAAACTCTGTC
* * *
15030 TAAAGTTTTGAAACTATGCC
1 TAAAGTTTCGAAACTCTGTC
*
15050 TAAAGTTT-GTAAACTCT-TGG
1 TAAAGTTTCG-AAACTCTGT-C
*
15070 AAAAGTTTCGAAACT-TGTC
1 TAAAGTTTCGAAACTCTGTC
15089 GTGCAGCAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
19 2 0.04
20 44 0.94
21 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (20 bp):
TAAAGTTTCGAAACTCTGTC
Found at i:18382 original size:21 final size:20
Alignment explanation
Indices: 18357--18395 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18347 TGTTAATTTA
18357 AATATTAAAATTTTATAAAAT
1 AATATT-AAATTTTATAAAAT
*
18378 AATATTATATTTTATAAA
1 AATATTAAATTTTATAAA
18396 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTAAATTTTATAAAAT
Found at i:18431 original size:17 final size:16
Alignment explanation
Indices: 18393--18442 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
18383 TATATTTTAT
*
18393 AAAT-ATTAAAAAATA
1 AAATAATTATAAAATA
*
18408 TAAATAATTCTATAAATA
1 -AAATAATTATA-AAATA
18426 AAATAATTATAAAATA
1 AAATAATTATAAAATA
18442 A
1 A
18443 CAGTATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.34
17 14 0.48
18 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAATTATAAAATA
Found at i:18772 original size:30 final size:31
Alignment explanation
Indices: 18732--18808 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
18722 GGTTAAATTG
*
18732 ATATTTTATCTAAAGTTT-AGAGAT-AAAATA
1 ATATTCTATCTAAAGTTTAAGAG-TCAAAATA
* * *
18762 ATATTGTATCTAAAGTTTAAGAGTCGAATTA
1 ATATTCTATCTAAAGTTTAAGAGTCAAAATA
18793 ATATTCTATCTAAAGT
1 ATATTCTATCTAAAGT
18809 CCAAGCATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 18 0.44
31 23 0.56
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (31 bp):
ATATTCTATCTAAAGTTTAAGAGTCAAAATA
Found at i:18803 original size:31 final size:30
Alignment explanation
Indices: 18725--18808 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
18715 ATTTAAGGGT
* *
18725 TAAATTGATATTTTATCTAAAGTTTAGAGA
1 TAAATTAATATTCTATCTAAAGTTTAGAGA
* *
18755 TAAAATAATATTGTATCTAAAGTTTA-AGA
1 TAAATTAATATTCTATCTAAAGTTTAGAGA
*
18784 GTCGAATTAATATTCTATCTAAAGT
1 -T-AAATTAATATTCTATCTAAAGT
18809 CCAAGCATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.07
30 24 0.52
31 19 0.41
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (30 bp):
TAAATTAATATTCTATCTAAAGTTTAGAGA
Found at i:22266 original size:21 final size:21
Alignment explanation
Indices: 22242--22281 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22232 TTTATTTTAT
22242 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
22263 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
22282 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:22329 original size:33 final size:33
Alignment explanation
Indices: 22276--22374 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
22266 TTTGTTTCAA
22276 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
22308 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
22341 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
22374 T
1 T
22375 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:22403 original size:13 final size:13
Alignment explanation
Indices: 22360--22414 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
22350 TTGGAAGTAT
22360 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
22373 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
22387 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
22400 TTAAGTATTTGAA
1 TTAAGTATTTCAA
22413 TT
1 TT
22415 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:22631 original size:21 final size:21
Alignment explanation
Indices: 22605--22652 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
22595 TGGAGCGTGG
22605 GGGAATCAGTACCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
* **
22626 GGGAATCGGTTTCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
22647 GGGAAT
1 GGGAAT
22653 TGGTTCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (21 bp):
GGGAATCAGTACCCTCTCATA
Found at i:22657 original size:21 final size:21
Alignment explanation
Indices: 22617--22657 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22607 GAATCAGTAC
22617 CCTCTCATAGGGAATCGGTTT
1 CCTCTCATAGGGAATCGGTTT
*
22638 CCTCTCATAGGGAATTGGTT
1 CCTCTCATAGGGAATCGGTT
22658 CCCTAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (21 bp):
CCTCTCATAGGGAATCGGTTT
Found at i:22851 original size:15 final size:15
Alignment explanation
Indices: 22826--22881 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
22816 ATCTGGAATA
*
22826 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
22841 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
22856 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
22873 TTAAAACCG
1 TTAAAACCG
22882 AAACTGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:22865 original size:17 final size:18
Alignment explanation
Indices: 22845--22878 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22835 GTTTTTTTAT
22845 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
22862 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
22879 CCGAAACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:24354 original size:57 final size:57
Alignment explanation
Indices: 24284--24392 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
24274 CATGCTTCTG
*
24284 TTTGTGTTTGCCTAAATGCACATAAGTGAGGTGATTCATTGTTCAAAACATTGTTGA
1 TTTGTATTTGCCTAAATGCACATAAGTGAGGTGATTCATTGTTCAAAACATTGTTGA
* *
24341 TTTGTATTTGCCTAAATGCACATAAGTGGGGTGATTCTTTGTTCAAAACATT
1 TTTGTATTTGCCTAAATGCACATAAGTGAGGTGATTCATTGTTCAAAACATT
24393 TCTGAATGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (57 bp):
TTTGTATTTGCCTAAATGCACATAAGTGAGGTGATTCATTGTTCAAAACATTGTTGA
Found at i:32336 original size:21 final size:19
Alignment explanation
Indices: 32312--32351 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
32302 ATATGAAATA
32312 AATATAAAAAAGTATATTTAT
1 AATATAAAAAA--ATATTTAT
*
32333 AATATTAAAAAATATTTAT
1 AATATAAAAAAATATTTAT
32352 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AATATAAAAAAATATTTAT
Found at i:32422 original size:19 final size:17
Alignment explanation
Indices: 32367--32434 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
32357 TTTAAAATTC
*
32367 AATTAATTATTTA-TTTA
1 AATTAA-TATTAATTTTA
*
32384 AATTAATATTATTTTTA
1 AATTAATATTAATTTTA
32401 AATTATATATTTAATTTTA
1 AATTA-ATA-TTAATTTTA
*
32420 AA-TAAT-TTAAATTTA
1 AATTAATATTAATTTTA
32435 GGTAAATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.18
16 4 0.09
17 17 0.39
18 5 0.11
19 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTAATATTAATTTTA
Found at i:34263 original size:32 final size:32
Alignment explanation
Indices: 34222--34286 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
34212 TAAAAGCTCT
34222 TAAAATGGTATCTATGTAAA-CATATTATTATA
1 TAAAATGGTATCTATGTAAATC-TATTATTATA
*
34254 TAAAATGGTATCTATTTAAATCTATTATTATA
1 TAAAATGGTATCTATGTAAATCTATTATTATA
34286 T
1 T
34287 TAATGTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (32 bp):
TAAAATGGTATCTATGTAAATCTATTATTATA
Found at i:34273 original size:16 final size:16
Alignment explanation
Indices: 34221--34273 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
34211 CTAAAAGCTC
34221 TTAAAATGGTATCTAT
1 TTAAAATGGTATCTAT
* **
34237 GTAAACATATTAT-TAT
1 TTAAA-ATGGTATCTAT
*
34253 ATAAAATGGTATCTAT
1 TTAAAATGGTATCTAT
34269 TTAAA
1 TTAAA
34274 TCTATTATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
TTAAAATGGTATCTAT
Found at i:35910 original size:65 final size:64
Alignment explanation
Indices: 35797--35939 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
35787 GCACCAATCC
* * *
35797 ATGCATCGATGCACACACCATGCATCGATGCACTGGGGATTTTATGAAAACATCGAATGTATTTG
1 ATGCATCGATGCACACACCATGCATCGATGCACTCGGGATTTTATG-AAACATCGAATGCACTTG
* * *
35862 ATGCATCGATGCATCA-GCCATGCATCGATGCACTCTGGCTATTT-TGAAACATCGAATGCACTT
1 ATGCATCGATGCA-CACACCATGCATCGATGCACTCGGGAT-TTTATGAAACATCGAATGCACTT
35925 G
64 G
35926 ATGCATCGATGCAC
1 ATGCATCGATGCAC
35940 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 29 0.41
65 35 0.50
66 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCGGGATTTTATGAAACATCGAATGCACTTG
Found at i:35939 original size:17 final size:19
Alignment explanation
Indices: 35911--35959 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
35901 TATTTTGAAA
35911 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
35929 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
35948 CACCGATGCACT
1 CATCGATGCACT
35960 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:36623 original size:64 final size:65
Alignment explanation
Indices: 36472--36631 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
36462 AATTAAATTG
* * *
36472 AACATCGAATGCATTTCATGCATTGATGCACATACCATACATCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATACATCGATGCACTCAGGATTTTATGAA
* * * * *
36537 AACATCGAATGCATTTGATGCATCGATGTACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATACATCGATGCACTCAGGAT-TTTATG
36600 -A
64 AA
*
36601 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
36632 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 48 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATACATCGATGCACTCAGGATTTTATGAA
Found at i:36643 original size:19 final size:19
Alignment explanation
Indices: 36619--36670 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
36609 ATGCACTTGA
36619 TGCATCGATGCACTCTTAG
1 TGCATCGATGCACTCTTAG
36638 TGCATCGATGCACTCTTAG
1 TGCATCGATGCACTCTTAG
*
36657 TGCACCGATGCACT
1 TGCATCGATGCACT
36671 AAGGGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCTTAG
Done.