Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009426.1 Hibiscus syriacus cultivar Beakdansim tig00113402_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: 116535
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3039 original size:79 final size:77
Alignment explanation
Indices: 2895--3044 Score: 180
Period size: 79 Copynumber: 1.9 Consensus size: 77
2885 AAATTAACAA
* *
2895 TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-T
1 TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTT
2959 TTAATGTTCATT
66 TTAATGTTCATT
* * *
2971 TAAAAT-TTATTTAATT-ATTCTGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACA
1 TAAAATATTATTTAATTAATTC--AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACA
*
3034 TTCTTTTAATG
61 ATCTTTTAATG
3045 CTTACTTACT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
74 4 0.06
75 10 0.16
76 16 0.26
77 1 0.02
78 3 0.05
79 21 0.34
80 7 0.11
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (77 bp):
TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTT
TTAATGTTCATT
Found at i:20021 original size:19 final size:20
Alignment explanation
Indices: 19997--20034 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19987 CGGCCAAGAG
19997 CATGTATCTTCA-TTAAAAT
1 CATGTATCTTCATTTAAAAT
*
20016 CATGTATTTTCATTTAAAA
1 CATGTATCTTCATTTAAAA
20035 AAATCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
CATGTATCTTCATTTAAAAT
Found at i:20826 original size:18 final size:17
Alignment explanation
Indices: 20777--20826 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
20767 AATTGGAGTG
20777 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
20795 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
20813 CAGAAAAGAAAAAA
1 CA-AAAAGAAAAAA
20827 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:26606 original size:11 final size:13
Alignment explanation
Indices: 26574--26603 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
26564 TGGCCAAAGA
26574 TGAAAAGGTATGT
1 TGAAAAGGTATGT
26587 TGAAAAGGTATG-
1 TGAAAAGGTATGT
26599 TGAAA
1 TGAAA
26604 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:38080 original size:14 final size:15
Alignment explanation
Indices: 38048--38089 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
38038 TGGTTTTGCT
38048 TTCTTTTTGAATTTA
1 TTCTTTTTGAATTTA
* *
38063 TTCTTTTT-ATTTTC
1 TTCTTTTTGAATTTA
38077 TTCTTTTCTGAAT
1 TTCTTTT-TGAAT
38090 GTTTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.50
15 9 0.41
16 2 0.09
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCTTTTTGAATTTA
Found at i:38101 original size:32 final size:28
Alignment explanation
Indices: 38048--38109 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 28
38038 TGGTTTTGCT
38048 TTCTTTTTGAATTTATTCTTTTTATTTTC
1 TTCTTTTTGAATTTATTCTTTTT-TTTTC
*
38077 TTCTTTTCTGAATGTTTTTTCTTTTTTTTTC
1 TTCTTTT-TGAA--TTTATTCTTTTTTTTTC
38108 TT
1 TT
38110 TTTGTACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 4 0.14
31 7 0.24
32 11 0.38
ACGTcount: A:0.10, C:0.11, G:0.05, T:0.74
Consensus pattern (28 bp):
TTCTTTTTGAATTTATTCTTTTTTTTTC
Found at i:44224 original size:20 final size:20
Alignment explanation
Indices: 44199--44245 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
44189 GATGCTCACC
44199 AACCAGCTAGTAAAGAGGTT
1 AACCAGCTAGTAAAGAGGTT
*
44219 AACCAGCTAGTGAAGAGGTT
1 AACCAGCTAGTAAAGAGGTT
44239 AACCAGC
1 AACCAGC
44246 CCGCCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (20 bp):
AACCAGCTAGTAAAGAGGTT
Found at i:49286 original size:11 final size:13
Alignment explanation
Indices: 49254--49283 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
49244 TGGCCAAAGA
49254 TGAAAAGGTATGT
1 TGAAAAGGTATGT
49267 TGAAAAGGTATG-
1 TGAAAAGGTATGT
49279 TGAAA
1 TGAAA
49284 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:54445 original size:13 final size:13
Alignment explanation
Indices: 54427--54454 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54417 GGCGTGAAGG
54427 TGGAAAATGGTGA
1 TGGAAAATGGTGA
54440 TGGAAAATGGTGA
1 TGGAAAATGGTGA
54453 TG
1 TG
54455 AATAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (13 bp):
TGGAAAATGGTGA
Found at i:54841 original size:19 final size:20
Alignment explanation
Indices: 54799--54841 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
54789 GAAACCCCTT
*
54799 TGAAAACACATGATTTTAAA
1 TGAAAACACATAATTTTAAA
*
54819 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTAAA
54838 TGAA
1 TGAA
54842 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTAAA
Found at i:58266 original size:17 final size:17
Alignment explanation
Indices: 58240--58274 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
58230 TATAGGAGTA
58240 TTTTTTTTCTTT-TTGT
1 TTTTTTTTCTTTCTTGT
58256 TTTTTTCTTCTTTCTTGT
1 TTTTTT-TTCTTTCTTGT
58274 T
1 T
58275 GCTTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTCTTGT
Found at i:59072 original size:19 final size:20
Alignment explanation
Indices: 59032--59080 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
59022 ACCCCTTTGA
**
59032 AAAATACATGATTTTTGTTG
1 AAAATACATGATTTTTAATG
59052 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
59071 AAGATACATG
1 AAAATACATG
59081 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:62540 original size:18 final size:19
Alignment explanation
Indices: 62502--62540 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
62492 ATCAGAAAAG
* *
62502 AAGCCCTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
62521 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
62539 AA
1 AA
62541 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:71199 original size:15 final size:15
Alignment explanation
Indices: 71164--71192 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
71154 GTGCTTCAAC
71164 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
71178 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
71193 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:73725 original size:19 final size:19
Alignment explanation
Indices: 73676--73726 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
73666 CCTTGGCTTG
*
73676 CTTTCTCTTTTTGAATTTT
1 CTTTCTTTTTTTGAATTTT
73695 CTTTTTCTTTTTTT-ATGATTTT
1 C--TTTCTTTTTTTGA--ATTTT
73717 CTTTCTTTTT
1 CTTTCTTTTT
73727 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 10 0.37
21 10 0.37
22 6 0.22
ACGTcount: A:0.08, C:0.14, G:0.04, T:0.75
Consensus pattern (19 bp):
CTTTCTTTTTTTGAATTTT
Found at i:76418 original size:19 final size:20
Alignment explanation
Indices: 76376--76418 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
76366 GAAACCCCTT
*
76376 TGAAAACACATGATTTTAAA
1 TGAAAACACATAATTTTAAA
*
76396 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTAAA
76415 TGAA
1 TGAA
76419 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTAAA
Found at i:78448 original size:16 final size:16
Alignment explanation
Indices: 78427--78459 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
78417 TTCTGCCACC
78427 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
78443 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
78459 T
1 T
78460 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:83884 original size:16 final size:16
Alignment explanation
Indices: 83863--83895 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
83853 TTCTGCCACC
83863 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
83879 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
83895 T
1 T
83896 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:84455 original size:19 final size:20
Alignment explanation
Indices: 84431--84469 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
84421 ACTAAGGAAG
*
84431 TGAAAA-CATATGTTATGCA
1 TGAAAATCATATATTATGCA
84450 TGAAAATCATATATTATGCA
1 TGAAAATCATATATTATGCA
84470 AGTAAGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
TGAAAATCATATATTATGCA
Found at i:91245 original size:58 final size:58
Alignment explanation
Indices: 91176--91290 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
91166 AAAAGATCTG
91176 ATTACCGCAAGATACGATAATCTCGCTTGATGTACGGTGCTTCTTCCAACTAGCTCTA
1 ATTACCGCAAGATACGATAATCTCGCTTGATGTACGGTGCTTCTTCCAACTAGCTCTA
91234 ATTACCGCAAGATACGATAATCTCGCTTGATGTACGGTGCTTCTTCCAACTAGCTCT
1 ATTACCGCAAGATACGATAATCTCGCTTGATGTACGGTGCTTCTTCCAACTAGCTCT
91291 GATACCAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (58 bp):
ATTACCGCAAGATACGATAATCTCGCTTGATGTACGGTGCTTCTTCCAACTAGCTCTA
Found at i:97401 original size:11 final size:13
Alignment explanation
Indices: 97369--97398 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
97359 TGGCCAAAGA
97369 TGAAAAGGTATGT
1 TGAAAAGGTATGT
97382 TGAAAAGGTATG-
1 TGAAAAGGTATGT
97394 TGAAA
1 TGAAA
97399 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:107316 original size:17 final size:17
Alignment explanation
Indices: 107291--107331 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
107281 CATAACACTC
*
107291 AAAAGAAAATTAAAAGT
1 AAAAGAAAAATAAAAGT
*
107308 AAAATAAAAATAAAAG-
1 AAAAGAAAAATAAAAGT
107324 -AAAGAAAA
1 AAAAGAAAA
107332 TTCAACAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAGAAAAATAAAAGT
Found at i:108188 original size:14 final size:15
Alignment explanation
Indices: 108165--108197 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
108155 TTTTTTGAAA
*
108165 TTTTGGCTTTTTTT-
1 TTTTGCCTTTTTTTG
108179 TTTTGCCTTTTTTTG
1 TTTTGCCTTTTTTTG
108194 TTTT
1 TTTT
108198 TTGTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (15 bp):
TTTTGCCTTTTTTTG
Found at i:110261 original size:20 final size:22
Alignment explanation
Indices: 110232--110271 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
110222 AGGAGAGTTT
110232 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
110252 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
110272 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:112794 original size:24 final size:21
Alignment explanation
Indices: 112760--112803 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
112750 TCCACAAGAC
*
112760 ATGTCCTTTGACATTTCAAAAG
1 ATGTCCTTTGA-AATTCAAAAG
112782 ATGTACCTCTTGAAATTCAAAA
1 ATGT-CCT-TTGAAATTCAAAA
112804 TGTGCCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAG
Done.