Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006770.1 Hibiscus syriacus cultivar Beakdansim tig00017106_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: 67998
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1935 original size:19 final size:21
Alignment explanation
Indices: 1889--1935 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
1879 ATATGTTTTG
1889 CATATG-TTTTATATTCATTT
1 CATATGTTTTTATATTCATTT
**
1909 GTTATGTTTTTATA-TCA-TT
1 CATATGTTTTTATATTCATTT
1928 CATATGTT
1 CATATGTT
1936 ATGGCAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (21 bp):
CATATGTTTTTATATTCATTT
Found at i:11216 original size:22 final size:22
Alignment explanation
Indices: 11189--11231 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11179 TGCTTGAATG
* *
11189 ATGCACATGGCAGCCTACATGA
1 ATGCACATGACAGCCGACATGA
11211 ATGCACATGACAGCCGACATG
1 ATGCACATGACAGCCGACATG
11232 GAAGTTATTT
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:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (22 bp):
ATGCACATGACAGCCGACATGA
Found at i:16235 original size:13 final size:13
Alignment explanation
Indices: 16213--16242 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16203 ACTAAACACC
16213 TTTC-ACATACCT
1 TTTCAACATACCT
16225 TTTCAACATACCT
1 TTTCAACATACCT
16238 TTTCA
1 TTTCA
16243 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:18530 original size:12 final size:11
Alignment explanation
Indices: 18513--18555 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
18503 TTGCAATTCC
18513 TTTATCTTTTCT
1 TTTATCTTTT-T
*
18525 TTTATCTTGTT
1 TTTATCTTTTT
*
18536 TTAATCTTATTT
1 TTTATCTT-TTT
18548 TTTATCTT
1 TTTATCTT
18556 GTTTCTAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATCTTTTT
Found at i:18550 original size:23 final size:23
Alignment explanation
Indices: 18516--18559 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
18506 CAATTCCTTT
18516 ATCTTTTCTTTTATCTTGTTTTA
1 ATCTTTTCTTTTATCTTGTTTTA
18539 ATCTTATT-TTTTATCTTGTTT
1 ATCTT-TTCTTTTATCTTGTTT
18560 CTAGCACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTTTCTTTTATCTTGTTTTA
Found at i:24891 original size:19 final size:17
Alignment explanation
Indices: 24869--24910 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
24859 AAATTTTGGC
24869 TTTTTTGGCTCTTTTTTT
1 TTTTTTGGC-CTTTTTTT
24887 GTTTTTT-GCCTTTTTTT
1 -TTTTTTGGCCTTTTTTT
24904 TTTTTTG
1 TTTTTTG
24911 AAAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 2 0.09
19 6 0.27
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.79
Consensus pattern (17 bp):
TTTTTTGGCCTTTTTTT
Found at i:30205 original size:6 final size:6
Alignment explanation
Indices: 30194--30222 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30184 TTCAACTTTC
30194 TTTCTT TTTCTT TTTC-T TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
30223 CCTTTTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:30215 original size:11 final size:11
Alignment explanation
Indices: 30190--30222 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
30180 CTGCTTCAAC
*
30190 TTTCTTTCT-T
1 TTTCTTTTTCT
30200 TTTCTTTTTCT
1 TTTCTTTTTCT
30211 TTTCTTTTTCT
1 TTTCTTTTTCT
30222 T
1 T
30223 CCTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:30216 original size:17 final size:16
Alignment explanation
Indices: 30190--30222 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
30180 CTGCTTCAAC
30190 TTTCTTTCTTTTTCTT
1 TTTCTTTCTTTTTCTT
30206 TTTCTTTTCTTTTTCTT
1 TTTC-TTTCTTTTTCTT
30223 CCTTTTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTT
Found at i:32562 original size:24 final size:24
Alignment explanation
Indices: 32530--32584 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
32520 TGGTATCTTC
32530 AGTTGAGTTTAGCTCCTCTAGCTA
1 AGTTGAGTTTAGCTCCTCTAGCTA
32554 AGTTGAGTTTAGCTCCTCTAGCTA
1 AGTTGAGTTTAGCTCCTCTAGCTA
*
32578 AGGTGAG
1 AGTTGAG
32585 CTTTCCTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (24 bp):
AGTTGAGTTTAGCTCCTCTAGCTA
Found at i:35033 original size:19 final size:20
Alignment explanation
Indices: 34986--35036 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
34976 GAAACCCCTT
**
34986 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
35006 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
35025 TGAAGATACATG
1 TGAAAATACATG
35037 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:38280 original size:23 final size:24
Alignment explanation
Indices: 38231--38283 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
38221 TTCTTTGCTT
* *
38231 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
38254 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
38277 TTTCTTT
1 TTTCTTT
38284 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:39002 original size:19 final size:20
Alignment explanation
Indices: 38955--39005 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
38945 GAAACCCCTT
**
38955 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
38975 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
38994 TGAAGATACATG
1 TGAAAATACATG
39006 TTGGTCGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:40259 original size:19 final size:20
Alignment explanation
Indices: 40235--40285 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40225 CGGCCAAGAG
* *
40235 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
40254 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
40274 CATGTATTTTCA
1 CATGTATTTTCA
40286 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:43859 original size:19 final size:20
Alignment explanation
Indices: 43822--43861 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43812 GGATAATAAT
43822 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
43842 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
43861 A
1 A
43862 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:44322 original size:19 final size:20
Alignment explanation
Indices: 44277--44325 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
44267 ACCCCTTTGA
44277 AAATACATGATTTTTAAATG
1 AAATACATGATTTTTAAATG
44297 ACAATACATGA-TTTT-AATG
1 A-AATACATGATTTTTAAATG
44316 AAGATACATG
1 AA-ATACATG
44326 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 12 0.44
20 5 0.19
21 9 0.33
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTTAAATG
Found at i:47841 original size:19 final size:20
Alignment explanation
Indices: 47804--47843 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
47794 GGATAATAAT
47804 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
47824 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
47843 A
1 A
47844 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:48299 original size:19 final size:21
Alignment explanation
Indices: 48256--48307 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
48246 GAAACCCCTT
*
48256 TGAAAATAAATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
48277 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
48296 TGAAGATACATG
1 TGAAAATACATG
48308 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:50563 original size:11 final size:11
Alignment explanation
Indices: 50549--50575 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
50539 TATCGATTTG
50549 TGAATCCATCA
1 TGAATCCATCA
50560 TGAATCCATCA
1 TGAATCCATCA
50571 TGAAT
1 TGAAT
50576 TTTCTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (11 bp):
TGAATCCATCA
Found at i:51432 original size:19 final size:21
Alignment explanation
Indices: 51389--51440 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
51379 GAAATCCCTT
51389 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
51410 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
51429 TGAAGATACATG
1 TGAAAATACATG
51441 CTCATGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:56722 original size:34 final size:33
Alignment explanation
Indices: 56684--56749 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
56674 TTGCTTTCTC
*
56684 TTTTTGAACTTCTTTTTCTTTTATTCTTTTCTAA
1 TTTTTGAACTTCTTTTTCTCTT-TTCTTTTCTAA
*** *
56718 TTTTTTTTCTTCTTTTTGTCTTTTCTTTTCTA
1 TTTTTGAACTTCTTTTTCTCTTTTCTTTTCTA
56750 TTTGCACTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (33 bp):
TTTTTGAACTTCTTTTTCTCTTTTCTTTTCTAA
Found at i:59210 original size:34 final size:33
Alignment explanation
Indices: 59172--59237 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
59162 TTGCTTTCTC
*
59172 TTTTTGAACTTCTTTTTCTTTTATTCTTTTCTAA
1 TTTTTGAACTTCTTTTTCTCTT-TTCTTTTCTAA
*** *
59206 TTTTTTTTCTTCTTTTTGTCTTTTCTTTTCTA
1 TTTTTGAACTTCTTTTTCTCTTTTCTTTTCTA
59238 TTTGCACTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (33 bp):
TTTTTGAACTTCTTTTTCTCTTTTCTTTTCTAA
Found at i:61724 original size:21 final size:20
Alignment explanation
Indices: 61670--61727 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
61660 CTGTTTGAAC
*
61670 TTGTTTTTCTTTTATTCTTT
1 TTGTTTTTCTTTTCTTCTTT
**
61690 TCTAAATTTT-TTTTCTTCTTT
1 T-T-GTTTTTCTTTTCTTCTTT
61711 TTGTCTTTTCTTTTCTT
1 TTGT-TTTTCTTTTCTT
61728 TTTGCACTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (20 bp):
TTGTTTTTCTTTTCTTCTTT
Found at i:62474 original size:19 final size:21
Alignment explanation
Indices: 62431--62480 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
62421 GAAACAACAT
62431 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
62452 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
62471 TGAAGATACA
1 TGAAAATACA
62481 AGCTCTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:66040 original size:15 final size:15
Alignment explanation
Indices: 66015--66050 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
66005 ACTATATATC
66015 AATCTAGGAATTTTGG
1 AATC-AGGAATTTTGG
*
66031 AATCAGGAATTTTTG
1 AATCAGGAATTTTGG
66046 AATCA
1 AATCA
66051 AGATGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (15 bp):
AATCAGGAATTTTGG
Found at i:66308 original size:19 final size:21
Alignment explanation
Indices: 66259--66310 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
66249 TGAAACCCCT
66259 TTGAAAATACATGATTTTTAA
1 TTGAAAATACATGATTTTTAA
*
66280 ATGAAAATACATGA-TTTT-A
1 TTGAAAATACATGATTTTTAA
*
66299 TTGAAGATACAT
1 TTGAAAATACAT
66311 TCTCTTGGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (21 bp):
TTGAAAATACATGATTTTTAA
Done.