Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007073.1 Hibiscus syriacus cultivar Beakdansim tig00018435_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: 69723
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:2513 original size:21 final size:21
Alignment explanation
Indices: 2484--2538 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2474 CTTGAAATGT
2484 TGCTTCTCTCGCTGCTCTCTC
1 TGCTTCTCTCGCTGCTCTCTC
* * *
2505 TGTTTCTCTTGTTGCTCTCTC
1 TGCTTCTCTCGCTGCTCTCTC
2526 TGCTTCTCTCGCT
1 TGCTTCTCTCGCT
2539 TCAACTTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.15, T:0.49
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCTCTCTC
Found at i:6862 original size:16 final size:16
Alignment explanation
Indices: 6841--6873 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6831 TGATGGAGAT
*
6841 TCTTTTTCTGGAATTA
1 TCTTTTTCTGAAATTA
6857 TCTTTTTCTGAAATTA
1 TCTTTTTCTGAAATTA
6873 T
1 T
6874 ATTAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TCTTTTTCTGAAATTA
Found at i:8696 original size:20 final size:20
Alignment explanation
Indices: 8646--8702 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
8636 AACGAAACAC
** *
8646 AACAAAATAATATTTAATATT
1 AACAAAAT-ATAAATAATATG
8667 AA-AAACATATAAATAATATG
1 AACAAA-ATATAAATAATATG
8687 AACAAAATATATAATA
1 AACAAAATATA-AATA
8703 TATAATAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AACAAAATATAAATAATATG
Found at i:15879 original size:35 final size:35
Alignment explanation
Indices: 15809--15879 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
15799 CTTTAGGTCC
* * **
15809 ATAAGGAATTACCAGTTGATTGGTGTTGAACCTAT
1 ATAAGGAATTACCAGTTGACTGGAGCAGAACCTAT
*
15844 ATAAGGAATTACCAGCTTGACT-GAGCAGAATCTAT
1 ATAAGGAATTACCAG-TTGACTGGAGCAGAACCTAT
15879 A
1 A
15880 GAGACGTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGACTGGAGCAGAACCTAT
Found at i:19470 original size:33 final size:34
Alignment explanation
Indices: 19433--19503 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
19423 CCTTTACAAC
*
19433 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* *
19466 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
19500 TCCC
1 TCCC
19504 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:19863 original size:20 final size:21
Alignment explanation
Indices: 19827--19867 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
19817 GAATAGTAAC
*
19827 GGTATCGGTACCCCTGTAGCA
1 GGTATCGATACCCCTGTAGCA
19848 GGTATCGATA-CCCTGTAGCA
1 GGTATCGATACCCCTGTAGCA
19868 TTCTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (21 bp):
GGTATCGATACCCCTGTAGCA
Found at i:19926 original size:20 final size:20
Alignment explanation
Indices: 19901--19946 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
19891 ACTATTCATC
19901 ACTGTTCAAACACTATCAG-T
1 ACTGTTCAAACACTATC-GTT
*
19921 ACTGTTCAAACAGTATCGTT
1 ACTGTTCAAACACTATCGTT
19941 ACTGTT
1 ACTGTT
19947 TATACATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (20 bp):
ACTGTTCAAACACTATCGTT
Found at i:20206 original size:21 final size:19
Alignment explanation
Indices: 20182--20239 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
20172 ATGTTTAATG
20182 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
20201 ACAAAAGAATATCAATTGTT-
1 A-AAAAG-ATACCAATTGTTA
*
20221 AAAAAGATACTAATTGTTA
1 AAAAAGATACCAATTGTTA
20240 CCATTTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 10 0.30
19 6 0.18
20 6 0.18
21 11 0.33
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:20235 original size:18 final size:18
Alignment explanation
Indices: 20182--20239 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
20172 ATGTTTAATG
*
20182 AAAAAGATACCAATTGTT
1 AAAAAGATACTAATTGTT
20200 AACAAAAGAATA-TCAATTGTT
1 -A-AAAAG-ATACT-AATTGTT
20221 AAAAAGATACTAATTGTT
1 AAAAAGATACTAATTGTT
20239 A
1 A
20240 CCATTTGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 11 0.32
19 7 0.21
20 6 0.18
21 10 0.29
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAAAGATACTAATTGTT
Found at i:22962 original size:34 final size:33
Alignment explanation
Indices: 22900--22970 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
22890 CCTTTACAAC
*
22900 TCCCTAGTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGATAAACTAGAACCTT
*
22933 TCCCTAGCTTTTACACGGGCTAAGA-TAGAACCTT
1 TCCCTAG-TTTTACACGGGATAA-ACTAGAACCTT
22967 TCCC
1 TCCC
22971 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 7 0.21
34 26 0.76
35 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGATAAACTAGAACCTT
Found at i:23140 original size:21 final size:21
Alignment explanation
Indices: 23115--23159 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
23105 TTGCTTGGAT
*
23115 AGTTGTGCTCTTACTTCTTCA
1 AGTTGTGCTCGTACTTCTTCA
*
23136 AGTTGTTCTCGTACTTCTTCA
1 AGTTGTGCTCGTACTTCTTCA
23157 AGT
1 AGT
23160 GTTCTCAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
AGTTGTGCTCGTACTTCTTCA
Found at i:25104 original size:8 final size:9
Alignment explanation
Indices: 25073--25102 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25063 TGGATTTGTT
25073 TGTTATGGA
1 TGTTATGGA
25082 TGTTATGGA
1 TGTTATGGA
25091 TGTT-TGGA
1 TGTTATGGA
25099 TGTT
1 TGTT
25103 TGAACTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (9 bp):
TGTTATGGA
Found at i:26021 original size:21 final size:21
Alignment explanation
Indices: 25997--26046 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
25987 TGACTTCACC
25997 AATGATCCCCCAATAATAAAA
1 AATGATCCCCCAATAATAAAA
26018 AATGATCCCCCAATAATAAAA
1 AATGATCCCCCAATAATAAAA
26039 AATGATCC
1 AATGATCC
26047 AAGGTGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (21 bp):
AATGATCCCCCAATAATAAAA
Found at i:29409 original size:15 final size:16
Alignment explanation
Indices: 29381--29410 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29371 TTTTGGGTCA
29381 GGTCAAACTCGGATCG
1 GGTCAAACTCGGATCG
29397 GGTCAAA-TCGGATC
1 GGTCAAACTCGGATC
29411 AAACGGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (16 bp):
GGTCAAACTCGGATCG
Found at i:32099 original size:18 final size:18
Alignment explanation
Indices: 32076--32111 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32066 TATACAAGTC
32076 TGACTATTCCAAGACTTG
1 TGACTATTCCAAGACTTG
32094 TGACTATTCCAAGACTTG
1 TGACTATTCCAAGACTTG
32112 AGCCTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TGACTATTCCAAGACTTG
Found at i:32118 original size:18 final size:18
Alignment explanation
Indices: 32077--32120 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
32067 ATACAAGTCT
*
32077 GACTATTCCAAGACTTGT
1 GACTATTCCAAGACTTGA
32095 GACTATTCCAAGACTTGA
1 GACTATTCCAAGACTTGA
*
32113 GCCTATTC
1 GACTATTC
32121 TAGATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (18 bp):
GACTATTCCAAGACTTGA
Found at i:32302 original size:13 final size:13
Alignment explanation
Indices: 32284--32308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32274 ACGTTACTAA
32284 AATATATATCTAG
1 AATATATATCTAG
32297 AATATATATCTA
1 AATATATATCTA
32309 TAGTTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
AATATATATCTAG
Found at i:32506 original size:90 final size:90
Alignment explanation
Indices: 32343--32605 Score: 474
Period size: 90 Copynumber: 2.9 Consensus size: 90
32333 TAATCCCAAA
* *
32343 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
*
32408 TAGGGTAACTTTGATATAAGAGGAT
66 TAGGGTAACTTGGATATAAGAGGAT
32433 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
32498 TAGGGTAACTTGGATATAAGAGGAT
66 TAGGGTAACTTGGATATAAGAGGAT
*
32523 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
*
32587 TAGGGTAACTTGGCTATAA
66 TAGGGTAACTTGGATATAA
32606 AAGGGTGTGT
Statistics
Matches: 168, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
89 29 0.17
90 139 0.83
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGAT
TAGGGTAACTTGGATATAAGAGGAT
Found at i:39199 original size:18 final size:18
Alignment explanation
Indices: 39178--39214 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39168 AATTGTTCTA
39178 ATAATTACTGCTAACGTT
1 ATAATTACTGCTAACGTT
39196 ATAATTACTGCTAACGTT
1 ATAATTACTGCTAACGTT
39214 A
1 A
39215 CAAGAACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTACTGCTAACGTT
Found at i:43725 original size:20 final size:20
Alignment explanation
Indices: 43680--43731 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
43670 TTTTCCATTA
*
43680 CAGTATCAATACCTTCCTCT
1 CAGTATCAATACCTTCCACT
**
43700 TGGTATCAATACC-TCCACAT
1 CAGTATCAATACCTTCCAC-T
*
43720 CAGTATCGATAC
1 CAGTATCAATAC
43732 TACTTAAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (20 bp):
CAGTATCAATACCTTCCACT
Found at i:57255 original size:43 final size:44
Alignment explanation
Indices: 57204--57301 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
57194 TTTTTTCTCT
*
57204 ACAAACGTCGCAATAGGTTT-GGTTATATAACGGCATTTTAGTC
1 ACAAACGTCGCAATAGGTTTGGGTTATATAACGGCATTTTAGGC
* * ** *
57247 ACAAACGTCACAATAGGTTTGGGTTATTTAGTGGCGTTTTAGGC
1 ACAAACGTCGCAATAGGTTTGGGTTATATAACGGCATTTTAGGC
*
57291 AAAAACGTCGC
1 ACAAACGTCGC
57302 TAAATGTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 19 0.41
44 27 0.59
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (44 bp):
ACAAACGTCGCAATAGGTTTGGGTTATATAACGGCATTTTAGGC
Found at i:59907 original size:21 final size:21
Alignment explanation
Indices: 59878--59932 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
59868 CTTGAAATGT
59878 TGCTTCTCTCGCTGCTCTCTC
1 TGCTTCTCTCGCTGCTCTCTC
* * *
59899 TGTTTCTCTTGTTGCTCTCTC
1 TGCTTCTCTCGCTGCTCTCTC
59920 TGCTTCTCTCGCT
1 TGCTTCTCTCGCT
59933 TCAACTTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.15, T:0.49
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCTCTCTC
Found at i:64292 original size:16 final size:16
Alignment explanation
Indices: 64271--64303 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
64261 TGATGGAGAT
*
64271 TCTTTTTCTGGAATTA
1 TCTTTTTCTGAAATTA
64287 TCTTTTTCTGAAATTA
1 TCTTTTTCTGAAATTA
64303 T
1 T
64304 ATTAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TCTTTTTCTGAAATTA
Found at i:66106 original size:19 final size:19
Alignment explanation
Indices: 66078--66127 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
66068 ACAACAAAAT
* *
66078 AATATTTAATATTAA-AAA
1 AATATATAATATGAACAAA
*
66096 CATATAATAATATGAACAAA
1 AATAT-ATAATATGAACAAA
66116 AATATATAATAT
1 AATATATAATAT
66128 AAATAGCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (19 bp):
AATATATAATATGAACAAA
Done.