Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005144.1 Hibiscus syriacus cultivar Beakdansim tig00011585_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: 71898
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4980 original size:2 final size:2
Alignment explanation
Indices: 4973--5059 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
4963 GTTTAAACCC
4973 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
5015 CT CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5057 CT C
1 CT C
5060 CCTCCCTCCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.01, C:0.51, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:7813 original size:17 final size:18
Alignment explanation
Indices: 7793--7834 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
7783 TATCTATATT
7793 TAAAATATA-TTTAAAAA
1 TAAAATATATTTTAAAAA
* *
7810 TAAAATTTATTTTAATAA
1 TAAAATATATTTTAAAAA
7828 TAAAATA
1 TAAAATA
7835 AAAATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATATTTTAAAAA
Found at i:14533 original size:21 final size:22
Alignment explanation
Indices: 14507--14547 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
14497 AATTGTGGGG
14507 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
*
14528 ATGTTTTTGGTATTTTTATT
1 ATGTTTTTAGTATTTTTATT
14548 TAGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:17840 original size:14 final size:13
Alignment explanation
Indices: 17802--17855 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
17792 TATTAATATG
*
17802 ATTAAAATAAAATA
1 ATTAAAATATAA-A
**
17816 ATTTAAAATATTGA
1 A-TTAAAATATAAA
17830 ATTAAACATATAAA
1 ATTAAA-ATATAAA
17844 ATTAAAATATAA
1 ATTAAAATATAA
17856 CTAAACATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 11 0.33
14 14 0.42
15 8 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
ATTAAAATATAAA
Found at i:19163 original size:3 final size:3
Alignment explanation
Indices: 19155--19211 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
19145 GACTGAAATG
19155 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
19201 TAA TAA -AA TAA
1 TAA TAA TAA TAA
19212 AAAAAACCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:19224 original size:31 final size:34
Alignment explanation
Indices: 19156--19224 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
19146 ACTGAAATGT
* *
19156 AATAATAATAATAATAAATAATAATAATAAATAA
1 AATAATAATAATAATAAATAATAATAAAAAACAA
*
19190 AATAATAATAATAAT-AA-AATAA-AAAAAACCA
1 AATAATAATAATAATAAATAATAATAAAAAACAA
19221 AATA
1 AATA
19225 GAAAAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.31
32 5 0.16
33 2 0.06
34 15 0.47
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (34 bp):
AATAATAATAATAATAAATAATAATAAAAAACAA
Found at i:19586 original size:118 final size:119
Alignment explanation
Indices: 19378--19710 Score: 560
Period size: 118 Copynumber: 2.8 Consensus size: 119
19368 GGATTAGTTA
*
19378 TTCTCATTATGAACTTTTCCACCGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
*
19443 AAGTTGAACAAATTCTTATCATTATGAACTTATTCTTTTTTTT-AGATGAGTCC
66 AAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTTTTTTTCAGATGAGTCC
* *
19496 TTCTCATTATGAACTTTTCCACTAGGGATGAAAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
* * *
19561 AAGTTGAACAAAGTATTCTCATTATGAACTTATTCTTTTTTTTCCAGATGAGTTC
66 AAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTTTTTTT-CAGATGAGTCC
* *
19616 TTCTCATTATGAACTTTTCCTCTGGGGATGACAATTTATCTCCTTTTGTGATGTAATCTAGCAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
*
19681 AAGTTGAACAAATTCTTCCCATTATGAACT
66 AAGTTGAACAAATTCTTCTCATTATGAACT
19711 CTTTCTGGAA
Statistics
Matches: 199, Mismatches: 14, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
118 102 0.51
120 97 0.49
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (119 bp):
TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
AAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTTTTTTTCAGATGAGTCC
Found at i:20042 original size:123 final size:122
Alignment explanation
Indices: 19778--20225 Score: 650
Period size: 123 Copynumber: 3.7 Consensus size: 122
19768 GAATTAAGGC
* * *
19778 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * **
19843 GAACACTTCTGGAAATGTTTATGCTT-ATCTATCTCCTTCTGTGATAGCTTC-ATGCAA
66 GAACTCTTCTGGAAAAGTGTATG-TTGATCTATCTCCTTCTGTGATAGAGTCTA-GCAA
*
19900 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
19965 GAACTTTATCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
66 GAACTCT-TCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
** * * *
20023 AAGGTTGAACATTTTCTTCTCATTATGAACTTTTTCTCCCTCTTCATATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
20088 GAACTTTCTCTGGAAAAATGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
66 GAACTCT-TCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
* * *
20146 AAGGTTGAACAAGTTCTTCTCATTACGAACTTTTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
20210 TGAACTCTTCTGGAAA
65 TGAACTCTTCTGGAAA
20226 TGTTGATTCA
Statistics
Matches: 298, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
122 78 0.26
123 219 0.73
124 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTCTTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
Found at i:20670 original size:22 final size:22
Alignment explanation
Indices: 20612--20674 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
20602 AAATCCAATA
* * * *
20612 AATCTTTCTTCTTTAAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
20634 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
20656 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
20675 ATGTAGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:21658 original size:18 final size:18
Alignment explanation
Indices: 21621--21658 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21611 TATATAAAAG
*
21621 AATAAATTGAATTTCTAA
1 AATAAATTGAATTTCAAA
21639 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
21657 AA
1 AA
21659 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:33560 original size:2 final size:2
Alignment explanation
Indices: 33553--33586 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
33543 ATAAAATTAA
33553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33587 AGCATGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33759 original size:14 final size:13
Alignment explanation
Indices: 33729--33768 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
33719 TGATTAAAAT
**
33729 AATTAAAATATTG
1 AATTAAAATATAA
33742 AATTAAACATATAA
1 AATTAAA-ATATAA
33756 AATTAAAATATAA
1 AATTAAAATATAA
33769 CTAAACATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (13 bp):
AATTAAAATATAA
Found at i:35026 original size:15 final size:15
Alignment explanation
Indices: 35006--35037 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34996 GTGTAATAAT
35006 AATAATAATAAAAAA
1 AATAATAATAAAAAA
35021 AATAATAATAAAAAA
1 AATAATAATAAAAAA
35036 AA
1 AA
35038 ACCAAATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAATAATAAAAAA
Found at i:35026 original size:18 final size:17
Alignment explanation
Indices: 35003--35038 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
34993 GAAGTGTAAT
35003 AATAATAATAATAAAAAA
1 AATAATAATAA-AAAAAA
35021 AATAATAATAAAAAAAA
1 AATAATAATAAAAAAAA
35038 A
1 A
35039 CCAAATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAATAATAAAAAAAA
Found at i:35033 original size:12 final size:12
Alignment explanation
Indices: 34999--35034 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
34989 GCATGAAGTG
*
34999 TAATAATAATAA
1 TAATAATAAAAA
*
35011 TAATAAAAAAAA
1 TAATAATAAAAA
35023 TAATAATAAAAA
1 TAATAATAAAAA
35035 AAAACCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:38373 original size:27 final size:27
Alignment explanation
Indices: 38343--38408 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
38333 TGGTAAAATA
38343 GAAAGTCATCTTCTGTTGCCACATCCT
1 GAAAGTCATCTTCTGTTGCCACATCCT
38370 GAAAGTCATCTTCTGTTGCCACATCCT
1 GAAAGTCATCTTCTGTTGCCACATCCT
*
38397 GAAATTC-TCTTC
1 GAAAGTCATCTTC
38409 ACAGAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.35
Consensus pattern (27 bp):
GAAAGTCATCTTCTGTTGCCACATCCT
Found at i:49167 original size:15 final size:15
Alignment explanation
Indices: 49143--49173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49133 ACCCTATTCC
49143 ATATGCAATGGGATA
1 ATATGCAATGGGATA
*
49158 ATATGTAATGGGATA
1 ATATGCAATGGGATA
49173 A
1 A
49174 GGAGGAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.26, T:0.29
Consensus pattern (15 bp):
ATATGCAATGGGATA
Found at i:49657 original size:12 final size:13
Alignment explanation
Indices: 49625--49657 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
49615 TAATATATCA
*
49625 TTTAAAATTATAT
1 TTTAAAAATATAT
49638 TTTAAAAAT-TAT
1 TTTAAAAATATAT
49650 TTTAAAAA
1 TTTAAAAA
49658 AATAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:63589 original size:45 final size:46
Alignment explanation
Indices: 63535--63656 Score: 167
Period size: 45 Copynumber: 2.7 Consensus size: 46
63525 AATGCTTGCG
63535 AACTAGATATCATGCGGTTAGGTTTATTTTTC-GAACAAGCATGCA
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCATGCA
* * *
63580 AACTAGATATCATACGGTTAGGTTTA-TTTTCTGAATAAGCATGCG
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCATGCA
* * *
63625 AATTAGATATCATGAGGTTAGGATTTCTTTTT
1 AACTAGATATCATGCGGTTAGG-TTTATTTTT
63657 GTGGATAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 5 0.07
45 55 0.82
46 3 0.04
47 4 0.06
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (46 bp):
AACTAGATATCATGCGGTTAGGTTTATTTTTCTGAACAAGCATGCA
Done.