Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007900.1 Hibiscus syriacus cultivar Beakdansim tig00110290_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: 270466
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:234575 original size:17 final size:17
Alignment explanation
Indices: 234553--234585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
234543 CAATGATTTT
*
234553 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
234570 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
234586 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:234602 original size:24 final size:22
Alignment explanation
Indices: 234570--234638 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
234560 AAATCATTAC
234570 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
234592 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
234617 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
234639 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:234881 original size:12 final size:13
Alignment explanation
Indices: 234845--235265 Score: 190
Period size: 12 Copynumber: 30.7 Consensus size: 13
234835 AATAATAACC
*
234845 AAATAATTATTAT
1 AAATCATTATTAT
234858 AAAATCATTATTAT
1 -AAATCATTATTAT
*
234872 -AATGATTATTAT
1 AAATCATTATTAT
234884 CAAATCATTACTAAATCAT
1 -AAATCATTA-T---T-AT
*
234903 CAAATCATTAAATATTT
1 -AAATCATT--AT-TAT
234920 AAATCATTA-T-T
1 AAATCATTATTAT
*
234931 AAATCATTTTTAT
1 AAATCATTATTAT
*
234944 -AATGATTATTACT
1 AAATCATTATTA-T
234957 AAATCATTATTAT
1 AAATCATTATTAT
*
234970 -AATGATTATTAT
1 AAATCATTATTAT
*
234982 CAAATCATTACTAT
1 -AAATCATTATTAT
*
234996 -AATGATTATTAT
1 AAATCATTATTAT
235008 CAAATCATTACTAAATCAT
1 -AAATCATTA-T---T-AT
*
235027 CAAATCATTAAATATTT
1 -AAATCATT--AT-TAT
235044 AAATCATTA-T-T
1 AAATCATTATTAT
*
235055 AAATCATTTTTAT
1 AAATCATTATTAT
*
235068 -AATGATTATTACT
1 AAATCATTATTA-T
235081 AAATCATTATTAT
1 AAATCATTATTAT
*
235094 -AATGATTATTAT
1 AAATCATTATTAT
*
235106 CAAATCATTACTAT
1 -AAATCATTATTAT
*
235120 -AATGATTATTAT
1 AAATCATTATTAT
235132 CAAATCATTACTAAATCAT
1 -AAATCATTA-T---T-AT
*
235151 CAAATCATTAAATATTT
1 -AAATCATT--AT-TAT
235168 AAATCATTA-T-T
1 AAATCATTATTAT
*
235179 AAATCATTTTTAT
1 AAATCATTATTAT
*
235192 -AATGATTATTACT
1 AAATCATTATTA-T
235205 AAATCATTATTAT
1 AAATCATTATTAT
*
235218 -AATGATTATTAT
1 AAATCATTATTAT
* * *
235230 CAAATTATTACTGT
1 -AAATCATTATTAT
*
235244 -AATGATTATTAT
1 AAATCATTATTAT
235256 CAAATCATTA
1 -AAATCATTA
235266 CTAAATCATC
Statistics
Matches: 322, Mismatches: 38, Indels: 94
0.71 0.08 0.21
Matches are distributed among these distances:
11 27 0.08
12 106 0.33
13 9 0.03
14 102 0.32
15 3 0.01
16 24 0.07
17 3 0.01
18 9 0.03
19 33 0.10
20 3 0.01
21 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (13 bp):
AAATCATTATTAT
Found at i:234888 original size:26 final size:26
Alignment explanation
Indices: 234850--235265 Score: 334
Period size: 26 Copynumber: 16.7 Consensus size: 26
234840 TAACCAAATA
*
234850 ATTATTATAAAATCATTATTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
234876 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
234901 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
234922 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
234948 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
234974 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
235000 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
235025 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
235046 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
235072 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
235098 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
235124 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
235149 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
235170 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
235196 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
* * *
235222 ATTATTATCAAATTATTACTGTAATG
1 ATTATTATCAAATCATTATTATAATG
235248 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
235266 CTAAATCATC
Statistics
Matches: 310, Mismatches: 56, Indels: 48
0.75 0.14 0.12
Matches are distributed among these distances:
21 12 0.04
22 6 0.02
23 42 0.14
24 18 0.06
25 18 0.06
26 211 0.68
27 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATTATCAAATCATTATTATAATG
Found at i:235019 original size:124 final size:124
Alignment explanation
Indices: 234806--235323 Score: 916
Period size: 124 Copynumber: 4.2 Consensus size: 124
234796 ATTTCATTAG
* * * * ** * *
234806 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACCA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
234868 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
234927 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
234992 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
235051 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
235116 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
235175 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATTATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
235240 CTGTAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
235299 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
235324 ATAAATACAT
Statistics
Matches: 383, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.05
123 16 0.04
124 349 0.91
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:238207 original size:26 final size:24
Alignment explanation
Indices: 238149--238207 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
238139 CTAATAAACC
*
238149 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
238173 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
238201 TAATAAT
1 TAATAAT
238208 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:239057 original size:28 final size:30
Alignment explanation
Indices: 239017--239079 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
239007 ATTTTTTATA
*
239017 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
239047 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
239075 TAATA
1 TAATA
239080 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:239086 original size:28 final size:28
Alignment explanation
Indices: 239021--239086 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
239011 TTTATATAAT
*
239021 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
239049 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
239077 ATAATTTATA
1 ATAATATATA
239087 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:239089 original size:21 final size:21
Alignment explanation
Indices: 239056--239104 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
239046 CTAATATAAT
239056 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
239077 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
239098 ATTAACT
1 A-TAACT
239105 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:239680 original size:20 final size:20
Alignment explanation
Indices: 239655--239727 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
239645 CCATGCACAG
239655 CATGCATCCCACAACTCCCC
1 CATGCATCCCACAACTCCCC
**
239675 CATGCATTCCCACGTC-CCATGCAC
1 CATGCA-TCCCACAACTCC---C-C
239699 AGCATGCATCCCACAACTCCCC
1 --CATGCATCCCACAACTCCCC
239721 CATGCAT
1 CATGCAT
239728 GCTCCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 15 0.37
21 7 0.17
22 1 0.02
23 2 0.05
24 1 0.02
25 7 0.17
26 8 0.20
ACGTcount: A:0.25, C:0.48, G:0.10, T:0.18
Consensus pattern (20 bp):
CATGCATCCCACAACTCCCC
Found at i:239694 original size:46 final size:46
Alignment explanation
Indices: 239635--239727 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
239625 CCATGCACAG
239635 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
239681 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
239727 T
1 T
239728 GCTCCAATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.47, G:0.11, T:0.18
Consensus pattern (46 bp):
TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
Found at i:243945 original size:84 final size:84
Alignment explanation
Indices: 243781--243953 Score: 274
Period size: 85 Copynumber: 2.0 Consensus size: 84
243771 TAAAAAGAGA
* * *
243781 CCCTTAAATCTCAATTTTACCACGATCCATAATACTTTGCTTGTTTTTTTATTGTAACAATAATA
1 CCCTTAAATCTCAATTTTACCACAATCCATAATACTTTACTTGTTTTTTTATTATAACAATAATA
243846 ATAAATCTAATTTTTTAGG
66 ATAAATCTAATTTTTTAGG
* * *
243865 CCCTTAAATCTCAATTTTACCATTAATCCATAATACTTTATTTGTTTTTTTATTATAACAATAGT
1 CCCTTAAATCTCAATTTTACCA-CAATCCATAATACTTTACTTGTTTTTTTATTATAACAATAAT
*
243930 AATAAATCTAATTTTTTGGG
65 AATAAATCTAATTTTTTAGG
243950 CCCT
1 CCCT
243954 CACTATTTCG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 22 0.27
85 59 0.73
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (84 bp):
CCCTTAAATCTCAATTTTACCACAATCCATAATACTTTACTTGTTTTTTTATTATAACAATAATA
ATAAATCTAATTTTTTAGG
Found at i:244868 original size:18 final size:18
Alignment explanation
Indices: 244835--244869 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
244825 ATATAGTTTG
* *
244835 AATACTTATTTTTATATT
1 AATACTTATATATATATT
244853 AATACTTATATATATAT
1 AATACTTATATATATAT
244870 ATATATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AATACTTATATATATATT
Found at i:253760 original size:28 final size:29
Alignment explanation
Indices: 253728--253783 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
253718 CTTTTTTGTC
253728 ATTAAACTT-TCAAA-AGTTACAAAATAAT
1 ATTAAACTTGTCAAACA-TTACAAAATAAT
253756 ATTAAACTTGTCAAACTATTACAAAATA
1 ATTAAACTTGTCAAAC-ATTACAAAATA
253784 TTCTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 9 0.36
29 5 0.20
30 10 0.40
31 1 0.04
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTAAACTTGTCAAACATTACAAAATAAT
Found at i:253829 original size:15 final size:15
Alignment explanation
Indices: 253809--253838 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
253799 AACAGTAATA
253809 AAATTTTGATAAATT
1 AAATTTTGATAAATT
253824 AAATTTTGATAAATT
1 AAATTTTGATAAATT
253839 GAAGGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AAATTTTGATAAATT
Found at i:266544 original size:15 final size:15
Alignment explanation
Indices: 266524--266554 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
266514 GAGTTAAGTC
266524 TAAAAATGTTTTGAA
1 TAAAAATGTTTTGAA
266539 TAAAAATGTTTTGAA
1 TAAAAATGTTTTGAA
266554 T
1 T
266555 TCAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
TAAAAATGTTTTGAA
Done.