Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007603.1 Hibiscus syriacus cultivar Beakdansim tig00022090_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: 35532
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:1060 original size:135 final size:139
Alignment explanation
Indices: 849--1122 Score: 436
Period size: 136 Copynumber: 2.0 Consensus size: 139
839 CTCTAACAAT
* *
849 TCAAAAAAATTATATTTTTAGTCTCTAAACCATTTTTGCTCACAATTTAGCCCTAAATAAAATAT
1 TCAAAAAAATAATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTAAATAAAATAT
914 AATTATAATGT-CCATTGCTCGATACTTAC-AGGTGATCCTAAATGTGGAGATGGAAGTTC-AAG
66 AATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAG--GGAAGTTCAAAG
976 TGTTAATGTAG
129 TGTTAATGTAG
987 TCAAAAAAA-AATA-TTTTAGTCTCTAAACCA-TTTTACTCAC-ATTTAGCCCTTAAATAAAATA
1 TCAAAAAAATAATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCC-TAAATAAAATA
* *
1048 TAATTATCATGTCCCATTGCTCGATACTTACAAGGTGATTCTAAATGTGGAGGGAAGTTCAAAGT
65 TAATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGGGAAGTTCAAAGT
1113 GTTAATGTAG
130 GTTAATGTAG
1123 CTATCATAGG
Statistics
Matches: 128, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
134 9 0.07
135 39 0.30
136 49 0.38
137 22 0.17
138 9 0.07
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (139 bp):
TCAAAAAAATAATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTAAATAAAATAT
AATTATAATGTCCCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGGGAAGTTCAAAGTG
TTAATGTAG
Found at i:1540 original size:28 final size:31
Alignment explanation
Indices: 1509--1578 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 31
1499 CTGAAAAATC
1509 ATTATATATTATTAAAATA-AAAG-TAT-AT
1 ATTATATATTATTAAAATATAAAGATATAAT
* * *
1537 ATTATATATCATTATAATATTAAGATATAAT
1 ATTATATATTATTAAAATATAAAGATATAAT
*
1568 ATCATATATTA
1 ATTATATATTA
1579 GAATTATGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 17 0.50
29 3 0.09
30 3 0.09
31 11 0.32
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTATATATTATTAAAATATAAAGATATAAT
Found at i:4459 original size:19 final size:20
Alignment explanation
Indices: 4421--4459 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4411 TATTAATTTT
4421 TTATTATAATATATTCTTGA
1 TTATTATAATATATTCTTGA
* *
4441 TTATTTTAAT-TATTGTTGA
1 TTATTATAATATATTCTTGA
4460 AAATAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATTATAATATATTCTTGA
Found at i:4664 original size:30 final size:29
Alignment explanation
Indices: 4605--4670 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
4595 TTGAAAAATC
*
4605 ATTATATATTATTAAAATAAAAGTATAAT
1 ATTATATATCATTAAAATAAAAGTATAAT
*
4634 ATTATATATCATTATAATTAAGAA-TATAAT
1 ATTATATATCATTA-AAATAA-AAGTATAAT
*
4664 ATCATAT
1 ATTATAT
4671 TATTAGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 17 0.53
31 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
ATTATATATCATTAAAATAAAAGTATAAT
Found at i:7723 original size:18 final size:18
Alignment explanation
Indices: 7689--7738 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
7679 AAGTTTTGTA
7689 ATTTA-TGAATAATATTAT
1 ATTTATTGAA-AATATTAT
7707 -TTTATTGAAAATCATTAT
1 ATTTATTGAAAAT-ATTAT
7725 ATATTATT-AAAATA
1 AT-TTATTGAAAATA
7739 AAAGTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 7 0.25
18 10 0.36
19 6 0.21
20 5 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (18 bp):
ATTTATTGAAAATATTAT
Found at i:9313 original size:6 final size:6
Alignment explanation
Indices: 9297--9327 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
9287 ATTATAAAAA
9297 ATATCTT ATATTT ATATTT ATATTT ATATTT
1 ATAT-TT ATATTT ATATTT ATATTT ATATTT
9328 CCAAGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:14207 original size:22 final size:22
Alignment explanation
Indices: 14159--14207 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
14149 TAAGAAAAAT
*
14159 GGGGAGAAGGTGTGTTATCGTAA
1 GGGG-GAAGGTGTGTTATAGTAA
*
14182 --GGGAATGTGTGTTATAGTAA
1 GGGGGAAGGTGTGTTATAGTAA
14202 GGGGGA
1 GGGGGA
14208 GTAATTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 16 0.73
21 2 0.09
22 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.45, T:0.27
Consensus pattern (22 bp):
GGGGGAAGGTGTGTTATAGTAA
Found at i:14241 original size:13 final size:13
Alignment explanation
Indices: 14211--14245 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
14201 AGGGGGAGTA
14211 ATTTTGCAAAATTG
1 ATTTT-CAAAATTG
14225 -TTTTCAAAATTG
1 ATTTTCAAAATTG
14237 ATTTTCAAA
1 ATTTTCAAA
14246 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (13 bp):
ATTTTCAAAATTG
Found at i:18556 original size:21 final size:22
Alignment explanation
Indices: 18530--18571 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18520 ATTATTATAA
*
18530 TAAAAAATT-AATATAATTTAT
1 TAAAAAATTCAATAAAATTTAT
18551 TAAAAAATTCAATAAAATTTA
1 TAAAAAATTCAATAAAATTTA
18572 ATAATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAATTCAATAAAATTTAT
Found at i:23459 original size:18 final size:17
Alignment explanation
Indices: 23419--23474 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
23409 TTGAGGACTT
23419 TATATTATTTATAAAAA
1 TATATTATTTATAAAAA
23436 TAATATT-TTTCATAAAAAA
1 T-ATATTATTT-AT-AAAAA
*
23455 TATATATATATATATAAAA
1 TATAT-TATTTATA-AAAA
23474 T
1 T
23475 TAAAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 14 0.44
20 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATTATTTATAAAAA
Found at i:23461 original size:20 final size:19
Alignment explanation
Indices: 23419--23473 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
23409 TTGAGGACTT
23419 TATATTATTTATAAAAATA
1 TATATTATTTATAAAAATA
23438 -ATATT-TTTCATAAAAAATA
1 TATATTATTT-AT-AAAAATA
*
23457 TATATATATATATAAAA
1 TATAT-TATTTATAAAA
23474 TTAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 3 0.10
18 7 0.23
19 7 0.23
20 8 0.27
21 3 0.10
22 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATTATTTATAAAAATA
Found at i:23488 original size:17 final size:18
Alignment explanation
Indices: 23462--23497 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
23452 AAATATATAT
*
23462 ATATATATAAAA-TTAAA
1 ATATAAATAAAATTTAAA
23479 ATATAAATAAAATTTAAA
1 ATATAAATAAAATTTAAA
23497 A
1 A
23498 AATAGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAATAAAATTTAAA
Found at i:25127 original size:2 final size:2
Alignment explanation
Indices: 25120--25156 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
25110 TTTCTTGGAA
25120 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25157 GTAAGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30176 original size:16 final size:16
Alignment explanation
Indices: 30157--30189 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30147 AAAAAATTAA
30157 TATAATTTATTAAAAG
1 TATAATTTATTAAAAG
30173 TATAATTTATTAAAAG
1 TATAATTTATTAAAAG
30189 T
1 T
30190 TTCAATAAAA
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:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TATAATTTATTAAAAG
Found at i:32766 original size:20 final size:20
Alignment explanation
Indices: 32737--32778 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
32727 TTTACTCATA
*
32737 ATTCTATAATATGATATTAT
1 ATTCTATAATATGATATGAT
* *
32757 ATTCTTTAATATTATATGAT
1 ATTCTATAATATGATATGAT
32777 AT
1 AT
32779 AATATTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTCTATAATATGATATGAT
Done.