Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002985.1 Hibiscus syriacus cultivar Beakdansim tig00006174_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: 66517
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Found at i:3628 original size:23 final size:23
Alignment explanation
Indices: 3594--3677 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
3584 CTCATATAAA
3594 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3617 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3640 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3663 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
3678 TATAAGATTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:7246 original size:105 final size:105
Alignment explanation
Indices: 7074--7801 Score: 1161
Period size: 105 Copynumber: 6.9 Consensus size: 105
7064 TTGAACAAGT
* * * *
7074 TCTTCTCATTATGAACTTCTTCTTCTTTTATCGGATGAGTTCTTATCATTATGAACTCTTCTGGA
1 TCTTCTCATTACGAAC--CTTC-TCCTTTA--GGACGAGTTCTTCTCATTATGAACTCTTCTGGA
* * * * *
7139 AATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAAGGAACAGGC
61 AATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
* * *
7184 TCTTCTCATTACGAACCTTCTCTTTTAAGACGAGTTTTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
7249 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATAC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
* * *
7289 TCTTCTCATTATGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
7354 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
7394 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
7459 TAGTTCACCTCATTCTGCGGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
*
7499 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
7564 TGGGTCACCTCCTTTTGTGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
7604 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
7669 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
*
7709 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGG-AATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
** *
7773 TGGGCCACCTCCTTCTGTGGTGGATTTGA
66 TGGTTCACCTCCTTCTGCGGTGGATTTGA
7802 TTGTTGTTGA
Statistics
Matches: 581, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
104 30 0.05
105 525 0.90
107 7 0.01
108 4 0.01
110 15 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (105 bp):
TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATGC
Found at i:8730 original size:19 final size:20
Alignment explanation
Indices: 8708--8796 Score: 91
Period size: 19 Copynumber: 4.6 Consensus size: 20
8698 TCTCGAACCC
8708 TCATTTTTC-TTTTTTCTTT
1 TCATTTTTCATTTTTTCTTT
8727 TCATTTTTTCATTTTTTTCTTT
1 TCA-TTTTTCA-TTTTTTCTTT
8749 T--TTTTTCATTTTTT-TTT
1 TCATTTTTCATTTTTTCTTT
**
8766 TCA-TTTTC-TTTTCACTTTT
1 TCATTTTTCATTTTTTC-TTT
8785 TCATTTTTCATT
1 TCATTTTTCATT
8797 CATTCATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
17 8 0.14
18 11 0.19
19 16 0.27
20 11 0.19
21 2 0.03
22 11 0.19
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (20 bp):
TCATTTTTCATTTTTTCTTT
Found at i:8745 original size:22 final size:21
Alignment explanation
Indices: 8711--8808 Score: 80
Period size: 23 Copynumber: 4.6 Consensus size: 21
8701 CGAACCCTCA
8711 TTTTTC-TTTTTTCTTTTCAT
1 TTTTTCATTTTTTCTTTTCAT
8731 TTTTTCATTTTTT-TCTTT--T
1 TTTTTCATTTTTTCT-TTTCAT
8750 TTTTTCATTTTTT-TTTTCATTT
1 TTTTTCATTTTTTCTTTTCA--T
*
8772 TCTTTTCACTTTTTCATTTTTCAT
1 T-TTTTCATTTTTTC--TTTTCAT
**
8796 TCATTCATTTTTT
1 TTTTTCATTTTTT
8809 TTTCAAGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.05
19 15 0.23
20 7 0.11
21 9 0.14
22 2 0.03
23 20 0.31
24 2 0.03
26 6 0.09
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCATTTTTTCTTTTCAT
Found at i:8772 original size:9 final size:9
Alignment explanation
Indices: 8724--8763 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
8714 TTCTTTTTTC
8724 TTTTCA-TT
1 TTTTCATTT
8732 TTTTCATTT
1 TTTTCATTT
*
8741 TTTTCTTTTT
1 TTTTC-ATTT
8751 TTTTCATTT
1 TTTTCATTT
8760 TTTT
1 TTTT
8764 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 6 0.21
9 14 0.50
10 8 0.29
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTCATTT
Found at i:8795 original size:7 final size:7
Alignment explanation
Indices: 8708--8807 Score: 67
Period size: 7 Copynumber: 15.1 Consensus size: 7
8698 TCTCGAACCC
8708 TCATTTT
1 TCATTTT
*
8715 TCTTTTT
1 TCATTTT
8722 TC--TTT
1 TCATTTT
8727 TCATTTTT
1 TCA-TTTT
8735 TCATTTT
1 TCATTTT
8742 T--TTCTT
1 TCATT-TT
*
8748 T-TTTTT
1 TCATTTT
8754 TCATTTT
1 TCATTTT
8761 T--TTTT
1 TCATTTT
8766 TCA-TTT
1 TCATTTT
8772 TC--TTT
1 TCATTTT
8777 TCACTTTT
1 TCA-TTTT
8785 TCATTTT
1 TCATTTT
*
8792 TCATTCAT
1 TCATT-TT
8800 TCATTTT
1 TCATTTT
8807 T
1 T
8808 TTTTCAAGCA
Statistics
Matches: 77, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
5 17 0.22
6 11 0.14
7 31 0.40
8 18 0.23
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (7 bp):
TCATTTT
Found at i:12234 original size:14 final size:14
Alignment explanation
Indices: 12215--12241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12205 AAATGAATGT
12215 AAAGAATGAAGAAA
1 AAAGAATGAAGAAA
12229 AAAGAATGAAGAA
1 AAAGAATGAAGAA
12242 TGAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAA
Found at i:27713 original size:23 final size:23
Alignment explanation
Indices: 27685--27768 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
27675 TATGGCATTA
27685 CGGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
*
27708 CAGTGCAATTCTACGTGGCACTC
1 CGGTGCAATTCTACGTGGCACTC
*
27731 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTC
*
27754 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
27769 AGCTGTGGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTC
Found at i:33046 original size:23 final size:23
Alignment explanation
Indices: 33020--33088 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
33010 CACCACAACT
*
33020 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
33043 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
33066 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
33089 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:33275 original size:103 final size:104
Alignment explanation
Indices: 33096--33308 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 104
33086 CCATATAATA
* *
33096 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
33160 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
33199 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 ATGTCCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
33263 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
33302 ATGTCCC
1 ATGTCCC
33309 GAAGAACCGC
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 103 0.97
104 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (104 bp):
ATGTCCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:34691 original size:22 final size:21
Alignment explanation
Indices: 34666--34725 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
34656 TTCGCTTGAG
*
34666 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
34688 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
34708 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
34726 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:41649 original size:21 final size:20
Alignment explanation
Indices: 41628--41666 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41618 TTCATCCATT
41628 TTTTATTTATT-T-AAAAATA
1 TTTTATTT-TTATGAAAAATA
41647 TTTTATTTTTATGAAAAATA
1 TTTTATTTTTATGAAAAATA
41667 AATTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 9 0.50
20 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTATTTTTATGAAAAATA
Found at i:43658 original size:23 final size:23
Alignment explanation
Indices: 43632--43700 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
43622 CACCACAGCT
*
43632 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
43655 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
43678 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
43701 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:43971 original size:30 final size:30
Alignment explanation
Indices: 43910--43978 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
43900 ACATAATTTG
* * *
43910 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTACATACCTT
* *
43940 TATCACATAGATATATCATTTACATATCTT
1 TATCACATAGACATATCATTTACATACCTT
43970 TATCACATA
1 TATCACATA
43979 ACTCATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
TATCACATAGACATATCATTTACATACCTT
Found at i:44463 original size:56 final size:55
Alignment explanation
Indices: 44360--44465 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 55
44350 CATAAATCCT
* *
44360 ATTCGATGTTTGTATGTAATATGGTGCATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATGTTTGTATGTAATAAGGTGCATCGATGCACTCCATATGCATCGATGGC
* * *
44415 ATTCGATGTTTGTATTTTAA-AAGAGTGCATCGATGCACTTCATGTGCATCG
1 ATTCGATGTTTGTA-TGTAATAAG-GTGCATCGATGCACTCCATATGCATCG
44466 GTACACCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
55 16 0.36
56 28 0.64
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (55 bp):
ATTCGATGTTTGTATGTAATAAGGTGCATCGATGCACTCCATATGCATCGATGGC
Found at i:50524 original size:23 final size:23
Alignment explanation
Indices: 50493--50561 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
50483 CACCACAGCT
* *
50493 CGTATAATTGCACTGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
50516 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
50539 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
50562 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:50805 original size:30 final size:30
Alignment explanation
Indices: 50771--50839 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
50761 ACATAATTTA
* *
50771 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATTATTTCCATACCTT
*
50801 TATCACATAGATATATTATTTCCATACCTT
1 TATCACATAGACATATTATTTCCATACCTT
50831 TATCACATA
1 TATCACATA
50840 ACTCATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (30 bp):
TATCACATAGACATATTATTTCCATACCTT
Found at i:52641 original size:60 final size:60
Alignment explanation
Indices: 52556--52696 Score: 255
Period size: 60 Copynumber: 2.4 Consensus size: 60
52546 AAATAATCGG
* *
52556 ATGACTATTTTATAACTTTTACTATTCGATGAACTCAACAAAATATTATCTTATAATTAA
1 ATGACTATCTTATAACTTTTACTATTCGATAAACTCAACAAAATATTATCTTATAATTAA
*
52616 ATGACTATCTTATAACTTTTACTATTCGATAAACTTAACAAAATATTATCTTATAATTAA
1 ATGACTATCTTATAACTTTTACTATTCGATAAACTCAACAAAATATTATCTTATAATTAA
52676 ATGACTATCTTATAACTTTTA
1 ATGACTATCTTATAACTTTTA
52697 TAATTAAGAC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (60 bp):
ATGACTATCTTATAACTTTTACTATTCGATAAACTCAACAAAATATTATCTTATAATTAA
Found at i:62693 original size:3 final size:3
Alignment explanation
Indices: 62687--62711 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
62677 GGTGGTCCTC
62687 GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG G
62712 AAGAGTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Done.