Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007144.1 Hibiscus syriacus cultivar Beakdansim tig00018682_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: 67040
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:935 original size:17 final size:17
Alignment explanation
Indices: 902--935 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
892 TTTAATATTT
* *
902 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
919 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
936 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:14628 original size:19 final size:19
Alignment explanation
Indices: 14604--14642 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
14594 TCGAATGCAT
14604 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
14623 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
14642 T
1 T
14643 GAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:14659 original size:65 final size:64
Alignment explanation
Indices: 14541--14704 Score: 181
Period size: 65 Copynumber: 2.5 Consensus size: 64
14531 TATTCAAAGG
*
14541 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAATTAATTGAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC-ATGAATTAATTAAACATCGAATGCAT
14604 TC
63 TC
**
14606 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAATTTTTTCAAAACATCGAATGCATT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATTAATT--AAACATCGAATGCATT
*
14670 T
64 C
* * ***
14671 GATGCATCGATGCACAAGCCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
14705 AAGCCATGCA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 8 0.09
64 16 0.19
65 60 0.70
66 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATTAATTAAACATCGAATGCATTC
Found at i:14696 original size:19 final size:19
Alignment explanation
Indices: 14672--14741 Score: 140
Period size: 19 Copynumber: 3.7 Consensus size: 19
14662 AATGCATTTG
14672 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
14691 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
14710 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
14729 ATGCATCGATGCA
1 ATGCATCGATGCA
14742 TCAGGCTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:20560 original size:20 final size:21
Alignment explanation
Indices: 20531--20586 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
20521 TTTGTGCTTC
*
20531 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
20551 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
20573 ATGCATCGATGCAT
1 ATGCATCGATGCAT
20587 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:22154 original size:21 final size:21
Alignment explanation
Indices: 22112--22155 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22102 ACCCCGGGAG
*
22112 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
22133 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
22154 CT
1 CT
22156 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:23207 original size:19 final size:19
Alignment explanation
Indices: 23183--23221 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23173 TCGAATGCAT
*
23183 TCCATGTACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
23202 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
23221 T
1 T
23222 GAATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:23238 original size:65 final size:63
Alignment explanation
Indices: 23120--23328 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 63
23110 TATTCAAAGG
*
23120 CATGTACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGTACCGATGCACTC--TCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATT
23184 C
63 C
**
23185 CATGTACCGATGCACTCTCCATGCATCGATGCACTC-TGAATTTTTTCAAAACATCGAATGCATT
1 CATGTACCGATGCACTCTCCATGCATCGATGCA-TCATGAATTAATT--AAACATCGAATGCATT
*
23249 T
63 C
* * * *** * * * * *
23250 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTACTCAAACATCGAATGCATTT
1 CATGTACCGATGCACTCTCCATGCATCGATGCATCATG-AATTAATTAAACATCGAATGCATTC
* *
23314 CATGCATCGATGCAC
1 CATGTACCGATGCAC
23329 ACTTGGTGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 8 0.07
64 49 0.40
65 59 0.48
66 6 0.05
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGTACCGATGCACTCTCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTC
Found at i:23325 original size:64 final size:65
Alignment explanation
Indices: 23169--23329 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
23159 GAATTAATTG
* * * *** * **
23169 AACATCGAATGCATTCCATGTACCGATGCACTCTCCATGCATCGATGCACTCTGAATTTTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATTTACTCAA
* **
23234 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTACTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAAT-TTACTCA
23297 A
65 A
23298 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
23330 CTTGGTGCAC
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATTTACTCAA
Found at i:25072 original size:30 final size:30
Alignment explanation
Indices: 24997--25072 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
24987 TAATGGCAGA
* * *
24997 AAACA-TCATGTATAAAATTGAGAATTTTT
1 AAACATTCATGTATGAAACTGAGAATTTAT
*
25026 AAACATT-ATATATGAAACTGAGAATTTGAT
1 AAACATTCATGTATGAAACTGAGAATTT-AT
*
25056 ATA-ATTCATGTATGAAA
1 AAACATTCATGTATGAAA
25073 GGGGTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (30 bp):
AAACATTCATGTATGAAACTGAGAATTTAT
Found at i:25859 original size:19 final size:19
Alignment explanation
Indices: 25835--25876 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
25825 ATAGAGAAAT
*
25835 GTTGAAATGAAGGTCAACA
1 GTTGAAATAAAGGTCAACA
25854 GTTGAAATAAAGGTCAACA
1 GTTGAAATAAAGGTCAACA
25873 GTTG
1 GTTG
25877 TAATCTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (19 bp):
GTTGAAATAAAGGTCAACA
Found at i:29871 original size:31 final size:32
Alignment explanation
Indices: 29836--29903 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
29826 CGTTTAGCAT
* *
29836 CTAAACTATCATTTTTGTTCCATTTTAGTA-C
1 CTAAACTATCACTTTTATTCCATTTTAGTACC
**
29867 CTAAACTATCACTTTTATTCTTTTTTAGTACC
1 CTAAACTATCACTTTTATTCCATTTTAGTACC
29899 CTAAA
1 CTAAA
29904 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (32 bp):
CTAAACTATCACTTTTATTCCATTTTAGTACC
Found at i:34504 original size:15 final size:15
Alignment explanation
Indices: 34484--34513 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34474 ATATTTTATT
*
34484 TTTAAAAAAAGTAAA
1 TTTAAAAAAAATAAA
34499 TTTAAAAAAAATAAA
1 TTTAAAAAAAATAAA
34514 GTTTTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:35129 original size:23 final size:23
Alignment explanation
Indices: 35103--35150 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
35093 GCGATTATTA
35103 ATTTTAATCTTGTTTTTCAAATC
1 ATTTTAATCTTGTTTTTCAAATC
** *
35126 ATTTTCTTGTTGTTTTTCAAATC
1 ATTTTAATCTTGTTTTTCAAATC
35149 AT
1 AT
35151 GTCCTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTTTAATCTTGTTTTTCAAATC
Found at i:36945 original size:14 final size:15
Alignment explanation
Indices: 36911--36953 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
36901 AATATTTATT
*
36911 ATAAATATTGAATACA
1 ATAAATATT-AATAAA
36927 ATAAATATT-ATAAA
1 ATAAATATTAATAAA
*
36941 ATAAATAATAATA
1 ATAAATATTAATA
36954 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 3 0.12
16 9 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAAATATTAATAAA
Found at i:37122 original size:33 final size:32
Alignment explanation
Indices: 37085--37159 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
37075 TATAAATTAT
** *
37085 TTATTAAATTAAAATATTAAATATGTAATAATA
1 TTATTAAATTAAAATAAGAAAAATGTAAT-ATA
* *
37118 TTATTATATTAAAATAAGAAAAATGTACTATA
1 TTATTAAATTAAAATAAGAAAAATGTAATATA
37150 TTATTAAATT
1 TTATTAAATT
37160 TATTAATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (32 bp):
TTATTAAATTAAAATAAGAAAAATGTAATATA
Found at i:40550 original size:2 final size:2
Alignment explanation
Indices: 40543--40569 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40533 ATCCCAGATA
40543 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40570 ATAGGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40853 original size:23 final size:23
Alignment explanation
Indices: 40806--40856 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
40796 ATATTCTTTA
*
40806 TCTTTATAGCACGTTTATATTTG
1 TCTTTATAGCACGTTTATATCTG
* * *
40829 TCTTTGTAGCACGTTTTTCTCTG
1 TCTTTATAGCACGTTTATATCTG
40852 TCTTT
1 TCTTT
40857 TGGTAGCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.55
Consensus pattern (23 bp):
TCTTTATAGCACGTTTATATCTG
Found at i:52615 original size:21 final size:20
Alignment explanation
Indices: 52576--52613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52566 AGATTACGCA
52576 GGGGGTACAGATTCCCCCTG
1 GGGGGTACAGATTCCCCCTG
52596 GGGGGTATC-GATTCCCCC
1 GGGGGTA-CAGATTCCCCC
52614 CTAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGTACAGATTCCCCCTG
Found at i:55450 original size:21 final size:21
Alignment explanation
Indices: 55424--55464 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55414 AGATTACGCA
*
55424 GGGGGTA-CAGATTCCCCCCTG
1 GGGGGTATC-GATTACCCCCTG
55445 GGGGGTATCGATTACCCCCT
1 GGGGGTATCGATTACCCCCT
55465 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.22
Consensus pattern (21 bp):
GGGGGTATCGATTACCCCCTG
Found at i:56385 original size:22 final size:22
Alignment explanation
Indices: 56356--56412 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
56346 CTACGCAGTC
*
56356 CTTT-GGGACATATACAGT-GGT
1 CTTTCGGGACAAATACA-TAGGT
56377 CTTTCGGGACAAATACATAGGT
1 CTTTCGGGACAAATACATAGGT
*
56399 CCTTCGGGACAAAT
1 CTTTCGGGACAAAT
56413 TTCATATGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (22 bp):
CTTTCGGGACAAATACATAGGT
Found at i:60324 original size:2 final size:2
Alignment explanation
Indices: 60312--60365 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
60302 GATACTTTAC
60312 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60353 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
60366 TAATTACTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66532 original size:51 final size:51
Alignment explanation
Indices: 66473--66574 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
66463 TATCCACATA
66473 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAACCAAATTCAG
1 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAACCAAATTCAG
*
66524 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAAGCAAATTCAG
1 CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAACCAAATTCAG
66575 ATGCATAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (51 bp):
CAAACAGAAAGTAGTTTGTTAGTATTACTATAATTGCAAAACCAAATTCAG
Done.