Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007036.1 Hibiscus syriacus cultivar Beakdansim tig00018239_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: 73984
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15426 original size:14 final size:14
Alignment explanation
Indices: 15381--15426 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
15371 CCCTAATTTA
*
15381 AAATCTTAAATTAT
1 AAATCTTAAATCAT
*
15395 AAACCTTAAACTC-T
1 AAATCTTAAA-TCAT
15409 AAATCTTAAATCAT
1 AAATCTTAAATCAT
15423 AAAT
1 AAAT
15427 TTCAACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.07
14 24 0.89
15 1 0.04
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCTTAAATCAT
Found at i:18594 original size:18 final size:18
Alignment explanation
Indices: 18571--18605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18561 ACAATGATGG
*
18571 TTATGGTGGATTTGGTGA
1 TTATGGAGGATTTGGTGA
*
18589 TTATGGAGGTTTTGGTG
1 TTATGGAGGATTTGGTG
18606 GTGATGGTCT
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:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (18 bp):
TTATGGAGGATTTGGTGA
Found at i:23343 original size:20 final size:20
Alignment explanation
Indices: 23326--23364 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23316 TGTTTATGTA
23326 TGATATATTGACTTTATGAG
1 TGATATATTGACTTTATGAG
* *
23346 TGATATGTTGACTCTATGA
1 TGATATATTGACTTTATGA
23365 TAATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.44
Consensus pattern (20 bp):
TGATATATTGACTTTATGAG
Found at i:35798 original size:106 final size:106
Alignment explanation
Indices: 35613--37253 Score: 2655
Period size: 106 Copynumber: 15.5 Consensus size: 106
35603 ACACCTCAAT
35613 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
35678 AGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
35719 CAACTTCTCAATTTCAGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
35784 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* *
35825 CAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
35890 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAC
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* *
35931 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
35996 AGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
36037 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
36102 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
36142 CAACTT-TCCAATTTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGGACTCCAGACAACGC
1 CAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
36206 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AA
65 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * **
36247 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
36312 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
36353 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
36418 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * * *
36459 TAA-TTTTCCAA-TTCTAGAGTCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACA
1 CAACTTCT-CAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
36522 CAAGCTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAA
64 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
36565 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
36630 AGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
36671 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGTA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
36736 TGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
36777 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
36842 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * ** * *
36883 TAACTTCTTAATTTCAGAGCCAATTTCAACTTCACAATGAAAGATATTGAACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * *
36948 AGTTCAACTTTACGACGAAGGGACTGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* *
36989 CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
37054 AGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * *
37095 TAACTTCTTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * *
37160 AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACACA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* ** * *
37201 CAAATTCTCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
37254 TGGAACAATG
Statistics
Matches: 1430, Mismatches: 97, Indels: 16
0.93 0.06 0.01
Matches are distributed among these distances:
104 1 0.00
105 207 0.14
106 1216 0.85
107 6 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
Found at i:37826 original size:16 final size:14
Alignment explanation
Indices: 37787--37829 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 14
37777 CTTTTATTAG
37787 TAATATTATTATAT
1 TAATATTATTATAT
37801 TATATAATTATATATAT
1 TA-AT-ATTAT-TATAT
37818 ATAATATTATTA
1 -TAATATTATTA
37830 ATTCTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.08
15 4 0.16
16 10 0.40
17 7 0.28
18 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTATTATAT
Found at i:39127 original size:11 final size:11
Alignment explanation
Indices: 39111--39135 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39101 TTCCCACTTC
39111 TTTATTTATTT
1 TTTATTTATTT
39122 TTTATTTATTT
1 TTTATTTATTT
39133 TTT
1 TTT
39136 TCATTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:39172 original size:3 final size:3
Alignment explanation
Indices: 39160--39193 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
39150 TTCTATTTTC
39160 TAT T-T TAT TAT TATT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
39194 TAACTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:39188 original size:19 final size:18
Alignment explanation
Indices: 39160--39195 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
39150 TTCTATTTTC
39160 TATTTTATTATTATTTAT
1 TATTTTATTATTATTTAT
39178 TATTATTATTATTATTTA
1 TATT-TTATTATTATTTA
39196 ACTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTATTATTATTTAT
Found at i:55657 original size:2 final size:2
Alignment explanation
Indices: 55650--55674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55640 TTAATAAAAT
55650 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55675 TATTAGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62371 original size:159 final size:157
Alignment explanation
Indices: 62096--62562 Score: 574
Period size: 158 Copynumber: 3.0 Consensus size: 157
62086 TTCAATTCCT
* * *
62096 AAACCATCTTAGAATGCATATGTACTTTCAATTCCTC-TTTTGAAAATAAATTT-TATATTTTCA
1 AAACCATCTTAGAATACATATGTACTTTCAATTTCTCTTTTTGATAATAAATTTCTA-ATTTTCA
*
62159 ATTTAGTCCC-TAATTGTTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAATCTA
65 ATTTAGTCCCTTAA-T-TTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAATCCA
62223 TTTTTTTACCAAATTTGAATC-ACATGCTCCC
128 -TTTTTTACCAAATTTGAA-CAACATGCTCCC
* * * *
62254 AAACCATCGTAGAATACATATGTACTTTTAATTTCTCTTTTTTATAATGAAATTTCTACTTTTCA
1 AAACCATCTTAGAATACATATGTACTTTCAATTTCTCTTTTTGATAAT-AAATTTCTAATTTTCA
* *
62319 ATTTAGTCCCTTGATTTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTCCATT
65 ATTTAGTCCCTTAATTTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAATCCATT
*
62384 TTTTACCAAATTTGAACAACATGCTCCT
130 TTTTACCAAATTTGAACAACATGCTCCC
* ** * * *
62412 AAATCATCTTAGAATATTTATGTACTTTCAATTTCTCTTTTTGATAACACATTTTCTATTTTTCA
1 AAACCATCTTAGAATACATATGTACTTTCAATTTCTCTTTTTGATAATA-AATTTCTAATTTTCA
* * * * * *
62477 A-TT--TCCCTCAATTTTTCATAATTTCCTTATTTCTTCAATTCATCC-TCATTTTAAGTTC-GT
65 ATTTAGTCCCTTAATTTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAATCCATT
* * *
62537 TTATACTAAATTTGAACCACATGCTC
130 TTTTACCAAATTTGAACAACATGCTC
62563 ATATTCCACA
Statistics
Matches: 274, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
153 24 0.09
154 11 0.04
155 39 0.14
157 4 0.01
158 115 0.42
159 54 0.20
160 23 0.08
161 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (157 bp):
AAACCATCTTAGAATACATATGTACTTTCAATTTCTCTTTTTGATAATAAATTTCTAATTTTCAA
TTTAGTCCCTTAATTTTTTATAATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAATCCATTT
TTTACCAAATTTGAACAACATGCTCCC
Found at i:66535 original size:18 final size:18
Alignment explanation
Indices: 66487--66538 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
66477 AATTACAAAG
*
66487 CTATTTTATTGTCACATT
1 CTATTTTATTGTGACATT
66505 CTATTTTATTGTGACATT
1 CTATTTTATTGTGACATT
66523 CTATTTTATTGTGACA
1 CTATTTTATTGTGACA
66539 AAACTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (18 bp):
CTATTTTATTGTGACATT
Done.