Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007574.1 Hibiscus syriacus cultivar Beakdansim tig00021590_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: 161221
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:154347 original size:90 final size:90
Alignment explanation
Indices: 154204--154381 Score: 356
Period size: 90 Copynumber: 2.0 Consensus size: 90
154194 GATAACTACT
154204 CATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTTTTAATACCGAG
1 CATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTTTTAATACCGAG
154269 AAATCTTGAATTCTGATTCTGATAA
66 AAATCTTGAATTCTGATTCTGATAA
154294 CATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTTTTAATACCGAG
1 CATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTTTTAATACCGAG
154359 AAATCTTGAATTCTGATTCTGAT
66 AAATCTTGAATTCTGATTCTGAT
154382 GAGGAGAATA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (90 bp):
CATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGTTCTTTTAATACCGAG
AAATCTTGAATTCTGATTCTGATAA
Found at i:154774 original size:32 final size:33
Alignment explanation
Indices: 154721--154788 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
154711 GATCAGATAA
154721 CTCAAAGAACACTTCTAGAAGATGCTATTGGGT
1 CTCAAAGAACACTTCTAGAAGATGCTATTGGGT
154754 CTCAAAGAACA-TTCTAGAAGATGCTATTGGGT
1 CTCAAAGAACACTTCTAGAAGATGCTATTGGGT
154786 CTC
1 CTC
154789 CTTATTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 24 0.69
33 11 0.31
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (33 bp):
CTCAAAGAACACTTCTAGAAGATGCTATTGGGT
Found at i:155185 original size:95 final size:95
Alignment explanation
Indices: 154799--155280 Score: 830
Period size: 94 Copynumber: 5.1 Consensus size: 95
154789 CTTATTTCTA
* * * * * *
154799 CTATGAGCAAATTCATCTTTCAATATCCAATGATTGGTTCTGT--GGTTTC-TACCAAACCAGAT
1 CTATGAGCACATTCATCTTCCAA-ATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGAT
154861 CAGATAACTCAAAGAACACTTCCAGAAGATG
65 CAGATAACTCAAAGAACACTTCCAGAAGATG
154892 CTATGAGCACATTCATCTTCCAAATTCAATGATTGG-TTTTTCGGGGTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
154956 AGATAACTCAAAGAACACTTCCAGAAGATG
66 AGATAACTCAAAGAACACTTCCAGAAGATG
*
154986 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTT-GGGGTTTATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
155050 AGATAACTCAAAGAACACTTCCAGAAGATG
66 AGATAACTCAAAGAACACTTCCAGAAGATG
* *
155080 CTATGAGCACATTCATCTTCTAAATTCAAAGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
155145 AGATAACTCAAAGAACACTTCCAGAAGATG
66 AGATAACTCAAAGAACACTTCCAGAAGATG
*
155175 CTATGAGCACATTCATCTTCCAAATTTAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
155240 AGATAACTCAAAGAACACTTCCAGAAGATG
66 AGATAACTCAAAGAACACTTCCAGAAGATG
155270 CTATGAGCACA
1 CTATGAGCACA
155281 CGGCACTTGT
Statistics
Matches: 371, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
91 3 0.01
92 12 0.03
93 26 0.07
94 171 0.46
95 159 0.43
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (95 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
AGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:155199 original size:189 final size:188
Alignment explanation
Indices: 154799--155280 Score: 833
Period size: 189 Copynumber: 2.6 Consensus size: 188
154789 CTTATTTCTA
* * * * * *
154799 CTATGAGCAAATTCATCTTTCAATATCCAATGATTGG--TTCTGTGGTTTCTACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAA-ATTCAATGATTGGTTTTTTGGGGTTTATACCAAACCAGATC
*
154862 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTG
65 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAAGATTG
154927 GTTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 GTTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
154986 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTTATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTTATACCAAACCAGATCA
*
155051 GATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAAAGATTGG
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAAGATTGG
155116 TTTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 -TTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
155175 CTATGAGCACATTCATCTTCCAAATTTAATGATTGGTTTTTTCGGGGTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTT-GGGGTTTATACCAAACCAGATC
155240 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
65 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
155281 CGGCACTTGT
Statistics
Matches: 281, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
186 12 0.04
187 21 0.07
188 87 0.31
189 99 0.35
190 62 0.22
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (188 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTTATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAAGATTGG
TTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:156139 original size:6 final size:6
Alignment explanation
Indices: 156128--156196 Score: 81
Period size: 6 Copynumber: 11.5 Consensus size: 6
156118 TCTTGACCCC
*
156128 CTTTTT CTTTTT CTTTTT CTTTTT TTTCTTT CTTTTTCT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT C-TTTT-T CTTTTT CTTTTT
156179 C--TTT -TTTTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTT
156197 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
4 3 0.05
5 3 0.05
6 36 0.65
7 9 0.16
8 4 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:156173 original size:33 final size:32
Alignment explanation
Indices: 156129--156191 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 32
156119 CTTGACCCCC
156129 TTTTTCTTTTTCTTTTTCTTTTTTTTCTTTCT
1 TTTTTCTTTTTCTTTTTCTTTTTTTTCTTTCT
156161 TTTTCTCTTTTTCTTTTTCTTTTTTTTCTTT
1 TTTT-TCTTTTTCTTTTTCTTTTTTTTCTTT
156192 TTCTTCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (32 bp):
TTTTTCTTTTTCTTTTTCTTTTTTTTCTTTCT
Done.