Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002273.1 Hibiscus syriacus cultivar Beakdansim tig00004620_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: 802197
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:795363 original size:76 final size:76
Alignment explanation
Indices: 795265--795482 Score: 375
Period size: 76 Copynumber: 2.9 Consensus size: 76
795255 ACAGATGACT
* *
795265 CGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTATAGATGACCCTAAGGCTTTGAAAACAT
1 CGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACAT
795329 CAAAAAGCTCC
66 CAAAAAGCTCC
* *
795340 CGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTATAGATGACCCTAAGGCTTTGGAAACAT
1 CGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACAT
795405 CAAAAAGCTCC
66 CAAAAAGCTCC
* *
795416 CGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACAT
1 CGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACAT
795481 CA
66 CA
795483 TGCACTGTAG
Statistics
Matches: 134, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
75 6 0.04
76 128 0.96
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (76 bp):
CGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACAT
CAAAAAGCTCC
Found at i:795488 original size:45 final size:45
Alignment explanation
Indices: 795424--795527 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
795414 CCCGAAGGCT
*
795424 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
*
795469 TTTTGAAAACATCATGCACTGTAGGACTTACATATGACCCTAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
*
795514 CTTTGAAAACATCA
1 TTTTGAAAACATCA
795528 AAAAGCTCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
Found at i:795492 original size:121 final size:122
Alignment explanation
Indices: 795348--795604 Score: 444
Period size: 121 Copynumber: 2.1 Consensus size: 122
795338 CCCGAAGGCT
* * * *
795348 TTTTGGAAACATCATGCATTGTAGGACTTATAGATGACCCTAAGGCTTTGGAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795413 TCCCGAAGGC-TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
66 TCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
*
795469 TTTTGAAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
*
795534 TCCCGAAGGCTTTTTTGGTAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
66 TCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
*
795591 CTTTGAAAACATCA
1 TTTTGAAAACATCA
795605 AAAAGCTCCC
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 70 0.55
122 58 0.45
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (122 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG
Found at i:795571 original size:198 final size:197
Alignment explanation
Indices: 795218--795680 Score: 786
Period size: 198 Copynumber: 2.4 Consensus size: 197
795208 TTACAGATGA
* * *
795218 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGTTTTTGAAAA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTTGAAAA
*
795281 CATCATGCACTGAAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG
65 CATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG
* * *
795346 CTTTTTGGAAACATCATGCATTGTAGGACTTATAGATGACCCTAAGGCTTTGGAAACATCAAAAA
130 CTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAA
795411 GCT
195 GCT
*
795414 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
* *
795479 ATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
66 ATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
795544 TTTTTTGGTAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAA
131 -TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAA
795609 GCT
195 GCT
*
795612 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
795677 ATCA
66 ATCA
795681 AAAAGCTCCC
Statistics
Matches: 252, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
196 8 0.03
197 72 0.29
198 172 0.68
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (197 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
ATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAG
CT
Found at i:795672 original size:76 final size:76
Alignment explanation
Indices: 795469--796187 Score: 1264
Period size: 76 Copynumber: 9.5 Consensus size: 76
795459 GACCCTAAGG
* *
795469 TTTTGAAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795534 TCCCGAAGGCTT
66 TCCCGAAGGC-T
*
795546 TTTTGGTAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795611 TCCCGAAGGCT
66 TCCCGAAGGCT
* *
795622 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795687 TCCCGAAGGCT
66 TCCCGAAGGCT
*
795698 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGATCCTAAGGCTTTGAAAACATC-AAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795762 TCCCGAAGGCTT
66 TCCCGAAGGC-T
* *
795774 TTTTGGTAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795839 TCCCGAAGGCT
66 TCCCGAAGGCT
* *
795850 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795915 TCCCGAAGGCT
66 TCCCGAAGGCT
*
795926 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
795991 TCCCGAAGGCT
66 TCCCGAAGGCT
*
796002 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
*
796066 TCCTGAAGGC-
66 TCCCGAAGGCT
*
796076 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGATAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
796141 TCCCGAAGGCT
66 TCCCGAAGGCT
*
796152 TTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTTGGAAACATCATGCACTGTAGGACTTACAGATG
796188 TAGGAAATAG
Statistics
Matches: 612, Mismatches: 26, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
74 56 0.09
75 46 0.08
76 422 0.69
77 88 0.14
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (76 bp):
TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCT
Found at i:797057 original size:20 final size:20
Alignment explanation
Indices: 797032--797102 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
797022 AATAAAGCTT
797032 TCATCTTTGAAAAGAGAATA
1 TCATCTTTGAAAAGAGAATA
797052 TCATCTTT-AAAA-AGAATCCA
1 TCATCTTTGAAAAGAGAAT--A
*
797072 TCATCTTTGAAAAGA-ATCTA
1 TCATCTTTGAAAAGAGA-ATA
797092 TCATCTTTGAA
1 TCATCTTTGAA
797103 GAGTGTAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
18 5 0.11
19 4 0.09
20 29 0.64
21 5 0.11
22 2 0.04
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (20 bp):
TCATCTTTGAAAAGAGAATA
Found at i:799676 original size:13 final size:13
Alignment explanation
Indices: 799658--799684 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
799648 ATTATGTTAA
799658 TATTTTTATTTTT
1 TATTTTTATTTTT
799671 TATTTTTATTTTT
1 TATTTTTATTTTT
799684 T
1 T
799685 TCTTTCGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTATTTTT
Done.