Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008775.1 Hibiscus syriacus cultivar Beakdansim tig00111887_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: 150276
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
File 2 of 2
Found at i:131638 original size:30 final size:31
Alignment explanation
Indices: 131597--131656 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
131587 TAGCCATAGT
*
131597 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
131627 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
131657 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:131713 original size:29 final size:29
Alignment explanation
Indices: 131671--131742 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
131661 TTTTCTGCAT
**
131671 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
131700 ATTCATGTCATGTAATATATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
131729 ATTCATGTCATGTA
1 ATTCATGTCATGTA
131743 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:132142 original size:67 final size:66
Alignment explanation
Indices: 132049--132198 Score: 189
Period size: 67 Copynumber: 2.2 Consensus size: 66
132039 TTTTCTCATG
* * *
132049 GGGGAATCGGTTTCCCCCCCTGGGGTATCGGTTCCCCT-ATAGCATTCTGGAATTTC-TTATACG
1 GGGGTATCGG-TTCCCCCCCTGGGGTATCGATTCCCCTCATA-CATTCTGGAAATTCATT-T-CG
132112 ATG-A
62 ATGAA
* *
132116 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTACATTCTGGAAATTCATTTCGTTG
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCATACATTCTGGAAATTCATTTCGATG
132181 AA
65 AA
132183 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
132199 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
66 14 0.19
67 56 0.76
68 4 0.05
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCATACATTCTGGAAATTCATTTCGATGA
A
Found at i:132208 original size:21 final size:21
Alignment explanation
Indices: 132178--132219 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
132168 ATTCATTTCG
* *
132178 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
132199 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
132220 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:134509 original size:28 final size:26
Alignment explanation
Indices: 134478--134568 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 26
134468 CTGTATAAAT
*
134478 ACTTAAATTCATAATATTTTATATATTA
1 ACTTAAATT-AAAATATTTTAT-TATTA
*
134506 ACTTAAA-AAAAATATTTT-TGTATTA
1 ACTTAAATTAAAATATTTTAT-TATTA
134531 ACTT--ATTAAATATATTTTATTATTA
1 ACTTAAATTAAA-ATATTTTATTATTA
*
134556 ACTTAATTTAAAA
1 ACTTAAATTAAAA
134569 ATATATTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 26 0.49
26 11 0.21
27 5 0.09
28 7 0.13
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (26 bp):
ACTTAAATTAAAATATTTTATTATTA
Found at i:134533 original size:25 final size:25
Alignment explanation
Indices: 134490--134579 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 25
134480 TTAAATTCAT
134490 AATATTTTATATATTAACTTAAAAAA
1 AATATTTTAT-TATTAACTTAAAAAA
**
134516 AATATTTT-TGTATTAACTTATTAAA
1 AATATTTTAT-TATTAACTTAAAAAA
*
134541 TATATTTTATTATTAACTTAATTTAAAA
1 AATATTTTATTATTAACTTAA---AAAA
134569 ATATATTTTAT
1 A-ATATTTTAT
134580 GTCAAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
25 31 0.60
26 9 0.17
28 3 0.06
29 9 0.17
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (25 bp):
AATATTTTATTATTAACTTAAAAAA
Found at i:135865 original size:22 final size:23
Alignment explanation
Indices: 135822--135864 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
135812 GGCCCGAACC
135822 CGACCCGATAAATAACTTAAAACT
1 CGACCCGA-AAATAACTTAAAACT
135846 CGACCCG-AAATAA-TTAAAA
1 CGACCCGAAAATAACTTAAAA
135865 ATATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
24 7 0.37
ACGTcount: A:0.49, C:0.23, G:0.09, T:0.19
Consensus pattern (23 bp):
CGACCCGAAAATAACTTAAAACT
Found at i:143968 original size:3 final size:3
Alignment explanation
Indices: 143960--144027 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
143950 AACTCTAAAA
143960 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
144008 TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
144028 CAGATCACAG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.