Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009134.1 Hibiscus syriacus cultivar Beakdansim tig00112634_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: 270421
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:236250 original size:31 final size:32
Alignment explanation
Indices: 236222--236281 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
236212 CCGTTTTGAG
* *
236222 ATAATTTAATCAATTTTAATGA-TATTTTGTA
1 ATAATTTAATAAACTTTAATGATTATTTTGTA
*
236253 ATAATTTTATAAACTTTAATGATTATTTT
1 ATAATTTAATAAACTTTAATGATTATTTT
236282 TATAACTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (32 bp):
ATAATTTAATAAACTTTAATGATTATTTTGTA
Found at i:238770 original size:30 final size:31
Alignment explanation
Indices: 238736--238801 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
238726 AATAATAGTT
* *
238736 CATTTAATC-ATAATTTTTCATATAATGACC
1 CATTTAATCAATAATTTTTCACATAAAGACC
* * *
238766 CATTTTATCAATATTTTTTCACATAAAGACT
1 CATTTAATCAATAATTTTTCACATAAAGACC
238797 CATTT
1 CATTT
238802 GAATTATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (31 bp):
CATTTAATCAATAATTTTTCACATAAAGACC
Found at i:247098 original size:95 final size:94
Alignment explanation
Indices: 246953--247235 Score: 322
Period size: 95 Copynumber: 3.0 Consensus size: 94
246943 AAATAATGAA
** * * * * *
246953 AACAATAATGGTAAGCTAATATGTCCAAAAACCAAGTGCAACTAAATATCCAGATCGATAATCAA
1 AACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGA-CAATAATCAA
*
247018 ACCAACTGCTATAAAAATAACAATGAAAAT
65 ACCAACTGCTATAAAAACAACAATGAAAAT
* ** *
247048 AATAATAATAATAAGCTAATATGTCTAAAAATCGTGTATAACAAAATATCCAGACTAATAATCAA
1 AACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGAC-AATAATCAA
* **
247113 ATCAACTATTAT-AAAACAACAAT--AAA-
65 ACCAACTGCTATAAAAACAACAATGAAAAT
* * * *
247139 AACAATAATAATAAGTTAATATGTCTAAAAATCAAGTACAACAAAATATCTATACCAATAATTAA
1 AACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGA-CAATAATCAA
* *
247204 ACTATCTGCTATAAAAACAACAATGAAAAT
65 ACCAACTGCTATAAAAACAACAATGAAAAT
247234 AA
1 AA
247236 AAAAGAAGTC
Statistics
Matches: 154, Mismatches: 28, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
91 62 0.40
92 15 0.10
94 14 0.09
95 63 0.41
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (94 bp):
AACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGACAATAATCAAA
CCAACTGCTATAAAAACAACAATGAAAAT
Found at i:247182 original size:91 final size:93
Alignment explanation
Indices: 246951--247232 Score: 300
Period size: 91 Copynumber: 3.0 Consensus size: 93
246941 AAAAATAATG
** * * * * *
246951 AAAACAATAATGGTAAGCTAATATGTCCAAAAACCAAGTGCAACTAAATATCCAGATCGATAATC
1 AAAACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGATCAATAATC
* *
247016 AAACCAACTGCTATAAAAATAACAATGAA
66 AAACCAACTACTATAAAAACAACAAT-AA
* ** *
247045 AATAATAATAATAATAAGCTAATATGTCTAAAAATCGTGTATAACAAAATATCCAGA-CTAATAA
1 AA-AACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGATC-AATAA
* *
247109 TCAAATCAACTATTAT-AAAACAACAAT-A
64 TCAAACCAACTACTATAAAAACAACAATAA
* * * * *
247137 AAAACAATAATAATAAGTTAATATGTCTAAAAATCAAGTACAACAAAATATCTATACCAATAATT
1 AAAACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGATCAATAATC
* * * *
247202 AAACTATCTGCTATAAAAACAACAATGA
66 AAACCAACTACTATAAAAACAACAATAA
247230 AAA
1 AAA
247233 TAAAAAAGAA
Statistics
Matches: 155, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
91 62 0.40
92 15 0.10
93 4 0.03
94 13 0.08
95 61 0.39
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (93 bp):
AAAACAATAATAATAAGCTAATATGTCTAAAAATCAAGTACAACAAAATATCCAGATCAATAATC
AAACCAACTACTATAAAAACAACAATAA
Found at i:247274 original size:27 final size:27
Alignment explanation
Indices: 247243--247305 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
247233 TAAAAAAGAA
* *
247243 GTCTCAAAATCAAGTAGAACAAAGTAT
1 GTCTCAAAACCAAGTAGAACAAAATAT
*
247270 GTCTCAACACCAAGTAGAACAAAATAT
1 GTCTCAAAACCAAGTAGAACAAAATAT
*
247297 GTCTAAAAA
1 GTCTCAAAA
247306 ATAACATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (27 bp):
GTCTCAAAACCAAGTAGAACAAAATAT
Found at i:253951 original size:21 final size:19
Alignment explanation
Indices: 253917--253956 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
253907 AGACTATAAT
253917 TATTAATAAAAAAATATTTA
1 TATTAATAAAAAAAT-TTTA
*
253937 TATTATATTAAAAAATTTTA
1 TATTA-ATAAAAAAATTTTA
253957 AATTTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTAATAAAAAAATTTTA
Found at i:262482 original size:23 final size:23
Alignment explanation
Indices: 262452--262498 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
262442 AAATTAGAAA
262452 TTACTCCCCCTTACTTTAACACT
1 TTACTCCCCCTTACTTTAACACT
262475 TTACTCCCCCTTACTTTAACACT
1 TTACTCCCCCTTACTTTAACACT
262498 T
1 T
262499 ATTCTTCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.40
Consensus pattern (23 bp):
TTACTCCCCCTTACTTTAACACT
Found at i:264767 original size:21 final size:21
Alignment explanation
Indices: 264741--264780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
264731 CAGAACCCCA
*
264741 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
264762 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
264781 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:264814 original size:20 final size:20
Alignment explanation
Indices: 264739--264822 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
264729 AACAGAACCC
*
264739 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGGATCGATTCCCT
* *
264758 CTGTGGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGG-ATCGATT-CCC-T
** * *
264782 CAAAGGGGAATCGGTTCCCT
1 CAGGGGGGGATCGATTCCCT
264802 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGGATCGATTCCCT
264822 C
1 C
264823 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.04
20 23 0.47
21 9 0.18
22 10 0.20
23 4 0.08
24 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
CAGGGGGGGATCGATTCCCT
Found at i:268661 original size:22 final size:21
Alignment explanation
Indices: 268619--268658 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
268609 GAGTTTGTTT
*
268619 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
268640 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
268659 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Done.