Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_72 ID=scaffold_72-JGI_221_v2.0
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: 17934
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.30
Warning! 1343 characters in sequence are not A, C, G, or T
Found at i:275 original size:96 final size:96
Alignment explanation
Indices: 1--672 Score: 998
Period size: 96 Copynumber: 7.0 Consensus size: 96
* * * * * *
1 GGGGAAAGTGAGACTCGCCATTGTAGCTTCAATCCGTTCCGATGCATCGCCTG-AAGTATGCTTC
1 GGGG-AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTT
** * *
65 G-TATGTGTGGTGTTCGATCTTTT-AACTGCAAT
65 GCCGT-TGTGG-CTTCGATCTTTTAAATTGCAAT
* *
97 GGGGAAGTGAGACT-GCCCGTTGTAGCTGCAATCTGTTCCGCCGCATCGCCTGAAAAGTAAGATT
1 GGGGAAGTGAGACTCG-CCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTG-AAAGTAAGATT
* *
161 TGCCGTTGTGGCTTCGATCTGTCAAATTGCAAT
64 TGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
* *
194 GGGGAAGTGAGACTCGCCGTTGTAGATTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTAG
1 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
259 CCGTTGTGGCTTCGATCTTTTAAA-T--ATAT
66 CCGTTGTGGCTTCGATCTTTTAAATTGCA-AT
* *
288 GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCAGCTGCATCGCCTGAAAGTAAGATTA
1 -GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTT
353 GCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
65 GCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
* *
385 GGGGAAGTGAGACTCGCCGTTGTAGCTTTAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCG
1 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
*
450 CCGTTGTGGCTTCGATTTTTTAAATTGCAAT
66 CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
*
481 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTT
1 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
546 CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
66 CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
* * *
577 AGGGAAGTGAGACTCGCTGTTGTAACTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
1 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
*
642 CCGTTGTGGCTTCGATCTTTTAAATTACAAT
66 CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
673 CTATGGTTAC
Statistics
Matches: 530, Mismatches: 35, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
93 1 0.00
94 3 0.01
95 129 0.24
96 323 0.61
97 71 0.13
98 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (96 bp):
GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTG
CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
Found at i:522 original size:287 final size:288
Alignment explanation
Indices: 1--672 Score: 998
Period size: 287 Copynumber: 2.3 Consensus size: 288
* * * * * * *
1 GGGGAAAGTGAGACTCGCCATTGTAGCTTCAATCCGTTCCGATGCATCGCCTG-AAGTATGCTTC
1 GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
** * *
65 G-TATGTGTGGTGTTCGATCTTTT-AACTGCAATGGGGAAGTGAGACTGCCCGTTGTAGCTGCAA
66 GCCGT-TGTGG-CTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTGCCCGTTGTAGCTGCAA
*
128 TCTGTTCCGCCGCATCGCCTGAAAAGTAAGATTTGCCGTTGTGGCTTCGATCTGTCAAATTGCAA
129 TCTGTTCCGCCGCATCGCCTGAAAAGTAAGATTCGCCGTTGTGGCTTCGATCTGTCAAATTGCAA
193 TGGGGAAGTGAGACTCGCCGTTGTAGATTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
194 TGGGGAAGTGAGACTCGCCGTTGTAGATTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
258 GCCGTTGTGGCTTCGATCTTTTAAA-TATAT
259 GCCGTTGTGGCTTCGATCTTTTAAATTA-AT
*
288 GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCAGCTGCATCGCCTGAAAGTAAGATTA
1 GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
**
353 GCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACT-CGCCGTTGTAGCTTTAAT
66 GCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTGC-CCGTTGTAGCTGCAAT
* * * *
417 CTGTTCCGCTGCATCGCCTG-AAAGTAAGATTCGCCGTTGTGGCTTCGATTTTTTAAATTGCAAT
130 CTGTTCCGCCGCATCGCCTGAAAAGTAAGATTCGCCGTTGTGGCTTCGATCTGTCAAATTGCAAT
* **
481 GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTT
195 GGGGAAGTGAGACTCGCCGTTGTAGATTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTAG
546 CCGTTGTGGCTTCGATCTTTTAAATTGCAAT
260 CCGTTGTGGCTTCGATCTTTTAAATT--AAT
* * * *
577 -AGGGAAGTGAGACTCGCTGTTGTAACTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTT
1 GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
*
641 GCCGTTGTGGCTTCGATCTTTTAAATTACAAT
66 GCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
673 CTATGGTTAC
Statistics
Matches: 350, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
287 186 0.53
288 160 0.46
289 3 0.01
290 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (288 bp):
GGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTA
GCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTGCCCGTTGTAGCTGCAATC
TGTTCCGCCGCATCGCCTGAAAAGTAAGATTCGCCGTTGTGGCTTCGATCTGTCAAATTGCAATG
GGGAAGTGAGACTCGCCGTTGTAGATTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTAGC
CGTTGTGGCTTCGATCTTTTAAATTAAT
Found at i:13566 original size:3 final size:3
Alignment explanation
Indices: 13558--13636 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
13548 AAATAAAGCC
** * * *
13558 AAT AAT AATT AAT AAT AGC AGT AAT GAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13604 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13637 GACACTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:14770 original size:14 final size:15
Alignment explanation
Indices: 14739--14774 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
14729 TTTTATGAAA
*
14739 TTGGGCTTGGGTGTT
1 TTGGGCTTCGGTGTT
14754 TTGGGCTTCGG-GTT
1 TTGGGCTTCGGTGTT
14768 TTGGGCT
1 TTGGGCT
14775 GTATTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.44, T:0.44
Consensus pattern (15 bp):
TTGGGCTTCGGTGTT
Found at i:14836 original size:82 final size:82
Alignment explanation
Indices: 14708--14868 Score: 322
Period size: 82 Copynumber: 2.0 Consensus size: 82
14698 GTTTCAGTCT
14708 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
1 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
14773 CTGTATTTGGGTTAAGA
66 CTGTATTTGGGTTAAGA
14790 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
1 CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
14855 CTGTATTTGGGTTA
66 CTGTATTTGGGTTA
14869 GTTTTAGGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (82 bp):
CTGAAACCCTAGGCAGATTTTTTTTATGAAATTGGGCTTGGGTGTTTTGGGCTTCGGGTTTTGGG
CTGTATTTGGGTTAAGA
Found at i:14852 original size:14 final size:15
Alignment explanation
Indices: 14821--14856 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
14811 TTTTATGAAA
*
14821 TTGGGCTTGGGTGTT
1 TTGGGCTTCGGTGTT
14836 TTGGGCTTCGG-GTT
1 TTGGGCTTCGGTGTT
14850 TTGGGCT
1 TTGGGCT
14857 GTATTTGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.11, G:0.44, T:0.44
Consensus pattern (15 bp):
TTGGGCTTCGGTGTT
Found at i:15214 original size:6 final size:6
Alignment explanation
Indices: 15203--15229 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15193 GGGGCGTCGC
15203 CGGTGG CGGTGG CGGTGG CGGTGG CGG
1 CGGTGG CGGTGG CGGTGG CGGTGG CGG
15230 CTGAAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.67, T:0.15
Consensus pattern (6 bp):
CGGTGG
Found at i:17248 original size:25 final size:25
Alignment explanation
Indices: 17212--17283 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
17202 GCCCATTTTC
17212 ACAGCTCATGTGAGCATTATGATTT
1 ACAGCTCATGTGAGCATTATGATTT
* * *
17237 GCAGCTCGTGTGAGCATTCTGATTT
1 ACAGCTCATGTGAGCATTATGATTT
*
17262 ACAACTCATGTGAGCATATATG
1 ACAGCTCATGTGAGCAT-TATG
17284 TATAGGAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 36 0.92
26 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (25 bp):
ACAGCTCATGTGAGCATTATGATTT
Done.