Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_349 ID=scaffold_349-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: 8814
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.28
Warning! 816 characters in sequence are not A, C, G, or T
Found at i:92 original size:18 final size:19
Alignment explanation
Indices: 69--113 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
59 ATATATATTG
69 TATATATTTTAAATGTT-T
1 TATATATTTTAAATGTTAT
* *
87 TATATATGTTATATGTTAT
1 TATATATTTTAAATGTTAT
106 TAT-TATTT
1 TATATATTT
114 ATTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATATATTTTAAATGTTAT
Found at i:5473 original size:46 final size:50
Alignment explanation
Indices: 5418--5524 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 50
5408 AAAGGTGGGA
* *
5418 CCAATGTGAAAGCCTACAAA-GGGCGCTTTGAGT-AAAAAAAAA-AG-GG
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGAGAGG
*
5464 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAAGAGAGG
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGAGAGG
*
5514 CTAAGGTGAAA
1 CCAAGGTGAAA
5525 ACTCGCAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
46 18 0.34
47 12 0.23
48 9 0.17
49 2 0.04
50 12 0.23
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.15
Consensus pattern (50 bp):
CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGAGAGG
Found at i:7445 original size:132 final size:132
Alignment explanation
Indices: 7255--7503 Score: 394
Period size: 132 Copynumber: 1.9 Consensus size: 132
7245 CCCCAAGCAG
* *
7255 TAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
*
7320 AGTAATTCTA-CTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTACAGATCTTGCCTTCCTGCA
66 AGTAATTCTATC-TCCCTGGGCAAC-GCGGAATAGATTGAAGATTACAGATCTTGCCTTCCTGCA
7384 TAGA
129 TAGA
* * *
7388 TAGT-GAGCAGATCAAGGATGGCGGATTTTACTTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
* *
7452 GGTAATTCTATCTCCCTGGGCAACGTGGAATAGATTGAAGATTACAGATCTT
66 AGTAATTCTATCTCCCTGGGCAACGCGGAATAGATTGAAGATTACAGATCTT
7504 ATCTCCCTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 27 0.25
132 75 0.70
133 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (132 bp):
TAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
AGTAATTCTATCTCCCTGGGCAACGCGGAATAGATTGAAGATTACAGATCTTGCCTTCCTGCATA
GA
Found at i:7593 original size:44 final size:45
Alignment explanation
Indices: 7530--7674 Score: 138
Period size: 44 Copynumber: 3.3 Consensus size: 45
7520 AAGTAGATCA
7530 AAGTTGCAGTGGGGCAGACT-AAGGA-AGC-AAGTCTTATC-CTCCTG
1 AAGTTGCAGTGGGGCAGACTGAA-GATAGCGAA-TCTTATCTC-CCTG
* *
7574 AAGTTACAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
* ** * * ** *
7619 AAGTTGCAGTGGAGCAGGTTAAAGCTA-ATAATCCTATCTCCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
7663 AAGTTGCAGTGG
1 AAGTTGCAGTGG
7675 AGCGGATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
44 47 0.55
45 35 0.41
46 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (45 bp):
AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
Found at i:7622 original size:45 final size:44
Alignment explanation
Indices: 7530--7635 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 44
7520 AAGTAGATCA
7530 AAGTTGCAGTGGGGCAGACTAAGGAAGCAAGTCTTATCCTCCTG
1 AAGTTGCAGTGGGGCAGACTAAGGAAGCAAGTCTTATCCTCCTG
* *
7574 AAGTTACAGTGGGGCAGACTGAA-GATGGCGAA-TCTTAT-CTCCCTG
1 AAGTTGCAGTGGGGCAGACT-AAGGA-AGC-AAGTCTTATCCT-CCTG
*
7619 AAGTTGCAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
7636 GTTAAAGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 23 0.43
45 29 0.54
46 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (44 bp):
AAGTTGCAGTGGGGCAGACTAAGGAAGCAAGTCTTATCCTCCTG
Found at i:7701 original size:44 final size:44
Alignment explanation
Indices: 7605--7843 Score: 179
Period size: 44 Copynumber: 5.5 Consensus size: 44
7595 AAGATGGCGA
* * *
7605 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTAAAGCTA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACCACA-G
*
7649 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* * * *** *
7693 ATCTTATCTCTCTGAAGTTGTAGAGG-GCGGA-TCGCATC-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* * ** *
7734 -TCTTATCTCCCTGCAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AACCACAG
* * * * *
7777 ATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAAAACCACAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
* *
7821 ATCTCATCTCTCTGAAGTTGCAG
1 ATCTTATCTCCCTGAAGTTGCAG
7844 CAGAGTAGAT
Statistics
Matches: 150, Mismatches: 36, Indels: 18
0.74 0.18 0.09
Matches are distributed among these distances:
40 21 0.14
41 7 0.05
42 6 0.04
43 11 0.07
44 104 0.69
45 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
Found at i:7763 original size:128 final size:128
Alignment explanation
Indices: 7605--7938 Score: 360
Period size: 128 Copynumber: 2.6 Consensus size: 128
7595 AAGATGGCGA
7605 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCTAATAATCCTATCTCCCTGAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GTTAAAGCTAATAATCCTATCTCCCTGAAGTTGC
* * * *
7670 AGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAG-AGGGCGGATCGCATCCAG
65 AGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTGAAGTTGCAGCAGAGCAGATCGCAT-CAG
* ** * * *
7734 -TCTTATCTCCCTGCAGTTGCAGTGGAGCAGACAGAAG-AAACCAATCCTATCTCCTTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGTTA-AAGCTAA-TAATCCTATCTCCCTGAAGTTG
* * * *
7797 CAATGGAGTGGATTAAAACCACATATCTCATCTCTCTGAAGTTGCAGCAGAGTAGATCGCATCAG
64 CAGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCAG
* * * * * *
7862 AT-TTAT-T--TTTAAGTTGTAGTAGAACAAGTTAAAGCT-ATAAGTCTTATCTCCCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGTTAAAGCTAATAA-TCCTATCTCCCTGAAGTTG
* *
7922 CAGTGGAACAGATTAAA
64 CAGTGGAGCGGATTAAA
7939 GACAACAAAT
Statistics
Matches: 168, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
124 2 0.01
125 46 0.27
126 3 0.02
127 5 0.03
128 100 0.60
129 12 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (128 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGTTAAAGCTAATAATCCTATCTCCCTGAAGTTGCA
GTGGAGCGGATTAAAACCACAGATCTCATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCAG
Done.