Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_960 ID=scaffold_960-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: 1960
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Found at i:789 original size:45 final size:45
Alignment explanation
Indices: 633--789 Score: 163
Period size: 45 Copynumber: 3.5 Consensus size: 45
623 AGTTGCTGAA
*
633 AATTGAGATGTTTTA-TCGCTGTAATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTAAGT-GCTGTAATTGAGGTGTATAAATGTTGTT
* * * * * ** * **
678 AATTGATATGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGA
1 AATTGAGATGTTTAAGTGCTG-TAATTGAGGTGTATAAATGTTGTT
* *
724 AATTGAGATGTTTTATTGCTGTAATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTAAGTGCTGTAATTGAGGTGTATAAATGTTGTT
*
769 AATTGATATGTTTAAGTGCTG
1 AATTGAGATGTTTAAGTGCTG
790 CAAATTGAAG
Statistics
Matches: 84, Mismatches: 26, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
45 50 0.60
46 34 0.40
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.43
Consensus pattern (45 bp):
AATTGAGATGTTTAAGTGCTGTAATTGAGGTGTATAAATGTTGTT
Found at i:835 original size:91 final size:91
Alignment explanation
Indices: 601--820 Score: 388
Period size: 91 Copynumber: 2.4 Consensus size: 91
591 GAAATTTGAT
*
601 AGTGCTGCAAATTGAAGTATTTAGTTGCTGAAAATTGAGATGTTTTATCGCTGTAATTGAGGTGT
1 AGTGCTGCAAATTGAAGTATTTAGTTGCTGAAAATTGAGATGTTTTATTGCTGTAATTGAGGTGT
666 ATAAATGTTGTTAATTGATATGTTTA
66 ATAAATGTTGTTAATTGATATGTTTA
*
692 AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATTGCTGTAATTGAGGTGT
1 AGTGCTGCAAATTGAAGTATTTAGTTGCTGAAAATTGAGATGTTTTATTGCTGTAATTGAGGTGT
757 ATAAATGTTGTTAATTGATATGTTTA
66 ATAAATGTTGTTAATTGATATGTTTA
* *
783 AGTGCTGCAAATTGAAGTGTTTAAG-TGCTGCAAATTGA
1 AGTGCTGCAAATTGAAGTATTT-AGTTGCTGAAAATTGA
821 AGTGTTTAGT
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 122 0.98
92 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (91 bp):
AGTGCTGCAAATTGAAGTATTTAGTTGCTGAAAATTGAGATGTTTTATTGCTGTAATTGAGGTGT
ATAAATGTTGTTAATTGATATGTTTA
Found at i:881 original size:23 final size:23
Alignment explanation
Indices: 601--880 Score: 161
Period size: 23 Copynumber: 12.3 Consensus size: 23
591 GAAATTTGAT
*
601 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
623 AGTTGCTGAAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* * *
647 A-TCGCTG-TAATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * **
669 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
*
692 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
714 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* * * *
738 ATTGCTG-TAATTGAGGTGTATA
1 AGTGCTGCAAATTGAAGTGTTTA
* * **
760 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
783 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
806 AGTGCTGCAAATTGAAGTGTTT-
1 AGTGCTGCAAATTGAAGTGTTTA
*
828 AGTTGCTGCAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
** *
852 A-TCGCTATAAATTGAAGTGTTAA
1 AGT-GCTGCAAATTGAAGTGTTTA
875 AGTGCT
1 AGTGCT
881 ACTTTCCATT
Statistics
Matches: 203, Mismatches: 33, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
22 43 0.21
23 154 0.76
24 6 0.03
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.40
Consensus pattern (23 bp):
AGTGCTGCAAATTGAAGTGTTTA
Found at i:1845 original size:43 final size:43
Alignment explanation
Indices: 1797--1956 Score: 205
Period size: 43 Copynumber: 3.7 Consensus size: 43
1787 GAGAAAGTGT
* * * *
1797 CGCTAAAGGTCTTGTTTTTTAGCAGCGCTTCAGGAAAAAGCGC
1 CGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGAGGAAAAAGCGC
*
1840 CGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGAGGGAAAAGCGC
1 CGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGAGGAAAAAGCGC
* * * * *
1883 CGCTAGAGGTCTTGGTCTTTAGCGGCGTTTGTGAAAAAAACGC
1 CGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGAGGAAAAAGCGC
*
1926 CGCTAAAGGTCATT-GTCTTTAGCGGCGTTTG
1 CGCTAAAGGTC-TTGGTTTTTAGCGGCGTTTG
1957 TAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 102 0.98
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
CGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGAGGAAAAAGCGC
Found at i:1957 original size:43 final size:43
Alignment explanation
Indices: 1770--1957 Score: 189
Period size: 43 Copynumber: 4.4 Consensus size: 43
1760 TTTTCGTGAC
* * * * * * *
1770 CTTTAGTGGCGTTTTTGGAGAAAGTGTCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGGT
* * * ** *
1813 TTTTAGCAGCGCTTCAGGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGGT
* * ** *
1856 TTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAGAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGGT
*
1899 CTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAGGTCATT-GT
1 CTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTC-TTGGT
1942 CTTTAGCGGCGTTTGT
1 CTTTAGCGGCGTTTGT
1958 AGG
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
43 121 0.98
44 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGGT
Done.