Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_674 ID=scaffold_674-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: 4736
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Found at i:1853 original size:51 final size:51
Alignment explanation
Indices: 1637--2080 Score: 363
Period size: 51 Copynumber: 8.8 Consensus size: 51
1627 TTTTATCATT
* *
1637 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTC
* * *
1686 C-AGTTCACGTAGTAGCCTTCACATAGTACGACACACGTGATC-AAGTTTTAC
1 CGA-TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTT-C
* * * *
1737 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGA-CTAAAGCTTTT
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAAGCTTTC
* * * * * * * * *
1787 TGGTACCCATTGTAGCCTTCACTTAGTACTACACATGTAATCATAG-TTTAC
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTT-C
* * *
1838 CGATACACGTAGTAGCATTCACACAGTACTACACACGTGCTCAAAGC-TTC
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTC
* * * * * * *
1888 TCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TTTAT
1 -CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AAGCTTT-C
* *
1940 CGATACACGTAGTAGCCTTAACACAGTACTACACACGTGATCAAAGCTATT-
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCT-TTC
* * * * * * ** * *
1991 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGA-CCCATCATTC
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTC
*
2041 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA
2081 CCATCACTTT
Statistics
Matches: 310, Mismatches: 67, Indels: 35
0.75 0.16 0.08
Matches are distributed among these distances:
48 1 0.00
49 41 0.13
50 84 0.27
51 179 0.58
52 3 0.01
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (51 bp):
CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTC
Found at i:1876 original size:102 final size:102
Alignment explanation
Indices: 1637--2081 Score: 489
Period size: 102 Copynumber: 4.4 Consensus size: 102
1627 TTTTATCATT
* * *
1637 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-TC--AG-TTTTACAGTTCACGTAG
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACTCAAAGCTTTT-CGGTACACATAG
* * * *
1698 TAGCCTTCACATAGTACGACACACGTGATCA-AGTTTTAC
65 TAGCCTTCACATAGTACTACACATGTAACCATA--TTTAC
* * * * * *
1737 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACT-AAAGCTTTTTGGTACCCATTGT
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACTCAAAGCTTTTCGGTACACATAGT
* *
1800 AGCCTTCACTTAGTACTACACATGTAATCATAGTTTAC
66 AGCCTTCACATAGTACTACACATGTAACCATA-TTTAC
* * *
1838 CGATACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTTCTCGGTACACATAGT
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACTCAAAGCTTTTCGGTACACATAGT
* * *
1902 AGCCTTCACTTAGTACTACACATGTGACCATTATTTAT
66 AGCCTTCACATAGTACTACACATGTAACCA-TATTTAC
* * * *
1940 CGATACACGTAGTAGCCTTAACACAGTACTACACACGTGA-TCAAAGCTATTCGGTACGCATAGT
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACTCAAAGCTTTTCGGTACACATAGT
* * *
2004 AGCCTGCACATAGTACTACACATGCGACCCATCA-TT-C
66 AGCCTTCACATAGTACTACACATG-TAACCAT-ATTTAC
*
2041 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGAC
2082 CATCACTTTC
Statistics
Matches: 293, Mismatches: 40, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
99 34 0.12
100 3 0.01
101 81 0.28
102 169 0.58
103 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACTCAAAGCTTTTCGGTACACATAGT
AGCCTTCACATAGTACTACACATGTAACCATATTTAC
Found at i:2103 original size:203 final size:200
Alignment explanation
Indices: 1631--2114 Score: 518
Period size: 203 Copynumber: 2.4 Consensus size: 200
1621 TATTATTTTT
* *
1631 ATCATT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTG--ATCAGTTTTACAGTTCA
1 ATCATTCCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGCCATCACTTTCAC-GTTCA
* * *
1693 CGTAGTAGCCTTCACATAGTACGACACACGTGATCAAGTTTTACGGCTCACGTAGTAGCCTTCAC
65 CATAGTAGCCTTCACATAGTACGACACACGTGATCAAGTTTTACGGATCACGTAGTAGCCTTAAC
* * * * * * *
1758 ATAGTACTACATACGTGACTAAAGCTTTTTGGTACCCATTGTAGCCTTCACTTAGTACTACACAT
130 ACAGTACTACACACGTGACTAAAGCTATTCGGTACCCATAGTAGCCTGCACATAGTACTACACAT
* *
1823 GTAATC
195 GGAACC
* * * *
1829 AT-AGTTTACCGATACACGTAGTAGCATTCACACAGTACTACACACGTGCTCA-AAGCTTCTC-G
1 ATCA--TT-CCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGC-CATCA-CTT-TCAC
* * * * * *
1891 GTACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTATC-GATACACGTAGTA
60 GTTCACATAGTAGCCTTCACATAGTACGACACACGTGATCAAGT-TTTA-CGGAT-CACGTAGTA
*
1954 GCCTTAACACAGTACTACACACGTGA-TCAAAGCTATTCGGTACGCATAGTAGCCTGCACATAGT
122 GCCTTAACACAGTACTACACACGTGACT-AAAGCTATTCGGTACCCATAGTAGCCTGCACATAGT
*
2018 ACTACACATGCGACCC
186 ACTACACATG-GAACC
* *
2034 ATCATTCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTTTCACTTTCA
1 ATCATTCCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG-CCATCACTTTCACGTTCA
* *
2099 CATAGTGGCCTACACA
65 CATAGTAGCCTTCACA
2115 CAGTCCGTGC
Statistics
Matches: 232, Mismatches: 36, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
197 1 0.00
198 2 0.01
199 2 0.01
201 37 0.16
202 5 0.02
203 99 0.43
204 80 0.34
205 5 0.02
206 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (200 bp):
ATCATTCCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGCCATCACTTTCACGTTCAC
ATAGTAGCCTTCACATAGTACGACACACGTGATCAAGTTTTACGGATCACGTAGTAGCCTTAACA
CAGTACTACACACGTGACTAAAGCTATTCGGTACCCATAGTAGCCTGCACATAGTACTACACATG
GAACC
Done.