Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_249 ID=scaffold_249-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: 8979
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:5991 original size:44 final size:44
Alignment explanation
Indices: 5942--6347 Score: 159
Period size: 44 Copynumber: 9.2 Consensus size: 44
5932 AATAGCAGAT
* * *
5942 CTTGCCTTCCTGCACCGACAGTGAAGCAGATCAAAGACACTAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACTAGC
**** * * * * * *
5986 CTTGCCTCCCTGGGTTG-CAGTGGAGCAGGTTAAAAATAGC-AGAA
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACA-CTAG-C
* * *
6030 CTTGCCTTCCTGCACCAACAGCGAAGCAGATCAAATACACTAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACTAGC
**** * * * * *
6074 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGC-AGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACA-CTAG-C
* * **
6118 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACTAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACTAGC
**** * * * *
6162 CTTGCCTCCCTGGGTTG-CAGC-AGAGCAG-GCTAAAAATAGTAGAT
1 CTTGCCTCCCTGCACCGACAGCGA-AGCAGATC-AAAAACACTAG-C
* * * *
6206 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCAAATACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACTAGC
* **** * * * *
6250 TTTGCCTCCCTGGGTTG-CAGC-AGAGCAG-GCTAAAAATAGTAGAT
1 CTTGCCTCCCTGCACCGACAGCGA-AGCAGATC-AAAAACACTAG-C
* * *
6294 ATTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACA-TCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACT-AGC
6338 CTTGCCTCCC
1 CTTGCCTCCC
6348 GGGGTTACAG
Statistics
Matches: 247, Mismatches: 94, Indels: 42
0.64 0.25 0.11
Matches are distributed among these distances:
42 4 0.02
43 67 0.27
44 107 0.43
45 65 0.26
46 4 0.02
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATCAAAAACACTAGC
Found at i:5992 original size:88 final size:88
Alignment explanation
Indices: 5843--6412 Score: 872
Period size: 88 Copynumber: 6.5 Consensus size: 88
5833 AGATCAGTAG
* ** * *
5843 AAATAGCAGATCTTGCCTTCCTGCACCGACAGGGAAGCAGATTGAAGACACCAGCTTTGCCTCCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
*
5908 TGGGTTGCAGCGGAGTAGGCTAA
66 TGGGTTGCAGCGGAGCAGGCTAA
*
5931 AAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
* *
5996 TGGGTTGCAGTGGAGCAGGTTAA
66 TGGGTTGCAGCGGAGCAGGCTAA
* * *
6019 AAATAGCAGAACTTGCCTTCCTGCACCAACAGCGAAGCAGATCAAATACACTAGCCTTGCCTCCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
*
6084 TGGGTTGCAGCGGAGCAGGTTAA
66 TGGGTTGCAGCGGAGCAGGCTAA
* *
6107 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACTAGCCTTGCCTCCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
*
6172 TGGGTTGCAGCAGAGCAGGCTAA
66 TGGGTTGCAGCGGAGCAGGCTAA
* * * * *
6195 AAATAGTAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCAAATACACCAGCTTTGCCTCCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
*
6260 TGGGTTGCAGCAGAGCAGGCTAA
66 TGGGTTGCAGCGGAGCAGGCTAA
* *
6283 AAATAGTAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACA-TCAGCCTTGCCTCC
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACT-AGCCTTGCCTCC
* * *
6347 CGGGGTTACAGCGGAGCAGGTTAA
65 CTGGGTTGCAGCGGAGCAGGCTAA
*
6371 AAATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGAT
1 AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGAT
6413 TGATGACCCC
Statistics
Matches: 442, Mismatches: 39, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
88 442 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (88 bp):
AAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCC
TGGGTTGCAGCGGAGCAGGCTAA
Found at i:6494 original size:44 final size:44
Alignment explanation
Indices: 6426--6757 Score: 392
Period size: 44 Copynumber: 7.7 Consensus size: 44
6416 TGACCCCAGC
* * *
6426 CCTATCTCCCTGGACAACAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
6470 CCTATCTCCCTAGTCAGCAATGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
6514 TCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
6552 TCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
6596 CCTATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * * *
6640 TCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTGTTG-GT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG-TGAAT
* *
6684 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
6728 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
6758 GGAAAATAGC
Statistics
Matches: 246, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
38 33 0.13
39 2 0.01
40 1 0.00
42 1 0.00
43 4 0.02
44 203 0.83
45 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:6652 original size:126 final size:129
Alignment explanation
Indices: 6426--6757 Score: 492
Period size: 126 Copynumber: 2.6 Consensus size: 129
6416 TGACCCCAGC
* * *
6426 CCTATCTCCCTGGACAACAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTAGTCAGCAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
6491 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGA-AT-T
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATATGT
6553 -CTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
* * * *
6617 GGAATGGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTGTTG
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGA-T-AT-
6682 GT
128 GT
* * * *
6684 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCCTGAG-CAGCAG
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTG-GTCAGCAG
*
6748 TGGAGTAGGT
65 TGGAATAGGT
6758 GGAAAATAGC
Statistics
Matches: 185, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
126 117 0.63
129 1 0.01
131 1 0.01
132 65 0.35
133 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (129 bp):
CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATATGT
Found at i:7156 original size:44 final size:44
Alignment explanation
Indices: 7059--7178 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
7049 CAAGATGGCA
* *
7059 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGAT
* *
7103 AAT-TCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC-TT
1 AATCT-TATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGAT
* * *
7146 GGATCTTATCTCTCTGAAGTTGCAGAG-AGCAGA
1 -AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
7179 ACGCATCTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
43 7 0.11
44 57 0.88
45 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGAT
Found at i:7217 original size:128 final size:129
Alignment explanation
Indices: 7061--7314 Score: 325
Period size: 128 Copynumber: 2.0 Consensus size: 129
7051 AGATGGCAAA
* ** * *
7061 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AGCCGATAATTCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAAC-A-AATCCTATCTCCCTAAAGTTG
* * *
7124 CAGTGAAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAACGCATCTA
64 CAGTGAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATCTA
7188 G
129 G
* *
7189 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTGCA
* * * ** *
7254 GTGGAGTGGATTAGAATGATGGATCTTATCTCTCTGAAATTACAGTAGAGCAGATCGCATC
66 GTGAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATC
7315 AAATTCATCT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
128 87 0.81
129 18 0.17
130 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTGCA
GTGAAGCGGATTAAAACCATGGATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATCTAG
Found at i:8771 original size:35 final size:35
Alignment explanation
Indices: 8705--8770 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
8695 TTAAGCTTTA
8705 ATTTTTATTTATTTATTATTATTATGATTTTTATG
1 ATTTTTATTTATTTATTATTATTATGATTTTTATG
* *
8740 ATTTTTA-TTATCTTGTTATT-TTATTATTTTT
1 ATTTTTATTTAT-TTATTATTATTATGATTTTT
8771 TTTAAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (35 bp):
ATTTTTATTTATTTATTATTATTATGATTTTTATG
Done.