Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_348 ID=scaffold_348-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: 8106
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:4193 original size:20 final size:20
Alignment explanation
Indices: 4168--4208 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4158 GCAAATGTTC
4168 TTTCATTCTTTACGATTTTT
1 TTTCATTCTTTACGATTTTT
**
4188 TTTCATTCTTTTGGATTTTT
1 TTTCATTCTTTACGATTTTT
4208 T
1 T
4209 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTCATTCTTTACGATTTTT
Found at i:5150 original size:21 final size:20
Alignment explanation
Indices: 5126--5166 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5116 AGTGATGTGA
*
5126 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAG-TAAAAATG
5147 AAAAATGAAAAGTAAAAATG
1 AAAAATGAAAAGTAAAAATG
5167 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAGTAAAAATG
Found at i:5151 original size:7 final size:7
Alignment explanation
Indices: 5126--5166 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
5116 AGTGATGTGA
5126 AAAAATG
1 AAAAATG
5133 AAAAGATG
1 AAAA-ATG
5141 -AAAATG
1 AAAAATG
5147 AAAAATG
1 AAAAATG
*
5154 AAAAGT-
1 AAAAATG
5160 AAAAATG
1 AAAAATG
5167 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 8 0.28
7 18 0.62
8 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:5156 original size:13 final size:13
Alignment explanation
Indices: 5127--5166 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
5117 GTGATGTGAA
5127 AAAATGAAAAGATG
1 AAAATGAAAA-ATG
5141 AAAATGAAAAATG
1 AAAATGAAAAATG
5154 AAAA-GTAAAAATG
1 AAAATG-AAAAATG
5167 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 14 0.56
14 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:5553 original size:13 final size:13
Alignment explanation
Indices: 5535--5559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5525 TAAATCAATT
5535 TCTTTGTTATCCA
1 TCTTTGTTATCCA
5548 TCTTTGTTATCC
1 TCTTTGTTATCC
5560 TCGACAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:6977 original size:50 final size:50
Alignment explanation
Indices: 6423--6992 Score: 346
Period size: 50 Copynumber: 11.4 Consensus size: 50
6413 TCCTTAGCAG
* * * * *
6423 TGCAATGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGACAT
* ** * * * * ** * *
6473 TGCAATTAAAAAGATTGAAGCCACAATGGCGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGA-CAT
* * *
6523 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATTTGGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGACAT
* ** * * * ** * *
6573 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGA-CAT
*
6623 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGG-TTCCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTT-CCCTGACAT
* * ** * * * * * ** * *
6673 CGCAATTAAAAAGATTAAAGCCACAACGACGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGA-CAT
* *
6723 TGCAGTGGAACAGATTGAAGCTACGACAGCGGATCTGG-TTCCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTT-CCCTGACAT
* * ** * * * ** * *
6773 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGA-CAT
*
6823 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGG-TTCCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTT-CCCTGACAT
* * ** * * * ** * *
6873 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGA-CAT
* * * *
6923 TGCAGTGGAATAGATTGAAGATACGACGGCGGATCTGGTTTCCCCGACAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGACAT
* *
6973 TGCAGTTGAACAAATTGAAG
1 TGCAGTGGAACAGATTGAAG
6993 ATTACAGATC
Statistics
Matches: 370, Mismatches: 134, Indels: 32
0.69 0.25 0.06
Matches are distributed among these distances:
49 26 0.07
50 319 0.86
51 25 0.07
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGCTTCCCTGACAT
Found at i:6992 original size:100 final size:100
Alignment explanation
Indices: 6408--6967 Score: 985
Period size: 100 Copynumber: 5.6 Consensus size: 100
6398 ACCATAGATT
* * * *
6408 TTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
* *
6473 TGCAATTAAAAAGATTGAAGCCACAATGGCGGATC
66 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* *
6508 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATTTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
*
6573 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
6608 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
* *
6673 CGCAATTAAAAAGATTAAAGCCACAACGACGGATC
66 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
*
6708 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACAGCGGATCTGGTTCCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
6773 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
6808 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
6873 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* *
6908 TTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGATACGACGGCGGATCTGGTTTCCCC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGG-TTCCCC
6968 GACATTGCAG
Statistics
Matches: 443, Mismatches: 16, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
100 437 0.99
101 6 0.01
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTCCCCTGATAT
CGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:7056 original size:44 final size:44
Alignment explanation
Indices: 6989--7144 Score: 102
Period size: 44 Copynumber: 3.5 Consensus size: 44
6979 TGAACAAATT
* * * *
6989 GAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
1 GAAGATGACGGATTTTACCTCCCTAAGCAATAGTGGAGCAGATC
* ** * * * *
7033 GAAGATGACGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATT
1 GAAGATGACGGATTTTACCTCCCT-AAGCAATAGTGGAGCAGATC
** * * * *
7078 GAAG-CCA-GTAATTCTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 GAAGATGACG-GATTTTACCTCCCTAAGCAATAGTGGAGCAGATC
*
7121 -AAGGATGGCGGATTTTACCTCCCT
1 GAA-GATGACGGATTTTACCTCCCT
7145 GAGGTTACAG
Statistics
Matches: 77, Mismatches: 30, Indels: 10
0.66 0.26 0.09
Matches are distributed among these distances:
42 2 0.03
43 14 0.18
44 43 0.56
45 18 0.23
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
GAAGATGACGGATTTTACCTCCCTAAGCAATAGTGGAGCAGATC
Found at i:7201 original size:88 final size:88
Alignment explanation
Indices: 7004--7184 Score: 328
Period size: 88 Copynumber: 2.1 Consensus size: 88
6994 TTACAGATCT
7004 TATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGAGGTTACAGTG
7069 GAGTACATTGAAGCCAGTAATTC
66 GAGTACATTGAAGCCAGTAATTC
* *
7092 TATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGGCGGATTTTACCTCCCTGAGGTTACAGT
1 TATCTCCCTAAGCAATAGTGGAGCAGATCGAA-GATGACGGATTTTACCTCCCTGAGGTTACAGT
7156 GGAGTACATTGAAGCCAGTAATTC
65 GGAGTACATTGAAGCCAGTAATTC
7180 TATCT
1 TATCT
7185 TCCTGGGCAA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
87 2 0.02
88 88 0.98
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (88 bp):
TATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGAGGTTACAGTG
GAGTACATTGAAGCCAGTAATTC
Found at i:7232 original size:88 final size:88
Alignment explanation
Indices: 7004--7207 Score: 266
Period size: 88 Copynumber: 2.3 Consensus size: 88
6994 TTACAGATCT
* * * * *
7004 TATCTCCCTAAGCAATAGTGGAGCAGATCGAA-GATGACGGATTTTACCTCCCTGAGGTTACAGT
1 TATCTCCCTAAGCAACAGTGGAACAGATC-AAGGATGGCAGATCTTACCTCCCTGAGGTTACAGT
7068 GGAGTACATTGAAGCCAGTAATTC
65 GGAGTACATTGAAGCCAGTAATTC
** * * *
7092 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAACAGTGGAACAGATCAAGGATGGCAGATCTTACCTCCCTGAGGTTACAGTG
7157 GAGTACATTGAAGCCAGTAATTC
66 GAGTACATTGAAGCCAGTAATTC
* ** *
7180 TATCTTCCTGGGCAACAGTGGAATAGAT
1 TATCTCCCTAAGCAACAGTGGAACAGAT
7208 TGAAGATTGC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
87 2 0.02
88 104 0.98
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
TATCTCCCTAAGCAACAGTGGAACAGATCAAGGATGGCAGATCTTACCTCCCTGAGGTTACAGTG
GAGTACATTGAAGCCAGTAATTC
Found at i:7245 original size:132 final size:132
Alignment explanation
Indices: 7092--7339 Score: 428
Period size: 132 Copynumber: 1.9 Consensus size: 132
7082 CCAGTAATTC
7092 TATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGGCGGATTTTACCTCCCTGAGGTTACAGT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GATGGCGGATTTTACCTCCCTGAGGTTACAGT
*
7156 GGAGTACATTGAAGCCAGTAATTCTATCTT-CCTGGGCAACAGTGGAATAGATTGAAGATTGCAT
65 GGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTAGGCAACAGTGGAATAGATTGAAGATTGCAT
7220 ATCT
129 ATCT
*
7224 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTTCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTG
* *
7289 GAGTACATTGAAGCCTGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGAT
66 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAACAGTGGAATAGAT
7340 CAAAGATAAC
Statistics
Matches: 110, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
131 3 0.03
132 105 0.95
133 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (132 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTG
GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAACAGTGGAATAGATTGAAGATTGCATAT
CT
Found at i:7495 original size:45 final size:44
Alignment explanation
Indices: 7335--7495 Score: 193
Period size: 44 Copynumber: 3.6 Consensus size: 44
7325 AGCAGTGGAA
7335 TAGATCAAAGATAA-CAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCAAAGA-AAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
* * * * * *
7379 TAGATCAAAGATAGCAGATATTGTCTCCCA--TACTGGTGGCGAAG
1 TAGATCAAAGAAAGCAGATCTTGTCT-TCATGTATTGG-CGTGAAG
* *
7423 TAGATCGAAGAAAGCAGATCTTTTCTTCATGTATTGGCGTGAAG
1 TAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
7467 TAGATCAAAGAAGAGCAGATCTTGTCTTC
1 TAGATCAAAGAA-AGCAGATCTTGTCTTC
7496 CCATACTGGT
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
43 8 0.08
44 65 0.68
45 22 0.23
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (44 bp):
TAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
Done.