Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_702 ID=scaffold_702-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: 5219
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.22
Warning! 741 characters in sequence are not A, C, G, or T
Found at i:136 original size:19 final size:18
Alignment explanation
Indices: 112--157 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
102 AACGTCTCTT
*
112 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTGCAT-CA
131 TTTGCATTTCATTGCATCA
1 TTTGCA-TTCATTGCATCA
*
150 TATGCATT
1 TTTGCATT
158 AAACACCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTGCATCA
Found at i:2815 original size:51 final size:52
Alignment explanation
Indices: 2702--2817 Score: 153
Period size: 52 Copynumber: 2.2 Consensus size: 52
2692 TAAAAGGTGG
* * *
2702 GACCAAGGTGAAAGCCTACAAAGGGTGCTTTGAGTCAAAAAAAAAAAGAAGA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAAAAAAAGAAGA
* * *
2754 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAAAAATGGAGA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAAAAAAAGAAGA
* *
2805 GGCTAAGGTGAAA
1 GACCAAGGTGAAA
2818 ACTCGCAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 24 0.44
52 31 0.56
ACGTcount: A:0.46, C:0.14, G:0.28, T:0.13
Consensus pattern (52 bp):
GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAAAAAAAGAAGA
Found at i:4228 original size:46 final size:46
Alignment explanation
Indices: 4085--4229 Score: 134
Period size: 44 Copynumber: 3.2 Consensus size: 46
4075 ATCGAATATA
* * *
4085 CAGATCTGGCATTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
1 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAA--AGAAAG
* * *** * * *
4133 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAGATAA-
1 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGA-AAG
4177 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAG
1 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAG
*
4223 TAGATCT
1 CAGATCT
4230 TGTCTTCATG
Statistics
Matches: 74, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
44 20 0.27
45 14 0.19
46 13 0.18
47 10 0.14
48 17 0.23
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (46 bp):
CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAAGAAAG
Found at i:4272 original size:90 final size:91
Alignment explanation
Indices: 4084--4292 Score: 289
Period size: 90 Copynumber: 2.3 Consensus size: 91
4074 GATCGAATAT
* *
4084 ACAGATCTGGCATTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCAT
1 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAA-GAAAAAGCAGATCTTGTCTTCAT
*
4149 GTACTGGCGTGAAGTAGATCAAAGATA
65 GTACTAGCGTGAAGTAGATCAAAGATA
* *
4176 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAA-AGAAAGTAGATCTTGTCTTCATG
1 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAAAGCAGATCTTGTCTTCATG
4240 TA-TCAGCGTGAAGTAGATCAAAG-TCA
66 TACT-AGCGTGAAGTAGATCAAAGAT-A
* * * *
4266 ATAGATCTTGTCTCCCCATACTGGTGG
1 ACAGATCTCGCCTTCCCATACTGGTGG
4293 TGGAGTAGAT
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
89 2 0.02
90 65 0.61
92 39 0.37
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (91 bp):
ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAAAGCAGATCTTGTCTTCATG
TACTAGCGTGAAGTAGATCAAAGATA
Found at i:4407 original size:45 final size:43
Alignment explanation
Indices: 4299--4420 Score: 145
Period size: 45 Copynumber: 2.8 Consensus size: 43
4289 GTGGTGGAGT
* *
4299 AGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGAAAC
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAAAAC
* *** * * *
4342 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAAAAAAC
1 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAAAAAC
4387 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
4421 TAATGATAGT
Statistics
Matches: 61, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 17 0.28
44 19 0.31
45 25 0.41
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAAAAC
Found at i:4697 original size:44 final size:46
Alignment explanation
Indices: 4638--4728 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
4628 AATCGATTGA
* * * *
4638 AAAAGCAGATTTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 AAAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
*
4683 AAAA-CAGATCTTGTCTTCCTATACTGGTAGTGAAGTAGATCGAAG
1 AAAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
4728 A
1 A
4729 TATATGTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (46 bp):
AAAAGCAGATCTTGTCTTCATATACTGGTAGTGAAGTAGATCGAAG
Done.