Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_260 ID=scaffold_260-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: 9481
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.30
Warning! 620 characters in sequence are not A, C, G, or T
Found at i:2539 original size:132 final size:132
Alignment explanation
Indices: 2370--2986 Score: 882
Period size: 132 Copynumber: 4.7 Consensus size: 132
2360 ATTTTGTCTG
* ** ** * *
2370 CTCCACTGCAACTTCAGGGAGGTAAAATCTGTTATCTTTGACCTGCTCCACTACTGCTTGGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * * * *
2435 ATAAGATCTGAAATCTTCAATCTATTCCACTACTGTCTAGGAAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
2500 TA
131 TA
* * * * *
2502 CTCCACTATAACCAC-GAGGAGGTAAAATCCGCCATCTTCGATCTACTTCGCTGTCTA-TGC--A
1 CTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTGC-TC-C--ACTACTGCTTA
* * *
2563 GGAAGGCAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTT
61 GGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTT
2628 CAATGTA
126 CAATGTA
* * *
2635 CTCCACTGTAACCACAGGGAGGTAAAATCTTCCATTTTTTATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
2700 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
2765 TA
131 TA
* * * * *
2767 CTCCACTGTAACCACAAGGAGGTAAAATCTACCATTTTTTATCTGCCCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
2832 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
2897 TA
131 TA
* *
2899 CTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCCCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
2964 ACAAGATCTGAAATCTTCAATCT
66 ACAAGATCTGAAATCTTCAATCT
2987 GCTTCTCTAT
Statistics
Matches: 435, Mismatches: 41, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
129 3 0.01
130 3 0.01
131 2 0.00
132 316 0.73
133 103 0.24
134 2 0.00
135 3 0.01
136 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
TA
Found at i:2952 original size:264 final size:264
Alignment explanation
Indices: 2370--2986 Score: 916
Period size: 265 Copynumber: 2.3 Consensus size: 264
2360 ATTTTGTCTG
* ** ** * *
2370 CTCCACTGCAACTTCAGGGAGGTAAAATCTGTTATCTTTGACCTGCTCCACTACTGCTTGGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* *
2435 ATAAGATCTGAAATCTTCAATCTATTCCACTACTGTCTAGGAAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCACTACTGTCCAGGAAAGTAGAATTACTGGCTTCAATG
* * **
2500 TACTCCACTATAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTACTTCGCTGTCTATGCAGG
131 TACTCCACTATAACCACAAGGAGGTAAAATCCACCATCTTCGATCTAC-TCGCTCACTATGCAGG
*
2565 AAGGCAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCA
195 AAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCA
2630 ATGTA
260 ATGTA
* * *
2635 CTCCACTGTAACCACAGGGAGGTAAAATCTTCCATTTTTTATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* *
2700 ACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCACTACTGTCCAGGAAAGTAGAATTACTGGCTTCAATG
* * * ** *
2765 TACTCCACTGTAACCACAAGGAGGTAAAATCTACCATTTTTTATCTGC-C-C-CACTACTGCTTA
131 TACTCCACTATAACCACAAGGAGGTAAAATCCACCATCTTCGATCTACTCGCTCACTA-TGC--A
* *
2827 GGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTT
193 GGAAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTT
2892 CAATGTA
258 CAATGTA
* *
2899 CTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCCCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
2964 ACAAGATCTGAAATCTTCAATCT
66 ACAAGATCTGAAATCTTCAATCT
2987 GCTTCTCTAT
Statistics
Matches: 317, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
261 3 0.01
262 4 0.01
263 1 0.00
264 153 0.48
265 156 0.49
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (264 bp):
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTATTCCACTACTGTCCAGGAAAGTAGAATTACTGGCTTCAATG
TACTCCACTATAACCACAAGGAGGTAAAATCCACCATCTTCGATCTACTCGCTCACTATGCAGGA
AGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
TGTA
Found at i:4823 original size:17 final size:17
Alignment explanation
Indices: 4801--4839 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4791 CCCAATGGAA
4801 GTTTTT-TGTTTCTTTTT
1 GTTTTTGTGTTT-TTTTT
4818 GTTTTTGTGTTTTTTTT
1 GTTTTTGTGTTTTTTTT
*
4835 CTTTT
1 GTTTT
4840 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (17 bp):
GTTTTTGTGTTTTTTTT
Done.