Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_603 ID=scaffold_603-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: 6133
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.28
Warning! 802 characters in sequence are not A, C, G, or T
Found at i:888 original size:44 final size:45
Alignment explanation
Indices: 804--891 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
794 GACTTGTATA
* *
804 TTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCTGCTTTC
1 TTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTTTC
* *
849 TTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTT
1 TTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTTT
892 TTCAATCGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 25 0.64
45 14 0.36
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (45 bp):
TTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTTTC
Found at i:1076 original size:44 final size:44
Alignment explanation
Indices: 1006--1421 Score: 330
Period size: 44 Copynumber: 9.4 Consensus size: 44
996 GTCTATGTAG
* * * *
1006 GAAGGCAAGATCTGCTATATTTGATCTACTTCACACCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAGTACAT
** * ***
1050 GAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACACCAGTACAT
* * * *
1095 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAGTACAT
* * * * * * *
1139 GAAGACAAGATCTGTTTTATTCAATCTGCTTTACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAGTACAT
* * * * * ***
1183 AAAGATAAGATTTGCTCTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACACCAGTACAT
* * ***
1228 GAAGACAAGATATGCTTTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCA-CACCAGTACAT
* * * * *
1273 GGAGATAAGATCTGGTATC-TCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTC-GATCTACTTCACACCAGTACAT
* *
1317 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAGTACAT
* * * * * * * *
1361 GAAGACAAGATCTACTATCTTTGATCCACTTCGCTACCAATATAG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCAC-ACCAGTACAT
*
1406 GAAGACAGGATCTGCT
1 GAAGACAAGATCTGCT
1422 ACTTTTCAAC
Statistics
Matches: 293, Mismatches: 73, Indels: 11
0.78 0.19 0.03
Matches are distributed among these distances:
44 168 0.57
45 125 0.43
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAGTACAT
Found at i:1134 original size:89 final size:89
Alignment explanation
Indices: 1004--1421 Score: 385
Period size: 89 Copynumber: 4.7 Consensus size: 89
994 CTGTCTATGT
* * **
1004 AGGAAGGCAAGATCTGCTATATTTGATCTACTTCACACCAGTACATGAAGACAAGATCTATTTTC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTC
*
1069 TTCGATCTACTTCGCCACCAGTAT
66 TTCGATCTACTTCGCCACCAGTAC
* * * * *
1093 GGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTA
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTC
* *
1158 TTCAATCTGCTTTACGCCA--A-TAC
66 TTCGATCTAC-TT-CGCCACCAGTAC
** * * * * * *** *
1181 ATAAAGATAAGATTTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGCTTT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGCTTT
* * *
1246 CTTCGATCTACTCCACCACCAGTAT
65 CTTCGATCTACTTCGCCACCAGTAC
* * * * * *
1271 GGGGAGATAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTC
* * *
1336 TTTGATCTACTTC-ACGCCAGTAC
66 TTCGATCTACTTCGCCACCAGTAC
* * * * * * * *
1359 ATGAAGACAAGATCTACTATCTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCAC-ACCAGTACATGAAGACAAGATCTGCT
1422 ACTTTTCAAC
Statistics
Matches: 257, Mismatches: 65, Indels: 14
0.76 0.19 0.04
Matches are distributed among these distances:
87 4 0.02
88 63 0.25
89 156 0.61
90 29 0.11
91 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (89 bp):
AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCGCCACCAGTAC
Found at i:1394 original size:178 final size:178
Alignment explanation
Indices: 1006--1421 Score: 546
Period size: 178 Copynumber: 2.3 Consensus size: 178
996 GTCTATGTAG
* * * * * **
1006 GAAGGCAAGATCTGCTATATTTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTATTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTTTCT
* * *
1070 TCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGT
66 TCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGT
* * *
1135 ACATGAAGACAAGATCTGTTTTATTCAATCTGCTTTACGCCAATACAT
131 ACATGAAGACAAGATCTGCTTTATTCAATCTACTTCACGCCAATACAT
* * * * * * *
1183 AAAGATAAGATTTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGCTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTTTCT
* *
1248 TCGATCTACTCCACCACCAGTATGGGGAGATAAGATCTGGTATCTCTGATCTACTTCACGCCAGT
66 TCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGT
* ** *
1313 ACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
131 ACATGAAGACAAGATCTGCTTTATTCAATCTACTTCACGCCAATACAT
* * * * *
1361 GAAGACAAGATCTACTATCTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCT
1422 ACTTTTCAAC
Statistics
Matches: 200, Mismatches: 38, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
177 25 0.12
178 175 0.88
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (178 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTTTCT
TCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGT
ACATGAAGACAAGATCTGCTTTATTCAATCTACTTCACGCCAATACAT
Done.