Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_372 ID=scaffold_372-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: 8035
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.32
Warning! 263 characters in sequence are not A, C, G, or T
Found at i:1033 original size:44 final size:45
Alignment explanation
Indices: 973--1089 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
963 TCAATCCACT
** * * *
973 CCACTGCAATGCCAGGGAGATAGGATTTG-TTTATTCGGTCTGCC
1 CCACTGCAATTTCAGGGAGATAAGACTTGCTCTATTCGGTCTGCC
* * * *
1017 CCACTGCAATTTCAGGGGGATAAGACTTGCTCTCTTGGGTCTGCT
1 CCACTGCAATTTCAGGGAGATAAGACTTGCTCTATTCGGTCTGCC
*
1062 CCACTGCAACTTCAGGGAGATAAGACTT
1 CCACTGCAATTTCAGGGAGATAAGACTT
1090 TCTTTCTTGA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 24 0.39
45 37 0.61
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (45 bp):
CCACTGCAATTTCAGGGAGATAAGACTTGCTCTATTCGGTCTGCC
Found at i:1069 original size:45 final size:44
Alignment explanation
Indices: 1009--1133 Score: 151
Period size: 45 Copynumber: 2.8 Consensus size: 44
999 TTGTTTATTC
*
1009 GGTCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGCTCTCTTG
1 GGTCTG-CCCACTGCAACTTCAGGGGGATAAGACTTGCTCTCTTG
* * *
1054 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTTCTTTCTTG
1 GGTCTGC-CCACTGCAACTTCAGGGGGATAAGACTTGCTCTCTTG
* * * *
1099 AGTTTGCCTCATTGCAACCTCAGGGGGATAAGACT
1 GGTCTGCC-CACTGCAACTTCAGGGGGATAAGACT
1134 AGATGCAATC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.03
45 67 0.97
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (44 bp):
GGTCTGCCCACTGCAACTTCAGGGGGATAAGACTTGCTCTCTTG
Found at i:1201 original size:41 final size:43
Alignment explanation
Indices: 1154--1257 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 43
1144 TGCTCTCTGT
*
1154 AACTTCAGAGAGATAAGAT-CT-CTTTTAATCCGCTCCACTGC
1 AACTTCAGGGAGATAAGATACTGCTTTTAATCCGCTCCACTGC
* * * *
1195 AACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCTCCACTGC
1 AACTTCAGGGAGATAAGA-TACTGCTTTTAATCCGCTCCACTGC
1239 AACTTCAGGGAGATAAGAT
1 AACTTCAGGGAGATAAGAT
1258 TCGCCATCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
41 16 0.30
42 1 0.02
43 2 0.04
44 35 0.65
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (43 bp):
AACTTCAGGGAGATAAGATACTGCTTTTAATCCGCTCCACTGC
Found at i:1858 original size:44 final size:44
Alignment explanation
Indices: 1809--1941 Score: 212
Period size: 44 Copynumber: 3.0 Consensus size: 44
1799 AGGAAAGTAA
1809 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * *
1853 GATTCACAATCTTTAACCTATTTCACTGTTGACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * *
1897 GATTCACAATTTTCAGCCTATTCCACTGCTGTCCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
1941 G
1 G
1942 GCTGGGGTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
Found at i:2071 original size:44 final size:45
Alignment explanation
Indices: 1955--2085 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 45
1945 GGGGTCATCG
* * * * *
1955 ATCTACTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCA
1 ATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTCA
* * ** * *
2000 ATCTGCTTCGCT-ACAACCCAGGGAGGCAAGA-CTGGTATCTTCA
1 ATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTCA
2043 ATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTT
1 ATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTT
2086 TGATCTACTT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 22 0.32
44 27 0.40
45 19 0.28
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (45 bp):
ATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTCA
Found at i:2107 original size:44 final size:44
Alignment explanation
Indices: 2059--2515 Score: 301
Period size: 44 Copynumber: 10.5 Consensus size: 44
2049 TTCGCTGTCG
* * * *
2059 ATACAGGAAGGCAAGATCTGCTATCTTTGATCTACTTCATGCCA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
* * *
2103 ATACATGAAGACAAGATCTG-TCATCTTTGATCTACCTCACACCA
1 ATACATGAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCA
* * * * *
2147 ATACATGAATACAAGATCTACTTTCTTCGATCTACTTCGCCACCA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCA
* * * *
2192 GTA-TTGGAAGACAAGATCTGTTATCTTCGATCTACTTCAAGCCA
1 ATACAT-GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
* * * * * **
2236 ATACATGAAGACAATATCTGCTATCTTCAACCTGCTCCACTACA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
** * * * * * * * * *
2280 ACCCAGGGAGGCAAG-GCTGGTATCTTCAATCTGCTTCACTGTCG
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCA
* * * * *
2324 ATGCAGGAAGGC-A-A---G--AT-TT-GATCTACTTTATGCCA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
* *
2359 ATACATGAAGACAAGATCTG-TCATCTTTGATATACTTCACGCCA
1 ATACATGAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCA
* * * * *
2403 ATACATGAATACAAAATCTGCTTTCTTCGATCTACTTCGCCACCA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCA
*** *
2448 ATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCA
1 ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
* *
2492 ATACATGAAGAAAATATCTGCTAT
1 ATACATGAAGACAAGATCTGCTAT
2516 ATTCAACCTG
Statistics
Matches: 314, Mismatches: 81, Indels: 36
0.73 0.19 0.08
Matches are distributed among these distances:
35 11 0.04
36 9 0.03
37 3 0.01
38 2 0.01
40 2 0.01
42 2 0.01
43 24 0.08
44 188 0.60
45 73 0.23
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (44 bp):
ATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA
Found at i:2459 original size:256 final size:256
Alignment explanation
Indices: 1977--2596 Score: 945
Period size: 256 Copynumber: 2.4 Consensus size: 256
1967 GTCGGTGCAG
* * * * * * *
1977 GAAGGCAAGATCTGCTATTTTCAATCTGCTTCGCTACAACCCAGGGAGGCAAGACTGGTATCTTC
1 GAAGACAATATCTGCTATATTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
*
2042 AATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTTGATCTACTTCATGCCAATAC
66 AATCTGCTTCGCTGTCGATGCAGGAAGGC-A-A---G--A--TTTGATCTACTTCATGCCAATAC
* *
2107 ATGAAGACAAGATCTGTCATCTTTGATCTACCTCACACCAATACATGAATACAAGATCTACTTTC
122 ATGAAGACAAGATCTGTCATCTTTGATATACCTCACACCAATACATGAATACAAAATCTACTTTC
* *
2172 TTCGATCTACTTCGCCACCAGTATTGGAAGACAAGATCTGTTATCTTCGATCTACTTCAAGCCAA
187 TTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCAAGCCAA
2237 TACAT
252 TACAT
*
2242 GAAGACAATATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
1 GAAGACAATATCTGCTATATTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
* *
2307 AATCTGCTTCACTGTCGATGCAGGAAGGCAAGATTTGATCTACTTTATGCCAATACATGAAGACA
66 AATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATTTGATCTACTTCATGCCAATACATGAAGACA
* * *
2372 AGATCTGTCATCTTTGATATACTTCACGCCAATACATGAATACAAAATCTGCTTTCTTCGATCTA
131 AGATCTGTCATCTTTGATATACCTCACACCAATACATGAATACAAAATCTACTTTCTTCGATCTA
*
2437 CTTCGCCACCAATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAT
196 CTTCGCCACCAATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCAAGCCAATACAT
* *
2498 GAAGAAAATATCTGCTATATTCAACCTGCTCCACTATAACCC-GAGGAGGCAAGGCTGGTATCTT
1 GAAGACAATATCTGCTATATTCAACCTGCTCCACTACAACCCAG-GGAGGCAAGGCTGGTATCTT
*
2562 CGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGAT
65 CAATCTGCTTCGCTGTCGATGCAGGAAGGCAAGAT
2597 CATTGCTTAC
Statistics
Matches: 331, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
255 1 0.00
256 241 0.73
258 1 0.00
260 1 0.00
263 1 0.00
264 1 0.00
265 85 0.26
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (256 bp):
GAAGACAATATCTGCTATATTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTC
AATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATTTGATCTACTTCATGCCAATACATGAAGACA
AGATCTGTCATCTTTGATATACCTCACACCAATACATGAATACAAAATCTACTTTCTTCGATCTA
CTTCGCCACCAATATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCAAGCCAATACAT
Done.