Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_59 ID=scaffold_59-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: 19295
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.35
Warning! 657 characters in sequence are not A, C, G, or T
Found at i:7815 original size:50 final size:50
Alignment explanation
Indices: 7752--7887 Score: 195
Period size: 50 Copynumber: 2.7 Consensus size: 50
7742 ATATCGGTGA
* *
7752 CGATGCCATGTCCCAGACATGGTTTTACA-TTG-ACTCTTCTCAGTCTGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTC--CTCAGTCTGTGC
* *
7802 CGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCCTCGGTCTGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTGC
*
7852 CGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
7888 ACTTACTGAC
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
50 72 0.92
51 2 0.03
52 4 0.05
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.28
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCAGTCTGTGC
Found at i:7980 original size:44 final size:44
Alignment explanation
Indices: 7914--7998 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
7904 CAACCATGGT
* * * *
7914 CTTTTCCGTCAATTCTTTCTTAATTTCCATGTTATAAACATAGA
1 CTTTTCCGTCAATTATTCCTTAATTGCCACGTTATAAACATAGA
*
7958 CTTTTCTGTCAATTATTCCTTAATTGCCACGTTATAAACAT
1 CTTTTCCGTCAATTATTCCTTAATTGCCACGTTATAAACAT
7999 GGACCTTGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (44 bp):
CTTTTCCGTCAATTATTCCTTAATTGCCACGTTATAAACATAGA
Found at i:10205 original size:15 final size:15
Alignment explanation
Indices: 10185--10214 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10175 CTCTTTCTTC
10185 AGAATGATATACCAA
1 AGAATGATATACCAA
*
10200 AGAATGATATGCCAA
1 AGAATGATATACCAA
10215 TATTCTTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (15 bp):
AGAATGATATACCAA
Found at i:12118 original size:35 final size:37
Alignment explanation
Indices: 12049--12120 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 37
12039 TAATGATAAT
* *
12049 AATAATAAAATATATAAAAATATATAAATGAAATGAA
1 AATAATAAAATATATAAAAATAGATAAATAAAATGAA
12086 AATAA-AAAATATA-AAAAATACGATAAA-AAAATGAA
1 AATAATAAAATATATAAAAATA-GATAAATAAAATGAA
12121 GACAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 14 0.44
36 13 0.41
37 5 0.16
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (37 bp):
AATAATAAAATATATAAAAATAGATAAATAAAATGAA
Found at i:13672 original size:58 final size:58
Alignment explanation
Indices: 13564--13674 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
13554 ATCCACTCCA
* * * ** *
13564 CTGCAACTTCAGAGAGATACAACTTGTAGCTTCAATCTACTCTGCTGCAACTTTAAGG
1 CTGCAACTTAAGAGAGATACAACTTATAACTTCAATCTACTCCACAGCAACTTTAAGG
* *
13622 CTGCAACTTAAGGGAGATA-AGACTTATAACTTCAATCTGCTCCACAGCAACTT
1 CTGCAACTTAAGAGAGATACA-ACTTATAACTTCAATCTACTCCACAGCAACTT
13675 CAGGGAGATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
57 1 0.02
58 43 0.98
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (58 bp):
CTGCAACTTAAGAGAGATACAACTTATAACTTCAATCTACTCCACAGCAACTTTAAGG
Found at i:14114 original size:143 final size:143
Alignment explanation
Indices: 13710--14450 Score: 997
Period size: 143 Copynumber: 5.2 Consensus size: 143
13700 TGCACTACTG
* * * ** *
13710 CAACTTCA-GAGAGATAAGATCCG---TAACTTATAGCTTTAATCTATTCCACTGCAACTTTAAG
1 CAACTTCAGGA-AGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGG
* * * * * * *
13771 GAAATAAGATTTGCTATCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTTGGTGACTTT
65 GAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTC
* *
13836 AATATGCTCCACTG
130 AATCTGCTCCACTA
* * * *
13850 CAACTTCAGGAAGATAAGATCGGCCATAATTTGTAGCTTTAATCTGTTCCACTG-TATGCCAGGG
1 CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGG
*
13914 AAATAAGATTCGCTGTCTTCAGTCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
66 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
*
13979 ATATGCTCCACTA
131 ATCTGCTCCACTA
* * *
13992 CAACTTCAGGAAGATAATATCCGCCATAATTTGTAGCTTTAATATGTTCCACTGCAACGCCAGGG
1 CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGG
14057 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
66 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
*
14122 ATCTGCTCCACTG
131 ATCTGCTCCACTA
*
14135 CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACACTAGGG
1 CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGG
* * * * ** *
14200 AAATAAGATTCGCTGTCTTTAGTCTGTTTCGCTGCAACTTTAGGGTGATAAGGCTATTGCCTTCA
66 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
*
14265 ATCTGCTCTACTA
131 ATCTGCTCCACTA
* * * * * *
14278 CAACTTCAGGAAGATAAGATCTGTCATAATTTATAGCTTTAATATGTTCCACTACAACGTTAGGG
1 CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGG
* * * * * *
14343 AAATAATATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGGCTTTA
66 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
14408 ATCTGCTCCACTA
131 ATCTGCTCCACTA
* * *
14421 CAACTTTAGAAAGATAAGATCCGCTATAAT
1 CAACTTCAGGAAGATAAGATCCGCCATAAT
14451 GATTTCAATC
Statistics
Matches: 530, Mismatches: 66, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
140 19 0.04
141 2 0.00
142 124 0.23
143 385 0.73
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
CAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGG
AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCA
ATCTGCTCCACTA
Found at i:15339 original size:10 final size:10
Alignment explanation
Indices: 15321--15373 Score: 70
Period size: 10 Copynumber: 5.0 Consensus size: 10
15311 TGGCCTCTCC
*
15321 CTTTCTTTTT
1 CTTTTTTTTT
15331 CTTTTTTTTT
1 CTTTTTTTTT
15341 CTTTTTTTCTCT
1 CTTTTTTT-T-T
15353 CTTTTTATTTT
1 CTTTTT-TTTT
15364 CTTTTTTTTT
1 CTTTTTTTTT
15374 AAGTGAAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 21 0.54
11 8 0.21
12 8 0.21
13 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:18302 original size:3 final size:3
Alignment explanation
Indices: 18288--18317 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18278 TAAAAAAGTT
*
18288 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18318 ATAANNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19256 original size:2 final size:2
Alignment explanation
Indices: 19251--19295 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19241 ATGTTTTTGA
19251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19293 AT A
1 AT A
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.