Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_481 ID=scaffold_481-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: 6549
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2613 original size:19 final size:19
Alignment explanation
Indices: 2577--2615 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
2567 CACTTTTTTT
2577 AAATAAAAAAAGAAAAAAG
1 AAATAAAAAAAGAAAAAAG
2596 AAATGAAAAAAAAGAAAAAA
1 AAAT--AAAAAAAGAAAAAA
2616 AAAGAGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
21 14 0.78
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (19 bp):
AAATAAAAAAAGAAAAAAG
Found at i:3611 original size:44 final size:44
Alignment explanation
Indices: 3558--4574 Score: 551
Period size: 44 Copynumber: 22.6 Consensus size: 44
3548 CATATCAAAC
* *
3558 CTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTACTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
** *
3602 CTTATCTCCCTGAAGTTGCAGTGGAGCAGCCTGAAGATAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGT
* * * * * * *
3647 CTTATTTCCTTGAAATTGCAGTGGAACAGATTAAAGCTATAAATAATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG-T-T--A-CA-AG-T
* * * * **
3698 CTTATCTCTCTGAAGTTGCAGTAGAGCA-GAT-CA--TATCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGT
** * *
3739 CTTATCTCCCTGAAGTTAAAGTGTAGCAAGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
* * * ** **
3783 CTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAAGACAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGT
* ** * * *
3828 CTTATTTCCCTGAAGTTGCAACGGACCAGATTGAAGCTACAAGTTGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAA---GT
* *
3875 AAACCTTATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
*
3923 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
*
3967 TTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
* *
4011 TTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
* * ** * *
4055 CTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGATAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGT
* * * * ** *
4100 CTTATTTCCCTAAAGTTGTAGTGGAACATATT-ACAGCTATAAATTATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGA-AG-T-T--A-CA-AG-T
* ** * * *
4151 CTTATCTCTCTGAAGTTGCAGTAAAGCA-GATCATAG-TA-AACT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGA-AGTTACAAGT
*
4193 -TTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
* ** *
4236 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGT
* * ** * *
4281 CTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG-T-T--A-CA-AG-T
* * * ** * **
4332 CTTATCTCTCTGAAGTTGCAGTAGAACA-AAT-CA--TAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGT
* ** * *
4373 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGT
* * * * * * * *
4418 CTTATCTCTCTGAAGCTGCAGTAGAGCAGATTAAAGCTATAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
* * * * * *
4462 TTTATCTCCCTGAAGATACAGTGGAGCAGGATAAAGTTATTAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGT
* * * * *
4506 CTTATCTCCCTAAAGATGTAGTGGAGCAGATTGAAGATACTAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTAC-AAGT
* ** *
4550 ATTATCTCCCAAAAGTTGTAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
4575 ATAGATTAAA
Statistics
Matches: 758, Mismatches: 162, Indels: 106
0.74 0.16 0.10
Matches are distributed among these distances:
41 72 0.09
42 12 0.02
43 13 0.02
44 353 0.47
45 170 0.22
46 8 0.01
47 4 0.01
48 6 0.01
49 8 0.01
50 4 0.01
51 108 0.14
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGT
Found at i:3786 original size:181 final size:181
Alignment explanation
Indices: 3465--3995 Score: 715
Period size: 181 Copynumber: 2.9 Consensus size: 181
3455 AAGCCACTAG
* *
3465 TCTTATCTCCCT-AAAGTTGCAGTGGAACAGATTGAAGCTATAAATTCTAGATCTTATCTCTCTA
1 TCTTATTTCCCTGAAA-TTGCAGTGGAACAGATTGAAGCTATAAATTATAGATCTTATCTCTCTA
* *
3529 AAGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAG
65 AAGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAG
* * *
3594 TTACTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGCCTGAAGATAGCGAA
130 TTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAA
* * * *
3646 TCTTATTTCCTTGAAATTGCAGTGGAACAGATTAAAGCTATAAATAATAGATCTTATCTCTCTGA
1 TCTTATTTCCCTGAAATTGCAGTGGAACAGATTGAAGCTATAAATTATAGATCTTATCTCTCTAA
* * *
3711 AGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTAAAGTGTAGCAAGTTGAAGT
66 AGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGT
* * *
3776 TACAAGTCTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAAGACAGCGAA
131 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAA
* ** * * * * * *
3827 TCTTATTTCCCTGAAGTTGCAACGGACCAGATTGAAGCTACAAGTTGTAAACCTTATCTCTCTAA
1 TCTTATTTCCCTGAAATTGCAGTGGAACAGATTGAAGCTATAAATTATAGATCTTATCTCTCTAA
* * * **
3892 AGTTGCAGTGGAGCAGGTTGA-AGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTG
66 AGTTGCAGTAGAGCA-GATCATA--T-CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTG
*
3956 AAGTTACAAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAG
127 AAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
3996 GTTGAAGTTA
Statistics
Matches: 303, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
181 227 0.75
182 6 0.02
183 1 0.00
184 69 0.23
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (181 bp):
TCTTATTTCCCTGAAATTGCAGTGGAACAGATTGAAGCTATAAATTATAGATCTTATCTCTCTAA
AGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGT
TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAA
Found at i:3959 original size:21 final size:21
Alignment explanation
Indices: 3933--4051 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
3923 CTTATCTCCC
3933 TGAAGTTACAGTGGAGCAGGT
1 TGAAGTTACAGTGGAGCAGGT
** * ****
3954 TGAAGTTACAAGTTTTATCTCCC
1 TGAAGTTAC-AG-TGGAGCAGGT
*
3977 TGAAGTTGCAGTGGAGCAGGT
1 TGAAGTTACAGTGGAGCAGGT
** * ****
3998 TGAAGTTACAAGTTTTATCTCCC
1 TGAAGTTAC-AG-TGGAGCAGGT
4021 TGAAGTTACAGTGGAGCAGGT
1 TGAAGTTACAGTGGAGCAGGT
4042 TGAAGTTACA
1 TGAAGTTACA
4052 AGTCTTATCT
Statistics
Matches: 64, Mismatches: 30, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
21 33 0.52
22 8 0.12
23 23 0.36
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
TGAAGTTACAGTGGAGCAGGT
Found at i:4047 original size:272 final size:270
Alignment explanation
Indices: 3697--4305 Score: 739
Period size: 272 Copynumber: 2.3 Consensus size: 270
3687 AAATAATAGA
* * * * * * *
3697 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACCTTATCTCCCTGAAGTTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTAC
* * *
3758 AGTGTAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAAGACAG
66 AGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTACAGCGGAGTAGACTAAAGACAG
* * * *
3823 CGAATCTTATTTCCCTGAAGTTGCAACGGACCAGATTGA-AGCTACAAGTTGTAAACCTTATCTC
131 CGAATCTTATTTCCCTAAAGTTGCAACGGAACAGATT-ACAGCTACAAATTATAAACCTTATCTC
** * * * *
3887 TCTAAAGTTGCAGTGGAGCAGGTTGA-AGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCA
195 TCTAAAGTTGCAGTAAAGCA-GATCATAG-TA-AACT-TTATCTCCCTAAAGTTACAGTGGAGCA
3951 GGTTGAAGTTACAAG
256 GGTTGAAGTTACAAG
* ** * *
3966 TTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-C-AAGTTTTATCTCCCTGAAGTTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TCTTATCTCCCTGAAGTTA
* * * *
4029 CAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGTAGACTAAAGATA
65 CAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTACAGCGGAGTAGACTAAAGACA
* ** * * * *
4094 GCGAATCTTATTTCCCTAAAGTTGTAGTGGAACATATTACAGCTATAAATTATAGATCTTATCTC
130 GCGAATCTTATTTCCCTAAAGTTGCAACGGAACAGATTACAGCTACAAATTATAAACCTTATCTC
* *
4159 TCTGAAGTTGCAGTAAAGCAGATCATAGTAAACTTTATCTCCCTAAAGTTGCAGTGGAGCAGGTT
195 TCTAAAGTTGCAGTAAAGCAGATCATAGTAAACTTTATCTCCCTAAAGTTACAGTGGAGCAGGTT
4224 GAAGTTACAAG
260 GAAGTTACAAG
* * *
4235 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTAC
4300 AGTGGA
66 AGTGGA
4306 ACATATTAAA
Statistics
Matches: 288, Mismatches: 43, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
269 102 0.35
270 28 0.10
271 10 0.03
272 146 0.51
273 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (270 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTAC
AGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTACAGCGGAGTAGACTAAAGACAG
CGAATCTTATTTCCCTAAAGTTGCAACGGAACAGATTACAGCTACAAATTATAAACCTTATCTCT
CTAAAGTTGCAGTAAAGCAGATCATAGTAAACTTTATCTCCCTAAAGTTACAGTGGAGCAGGTTG
AAGTTACAAG
Found at i:4486 original size:181 final size:181
Alignment explanation
Indices: 4012--4453 Score: 654
Period size: 181 Copynumber: 2.4 Consensus size: 181
4002 GTTACAAGTT
* * *
4012 TTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTACAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCTCTGAAGTTGCAGT
* * * *
4077 GGAGTAGACTAAAGATAGCGAATCTTATTTCCCTAAAGTTGTAGTGGAACATATTACAGCTATAA
66 GGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTATAA
* * * *
4142 ATTATAGATCTTATCTCTCTGAAGTTGCAGTAAAGCAGATCATAGTAAACT
131 ATTACAGATCTTATCTCTCTGAAGTTGCAGTAAAGCAAATCATAGCAAACC
*
4193 TTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCT-TCCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCT-CTGAAGTTGCAG
*
4257 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTATA
65 TGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTATA
4322 AATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAA-CAAATCATAGCAAACC
130 AATTACAGATCTTATCTCTCTGAAGTTGCAGTA-AAGCAAATCATAGCAAACC
* ** * * *
4374 TTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAATCTTATCTCTCTGAAGCTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGTCTTATCTCTCTGAAGTTGCAG
* *
4439 TAGAGCAGATTAAAG
65 TGGAGCAGACTAAAG
4454 CTATAAATTT
Statistics
Matches: 234, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
181 197 0.84
182 36 0.15
183 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (181 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCTCTGAAGTTGCAGT
GGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTATAA
ATTACAGATCTTATCTCTCTGAAGTTGCAGTAAAGCAAATCATAGCAAACC
Found at i:6175 original size:18 final size:18
Alignment explanation
Indices: 6154--6188 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6144 TATTTTATTA
*
6154 TATCGTTTTATTTATTTG
1 TATCGTTTTATATATTTG
*
6172 TATCTTTTTATATATTT
1 TATCGTTTTATATATTT
6189 TCAAACTCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (18 bp):
TATCGTTTTATATATTTG
Found at i:6218 original size:3 final size:3
Alignment explanation
Indices: 6200--6253 Score: 54
Period size: 3 Copynumber: 16.7 Consensus size: 3
6190 CAAACTCTAG
* *
6200 ATT ATTT ATT ATTT ATT ATT CATAT ATT ATT AAT ATT ATT ATT ATC ATT
1 ATT A-TT ATT A-TT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT
6249 ATT AT
1 ATT AT
6254 CTTTTTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 32 0.74
4 10 0.23
5 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:6237 original size:9 final size:10
Alignment explanation
Indices: 6205--6253 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
6195 TCTAGATTAT
*
6205 TTATTATTTA
1 TTATTATATA
6215 TTATTCATATA
1 TTATT-ATATA
6226 TTATTA-ATA
1 TTATTATATA
6235 TTATTATTATCA
1 TTATTA-TAT-A
6247 TTATTAT
1 TTATTAT
6254 CTTTTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.26
10 6 0.18
11 12 0.35
12 7 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATTATATA
Done.