Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_216 ID=scaffold_216-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: 9273
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--25 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
26 GAGGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1456 original size:44 final size:44
Alignment explanation
Indices: 1393--1675 Score: 176
Period size: 44 Copynumber: 6.5 Consensus size: 44
1383 GATCTACTCT
* *
1393 CTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCCAAGGTTTTAATCTGCTCCA
* * *
1437 CTGCAACTTCAGGGAGATAAGATTCGCCA--TCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGGGAGATAAGA-TC-CAAGGT-TTTAATCTGCTC-CA
* ** * *
1482 CTGCAACTTCA-AGAGGATAAGA--CTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGGA-GATAAGATCCAAGGTT--TTAATCTGCTCCA
* * * *** *
1526 CTGCAACTTCAGGGAGATAA-A-ACTA-GATGCGATCTGCT-CT
1 CTGCAACTTCAGGGAGATAAGATCCAAGGTTTTAATCTGCTCCA
* * *** *
1566 CTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCCAAGGTTTTAATCTGCTCCA
* * *
1610 CTGCAACTTCAGGGAGATAGGAT-CATTGGCTTT-ATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCCA-AGGTTTTAATCTGCTCCA
1653 CTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGGGAGATAAGAT
1676 TTGCCATCTT
Statistics
Matches: 184, Mismatches: 38, Indels: 35
0.72 0.15 0.14
Matches are distributed among these distances:
40 19 0.10
41 8 0.04
42 1 0.01
43 42 0.23
44 80 0.43
45 32 0.17
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATCCAAGGTTTTAATCTGCTCCA
Found at i:1614 original size:84 final size:83
Alignment explanation
Indices: 1378--1628 Score: 274
Period size: 89 Copynumber: 2.9 Consensus size: 83
1368 AGACAAATTT
* **
1378 GATGCGATCTACTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAA
1 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT-CTTGGTTTTAATCCGCTCCACTGCAA
* * *
1443 CTTCAGGGAGATAAGATTC
65 CTTCAGGGAGATAAAACTA
* * * * *
1462 GCCAT-CTTCAGTCTGCCTCACTGCAACTTCA-AGAGGATAAGA-CTTGCTTACTTAGTCTGCTC
1 G--ATGC--GA-TCTG-CTCTCTGCAACTTCAGAGA-GATAAGATCTTGGTT--TTAATCCGCTC
1524 CACTGCAACTTCAGGGAGATAAAACTA
57 CACTGCAACTTCAGGGAGATAAAACTA
*
1551 GATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAA
1 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT-TGGTTTTAATCCGCTCCACTGCAA
1616 CTTCAGGGAGATA
65 CTTCAGGGAGATA
1629 GGATCATTGG
Statistics
Matches: 137, Mismatches: 17, Indels: 26
0.76 0.09 0.14
Matches are distributed among these distances:
84 51 0.37
85 10 0.07
86 7 0.05
87 7 0.05
88 7 0.05
89 55 0.40
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (83 bp):
GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTTGGTTTTAATCCGCTCCACTGCAAC
TTCAGGGAGATAAAACTA
Found at i:2092 original size:44 final size:43
Alignment explanation
Indices: 1994--2189 Score: 162
Period size: 44 Copynumber: 4.4 Consensus size: 43
1984 GGACTAAATG
* * *
1994 TCTTCGATCTGCTTCACTGCCAGTACAAGAAGACAAGATCTGCTAT
1 TCTTCGATCTACTTCAC-G-CAATACATGAAGACAAGATCTGCT-T
* * * *
2040 T-TTTGATCTATTTCATGTCGATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACG-CAATACATGAAGACAAGATCTGCTT
* *** * * * *
2083 TCTTCGATCTACTTCGCCAC-CAGTATGGGAAGACGAGATTTACTA
1 TCTTCGATCTACTT---CACGCAATACATGAAGACAAGATCTGCTT
2128 TCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGC-AATACATGAAGACAAGATCTGCTT
*
2172 TCTTCGATCTATTTCACG
1 TCTTCGATCTACTTCACG
2190 ACAACCTAGG
Statistics
Matches: 115, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 65 0.57
45 41 0.36
46 1 0.01
47 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (43 bp):
TCTTCGATCTACTTCACGCAATACATGAAGACAAGATCTGCTT
Found at i:2231 original size:43 final size:43
Alignment explanation
Indices: 2172--2574 Score: 177
Period size: 43 Copynumber: 9.2 Consensus size: 43
2162 AGATCTGCTT
** *
2172 TCTTCGATCTATTTCACGACAACCTAGGGAGGCAAGGCTAGTA
1 TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
* * * *
2215 TCTTTGATCTGCTTCACTATCGGTA-C-AGGAAGGCAAGATCT-GCTA
1 TCTTCGATCTGCTTCACTA-C--AACCTAGGGAGGCAAG-GCTAG-TA
* * *
2260 TCTTCAACCTGCTCCACTACAACCTAGGGAGGCAAGGCTAGTA
1 TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
* * * * *
2303 TCTTCGATCTGCTTCACTGTCGGTA-C-AGGAAGGTAAGATCT-GCTA
1 TCTTCGATCTGCTTCACT-AC--AACCTAGGGAGGCAAG-GCTAG-TA
* * * * *
2348 TCTTCGACCTGCTCCACT-CGACCCAGGGAGGCAAGGCTGGTA
1 TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
* * ** *
2390 TCTTCGATCTGCTTCACTGTCGGTA-C-AGTAAGGCAAGATCT-GCTA
1 TCTTCGATCTGCTTCACT-AC--AACCTAGGGAGGCAAG-GCTAG-TA
* * * * *
2435 TCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTA
1 TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
* * * *
2478 TCTTCGATCTGCTTCGCTGTCGATA-C-A-GAAGGCAAGATCT-GCTA
1 TCTTCGATCTGCTTCACT-AC-A-ACCTAGGGAGGCAAG-GCTAG-TA
* * * * *
2522 TCTTCAATCTGCTCCACTACAACCCAAGGAGGCAAGGCTGGTA
1 TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
2565 TCTTCGATCT
1 TCTTCGATCT
2575 ACTTTACTGT
Statistics
Matches: 270, Mismatches: 56, Indels: 68
0.69 0.14 0.17
Matches are distributed among these distances:
41 2 0.01
42 25 0.09
43 89 0.33
44 87 0.32
45 63 0.23
46 4 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (43 bp):
TCTTCGATCTGCTTCACTACAACCTAGGGAGGCAAGGCTAGTA
Found at i:2384 original size:175 final size:174
Alignment explanation
Indices: 2126--2648 Score: 701
Period size: 175 Copynumber: 3.0 Consensus size: 174
2116 CGAGATTTAC
* * * * * * ** *
2126 TATCTTCGATCTACTTCAC-G-CTAATACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCAC
1 TATCTTCGATCTGCTTCACTGTC-GATACA-GAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* * * * *
2189 GACAACCTAGGGAGGCAAGGCTAGTATCTTTGATCTGCTTCACTATCGGTACAGGAAGGCAAGAT
64 TACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGAT
2254 CTGCTATCTTCAACCTGCTCCACTACAACCTAGGGAGGCAAGGCTAG
129 CTGCTATCTTCAACCTGCTCCACTACAACC-AGGGAGGCAAGGCTAG
* * *
2301 TATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGTAAGATCTGCTATCTTCGACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACA-GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* *
2366 -CGACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGTAAGGCAAGATC
65 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
*
2430 TGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGG
130 TGCTATCTTCAACCTGCTCCACTACAA-CCAGGGAGGCAAGGCTAG
* *
2476 TATCTTCGATCTGCTTCGCTGTCGATACAGAAGGCAAGATCTGCTATCTTCAATCTGCTCCACTA
1 TATCTTCGATCTGCTTCACTGTCGATACAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
* * *
2541 CAACCCAAGGAGGCAAGGCTGGTATCTTCGATCTACTTTACTGTCGGTACAGGAAGGCAAGATCT
66 CAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCT
* * * * *
2606 GTTATTTTTAACCTGCTCCGCTGCAAACCAGGGAGGCAAGGCT
131 GCTATCTTCAACCTGCTCCACTAC-AACCAGGGAGGCAAGGCT
2649 TTGTGCTTCC
Statistics
Matches: 309, Mismatches: 34, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
174 32 0.10
175 240 0.78
176 36 0.12
177 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (174 bp):
TATCTTCGATCTGCTTCACTGTCGATACAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
CAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCT
GCTATCTTCAACCTGCTCCACTACAACCAGGGAGGCAAGGCTAG
Found at i:2414 original size:87 final size:88
Alignment explanation
Indices: 2190--2648 Score: 706
Period size: 88 Copynumber: 5.2 Consensus size: 88
2180 CTATTTCACG
* * * *
2190 ACAACCTAGGGAGGCAAGGCTAGTATCTTTGATCTGCTTCACTATCGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
2255 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
2278 ACAACCTAGGGAGGCAAGGCTAGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGTAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
*
2343 TGCTATCTTCGACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
2366 -CGACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGTAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
2430 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
2453 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACA-GAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
*
2517 TGCTATCTTCAATCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
2540 ACAACCCAAGGAGGCAAGGCTGGTATCTTCGATCTACTTTACTGTCGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
* * * *
2605 TGTTATTTTTAACCTGCTCCGCT
66 TGCTATCTTCAACCTGCTCCACT
* *
2628 GCAAACCAGGGAGGCAAGGCT
1 ACAACCCAGGGAGGCAAGGCT
2649 TTGTGCTTCC
Statistics
Matches: 341, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
87 161 0.47
88 180 0.53
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (88 bp):
ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
TGCTATCTTCAACCTGCTCCACT
Found at i:4000 original size:20 final size:20
Alignment explanation
Indices: 3975--4019 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3965 CACCTTGGTC
3975 TTTTT-CCTTCTTCGTTTCTT
1 TTTTTCCCTTCTTCGTTT-TT
* *
3995 TTTTTCCCTTTTTTGTTTTT
1 TTTTTCCCTTCTTCGTTTTT
4015 TTTTT
1 TTTTT
4020 GTTTTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTCCCTTCTTCGTTTTT
Found at i:4014 original size:18 final size:18
Alignment explanation
Indices: 3993--4035 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3983 TCTTCGTTTC
3993 TTTTTTTCCCTTTTTTGT
1 TTTTTTTCCCTTTTTTGT
***
4011 TTTTTTTTTGTTTTTTGT
1 TTTTTTTCCCTTTTTTGT
4029 TTTTTTT
1 TTTTTTT
4036 AGTGAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (18 bp):
TTTTTTTCCCTTTTTTGT
Found at i:4017 original size:11 final size:11
Alignment explanation
Indices: 4003--4035 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3993 TTTTTTTCCC
4003 TTTTTTGTTTT
1 TTTTTTGTTTT
4014 TTTTTTGTTTT
1 TTTTTTGTTTT
4025 TTGTTTT-TTTT
1 TT-TTTTGTTTT
4036 AGTGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:4124 original size:14 final size:15
Alignment explanation
Indices: 4101--4133 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4091 AATGATGTTT
*
4101 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
4115 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
4130 TTCC
1 TTCC
4134 CAGCATGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Done.