Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_278 ID=scaffold_278-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: 8734
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:161 original size:3 final size:3
Alignment explanation
Indices: 143--212 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
133 AATGATAGTC
* * * **
143 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
191 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
213 CACTAAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:323 original size:30 final size:28
Alignment explanation
Indices: 248--324 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
238 AAATTGTTAG
*
248 AAAAAGGGATTAAATCGAAATAAAAACA
1 AAAAAGGGACTAAATCGAAATAAAAACA
* * * *
276 TAAATGCTGGGCGAAATCGAAATAAAAAAACA
1 AAAAAG--GGACTAAATCGAAAT--AAAAACA
308 AAAAAGGGACTAAATCG
1 AAAAAGGGACTAAATCG
325 TGATACACGC
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.11
30 21 0.58
32 11 0.31
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (28 bp):
AAAAAGGGACTAAATCGAAATAAAAACA
Found at i:1874 original size:50 final size:49
Alignment explanation
Indices: 1814--2792 Score: 540
Period size: 50 Copynumber: 19.6 Consensus size: 49
1804 CTCCAAACTG
* * *
1814 TTTAACTGCAATGTCGAGGAAGTAAGATTCGTCGTCGTAGCTTCAATCT
1 TTTAACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * ** * *
1863 ATTTAATTGCAATGTCAAGGAAGCAAAATTCACCGTTGTAGCTTCAATCT
1 -TTTAACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
** ** * * *
1913 GTTTCGCTGCACCGCCGAGGGAGTAAGATTCGCCGTTGT-GACTTCAATCTT
1 -TTTAACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAG-CTTCAATC-T
* **
1964 TTTAA-TCGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCT
1 TTTAACT-GCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
** * ** * * * *
2013 GTTCCACTGTACCGTCTAGAAAGTAAGATTCGCC-TTGATGGCTTCAATCT
1 -TTTAACTGCAATGTCGAGGAAGTGAGATTCGCCGTTG-TAGCTTCAATCT
* * * * * *
2063 TTTGAATTGCAATGTTGGGGAAGTGAGATTCGTCATCGTAGCTTCAATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
** ** * * *
2113 GTTCCACTGC-ATCCCTAGGGAAATGAGATTTGCCGTTGT-GACTTCAATCT
1 -TTTAACTGCAATGTCGA-GGAAGTGAGATTCGCCGTTGTAG-CTTCAATCT
* * * *
2163 TTTGAATTGTAATGTCGGGGAAGTGAGATTCGCCGTCGTAGCTTCAATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
*** * * * * * *
2213 GTTCCGCTGC-ATCGCCTG-GGAAATAAGATTCGCCATTGTGGCTTCGATCT
1 -TTTAACTGCAAT-GTC-GAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * *
2263 TTTAAACTGCAATGTCGGGGAAGTGAGATTCGACGTCGTAGCTTCAATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
*** * * * * *
2313 GTTCCGCTGC-ATCGTCCG-GGAAATAAGATTCGCCGTTGTGGTTTCGATCT
1 -TTTAACTGCAAT-GT-CGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
*
2363 TTTAAACTGCAATGTCTG-GGAAGTGAGATTCGCCGTCGTAGCTTCAAT-T
1 TTT-AACTGCAATGTC-GAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
** * * * * * *
2412 TGTTCCGCTGC-ATCGCCTG-GGAAATAAGATTCACCGTTGTGGCTTCGATCT
1 T-TT-AACTGCAAT-GTC-GAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* ** * *
2463 TTTAAATTGCAATGTCGAGGAAGCAAGATCCGCTGTTGTAGCTTCAATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * * *
2513 ATTCAACTGCACTGTCTG-GGAGGTGAGATTCGCTGTTGTAGCTTCAATCT
1 -TTTAACTGCAATGTC-GAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * * *
2563 TTTAAATTGCAATGTCGAGGAAGTGAGATTTGCCGTCGTAGCTTCGATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
*** * * * * *
2613 GTTCCGCTGC-ATCG-CCAGGGAGGTGAGATTCACTGTTGTAGCTTCAATAT
1 -TTTAACTGCAAT-GTCGA-GGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * *
2663 TTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCGTCGTAGCTTCAATCT
1 TTT-AACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
* * **
2713 GTTCT-GCTGC-ATCGTC-AGGGAGGTGAGATTCGTTGTTGTAGCTTCAATCT
1 -TT-TAACTGCAAT-GTCGA-GGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
*
2763 TTTAAATTGCAATGTC-AGGGAAGTGAGATT
1 TTT-AACTGCAATGTCGA-GGAAGTGAGATT
2793 TGTCGTCGTA
Statistics
Matches: 693, Mismatches: 187, Indels: 98
0.71 0.19 0.10
Matches are distributed among these distances:
48 1 0.00
49 41 0.06
50 612 0.88
51 38 0.05
52 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (49 bp):
TTTAACTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCT
Found at i:1940 original size:100 final size:100
Alignment explanation
Indices: 1828--2875 Score: 1060
Period size: 100 Copynumber: 10.5 Consensus size: 100
1818 ACTGCAATGT
* * ** ** *
1828 CGAGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTT-AATTGCAATGTCAAGGAAGCAAAAT
1 CGAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGTGAGAT
* * * *
1892 TCACCGTTGTAGCTTCAATCTGTTTCGCTGCACCGC
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * **
1928 CGAGGGAGTAAGATTCGCCGTTGT-GACTTCAATCTTTTTAATCGCAATGTCGGGGAAGCAAGAT
1 CGAGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
* * * * *
1992 TCGCCGTTGTAGCTTCAATCTGTTCCACTGTACCGT
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * * *
2028 CTAGAAAGTAAGATTCGCC-TTGATGGCTTCAATCTTTTGAATTGCAATGTTGGGGAAGTGAGAT
1 CGAGGAAGTAAGATTCGCCGTTG-TAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
* * *
2092 TCGTCATCGTAGCTTCAATCTGTTCCACTGCATC-C
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * * * *
2127 CTAGGGAAATGAGATTTGCCGTTGT-GACTTCAATCTTTTGAATTGTAATGTCGGGGAAGTGAGA
1 CGA-GGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGA
2191 TTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
64 TTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * * *
2228 CTG-GGAAATAAGATTCGCCATTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGTGAGAT
1 C-GAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
*
2292 TCGACGTCGTAGCTTCAATCTGTTCCGCTGCATCGTC
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCG-C
* * * * * *
2329 CG-GGAAATAAGATTCGCCGTTGTGGTTTCGATCTTTTAAACTGCAATGTCTGGGAAGTGAGATT
1 CGAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATT
*
2393 CGCCGTCGTAGCTTCAATTTGTTCCGCTGCATCGC
66 CGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * * * **
2428 CTG-GGAAATAAGATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGAGGAAGCAAGAT
1 C-GAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
* * * * **
2492 CCGCTGTTGTAGCTTCAATCTATTCAACTGCA-CTGTC
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATC-G-C
* * * * *
2529 TG-GGAGGTGAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGAGGAAGTGAGATT
1 CGAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATT
* *
2593 TGCCGTCGTAGCTTCGATCTGTTCCGCTGCATCGC
66 CGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * * * *
2628 C-AGGGAGGTGAGATTCACTGTTGTAGCTTCAATATTTTAAATTGCAATGTCGGGGAAGTGAGAT
1 CGA-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
* *
2692 TCGCCGTCGTAGCTTCAATCTGTTCTGCTGCATCGT
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * ** *
2728 C-AGGGAGGTGAGATTCGTTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGTGAGAT
1 CGA-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGAT
* * * * *
2792 TTGTCGTCGTAGGTTCGATCTGTTCTGCTGCATCGC
65 TCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
* * ** * * *
2828 C-AGGGAGGTGAGATTTACTGTTGTGGCTTCAATCTTTTGAATTGCAAT
1 CGA-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT
2876 CTATGGTTTT
Statistics
Matches: 828, Mismatches: 103, Indels: 34
0.86 0.11 0.04
Matches are distributed among these distances:
99 15 0.02
100 802 0.97
101 11 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (100 bp):
CGAGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATT
CGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC
Found at i:4194 original size:6 final size:6
Alignment explanation
Indices: 4183--4226 Score: 70
Period size: 6 Copynumber: 7.0 Consensus size: 6
4173 GGCCTCTCCA
4183 TTTTCT TTTTCT TTTTCT TTTTCTT TTTTCT TCTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT T-TTTCT TTTTCT
4227 CCTTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 24 0.67
7 12 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:4225 original size:13 final size:12
Alignment explanation
Indices: 4183--4226 Score: 70
Period size: 13 Copynumber: 3.5 Consensus size: 12
4173 GGCCTCTCCA
4183 TTTTCTTTTTCT
1 TTTTCTTTTTCT
4195 TTTTCTTTTTCTT
1 TTTTCTTTTTC-T
4208 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
4221 TTTTCT
1 TTTTCT
4227 CCTTTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 15 0.50
14 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:4281 original size:8 final size:7
Alignment explanation
Indices: 4254--4280 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4244 TTTTTTCGAT
4254 TTTTTTA
1 TTTTTTA
4261 TTTTTTA
1 TTTTTTA
4268 TTTTTTA
1 TTTTTTA
4275 TTTTTT
1 TTTTTT
4281 TCTCTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Done.