Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_309 ID=scaffold_309-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: 8329
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:365 original size:18 final size:19
Alignment explanation
Indices: 316--368 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
306 TTATATTGAA
316 AAATATACGTATATATACATGG
1 AAATATAC--ATATATACAT-G
338 AAATA-A-ATATATACAT-
1 AAATATACATATATACATG
354 AAATATACATATATA
1 AAATATACATATATA
369 TAAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 17 0.59
21 1 0.03
22 5 0.17
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (19 bp):
AAATATACATATATACATG
Found at i:604 original size:11 final size:11
Alignment explanation
Indices: 588--630 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
578 GGCCAAATTG
588 AAATTAAAAAT
1 AAATTAAAAAT
*
599 AAATTAAAGAT
1 AAATTAAAAAT
610 GAAATTTAAAAAT
1 -AAA-TTAAAAAT
*
623 AAAATAAA
1 AAATTAAA
631 CTTAATTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:623 original size:24 final size:23
Alignment explanation
Indices: 586--630 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
576 GAGGCCAAAT
*
586 TGAAATTAAAAATAAATTAAAGA
1 TGAAATTAAAAATAAAATAAAGA
609 TGAAATTTAAAAATAAAATAAA
1 TGAAA-TTAAAAATAAAATAAA
631 CTTAATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (23 bp):
TGAAATTAAAAATAAAATAAAGA
Found at i:1962 original size:44 final size:44
Alignment explanation
Indices: 1929--2012 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
1919 AAGATCTGTT
* *
1929 ATTTTAATCCGCTCCGCTATAACCTCAGGGAGATAGGATTATCG
1 ATTTTAATCCGCTCCACTATAACCTCAGGGAGATAAGATTATCG
* * * *
1973 GTTTTAATCTGCTTCACTGTAACCTCAGGGAGATAAGATT
1 ATTTTAATCCGCTCCACTATAACCTCAGGGAGATAAGATT
2013 TACCATCCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
ATTTTAATCCGCTCCACTATAACCTCAGGGAGATAAGATTATCG
Found at i:2077 original size:44 final size:44
Alignment explanation
Indices: 2029--2357 Score: 191
Period size: 44 Copynumber: 7.5 Consensus size: 44
2019 CCTCGATCTG
*
2029 CTCCACTACTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
* ** * ** ** * * * *
2073 CTCCATTGCTATTTAGGGAGA-CAAGGCTGGGGA-CTTCGATCTG
1 CTCCACTGCTGCTTAGGGAGATAAAATCT-GTAATTTTCAACCTA
* *
2116 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
* ** * * ** * * * *
2160 CTCAACTGCTGCCCAGGGAGA-CAAAGCTGGGGA-CTTCGATCTG
1 CTCCACTGCTGCTTAGGGAGATAAAATCT-GTAATTTTCAACCTA
* * *
2203 CTCCACTGTTGCTTAAGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
* * * ** *** * * * *
2247 CTCCACTGCTGCTCAGAGAGA-CAAGGCTGGGGTCTTCGATCTG
1 CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
* *
2290 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
* * *
2334 CTCCACTGTTGCTCAAGGAGATAA
1 CTCCACTGCTGCTTAGGGAGATAA
2358 GGCTGGTGTC
Statistics
Matches: 191, Mismatches: 87, Indels: 14
0.65 0.30 0.05
Matches are distributed among these distances:
43 86 0.45
44 105 0.55
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
CTCCACTGCTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTA
Found at i:2123 original size:87 final size:87
Alignment explanation
Indices: 2021--2378 Score: 554
Period size: 87 Copynumber: 4.1 Consensus size: 87
2011 TTTACCATCC
* * **
2021 TCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATTTTCAACCTACTCCATTGCTATT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
2086 TAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
* *
2108 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCAACTGCTGCC
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
2173 CAGGGAGACAAAGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
** *
2195 TCGATCTGCTCCACTGTTGCTTAAGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
* *
2260 CAGAGAGACAAGGCTGGGGTCT
66 CAGGGAGACAAGGCTGGGGACT
*
2282 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGTTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
* * * *
2347 CAAGGAGATAAGGCTGGTGTCT
66 CAGGGAGACAAGGCTGGGGACT
2369 TCGATCTGCT
1 TCGATCTGCT
2379 TCGCTGTCGG
Statistics
Matches: 247, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 247 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (87 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
CAGGGAGACAAGGCTGGGGACT
Found at i:2132 original size:43 final size:43
Alignment explanation
Indices: 2085--2310 Score: 159
Period size: 43 Copynumber: 5.2 Consensus size: 43
2075 CCATTGCTAT
*
2085 TTAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTACTGC
1 TTAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGCTGC
* * ** * * * * *
2128 TTAGGGAGATAAGATCT-GTAATTTTCAACCTACTCAACTGCTGC
1 TTAGGGAGACAAG-GCTGGGGA-CTTCGATCTGCTCCACTGCTGC
** * *
2172 CCAGGGAGACAAAGCTGGGGACTTCGATCTGCTCCACTGTTGC
1 TTAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGCTGC
* * * ** * * * *
2215 TTAAGGAGATAAGATCT-GTAATTTTCAACCTACTCCACTGCTGC
1 TTAGGGAGACAAG-GCTGGGGA-CTTCGATCTGCTCCACTGCTGC
* * * *
2259 TCAGAGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGC
1 TTAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGCTGC
2302 TTAGGGAGA
1 TTAGGGAGA
2311 TAAGATCTGT
Statistics
Matches: 126, Mismatches: 51, Indels: 12
0.67 0.27 0.06
Matches are distributed among these distances:
43 68 0.54
44 58 0.46
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (43 bp):
TTAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGCTGC
Found at i:2448 original size:88 final size:88
Alignment explanation
Indices: 2356--2768 Score: 664
Period size: 88 Copynumber: 4.7 Consensus size: 88
2346 TCAAGGAGAT
2356 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
*
2421 ACTCCGCTGCAACCCAGGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
* **
2444 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTATTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
* *
2509 GCTCCGCTACAACCTAGGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
* * **
2532 AAGGCTAGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTGCTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
*
2597 GCTCCGCTGTAACCCAGGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
* * *
2620 AAGGCTGGTGCCTTCGATCTACTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
* * *
2685 GCTCCGCTGTATCCCAAGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
*
2708 AAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
2769 CTGATCTGCT
Statistics
Matches: 298, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 298 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (88 bp):
AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
GCTCCGCTGCAACCCAGGGAGGC
Found at i:2605 original size:45 final size:45
Alignment explanation
Indices: 2550--2694 Score: 123
Period size: 45 Copynumber: 3.3 Consensus size: 45
2540 TGTCTTCGAT
* * *
2550 CTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTGCTTTTAAC
1 CTGCTCCGCTGTCGATGCAGGAAGGCAAGATCTGCTGCTTTTAAC
* ** * * * * ** *
2595 CTGCTCCGCTGT-AACCCAGGGAGGCAAG-GCTGGTGCCTTCGAT
1 CTGCTCCGCTGTCGATGCAGGAAGGCAAGATCTGCTGCTTTTAAC
* * **
2638 CTACTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTGTCGATGCAGGAAGGCAAGATCTGCTGCTTTTAAC
2683 CTGCTCCGCTGT
1 CTGCTCCGCTGT
2695 ATCCCAAGGA
Statistics
Matches: 69, Mismatches: 29, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 19 0.28
44 22 0.32
45 28 0.41
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (45 bp):
CTGCTCCGCTGTCGATGCAGGAAGGCAAGATCTGCTGCTTTTAAC
Done.