Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_412 ID=scaffold_412-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: 8343
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.29
Warning! 1005 characters in sequence are not A, C, G, or T
Found at i:1428 original size:21 final size:21
Alignment explanation
Indices: 1404--1463 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1394 ATTACAAAAT
1404 CATATCTTCTAAGATTGCATA
1 CATATCTTCTAAGATTGCATA
1425 CATA---TCTAAGATTGCAT-
1 CATATCTTCTAAGATTGCATA
*
1442 -ATATCATATCTAAGATTACATA
1 CATATC-T-TCTAAGATTGCATA
1464 TCCTTTGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
16 3 0.09
18 13 0.41
21 16 0.50
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (21 bp):
CATATCTTCTAAGATTGCATA
Found at i:1434 original size:18 final size:19
Alignment explanation
Indices: 1411--1465 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
1401 AATCATATCT
1411 TCTAAGATTGCATA-CATA
1 TCTAAGATTGCATATCATA
1429 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
*
1450 TCTAAGATTACATATC
1 TCTAAGATTGCATATC
1466 CTTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 3 0.09
21 14 0.42
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2168 original size:45 final size:44
Alignment explanation
Indices: 1893--2346 Score: 190
Period size: 44 Copynumber: 10.6 Consensus size: 44
1883 CTCTAATCCA
* * * * ** *
1893 CTCCACTACAACTT-AGGGAGACATGATTTTTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTACTTAGTCTG
* * * * * * *
1936 CCCCACTACAATTTCAGGGGGATAAGACTTGCTTTCTTGAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTACTT-AGTCTG
* * ** * * * *
1981 CTCCACTACAACTTTAGGGAGATAAGACCCGA-T-GTGA-TATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTACTTAGTCTG
* * * * * * *
2022 CTCTACTGTAACTTCAGAGAGATAAGATCTGCGGTT--TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGATTACTTAGTCTG
* * * *
2066 CTCCACTACAACTTCAGGGAGATAGGA-TT-ATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATT-AC-TTAGTCTG
2110 CTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCA-T-CTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-G--ATTACTT-AGTCTG
*
2155 C-CTCACTGCAACTTCA-AGAGGATAAGACTTGATTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGATTACTTAGTCTG
*
2199 CTCCACTGCAACTTCAGGGAGATAAGAC-T-A-GA--T-G-C-G
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTACTTAGTCTG
* * * *
2235 AT---CTGCAACTTCAGAGAGATAAGATCTGTGATT--TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGATTACTTAGTCTG
* * *
2276 CTCCACTGCAACTTCAGGGAGATAGGA-TT-ATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATT-AC-TTAGTCTG
*
2320 CTCCACTGCAACTTCAAGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
2347 TTCGCCATCT
Statistics
Matches: 317, Mismatches: 56, Indels: 75
0.71 0.12 0.17
Matches are distributed among these distances:
33 21 0.07
34 1 0.00
36 3 0.01
37 2 0.01
38 2 0.01
39 1 0.00
40 6 0.02
41 29 0.09
42 5 0.02
43 19 0.06
44 160 0.50
45 64 0.20
46 2 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGATTACTTAGTCTG
Found at i:2447 original size:50 final size:50
Alignment explanation
Indices: 2388--2561 Score: 159
Period size: 50 Copynumber: 3.5 Consensus size: 50
2378 TTGGGGAAAC
* *
2388 AAGATTCGCCGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGAGAAGT
1 AAGATTCACCGTCGTGGCTTCAATCTGTTCCATTACACCGCCAGAGAAGT
* * * * * ** ** *** * **
2438 AAGATTCGCCGTTGCGGCTTTAATCTTTTTAATTACAATGTTGGGGAAAC
1 AAGATTCACCGTCGTGGCTTCAATCTGTTCCATTACACCGCCAGAGAAGT
* * *
2488 AAGATTCACCGTCGTAGCTTCAATCTGTTCCATTACACCACCAGAGGAGT
1 AAGATTCACCGTCGTGGCTTCAATCTGTTCCATTACACCGCCAGAGAAGT
*
2538 AAGATTCACCGTCGTGGTTTCAAT
1 AAGATTCACCGTCGTGGCTTCAAT
2562 TCGCTCCACT
Statistics
Matches: 89, Mismatches: 35, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (50 bp):
AAGATTCACCGTCGTGGCTTCAATCTGTTCCATTACACCGCCAGAGAAGT
Found at i:2500 original size:100 final size:100
Alignment explanation
Indices: 2361--2549 Score: 306
Period size: 100 Copynumber: 1.9 Consensus size: 100
2351 CCATCTTCAG
* * *
2361 TCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTGGCTTCAATCTGTTCCACTACAC
1 TCTTTTAAATTACAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
2426 CGCCAGAGAAGTAAGATTCGCCGTTGCGGCTTTAA
66 CACCAGAGAAGTAAGATTCACCGTTGCGGCTTTAA
* *
2461 TCTTTTTAATTACAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCATTACAC
1 TCTTTTAAATTACAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACAC
*
2526 CACCAGAGGAGTAAGATTCACCGT
66 CACCAGAGAAGTAAGATTCACCGT
2550 CGTGGTTTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
TCTTTTAAATTACAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACAC
CACCAGAGAAGTAAGATTCACCGTTGCGGCTTTAA
Found at i:2633 original size:45 final size:45
Alignment explanation
Indices: 2583--2724 Score: 214
Period size: 45 Copynumber: 3.2 Consensus size: 45
2573 TAATGCCAAA
*
2583 GAGATAGGACTTTGTGATTTTCAACCTATTCTACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
**** * *
2628 GAGATAGGA-TTCACAATCTTCAACCTATTCCACTGTTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
2672 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
2717 GAGATAGG
1 GAGATAGG
2725 GCTGGGTCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 37 0.45
45 46 0.55
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (45 bp):
GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
Found at i:2811 original size:44 final size:44
Alignment explanation
Indices: 2761--2899 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 44
2751 CGGTGCAGGA
2761 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAAGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAAGG
* * * * ** * * *** *
2805 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTTGGCGC-AGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACCCAAGG
* * *
2848 AAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAACCCAGGG
1 -AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAAGG
2893 AGGCAAG
1 AGGCAAG
2900 CTGGTGTCTT
Statistics
Matches: 64, Mismatches: 27, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 21 0.33
44 25 0.39
45 18 0.28
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAAGG
Found at i:2956 original size:87 final size:87
Alignment explanation
Indices: 2724--2956 Score: 371
Period size: 88 Copynumber: 2.7 Consensus size: 87
2714 AGGGAGATAG
*
2724 GGCTGG-GTCATTGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTC-TTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2788 TCCGCTGCAACCCAAGGAGGCAA
65 TCCACTACAACCCAAGGAGGCAA
* *
2811 GGCTGGTGTCTTCGATCTGCTTCGCTGTTGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTT-GATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
2876 TCCACTACAACCCAGGGAGGCAA
65 TCCACTACAACCCAAGGAGGCAA
2899 -GCTGGTGTCTTGTATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTG-ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
2957 CTGATATGCT
Statistics
Matches: 135, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
86 1 0.01
87 62 0.46
88 72 0.53
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (87 bp):
GGCTGGTGTCTTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
CCACTACAACCCAAGGAGGCAA
Done.