Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_211 ID=scaffold_211-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: 9394
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:1339 original size:30 final size:28
Alignment explanation
Indices: 1265--1340 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
1255 TCGATACAAC
*
1265 GTCAGCTTGTGTGAGCAAATTCATAAAT
1 GTCAGCTTGTGTGAGCAAACTCATAAAT
** * * *
1293 GTCAGCTTGTACGAGCAAACCCTGATCATT
1 GTCAGCTTGTGTGAGCAAA--CTCATAAAT
1323 GTCAGCTTGTGTGAGCAA
1 GTCAGCTTGTGTGAGCAA
1341 TATAGTCTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 17 0.45
30 21 0.55
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
GTCAGCTTGTGTGAGCAAACTCATAAAT
Found at i:2531 original size:22 final size:22
Alignment explanation
Indices: 2487--2532 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2477 CCGTAACACC
*
2487 ATTTGTAGACAAGCCACCACTG
1 ATTTGTAGACAAACCACCACTG
* * *
2509 ATTTGTAGATAAACTACCTCTG
1 ATTTGTAGACAAACCACCACTG
2531 AT
1 AT
2533 AACACTTTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (22 bp):
ATTTGTAGACAAACCACCACTG
Found at i:2550 original size:51 final size:49
Alignment explanation
Indices: 2487--2619 Score: 140
Period size: 51 Copynumber: 2.7 Consensus size: 49
2477 CCGTAACACC
* * *
2487 ATTTGTAGACAAGCCACCACTGATTTGTAGATAAACTACCTCTGATAACA
1 ATTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTGATAA-A
* * * * * * * *
2537 CTTTCGTGGACAAGCCACCATTGGTATGCAAATATATTGCCACTGATAAA
1 ATTT-GTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTGATAAA
*
2587 ATTTTTGGACAAGCCACCACTGATTTGCAGATA
1 ATTTGTGGACAAGCCACCACTGATTTGCAGATA
2620 TACTGTCACT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
49 24 0.37
50 7 0.11
51 34 0.52
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (49 bp):
ATTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTGATAAA
Found at i:2621 original size:49 final size:51
Alignment explanation
Indices: 2494--2630 Score: 152
Period size: 49 Copynumber: 2.7 Consensus size: 51
2484 ACCATTTGTA
* * * * *
2494 GACAAGCCACCACTGATTTGTAGATAAACTACCTCTGATAACACTTTCGTG
1 GACAAGCCACCACTGATTTGCAGATATACTGCCACTGATAACAATTTCGTG
* * * * * *
2545 GACAAGCCACCATTGGTATGCAAATATATTGCCACTGATAA-AATTT-TTG
1 GACAAGCCACCACTGATTTGCAGATATACTGCCACTGATAACAATTTCGTG
*
2594 GACAAGCCACCACTGATTTGCAGATATACTGTCACTG
1 GACAAGCCACCACTGATTTGCAGATATACTGCCACTG
2631 CTTTCACCTT
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
49 33 0.48
50 4 0.06
51 32 0.46
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (51 bp):
GACAAGCCACCACTGATTTGCAGATATACTGCCACTGATAACAATTTCGTG
Found at i:8182 original size:44 final size:44
Alignment explanation
Indices: 8119--8496 Score: 274
Period size: 44 Copynumber: 8.6 Consensus size: 44
8109 GTCATCGTGG
8119 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
* * *
8163 CAAATCTTATTTCCCTGAAGTTGCAGTGTAATAGATTAAGGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
** ** *
8207 CAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-TTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT-AAAGCTA
* * ** * * * * *
8251 CAAGTTTTATCTCCCTGAAAATGCAGTAGAGTAGACTGAAGACTG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAG-CTA
* * * * **
8296 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAATTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
* * * * * * *
8340 CAAGTCTTATCTCCCTAAAGGTACAGTGGAACAGACTAAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
** ** * * *
8384 TCAAATCTTATCTCCCTGCTG-TGCAGTGGAGCAGACTAAAACCA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
* * * * * * * *
8428 CAAATCTCATCTCCTTAAAATTGTAGTGGAGTGGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
* * * *
8472 CAAGTCATATCTCTCTGAATTTGCA
1 CAAATCTTATCTCCCTGAAGTTGCA
8497 ATAGAGTGGA
Statistics
Matches: 253, Mismatches: 76, Indels: 10
0.75 0.22 0.03
Matches are distributed among these distances:
43 16 0.06
44 188 0.74
45 49 0.19
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA
Found at i:8320 original size:133 final size:132
Alignment explanation
Indices: 8125--8374 Score: 302
Period size: 133 Copynumber: 1.9 Consensus size: 132
8115 GTGGCAAATC
** * * *
8125 TTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATCTTATTTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAAATGCAGTAGAATAGACTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGT
* ** * * * *
8190 GTAATAGATTAAGGCTACAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAG
66 GGAATAGATTAAAACTACAAGCCTTATCTCCCTAAAGGTACAGTGGAACAGATTGAAATTACAAG
8255 TT
131 TT
* * * * *
8257 TTATCTCCCTGAAAATGCAGTAGAGTAGACTGAAGACTGCAGATCTTGTCTCCCTGAAGTTGCAG
1 TTATCTCCCTGAAAATGCAGTAGAATAGACTAAAG-CTACAAATCTTATCTCCCTGAAGTTGCAG
* * * *
8322 TGGAGTAGGTTAAAATTACAAGTCTTATCTCCCTAAAGGTACAGTGGAACAGA
65 TGGAATAGATTAAAACTACAAGCCTTATCTCCCTAAAGGTACAGTGGAACAGA
8375 CTAAAGATAT
Statistics
Matches: 96, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
132 29 0.30
133 67 0.70
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (132 bp):
TTATCTCCCTGAAAATGCAGTAGAATAGACTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGT
GGAATAGATTAAAACTACAAGCCTTATCTCCCTAAAGGTACAGTGGAACAGATTGAAATTACAAG
TT
Found at i:8338 original size:89 final size:87
Alignment explanation
Indices: 8121--8424 Score: 274
Period size: 89 Copynumber: 3.4 Consensus size: 87
8111 CATCGTGGCA
* ** * * **
8121 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATCTTATTTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATTACAAGTCTTATCTCCCTGAAAATG
* *
8186 CAGTGTAATAGATTAAGGCTAC
66 CAGTGTAATAGATGAAGACTAC
* * * *
8208 AAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTTTTATCTCCCTGAAAAT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATTACAAGTCTTATCTCCCTGAAAAT
* *
8273 GCAGTAG-AGTAGACTGAAGACTGC
65 GCAGT-GTAATAGA-TGAAGACTAC
* * *
8297 AGATCTTGTCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAATTACAAGTCTTATCTCCCT-AAAGG
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATTACAAGTCTTATCTCCCTGAAA-A
* * * *
8361 TACAGTGGAACAGACTAAAGA-TATC
64 TGCAGTGTAATAGA-TGAAGACTA-C
** * *
8386 AAATCTTATCTCCCTGCTG-TGCAGTGGAGCAGACTAAAA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAA
8425 CCACAAATCT
Statistics
Matches: 176, Mismatches: 33, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
87 2 0.01
88 83 0.47
89 89 0.51
90 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (87 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATTACAAGTCTTATCTCCCTGAAAATG
CAGTGTAATAGATGAAGACTAC
Found at i:8999 original size:15 final size:15
Alignment explanation
Indices: 8979--9010 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8969 CTGTCACCTG
*
8979 CAAGAAGCCAACAAA
1 CAAGAAGACAACAAA
8994 CAAGAAGACAACAAA
1 CAAGAAGACAACAAA
9009 CA
1 CA
9011 GAGGAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.25, G:0.12, T:0.00
Consensus pattern (15 bp):
CAAGAAGACAACAAA
Done.