Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1025 ID=scaffold_1025-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, 855
Length: 1425
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Found at i:150 original size:88 final size:88
Alignment explanation
Indices: 1--1425 Score: 1968
Period size: 88 Copynumber: 16.2 Consensus size: 88
* * *
1 CAATGGAGGAAGGCAAGATCTTTTGCCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
66 GTGTCTTCGAACTCCTTCGTTGT
66 GTGTCTTCGATCTGCTTCGCTGT
*
89 CAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
154 GTGTCTTTGATCTGATTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
* ** * * *
177 CAATCCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTTATTACAACCGAGGGAGGTAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
*
242 GTGTCTTCGATCTGCTTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
* *
265 CAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* *
330 GTGTCTTCGACCTACTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * *
353 CAATGCAGGAAGGTAAGATTTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
418 GTGTCTTCGACCTACTTCTCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * **
441 CAATGCAGGAAGGCAAGATCGGTTGTGTTCAACCAGCCCCATCACAACCGAGAGAGGCAACATTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
506 GTGTCTTTGACCTACTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * * *
529 CAATGCAGGAAGGCAAGATCGGTTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCAGGGCTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
594 GTGTCTTCGATATGATTCACTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * * * * *
617 CGATGCAGGAAGGTAAGATTTTTTGTCTTCAACCAGCTCCATCACAATCGAGGGAGGTAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
*
682 GTGTCTTCGACCTGCTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * * * **
705 CAATACAGGAAGGCAGGATCTTTTGCCTTCAATCAGCTCCATCACAATTGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* *
770 GTGTCTTTGACCTGCTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * * *
793 CAATGCAGGATGGCAAGATCTGTTGTCTTCAACCAGCTCTATCATAACCGAGGGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
858 GTGTCTTCGATCTGCTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* *
881 CAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* *
946 GTGTCTTCGACCTACTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* *
969 CAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCTAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
1034 GTGTCTTTGATCTGATTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
** * * *
1057 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTTATTACAACCGAGGGAGGTAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
*
1122 GTGTCTTCGATCTGCTTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
* *
1145 CAATGCAGGAAGGCAAGATCTTTTGTCTTCAACTAGCTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* *
1210 GTGTCTTCAACCTGCTTCGCTGT
66 GTGTCTTCGATCTGCTTCGCTGT
* * *
1233 CAATGCAGGAAGGCAAGATCTGCTGTCTTTAACCAGCTCCATCACAACCAAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
1298 GTGTCTTTGATCTGATTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
* * ** * * *
1321 AAATGCAGGAAGGCAAGATCTGTTGTGTTCAACCAGCTTTATTACAACCGAGGGAGGTAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
*
1386 GTGTCTTCGATCTGCTTCGCTAT
66 GTGTCTTCGATCTGCTTCGCTGT
1409 CAATGCAGGAAGGCAAG
1 CAATGCAGGAAGGCAAG
Statistics
Matches: 1182, Mismatches: 155, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 1182 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (88 bp):
CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
GTGTCTTCGATCTGCTTCGCTGT
Found at i:587 original size:44 final size:44
Alignment explanation
Indices: 375--587 Score: 107
Period size: 44 Copynumber: 4.8 Consensus size: 44
365 GTAAGATTTT
* * **
375 TTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAGGTTTG
1 TTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCAAGATCGG
* * ** * *
419 -TGTCTTCGACCTA-CTTCTCTGTCAA-TGCAGGAAGGCAAGATCGG
1 TTGTCTTCAACC-AGC-TCTATCACAACCG-AGGGAGGCAAGATCGG
* * * * * **
463 TTGTGTTCAACCAGCCCCATCACAACCGAGAGAGGCAACATTTG
1 TTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCAAGATCGG
** * ** *
507 -TGTCTTTGACCTA-CTTCGCTGTCA-ATGC-AGGAAGGCAAGATCGG
1 TTGTCTTCAACC-AGC-T--CTATCACAACCGAGGGAGGCAAGATCGG
551 TTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCA
1 TTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCA
588 GGGCTTGTGT
Statistics
Matches: 113, Mismatches: 42, Indels: 28
0.62 0.23 0.15
Matches are distributed among these distances:
42 5 0.04
43 23 0.20
44 58 0.51
45 23 0.20
46 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (44 bp):
TTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGCAAGATCGG
Found at i:1335 original size:44 final size:44
Alignment explanation
Indices: 1023--1337 Score: 112
Period size: 44 Copynumber: 7.2 Consensus size: 44
1013 CAACCTAGAG
* * *
1023 AGGCAAGGTTTGTGTCTTTGATCTGATTCGCTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTTAACCTGATTCGCTATAAATGCAGGA
* * * * * *** * ** *
1067 AGGCAAGATCTGTTGTCTTCAACCAGCTTTATTACAACCG-AGGG
1 AGGCAAGGTTTG-TGTCTTTAACCTGATTCGCTATAAATGCAGGA
* ** * * *
1111 AGGTAAGGTTTGTGTCTTCGATCTGCTTCGCTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTTAACCTGATTCGCTATAAATGCAGGA
* * * * *
1155 AGGCAAGATCTTTTGTCTTCAA-CT-AGCTC-C-ATCACAA--CCGAGA
1 AGGCAAGGT-TTGTGTCTTTAACCTGA-TTCGCTAT-A-AATGCAG-GA
* * * *
1198 GAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTTAACCTGATTCGCTATAAATGCAGGA
* * * * * *
1243 AGGCAAGATCTGCTGTCTTTAACCAG-CTC-C-ATCACAA-CCAAGA
1 AGGCAAGGTTTG-TGTCTTTAACCTGATTCGCTAT-A-AATGCAGGA
* *
1286 GAGGCAAGGTTTGTGTCTTTGATCTGATTCGCTATAAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTTAACCTGATTCGCTATAAATGCAGGA
1331 AGGCAAG
1 AGGCAAG
1338 ATCTGTTGTG
Statistics
Matches: 188, Mismatches: 61, Indels: 44
0.64 0.21 0.15
Matches are distributed among these distances:
42 5 0.03
43 46 0.24
44 87 0.46
45 45 0.24
46 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTTAACCTGATTCGCTATAAATGCAGGA
Done.