Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1026 ID=scaffold_1026-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:0.24, G:0.24, T:0.27
Found at i:197 original size:88 final size:88
Alignment explanation
Indices: 1--1425 Score: 1990
Period size: 88 Copynumber: 16.1 Consensus size: 88
* * * *
1 TCTGCTGTCTTCAACCAAGCTCCCATCACAACCGAGAGAGGCAAGGGTTGTGTCTTCGATCTGAT
1 TCTGTTGTCTTCAACC-AGCT-CCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCT
*
66 TCGCTTTCAAATGCAGGAAGGCAAGA
64 TCGCTGTC-AATGCAGGAAGGCAAGA
** * * *
92 TCTGTTGTCTTCAACCAGCTTTATCACAACCGAGGGAGGTAAGGTTTGTGTCTTCGATCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
157 GCTATCAATGCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
*
180 TCTTTTGTCTTCAACCAGCTCCATCACAACCCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
1 TCTGTTGTCTTCAACCAGCTCCATCACAA-CCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
* *
245 TGCTGTCAGTGCAGGAAGGCAAGA
65 CGCTGTCAATGCAGGAAGGCAAGA
* * * * *
269 TCTGCTGTCTTTAACCCAGCTCCCTCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGATT
1 TCTGTTGTCTTCAA-CCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
334 CGCTGTCAATGCAGGAAGGCAAGA
65 CGCTGTCAATGCAGGAAGGCAAGA
* * * * *
358 TCTTTTGTCTTCAACCAGCTCCATCACAACAGAGAGAGG-ATAGGTTTGTGTATTCGACCTACCT
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCGACCTGCTT
422 CGCTGTCAATGCA-GAAGGGCAAGA
65 CGCTGTCAATGCAGGAA-GGCAAGA
* * * *
446 TCTATTGTCTTCAACCAGCTCCATCACAATCGAGAAAGGCAAGGTTTGTGTCTTCAACCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
511 GCTGTCAATGCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
534 TCTGTTGTCTTCAACAAGCTCAATCACAACCAAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
599 GCTGTCAATCCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * * * * *
622 TCTGTTGTCTTCAAACAGCTCCATCACAACCGAGGGAGGCAGGGCTTGTGTCTTCGATCTGATAC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
687 GCTGTCAATGCAGGAAGGTAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
710 TTTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGTAAGGTTTGTGTCTTCGACCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
* * *
775 GCTGTCAATACAGGAAGGTAGGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
798 TCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAAGCAAGGATTGTGTCTTCGACCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
* *
863 GCTGTCAATGCCGGATGGCAAAGA
66 GCTGTCAATGCAGGAAGGC-AAGA
* * *
887 TCTGTTGTCTTCAACCAGCTCCATCAGAACCGAGTGAGGCAAGGTTTGTGTCTTCGATCTGCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
* *
952 GCTGTCAATACAGGAAGACAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * * *
975 TCTTTTGTCTTCAACCAGCTCCATCACAATCGAGAGAGACAAGGTTTGTGTCTTCGAACTCCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
1040 GCTGTCAATGCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
1063 TCTGCTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGATCTGATTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
* *
1128 GCTATCAATCCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
1151 TCTGTTGTCTTCAACCAGCTCTATCAGAACCGAGTGAGGCAAGGTTTGTGTCTTCGACCTGCATC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
1216 GCTGTCAATGGAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
1239 TCTTTTGCCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGAACTCCTTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
1304 GTTGTCAATGCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
* * * *
1327 TCTGCTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGATCTGATTC
1 TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
* *
1392 GCTATCAATCCAGGAAGGCAAGA
66 GCTGTCAATGCAGGAAGGCAAGA
1415 TCTGTTGTCTT
1 TCTGTTGTCTT
Statistics
Matches: 1178, Mismatches: 149, Indels: 17
0.88 0.11 0.01
Matches are distributed among these distances:
87 4 0.00
88 887 0.75
89 254 0.22
90 18 0.02
91 15 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
TCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTC
GCTGTCAATGCAGGAAGGCAAGA
Found at i:354 original size:44 final size:44
Alignment explanation
Indices: 39--1413 Score: 185
Period size: 44 Copynumber: 31.2 Consensus size: 44
29 CAACCGAGAG
* * *
39 AGGCAAGGGTTGTGTCTTCGATCTGATTCGCTTTCAAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATC-AATGCAGGA
* * * * * ** *
84 AGGCAAGATCTGTTGTCTTCAACCAGCTT---TATCACAACCGAGGG
1 AGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGC-AGGA
* * *
128 AGGTAAGGTTTGTGTCTTCGATCTGCTTCGCTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * ** *
172 AGGCAAGATCTTTTGTCTTCAACCAG-CTC-C-ATCACAACCCGAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGATTCGCTATCA-ATGCAG-GA
* * * *
216 GAGGCAAGGTTTGTGTCTTCGACCTGCTTTGCTGTCAGTGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * ** * * * *
261 AGGCAAGATCTGCTGTCTTTAACC-CAGCTCCCTCA-CAA--CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGACCTGA-TTCGCT-ATCAATGCAG-GA
* *
305 GAGGCAAGGTTTGTGTCTTCGATCTGATTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * *
350 AGGCAAGATCTTTTGTCTTCAACCAG-CTC-C-ATCACA-ACAGAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGATTCGCTATCA-ATGCAG-GA
* * *
393 GAGG-ATAGGTTTGTGTATTCGACCT-ACCTCGCTGTCAATGCA-GA
1 -AGGCA-AGGTTTGTGTCTTCGACCTGA-TTCGCTATCAATGCAGGA
* * * * *
437 AGGGCAAGATCTAT-TGTCTTCAACCAG-CTC-C-ATCACAAT-CGAGAA
1 A-GGCAAGGT-T-TGTGTCTTCGACCTGATTCGCTAT--CAATGC-AGGA
* * *
482 AGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * * *
526 AGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCAA-G-A-G-
1 AGGCAAGGTTTG-TGTCTTCGAC---CTGATTCGCTATCAATGCAGGA
* * * *
570 AGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATCCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * ** *
614 AGGCAAGATCTGTTGTCTTCAAACAG-CTC-C-ATCACAACCGAGGG
1 AGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGC-AGGA
* * * * *
658 AGGCAGGGCTTGTGTCTTCGATCTGATACGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * ** *
702 AGGTAAGATTTTTTGTCTTCAACCAG-CTC-C-ATCACAACCGAGGG
1 AGGCAAG-GTTTGTGTCTTCGACCTGATTCGCTATCA-ATGC-AGGA
* * * *
746 AGGTAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * **
790 AGG-TAGGATCTTTTGTCTTCAATCAG-CTC-C-ATCACAACCGAGAGA
1 AGGCAAGG-T-TTGTGTCTTCGACCTGATTCGCTATCA-ATGC-AG-GA
* * * *
835 A-GCAAGGATTGTGTCTTCGACCTGCTTCGCTGTCAATGCCGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * **
878 TGGCAAAGATCTGTTGTCTTCAACCAG-CTC-C-ATCAGAACCGAGTG-
1 AGGC-AAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGC-AG-GA
* * * *
923 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * *
967 AGACAAGATCTTTTGTCTTCAACCAG-CTC-C-ATCACAAT-C-GAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGATTCGCTAT--CAATGCAG-GA
* * ** *
1010 GAGACAAGGTTTGTGTCTTCGAACTCCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * *
1055 AGGCAAGATCTGCTGTCTTCAACCAG-CTC-C-ATCACA-ACCGAGA
1 AGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGCAG-GA
* * *
1098 GAGGCAAGGTTTGTGTCTTTGATCTGATTCGCTATCAATCCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * **
1143 AGGCAAGATCTGTTGTCTTCAACC--A-GCTCTATCAGAACCGAGTG-
1 AGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGC-AG-GA
* *
1187 AGGCAAGGTTTGTGTCTTCGACCTGCA-TCGCTGTCAATGGAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTG-ATTCGCTATCAATGCAGGA
* * * * * * * *
1231 AGGCAAGATCTTTTGCCTTCAACCAG-CTC-C-ATCACA-ACCGAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGATTCGCTATCA-ATGCAG-GA
* ** * *
1274 GAGGCAAGGTTTGTGTCTTCGAACTCCTTCGTTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
* * * * * * *
1319 AGGCAAGATCTGCTGTCTTCAACCAG-CTC-C-ATCACA-ACCGAGA
1 AGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATCA-ATGCAG-GA
* * *
1362 GAGGCAAGGTTTGTGTCTTTGATCTGATTCGCTATCAATCCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
1407 AGGCAAG
1 AGGCAAG
1414 ATCTGTTGTC
Statistics
Matches: 911, Mismatches: 291, Indels: 257
0.62 0.20 0.18
Matches are distributed among these distances:
40 8 0.01
42 46 0.05
43 199 0.22
44 336 0.37
45 230 0.25
46 80 0.09
47 4 0.00
48 8 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGATTCGCTATCAATGCAGGA
Done.