Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_736 ID=scaffold_736-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: 5314
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.25

Warning! 1146 characters in sequence are not A, C, G, or T


Found at i:25 original size:19 final size:19

Alignment explanation

Indices: 1--153 Score: 270 Period size: 19 Copynumber: 8.1 Consensus size: 19 * 1 GCAAACACGTTTAGAAAAC 1 GCAAACACGTTTCGAAAAC 20 GCAAACACGTTTCGAAAAC 1 GCAAACACGTTTCGAAAAC * 39 GCAAACACGTTTAGAAAAC 1 GCAAACACGTTTCGAAAAC 58 GCAAACACGTTTCGAAAAC 1 GCAAACACGTTTCGAAAAC 77 GCAAACACGTTTCGAAAAC 1 GCAAACACGTTTCGAAAAC * 96 GCAAACACGTTTAGAAAAC 1 GCAAACACGTTTCGAAAAC 115 GCAAACACGTTTCGAAAAC 1 GCAAACACGTTTCGAAAAC * 134 GCAAACACGTTTGGAAAAC 1 GCAAACACGTTTCGAAAAC 153 G 1 G 154 TCCATGTCTA Statistics Matches: 128, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 128 1.00 ACGTcount: A:0.44, C:0.24, G:0.17, T:0.16 Consensus pattern (19 bp): GCAAACACGTTTCGAAAAC Found at i:1370 original size:22 final size:22 Alignment explanation

Indices: 1344--1389 Score: 83 Period size: 22 Copynumber: 2.1 Consensus size: 22 1334 AGGAGACTTA * 1344 TTTTGACGAGTCCACTTGGATT 1 TTTTGACGAGTCCACTTGCATT 1366 TTTTGACGAGTCCACTTGCATT 1 TTTTGACGAGTCCACTTGCATT 1388 TT 1 TT 1390 GACTTGCTAA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 23 1.00 ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43 Consensus pattern (22 bp): TTTTGACGAGTCCACTTGCATT Found at i:4098 original size:22 final size:20 Alignment explanation

Indices: 4056--4099 Score: 52 Period size: 22 Copynumber: 2.1 Consensus size: 20 4046 GCGTTCTTCC * * 4056 GCAAAAATGAGTAAATTTAT 1 GCAAAAATAAGTAAATATAT 4076 GCAAAAACTAAGTCAAATATAT 1 GCAAAAA-TAAGT-AAATATAT 4098 GC 1 GC 4100 TTTATAAACG Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 20 7 0.35 21 4 0.20 22 9 0.45 ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25 Consensus pattern (20 bp): GCAAAAATAAGTAAATATAT Done.