Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold171
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: 1364075
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 108074 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1340705 original size:15 final size:15
Alignment explanation
Indices: 1340685--1340714 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1340675 TTAACCATAT
*
1340685 ACCATAAACTCTAAA
1 ACCATAAACCCTAAA
1340700 ACCATAAACCCTAAA
1 ACCATAAACCCTAAA
1340715 CACTAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (15 bp):
ACCATAAACCCTAAA
Found at i:1341099 original size:149 final size:147
Alignment explanation
Indices: 1340807--1341086 Score: 343
Period size: 148 Copynumber: 1.9 Consensus size: 147
1340797 TCAAAAACGC
* * * *
1340807 CGCTATTGCTTACCTTTTGTGGCATTTTTCTCATAAACACCACTAATGCTTGACATTTTTACAAT
1 CGCTATTGCTTACCTTTTGCGACATTTTTCTCATAAACACCACTAATACTTAACATTTTTACAAT
*** * *
1340872 TTTTATATTGAATTATTATACAGGGAGCAAAACAACATCGTTTTGTTTAAAATAAAATGATTTTT
66 TTTTATATTGAATTATTATACAGGGAGCAAAAC-ACATCGCCATGTTTAAAATAAAAAGATATTT
*
1340937 TGCGGCGTTTAAAACCGT
130 TGCAGCGTTTAAAACCGT
* ** * * **
1340955 CGCTATTGTTTACCTTTTGCGATGTTTTTCTCATAAACGCTACTAATACTTAATTTTTTTTACAA
1 CGCTATTGCTTACCTTTTGCGACATTTTTCTCATAAACACCACTAATACTTAA-CATTTTTACAA
* *
1341020 TTTTTATATTGAATTATTATATAGGGAGCAAAAC-GAT-GCCAT-TTTAAAATAAAAAGA-ATTT
65 TTTTTATATTGAATTATTATACAGGGAGCAAAACACATCGCCATGTTTAAAATAAAAAGATATTT
1341081 TGCAGC
130 TGCAGC
1341087 ATTTCTGATA
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
144 8 0.07
145 14 0.12
146 2 0.02
147 2 0.02
148 44 0.39
149 42 0.38
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (147 bp):
CGCTATTGCTTACCTTTTGCGACATTTTTCTCATAAACACCACTAATACTTAACATTTTTACAAT
TTTTATATTGAATTATTATACAGGGAGCAAAACACATCGCCATGTTTAAAATAAAAAGATATTTT
GCAGCGTTTAAAACCGT
Found at i:1343105 original size:41 final size:41
Alignment explanation
Indices: 1343060--1343167 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
1343050 AATTCGGCCA
* * *
1343060 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
*
1343101 AACATGTAGTGGCAGCATTAAATTCATCCAGACACATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
1343142 AACATGTAGTGGCAGCATTAAATTCG
1 AACATGTAGTGGCAGCATTAAATTCG
1343168 ACATATTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (41 bp):
AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:1350325 original size:23 final size:23
Alignment explanation
Indices: 1350297--1350342 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1350287 CGGTTTGGCA
1350297 CATAGCCCACGACACGGCTGTGT
1 CATAGCCCACGACACGGCTGTGT
1350320 CATAGCCCACGACACGGCTGTGT
1 CATAGCCCACGACACGGCTGTGT
1350343 AGCCCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.17
Consensus pattern (23 bp):
CATAGCCCACGACACGGCTGTGT
Found at i:1354125 original size:24 final size:24
Alignment explanation
Indices: 1354093--1354139 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1354083 ATTATACCCT
1354093 CCATCGAATTCCTACCTTAATTGC
1 CCATCGAATTCCTACCTTAATTGC
1354117 CCATCGAATTCCTACCTTAATTG
1 CCATCGAATTCCTACCTTAATTG
1354140 GTCCCTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (24 bp):
CCATCGAATTCCTACCTTAATTGC
Found at i:1355311 original size:2 final size:2
Alignment explanation
Indices: 1355304--1355330 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1355294 ACCACCAATT
1355304 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1355331 GCATTCGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1355758 original size:21 final size:21
Alignment explanation
Indices: 1355734--1355783 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1355724 TGCTCATCAA
1355734 ACTTATTTATCAAATATATAT
1 ACTTATTTATCAAATATATAT
*
1355755 ACTTGATCT-TCAAATATATAT
1 ACTT-ATTTATCAAATATATAT
1355776 A-TTATTTA
1 ACTTATTTA
1355784 CATATCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 17 0.68
22 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
ACTTATTTATCAAATATATAT
Found at i:1355959 original size:41 final size:40
Alignment explanation
Indices: 1355869--1355988 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 40
1355859 TGATTTAATA
* * * * * *
1355869 CACCGGCTTTTAGCCTGCTAGACTTATAGTCCGAATAATTT
1 CACCGGCATTAAGCCTGCTAGAC-AATAGTCTGAATTATAT
*
1355910 CACTGGCATTAAGCCTGCTAGACAATGAGTCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTATAT
*
1355951 CACCGGCATCAAGCCTGCTAGACAATAAGTCTGAATTA
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTA
1355989 CATTCGATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.03
41 66 0.97
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACAATAGTCTGAATTATAT
Found at i:1364006 original size:16 final size:16
Alignment explanation
Indices: 1363985--1364015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1363975 AGTAAGCTAT
*
1363985 TAAAGCTTAGCAAATC
1 TAAAGCTTAACAAATC
1364001 TAAAGCTTAACAAAT
1 TAAAGCTTAACAAAT
1364016 TATATAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (16 bp):
TAAAGCTTAACAAATC
Done.