Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold328
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: 936272
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 6 of 6
Found at i:918187 original size:79 final size:80
Alignment explanation
Indices: 918094--918251 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 80
918084 ATATGAGTGA
*
918094 AGTTTATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTGTTGTGA-TG
1 AGTTTATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATTG
918158 ATTTTAACAAATAAC
66 ATTTTAACAAATAAC
918173 AGTTTATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATTG
1 AGTTTATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATTG
918238 ATTTTAACAAATAA
66 ATTTTAACAAATAA
918252 AACACTAACT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
79 61 0.79
80 16 0.21
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (80 bp):
AGTTTATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATTG
ATTTTAACAAATAAC
Found at i:918282 original size:79 final size:79
Alignment explanation
Indices: 918098--918285 Score: 202
Period size: 79 Copynumber: 2.4 Consensus size: 79
918088 GAGTGAAGTT
* * * * *
918098 TATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTGTTGTGATGATTTT
1 TATACTATTATAATGACAATTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATGATTTT
* ***
918163 AACAAATAACAGTT
66 AACAAATAAAACAC
* * * *
918177 TATATTATTATTATTACATTTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATTGATTT
1 TATACTATTATAATGACAATTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGA-TGATTT
918242 TAACAAATAAAACAC
65 TAACAAATAAAACAC
*
918257 TA-ACTA-TA-AAGTGACTAATTGTTAGTTTG
1 TATACTATTATAA-TGAC-AATTATTAGTTTG
918286 TCAGAGTAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.01
78 5 0.05
79 71 0.74
80 19 0.20
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (79 bp):
TATACTATTATAATGACAATTATTAGTTTGCTGATTTTATTATTCAAATTTATTGTGATGATTTT
AACAAATAAAACAC
Found at i:927184 original size:18 final size:20
Alignment explanation
Indices: 927153--927189 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
927143 AAATCCAAAA
*
927153 TACAATAAGTTTGTCAAATG
1 TACAATAAGTTTGTAAAATG
927173 TACAA-AAG-TTGTAAAAT
1 TACAATAAGTTTGTAAAAT
927190 CAAAATCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (20 bp):
TACAATAAGTTTGTAAAATG
Found at i:928319 original size:14 final size:14
Alignment explanation
Indices: 928298--928338 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
928288 TTATATATTT
*
928298 TAAA-TAATATAAA
1 TAAATTAATAAAAA
928311 TAAATTAATAAAAA
1 TAAATTAATAAAAA
*
928325 TAAATCAATAAAAA
1 TAAATTAATAAAAA
928339 ATTATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATTAATAAAAA
Found at i:929397 original size:18 final size:18
Alignment explanation
Indices: 929376--929414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
929366 GGATTTAAAA
929376 TATTAAAATAATT-TATTT
1 TATTAAAAT-ATTATATTT
*
929394 TATTATAATATTATATTT
1 TATTAAAATATTATATTT
929412 TAT
1 TAT
929415 AATTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTAAAATATTATATTT
Found at i:929414 original size:15 final size:15
Alignment explanation
Indices: 929383--929425 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
929373 AAATATTAAA
*
929383 ATAATTTATTTTATT
1 ATAATTTATATTATT
929398 ATAATATTATATT-TT
1 ATAAT-TTATATTATT
*
929413 ATAATTTTTATTA
1 ATAATTTATATTA
929426 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.25
15 12 0.50
16 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATAATTTATATTATT
Found at i:935968 original size:19 final size:18
Alignment explanation
Indices: 935942--935980 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
935932 TCAATGCGTA
935942 AAATCTATATAACTATAT
1 AAATCTATATAACTATAT
935960 AAATACTATATAACTATAT
1 AAAT-CTATATAACTATAT
935979 AA
1 AA
935981 CTGTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATCTATATAACTATAT
Done.