Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00989.N5
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: 1885
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:1129 original size:93 final size:93
Alignment explanation
Indices: 970--1138 Score: 257
Period size: 93 Copynumber: 1.8 Consensus size: 93
960 CTAGGAAGCT
* * * * * * *
970 TGAGGCATGGTCTTGACAGACAATTGGTAGAGGTGCCGAGAACCTTGAATGGTAACTTGCCTTAC
1 TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
1035 ATGCATGAGCACAAGCATGAGCATGAAG
66 ATGCATGAGCACAAGCATGAGCATGAAG
* *
1063 TGAGGCATAGTCTTGACAGACAAGTGGTAGGGGTGCCAAGAACCATAAATGATAACTTGTATTAC
1 TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
1128 ATGCATGAGCA
66 ATGCATGAGCA
1139 TGAAAATAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (93 bp):
TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
ATGCATGAGCACAAGCATGAGCATGAAG
Found at i:1178 original size:75 final size:75
Alignment explanation
Indices: 1069--1213 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 75
1059 GAAGTGAGGC
* * * * * **
1069 ATAGTCTTGACAGACAAGTGGTAGGGGTGCCAAGAACCATAAATGATAACTTGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
1134 GAGCATGAAA
66 GAGCATGAAA
* *
1144 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
1209 GAGCA
66 GAGCA
1214 CAAGCCAGCG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (75 bp):
ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
GAGCATGAAA
Found at i:1288 original size:84 final size:84
Alignment explanation
Indices: 1144--1297 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 84
1134 GAGCATGAAA
* *
1144 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGAACTACATGCAT
1209 GAGCACAAGCCAGCGAGGC
66 GAGCACAAGCCAGCGAGGC
* * * * * *
1228 ATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGAATGGTAACTTC-AACTACATGCA
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAAC-ACGAACTACATGCA
1292 TGAGCA
65 TGAGCA
1298 TGAGCATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 60 0.98
85 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (84 bp):
ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGAACTACATGCAT
GAGCACAAGCCAGCGAGGC
Found at i:1682 original size:78 final size:78
Alignment explanation
Indices: 1595--1755 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
1585 TATCTTTGGT
* * *
1595 TGCTTTGCTTTACTTGATGTTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGATTACATC
1 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
1660 TAAACAAGTTGCA
66 TAAACAAGTTGCA
*
1673 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGACTACATC
1 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
1738 TAAACAAGTTGCA
66 TAAACAAGTTGCA
1751 TGCTT
1 TGCTT
1756 ACATGGATAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (78 bp):
TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
TAAACAAGTTGCA
Done.