Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g02546.N4
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, 691
Length: 1153
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Found at i:432 original size:3 final size:3
Alignment explanation
Indices: 426--487 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
416 AGAAGAAGAA
426 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
474 GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
488 GGAGGAGGAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:534 original size:9 final size:9
Alignment explanation
Indices: 531--589 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
521 GGACGATGAC
*
531 GACGATGAT
1 GACGACGAT
540 GACGACGAT
1 GACGACGAT
549 GACGACGAT
1 GACGACGAT
*
558 GACGACGAC
1 GACGACGAT
*
567 GACGACGGT
1 GACGACGAT
*
576 GACGACGGT
1 GACGACGAT
585 GACGA
1 GACGA
590 TGACAATGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.37, T:0.10
Consensus pattern (9 bp):
GACGACGAT
Found at i:542 original size:12 final size:12
Alignment explanation
Indices: 522--582 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
512 GGAGGAGGAG
522 GACGATGACGAC
1 GACGATGACGAC
*
534 GATGATGACGAC
1 GACGATGACGAC
* * *
546 GATGACGACGAT
1 GACGATGACGAC
*
558 GACGACGACGAC
1 GACGATGACGAC
*
570 GACGGTGACGAC
1 GACGATGACGAC
582 G
1 G
583 GTGACGATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.36, T:0.10
Consensus pattern (12 bp):
GACGATGACGAC
Found at i:582 original size:3 final size:3
Alignment explanation
Indices: 522--573 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
512 GGAGGAGGAG
* * * * *
522 GAC GAT GAC GAC GAT GAT GAC GAC GAT GAC GAC GAT GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
570 GAC G
1 GAC G
574 GTGACGACGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.10
Consensus pattern (3 bp):
GAC
Found at i:643 original size:3 final size:3
Alignment explanation
Indices: 635--661 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
625 GATCATTTTT
635 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
662 CTCATTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:806 original size:51 final size:51
Alignment explanation
Indices: 729--1033 Score: 164
Period size: 51 Copynumber: 6.3 Consensus size: 51
719 ATCAACACTT
* * * **
729 GAAGAAGAAGAAGACTCACCATTGCAATCATCATTGTCAATAGGGGAAGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATCATCATTGTCAACAGAAGAAGAA
* * * *
780 GATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAACAGAAGAAGAAGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATCATCATTGTCAAC---AGAAGAAGAA
*** * *
834 GAAGAAGAAGAAGACTCACTGTTACAATCATCAAAT-TCAAC------AGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATCATC-ATTGTCAACAGAAGAAGAA
* * * * * ** *
879 GAAGATGAAGAACATTCACCAGTGGGATCAAT-ACT-T-----GAAGAAGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATC-ATCATTGTCAACAGAAGAAGAA
* * *
924 GA------AGAAGACTCACCATTGCAATCATCATTGTCAACAGAGGAAGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATCATCATTGTCAACAGAAGAAGAA
* * * *
969 GATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAACAGAAGAAGAA
1 GAAGAAGAAGAAGACTCACAAATGCAATCATCATTGTCAACAGAAGAAGAA
1020 GAAGAAGAAGAAGA
1 GAAGAAGAAGAAGA
1034 AGAAGAAGAA
Statistics
Matches: 189, Mismatches: 42, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
38 2 0.01
39 18 0.10
40 1 0.01
44 3 0.02
45 40 0.21
46 2 0.01
51 83 0.44
54 38 0.20
55 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (51 bp):
GAAGAAGAAGAAGACTCACAAATGCAATCATCATTGTCAACAGAAGAAGAA
Found at i:827 original size:3 final size:3
Alignment explanation
Indices: 821--847 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
811 CATTTTCAAC
821 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
848 CTCACTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:827 original size:186 final size:187
Alignment explanation
Indices: 635--1036 Score: 716
Period size: 189 Copynumber: 2.1 Consensus size: 187
625 GATCATTTTT
*
635 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCATTGTTACAATCACCAAATTCAACAGAAGAAGATG
1 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
*
700 AGGAACATTCACCAATGGGATCAACACTT-GAAGAAGAAGAAGACTCACCATTGCAATCATCATT
66 AAGAACATTCACCAATGGGATCAACACTTAGAAGAAGAAGAAGACTCACCATTGCAATCATCATT
* *
764 GTCAATAGGGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAAC
131 GTCAACAGAGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAAC
*
821 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCATCAAATTCAACAGAAGAAGATG
1 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
* *
886 AAGAACATTCACCAGTGGGATCAATACTTGAAGAAGAAGAAGAAGACTCACCATTGCAATCATCA
66 AAGAACATTCACCAATGGGATCAACACTT--AGAAGAAGAAGAAGACTCACCATTGCAATCATCA
951 TTGTCAACAGAGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAAC
129 TTGTCAACAGAGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAAC
1010 AGAAGAAGAAGAAGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGAAGAAGAAGAAGA
1037 AGAAGAAGAA
Statistics
Matches: 206, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
186 89 0.43
189 117 0.57
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (187 bp):
AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
AAGAACATTCACCAATGGGATCAACACTTAGAAGAAGAAGAAGACTCACCATTGCAATCATCATT
GTCAACAGAGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAAC
Found at i:832 original size:54 final size:54
Alignment explanation
Indices: 729--890 Score: 177
Period size: 54 Copynumber: 3.1 Consensus size: 54
719 ATCAACACTT
* * * *
729 GAAGAAGAAGAAGACTCACCATTGCAATCATCATTGTCAATAG--G-GGAAGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAACAGAAGAAGAAGAA
* * * *
780 GATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAACAGAAGAAGAAGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAACAGAAGAAGAAGAA
** * ** *
834 GAAGAAGAAGAAGACTCACTGTTACAATCATCAAATTCAACAGAAGAAGATGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAACAGAAGAAGAAGAA
888 GAA
1 GAA
891 CATTCACCAG
Statistics
Matches: 90, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 36 0.40
53 1 0.01
54 53 0.59
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (54 bp):
GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAACAGAAGAAGAAGAA
Found at i:1016 original size:3 final size:3
Alignment explanation
Indices: 1010--1076 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
1000 CATTTTCAAC
1010 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1058 AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA A
1077 AGCAAAAAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Done.