Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_50906
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, 948
Length: 1581
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Found at i:566 original size:42 final size:43
Alignment explanation
Indices: 520--669 Score: 110
Period size: 42 Copynumber: 3.3 Consensus size: 43
510 GATTGGGATT
520 TTGAAG-AAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAA
1 TTGAAGCAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAA
* * * **
562 TTGAAGCAAAAA--AATGATGAATCTAATGATAAACTGGAAGCTGAGATTGGGATT
1 TTGAAGCAAAAATCAAAG-TGAA--T--TGA-AGA-TGG-A----A-ATTGTGAAA
616 TTGAAG-AAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAA
1 TTGAAGCAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAA
658 TTGAAGCAAAAA
1 TTGAAGCAAAAA
670 AATGATGAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 33
0.65 0.08 0.27
Matches are distributed among these distances:
41 3 0.04
42 22 0.27
43 11 0.14
44 1 0.01
46 3 0.04
47 3 0.04
48 6 0.07
49 3 0.04
50 3 0.04
52 1 0.01
53 6 0.07
54 16 0.20
55 3 0.04
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.24
Consensus pattern (43 bp):
TTGAAGCAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAA
Found at i:625 original size:96 final size:96
Alignment explanation
Indices: 500--693 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
490 AATACTGAAT
500 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
1 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
565 AAGCAAAAAAATGATGAATCTAATGATAAAC
66 AAGCAAAAAAATGATGAATCTAATGATAAAC
596 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
1 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
661 AAGCAAAAAAATGATGAATCTAATGATAAAC
66 AAGCAAAAAAATGATGAATCTAATGATAAAC
692 TG
1 TG
694 ACTGTATTCG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.25
Consensus pattern (96 bp):
TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
AAGCAAAAAAATGATGAATCTAATGATAAAC
Found at i:953 original size:42 final size:41
Alignment explanation
Indices: 877--1258 Score: 291
Period size: 42 Copynumber: 9.1 Consensus size: 41
867 TGAGACACAA
* * * * * *
877 GTCACTAAGAGTTTGCTTGAGCTTATGGGAACTGATCAAACG
1 GTCACAAAGAGCTTGCCTGAGCCTATGGG-ACTGACCAAAGG
** **
919 GTCACAAAGAGCTTGAATGAGCCTATGGAGACTGACCGGAGG
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
* * * *
961 GGCACCAAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGG
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* * * * *
1003 GTCACCAAGAACTTGCCTGGGCCTATGGGGAATGACCAAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* *
1045 GTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
*
1087 GT-AGCAAAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGG
1 GTCA-CAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* * * *
1129 GTCACCAAAGAG-TTGGCTGAGCCTACGGGGACTGACCAATGT
1 GTCA-CAAAGAGCTTGCCTGAGCCTA-TGGGACTGACCAAAGG
* * * * ** * *
1171 GTCCCAAAGACCTTGCCTAAGCCAATGGAGACCAACCAACGT
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
* * * * * *
1213 ATCACAAAGACCTTGCCTAAGCCTATGGAGATTGGCCAAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
1255 GTCA
1 GTCA
1259 TCAACTCTAA
Statistics
Matches: 279, Mismatches: 54, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
41 9 0.03
42 259 0.93
43 11 0.04
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (41 bp):
GTCACAAAGAGCTTGCCTGAGCCTATGGGACTGACCAAAGG
Found at i:1102 original size:126 final size:125
Alignment explanation
Indices: 919--1202 Score: 374
Period size: 126 Copynumber: 2.3 Consensus size: 125
909 TGATCAAACG
** * *
919 GTCACAAAGAGCTTGAATGAGCCTATGGAGACTGACCGGAGGGGCACCAAGAACTTGCCTGAGCC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAGGAGCA-CAAGAACTTGCCTGAGCC
* *
984 TATAGGGACTGACCAGAGGGTCACC-AAGAACTTGCCTGGGCCTATGGGGAATGACCAAAGT
65 TATAGGGACTGACCAGAGGGTCACCAAAG-ACTTGCCTGAGCCTACGGGGAATGACCAAAGT
* *
1045 GTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGTGTAGCA-AAGAGCTTGCCTGAGC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAG-G-AGCACAAGAACTTGCCTGAGC
* * * *
1109 CTATAGGGACTGACCAGAGGGTCACCAAAGAGTTGGCTGAGCCTACGGGGACTGACCAATGT
64 CTATAGGGACTGACCAGAGGGTCACCAAAGACTTGCCTGAGCCTACGGGGAATGACCAAAGT
* * * *
1171 GTCCCAAAGACCTTGCCTAAGCCAATGGAGAC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGAC
1203 CAACCAACGT
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
126 131 0.95
127 4 0.03
128 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (125 bp):
GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAGGAGCACAAGAACTTGCCTGAGCCT
ATAGGGACTGACCAGAGGGTCACCAAAGACTTGCCTGAGCCTACGGGGAATGACCAAAGT
Found at i:1221 original size:126 final size:126
Alignment explanation
Indices: 967--1238 Score: 343
Period size: 126 Copynumber: 2.2 Consensus size: 126
957 GAGGGGCACC
* *
967 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGGGCCTATGGG
1 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGAGCCTACGGG
* * * * ** *
1032 GAATGACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGTGTAGCA
66 GAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAAGTATAGCA
* * *
1093 AAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAA-AGAGTTGGCTGAGCCTACGG
1 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGA-ACTTGCCTGAGCCTACGG
* * *
1157 GGACTGACCAATGTGTCCCAAAGACCTTGCCTAAGCCAATGGAGACCAACC-AACGTATCA-CA
65 GGAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAA-GTAT-AGCA
* *
1219 AAGACCTTGCCTAAGCCTAT
1 AAGAACTTGCCTGAGCCTAT
1239 GGAGATTGGC
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
125 3 0.02
126 122 0.97
127 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.18
Consensus pattern (126 bp):
AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGAGCCTACGGG
GAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAAGTATAGCA
Done.