Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1725
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: 37125
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Found at i:5849 original size:27 final size:27
Alignment explanation
Indices: 5816--5967 Score: 225
Period size: 27 Copynumber: 5.6 Consensus size: 27
5806 TAAATTGTGC
*
5816 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
5843 AGCACTAAGTGTGCG-GTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
5870 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
5897 AGCACTAAGTGTGCGGAGTTTGATTATGT
1 AGCACTAAGTGTGC-GAG-TTGACTATGT
* *
5926 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
5953 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5968 GACTAAATAT
Statistics
Matches: 117, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
27 87 0.74
28 7 0.06
29 23 0.20
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:5940 original size:56 final size:56
Alignment explanation
Indices: 5816--5969 Score: 249
Period size: 56 Copynumber: 2.8 Consensus size: 56
5806 TAAATTGTGC
*
5816 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGC-G-GTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGGAGTTTGACTATGT
*
5870 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGGAGTTTGACTATGT
* * *
5926 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGA
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGGA
5970 CTAAATATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 40 0.43
55 1 0.01
56 52 0.56
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (56 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGGAGTTTGACTATGT
Found at i:13782 original size:28 final size:27
Alignment explanation
Indices: 13725--13876 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
13715 TAAATTGTGC
*
13725 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
13752 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
13780 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
13807 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
13835 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
13862 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13877 GACTTAAATA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:13789 original size:55 final size:55
Alignment explanation
Indices: 13725--13876 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
13715 TAAATTGTGC
*
13725 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
13780 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
13835 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
13877 GACTTAAATA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:21761 original size:28 final size:27
Alignment explanation
Indices: 21704--21855 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
21694 TAAATTGTGC
*
21704 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
21731 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
21759 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
21786 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
21814 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
21841 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21856 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:21768 original size:55 final size:55
Alignment explanation
Indices: 21704--21855 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
21694 TAAATTGTGC
*
21704 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
21759 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
21814 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
21856 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:27325 original size:39 final size:39
Alignment explanation
Indices: 27121--27343 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
27111 TTGAATGCTG
* * * * * *
27121 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
27161 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
27201 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
27241 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
27281 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
27320 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
27344 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:27363 original size:79 final size:80
Alignment explanation
Indices: 27196--27378 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
27186 GTGCGAGATA
* * *
27196 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
27261 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
27276 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
27340 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
27355 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
27379 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:35208 original size:39 final size:39
Alignment explanation
Indices: 35004--35226 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
34994 TTGAATGCTG
* * * * * *
35004 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
35044 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
35084 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
35124 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
35164 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
35203 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35227 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:35246 original size:79 final size:80
Alignment explanation
Indices: 35079--35261 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
35069 GTGCGAGATA
* * *
35079 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
35144 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
35159 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
35223 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
35238 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
35262 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Done.