Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3547
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: 35268
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8409 original size:3 final size:3
Alignment explanation
Indices: 8401--8438 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8391 AACAAATAGG
8401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
8439 GGACTAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16986 original size:20 final size:19
Alignment explanation
Indices: 16956--16993 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16946 TTATTAAAAA
16956 TTAAAAAAAAAATCATATT
1 TTAAAAAAAAAATCATATT
*
16975 TTAAAGAAAAAAATTATAT
1 TTAAA-AAAAAAATCATAT
16994 ATAACAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
TTAAAAAAAAAATCATATT
Found at i:19043 original size:26 final size:26
Alignment explanation
Indices: 19007--19056 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
18997 AAAGTGTAAG
19007 TCATTTTCCGGAAAAGAGCTCATCAA
1 TCATTTTCCGGAAAAGAGCTCATCAA
19033 TCATTTTCCGGAAAAGAGCTCATC
1 TCATTTTCCGGAAAAGAGCTCATC
19057 TGTAGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (26 bp):
TCATTTTCCGGAAAAGAGCTCATCAA
Found at i:19246 original size:22 final size:20
Alignment explanation
Indices: 19201--19251 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
19191 TTATATTTAG
*
19201 TAATATAATAAATTATTAATA
1 TAATA-AATAAATTATTAAAA
19222 TAATAAATAAAATTCATTAAAA
1 TAATAAAT-AAATT-ATTAAAA
19244 TAATAAAT
1 TAATAAAT
19252 TATTTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
22 14 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAAATAAATTATTAAAA
Found at i:19287 original size:13 final size:14
Alignment explanation
Indices: 19271--19312 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
19261 TTTCAATTTT
19271 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
19284 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
19299 ATTTTAAATAATAT
1 ATTTT-AATAATAT
19313 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:19297 original size:16 final size:16
Alignment explanation
Indices: 19275--19311 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
19265 AATTTTATTT
19275 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
19292 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
19307 TAATA
1 TAATA
19312 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:19364 original size:15 final size:15
Alignment explanation
Indices: 19344--19395 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 15
19334 ATTCAATATT
19344 AATATTTTAATAATA
1 AATATTTTAATAATA
*
19359 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
19378 AATATTTTAATAATA
1 AATATTTTAATAATA
19393 AAT
1 AAT
19396 GGTTTGTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 13 0.42
16 2 0.06
17 4 0.13
18 2 0.06
19 10 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:20412 original size:15 final size:15
Alignment explanation
Indices: 20392--20421 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20382 TCTCACTTGT
20392 GTCACTTGTAGAGTC
1 GTCACTTGTAGAGTC
*
20407 GTCACTTGTGGAGTC
1 GTCACTTGTAGAGTC
20422 TTAAAAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (15 bp):
GTCACTTGTAGAGTC
Found at i:22531 original size:14 final size:14
Alignment explanation
Indices: 22512--22543 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
22502 TCCAATCACC
22512 GGGCCAGATTGGTT
1 GGGCCAGATTGGTT
*
22526 GGGCCAGTTTGGTT
1 GGGCCAGATTGGTT
22540 GGGC
1 GGGC
22544 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.47, T:0.28
Consensus pattern (14 bp):
GGGCCAGATTGGTT
Found at i:27650 original size:14 final size:14
Alignment explanation
Indices: 27631--27662 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27621 TCCAATCACC
27631 GGGCCAGATTGGTT
1 GGGCCAGATTGGTT
*
27645 GGGCCAGTTTGGTT
1 GGGCCAGATTGGTT
27659 GGGC
1 GGGC
27663 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.47, T:0.28
Consensus pattern (14 bp):
GGGCCAGATTGGTT
Found at i:33188 original size:15 final size:15
Alignment explanation
Indices: 33168--33198 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33158 GTATAAAGAT
33168 TGAATTAGTTCATTC
1 TGAATTAGTTCATTC
33183 TGAATTAGTTCATTC
1 TGAATTAGTTCATTC
33198 T
1 T
33199 ATAGTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TGAATTAGTTCATTC
Done.