Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold91
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: 988755
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.27
Warning! 189020 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:950035 original size:22 final size:22
Alignment explanation
Indices: 950009--950056 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
949999 TAGTAAACTT
* *
950009 ATAAATTGATTACTTGAATATA
1 ATAAATTAATTAATTGAATATA
* *
950031 ATAAATTAATTAATTTAATTTA
1 ATAAATTAATTAATTGAATATA
950053 ATAA
1 ATAA
950057 CTTATATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
ATAAATTAATTAATTGAATATA
Found at i:954604 original size:29 final size:29
Alignment explanation
Indices: 954562--954619 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
954552 ATTGTTGGAG
*
954562 AACGCAGGTTTATGTTGGTTAATAGTGGT
1 AACGCAGCTTTATGTTGGTTAATAGTGGT
*
954591 AACGCAGCTTTATGTTGGTTGATAGTGGT
1 AACGCAGCTTTATGTTGGTTAATAGTGGT
954620 TCATAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (29 bp):
AACGCAGCTTTATGTTGGTTAATAGTGGT
Found at i:955367 original size:87 final size:87
Alignment explanation
Indices: 955265--955446 Score: 348
Period size: 87 Copynumber: 2.1 Consensus size: 87
955255 CAGGTATGTC
955265 TACTACTTTCTTCGTTTGAATTGCCTTTGCACGTTACCTGATAATTGTTTTCAGTGCCATCATTC
1 TACTACTTTCTTCGTTTGAATTGCCTTTGCACGTTACCTGATAATTGTTTTCAGTGCCATCATTC
*
955330 ATATGTTTACATATTTTGCAGG
66 ATATGTCTACATATTTTGCAGG
955352 TACTACTTTCTTCGTTTGAATTGCCTTTGCACGTTACCTGATAATTGTTTTCAGTGCCATCATTC
1 TACTACTTTCTTCGTTTGAATTGCCTTTGCACGTTACCTGATAATTGTTTTCAGTGCCATCATTC
955417 ATATGTCTACATATTTTGCAGG
66 ATATGTCTACATATTTTGCAGG
955439 T-CTACTTT
1 TACTACTTT
955447 GGAAAGACGA
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 7 0.07
87 87 0.93
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (87 bp):
TACTACTTTCTTCGTTTGAATTGCCTTTGCACGTTACCTGATAATTGTTTTCAGTGCCATCATTC
ATATGTCTACATATTTTGCAGG
Found at i:959134 original size:18 final size:19
Alignment explanation
Indices: 959097--959135 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
959087 ATTACAAAAT
*
959097 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
959116 AATTTAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
959134 AA
1 AA
959136 AAATCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:960007 original size:8 final size:8
Alignment explanation
Indices: 959996--960052 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
959986 TTTATTAATT
959996 TTTTAAAA
1 TTTTAAAA
960004 TTTTAAAA
1 TTTTAAAA
* *
960012 ATTAAAAA
1 TTTTAAAA
*
960020 ATTTAAAA
1 TTTTAAAA
960028 -TTTAAAA
1 TTTTAAAA
*
960035 CTATTAAAA
1 -TTTTAAAA
960044 TTATTAAAA
1 TT-TTAAAA
960053 GGTATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 7 0.17
8 22 0.54
9 12 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTTAAAA
Found at i:967972 original size:26 final size:25
Alignment explanation
Indices: 967929--967981 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
967919 TTTGGGATGG
967929 AATGAGAGTAAATATTTT-AGGAGAA
1 AATGAGAGTAAATATTTTGAGG-GAA
967954 AATGAGAAGTAAA-AGTTTTGAGGGAA
1 AATGAG-AGTAAATA-TTTTGAGGGAA
967980 AA
1 AA
967982 GTAAAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.28
26 15 0.60
27 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.25
Consensus pattern (25 bp):
AATGAGAGTAAATATTTTGAGGGAA
Found at i:971233 original size:24 final size:24
Alignment explanation
Indices: 971205--971250 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
971195 AAATATTTTT
971205 TTATTTTATTTAATACTAATATAA
1 TTATTTTATTTAATACTAATATAA
*
971229 TTATTTTATTTAATATTAATAT
1 TTATTTTATTTAATACTAATAT
971251 TAATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTTTATTTAATACTAATATAA
Found at i:971270 original size:30 final size:30
Alignment explanation
Indices: 971214--971276 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
971204 TTTATTTTAT
* *
971214 TTAATACTAATATAATTATTTTATTTAATA
1 TTAATACTAATATAATAATTTAATTTAATA
* *
971244 TTAATATTAATATAA-AATTTAAATTTATTA
1 TTAATACTAATATAATAATTT-AATTTAATA
971274 TTA
1 TTA
971277 TCTTTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAATACTAATATAATAATTTAATTTAATA
Found at i:981480 original size:22 final size:22
Alignment explanation
Indices: 981454--981496 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
981444 TTAAAAATTA
* *
981454 TTTTGAACTTCCTTTTTTTTTT
1 TTTTGAAATTCCATTTTTTTTT
*
981476 TTTTGAAATTCGATTTTTTTT
1 TTTTGAAATTCCATTTTTTTT
981497 AATCAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTTGAAATTCCATTTTTTTTT
Done.