Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold610
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: 54397
ACGTcount: A:0.11, C:0.06, G:0.07, T:0.15
Warning! 33429 characters in sequence are not A, C, G, or T
Found at i:35192 original size:26 final size:23
Alignment explanation
Indices: 35163--35219 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
35153 CCCTTCACAT
35163 TCCGTCCCGGTTCAGTTGTTTTAG
1 TCCGT-CCGGTTCAGTTGTTTTAG
35187 T--GTCCGGTTCAGTTGTTTTAG
1 TCCGTCCGGTTCAGTTGTTTTAG
35208 T--GTCCGGTTCAG
1 TCCGTCCGGTTCAG
35220 ATTTTTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 30 0.91
22 2 0.06
24 1 0.03
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (23 bp):
TCCGTCCGGTTCAGTTGTTTTAG
Found at i:35226 original size:21 final size:21
Alignment explanation
Indices: 35169--35219 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
35159 ACATTCCGTC
35169 CCGGTTCAGTTGTTTTAGTGT
1 CCGGTTCAGTTGTTTTAGTGT
35190 CCGGTTCAGTTGTTTTAGTGT
1 CCGGTTCAGTTGTTTTAGTGT
35211 CCGGTTCAG
1 CCGGTTCAG
35220 ATTTTTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.18, G:0.29, T:0.43
Consensus pattern (21 bp):
CCGGTTCAGTTGTTTTAGTGT
Found at i:39134 original size:75 final size:76
Alignment explanation
Indices: 39010--39164 Score: 276
Period size: 75 Copynumber: 2.1 Consensus size: 76
39000 AGGTACAAGT
*
39010 TATTTTGTCCTCACGACTAACTAAGCAGTAAACATTTCTGCCCTCTATCATAGAGGAAACTACAA
1 TATTTTGTCCTCACGACTAACTAAGCAGTAAACATTTATGCCCTCTATCATAGAGGAAACTACAA
39075 TTGTGGCTGGG
66 TTGTGGCTGGG
* *
39086 TATTTTGTCGT-ACGACTAACTGAGCAGTAAACATTTATGCCCTCTATCATAGAGGAAACTACAA
1 TATTTTGTCCTCACGACTAACTAAGCAGTAAACATTTATGCCCTCTATCATAGAGGAAACTACAA
39150 TTGTGGCTGGG
66 TTGTGGCTGGG
39161 TATT
1 TATT
39165 AATTTGGAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 66 0.87
76 10 0.13
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (76 bp):
TATTTTGTCCTCACGACTAACTAAGCAGTAAACATTTATGCCCTCTATCATAGAGGAAACTACAA
TTGTGGCTGGG
Found at i:43161 original size:22 final size:22
Alignment explanation
Indices: 43136--43179 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43126 ATGTATATTT
43136 TATACATTT-TGTATAATTAATG
1 TATACATTTGT-TATAATTAATG
* *
43158 TATATATTTGTTTTAATTAATG
1 TATACATTTGTTATAATTAATG
43180 CATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
TATACATTTGTTATAATTAATG
Found at i:47036 original size:29 final size:29
Alignment explanation
Indices: 47004--47063 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
46994 TGGGAACATC
47004 TCTGTTTTTTAGTTTTTGATACATGCTTT
1 TCTGTTTTTTAGTTTTTGATACATGCTTT
47033 TCTGTTTTTTAGTTTTTGATACATGCTTT
1 TCTGTTTTTTAGTTTTTGATACATGCTTT
47062 TC
1 TC
47064 ACTTGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.12, G:0.13, T:0.62
Consensus pattern (29 bp):
TCTGTTTTTTAGTTTTTGATACATGCTTT
Found at i:51724 original size:31 final size:32
Alignment explanation
Indices: 51683--51744 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
51673 CAACCAGGGA
51683 TATCCCATTCT-AGGGATATCCCGGCTTGGGT
1 TATCCCATTCTGAGGGATATCCCGGCTTGGGT
* *
51714 TATCCTATTCTGGGGGATATCCCGGCTTGGG
1 TATCCCATTCTGAGGGATATCCCGGCTTGGG
51745 GTATAGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (32 bp):
TATCCCATTCTGAGGGATATCCCGGCTTGGGT
Done.