Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2757
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: 7467
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Found at i:944 original size:38 final size:40
Alignment explanation
Indices: 902--998 Score: 126
Period size: 41 Copynumber: 2.5 Consensus size: 40
892 CCATCTTTTC
* * *
902 TCTCTCTTCCTATCATCCTCC-TCTTTATTATCT-TCCTA
1 TCTCTCCTCCTATCATCCTCCATCTCTACTATCTCTCCTA
* *
940 TCTCTCCTCCTATCACCCTCCTATCTCTACTATCTCTCCTC
1 TCTCTCCTCCTATCATCCTCC-ATCTCTACTATCTCTCCTA
981 TCTCTCCTCCTATCATCC
1 TCTCTCCTCCTATCATCC
999 CTCTTATCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
38 19 0.38
40 10 0.20
41 21 0.42
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.43
Consensus pattern (40 bp):
TCTCTCCTCCTATCATCCTCCATCTCTACTATCTCTCCTA
Found at i:3088 original size:17 final size:16
Alignment explanation
Indices: 3066--3112 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
3056 GGTTTTCCTC
3066 TCTTTTTTTGTATTTGT
1 TCTTTTTTTGTATTT-T
*
3083 TCTTTTTTTTTATTTT
1 TCTTTTTTTGTATTTT
* *
3099 TATTTTTTGGTATT
1 TCTTTTTTTGTATT
3113 CTTGAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.79
Consensus pattern (16 bp):
TCTTTTTTTGTATTTT
Found at i:3090 original size:16 final size:16
Alignment explanation
Indices: 3068--3112 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3058 TTTTCCTCTC
*
3068 TTTTTTTGTATTTGTTC
1 TTTTTTTGTATTT-TTA
*
3085 TTTTTTTTTATTTTTA
1 TTTTTTTGTATTTTTA
*
3101 TTTTTTGGTATT
1 TTTTTTTGTATT
3113 CTTGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTTTTTGTATTTTTA
Found at i:4241 original size:12 final size:12
Alignment explanation
Indices: 4221--4264 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
4211 AGAAAGAAGA
*
4221 GATAAGAGGGAT
1 GATAGGAGGGAT
4233 GATAGGAGGGAT
1 GATAGGAGGGAT
4245 GATAGGAGGAGA-
1 GATAGGAGG-GAT
4257 GATAGGAG
1 GATAGGAG
4265 AGATAATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.48, T:0.14
Consensus pattern (12 bp):
GATAGGAGGGAT
Found at i:4273 original size:12 final size:12
Alignment explanation
Indices: 4230--4278 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4220 AGATAAGAGG
*
4230 GATGATAGGAGG
1 GATGATAGGAGA
4242 GATGATAGGAGGA
1 GATGATAGGA-GA
4255 GA-GATAGGAGA
1 GATGATAGGAGA
*
4266 GATAATA-GAGA
1 GATGATAGGAGA
4277 GA
1 GA
4279 GGACGGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 20 0.61
13 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATGATAGGAGA
Found at i:7285 original size:16 final size:16
Alignment explanation
Indices: 7264--7297 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7254 AAGTAGGATG
*
7264 ATGGTTCTATGTGCCT
1 ATGGTTCTATGTGACT
*
7280 ATGGTTCTGTGTGACT
1 ATGGTTCTATGTGACT
7296 AT
1 AT
7298 AGAGAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (16 bp):
ATGGTTCTATGTGACT
Done.