Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5588.1
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: 20729
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Found at i:6994 original size:40 final size:40
Alignment explanation
Indices: 6939--7066 Score: 177
Period size: 40 Copynumber: 3.2 Consensus size: 40
6929 TATTCGAATG
* * *
6939 ATATCCGAGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
6979 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
* * **
7019 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGT-AGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCA-CT
7059 ATATCCGG
1 ATATCCGG
7067 TTAAATTCCG
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 78 0.99
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
Found at i:7010 original size:176 final size:180
Alignment explanation
Indices: 6664--7019 Score: 483
Period size: 176 Copynumber: 2.0 Consensus size: 180
6654 ATTGCAAGAA
*
6664 TGATAAGTGTCTTGTGTTTGAGTTTTGCTAATGAAAATGAAATACAAATGTGTCATGATTTATTG
1 TGATAAGTGTCTTGTGTTTGAGTTTAGCTAATGAAAATGAAATACAAATGTGTCATGATTTATTG
* * * *
6729 GATTTATTGTTCAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCGAAGGCTTTGTGC
66 GA-TTA-T-TT--ATGTGCATGATTATTCGAATGATATCCGAGCTAAGTCCCGAAGGCTTTGTGC
*
6794 TAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAGGTT
126 TAAGTGACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGTCACTAAGGTT
***
6849 TGATAAGTGTCTTGTGTTTGAGCTTTAG-TAATGAAAATGAAATATGGATGTGTCATGATTTATT
1 TGATAAGTGTCTTGTGTTTGAG-TTTAGCTAATGAAAATGAAATACAAATGTGTCATGATTTATT
6913 -GA-TA-TT-TGTGCATGATTATTCGAATGATATCCGAGCTAAGTCCCGAAGGCATTTGTGCT-A
65 GGATTATTTATGTGCATGATTATTCGAATGATATCCGAGCTAAGTCCCGAAGGC-TTTGTGCTAA
* * *
6973 GTGACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTCACTA
129 GTGACCATATCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTCACTA
7020 TAACCGGGCT
Statistics
Matches: 156, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
175 1 0.01
176 82 0.53
177 8 0.05
179 2 0.01
182 2 0.01
184 2 0.01
185 55 0.35
186 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (180 bp):
TGATAAGTGTCTTGTGTTTGAGTTTAGCTAATGAAAATGAAATACAAATGTGTCATGATTTATTG
GATTATTTATGTGCATGATTATTCGAATGATATCCGAGCTAAGTCCCGAAGGCTTTGTGCTAAGT
GACCATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGTCACTAAGGTT
Found at i:7487 original size:56 final size:56
Alignment explanation
Indices: 7401--7515 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
7391 GCTTACTCCA
** *
7401 TTTCTTTGTTTCTCTGTTTTATAGATTTTGGCTCGTCAGCTATCGGATTCGGGATT
1 TTTCTTTGAATCTCTGTTTTATAGATTTTGGCTCGTCAGCTATCAGATTCGGGATT
*
7457 TTTCTTTGAATCTCTGTTTTATAGATTTTGGTTCGTCAGCTATCAGATTCGGGATT
1 TTTCTTTGAATCTCTGTTTTATAGATTTTGGCTCGTCAGCTATCAGATTCGGGATT
7513 TTT
1 TTT
7516 GGAAGTCGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (56 bp):
TTTCTTTGAATCTCTGTTTTATAGATTTTGGCTCGTCAGCTATCAGATTCGGGATT
Found at i:15486 original size:40 final size:40
Alignment explanation
Indices: 15050--15472 Score: 676
Period size: 40 Copynumber: 10.6 Consensus size: 40
15040 TGAATGATGT
* * * *
15050 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
15090 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
* * *
15130 CCGGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
15168 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
15208 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
15248 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
15288 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
15328 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
15368 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
15408 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
15448 CCGGGCTACGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
15473 AACGAGTAGC
Statistics
Matches: 363, Mismatches: 14, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
38 10 0.03
39 49 0.13
40 296 0.82
41 8 0.02
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Done.