Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1447
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: 33669
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:6065 original size:43 final size:43
Alignment explanation
Indices: 5918--6074 Score: 110
Period size: 43 Copynumber: 3.7 Consensus size: 43
5908 TGTGATTTTG
* *
5918 TGTAAGATCACGTCT-GGA-ACGTTGGCATCGAT-TTGAGATTTACA
1 TGTAAGACCACGTCTGGGATA-G-TGGCATCGATATT-TGA-TTACA
* * * * ***
5962 CGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTTTG
1 TGTAAGACCACGTCTGGGATAGTGGCATCGATATTTGATTACA
* *
6004 TGTAACACGC-CCTCTGGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGAC-CACGTCTGGGATAGTGGCATCGATATTTGATTACA
*
6047 TGTAAGACCACGTTTGGGAT-GTTGGCAT
1 TGTAAGACCACGTCTGGGATAG-TGGCAT
6075 TGTACTAGCT
Statistics
Matches: 86, Mismatches: 20, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
42 26 0.30
43 34 0.40
44 22 0.26
45 3 0.03
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATAGTGGCATCGATATTTGATTACA
Found at i:22107 original size:71 final size:67
Alignment explanation
Indices: 22030--22171 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
22020 TCACCAGATA
* * * *
22030 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCATCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
22095 GGCTGC
62 GGCTGC
* * *
22101 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGTAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
22166 GC
66 GC
22168 CAGA
1 CAGA
22172 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 39 0.61
71 25 0.39
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:22149 original size:27 final size:26
Alignment explanation
Indices: 22101--22152 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
22091 GCGAGGCTGC
*
22101 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
22127 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
22153 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:22448 original size:19 final size:19
Alignment explanation
Indices: 22426--22500 Score: 150
Period size: 19 Copynumber: 3.9 Consensus size: 19
22416 TGGCCTATTA
22426 GCCCGTTTTCGGCCCATTG
1 GCCCGTTTTCGGCCCATTG
22445 GCCCGTTTTCGGCCCATTG
1 GCCCGTTTTCGGCCCATTG
22464 GCCCGTTTTCGGCCCATTG
1 GCCCGTTTTCGGCCCATTG
22483 GCCCGTTTTCGGCCCATT
1 GCCCGTTTTCGGCCCATT
22501 AAGCCCAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 56 1.00
ACGTcount: A:0.05, C:0.37, G:0.25, T:0.32
Consensus pattern (19 bp):
GCCCGTTTTCGGCCCATTG
Found at i:22477 original size:38 final size:38
Alignment explanation
Indices: 22417--22506 Score: 153
Period size: 38 Copynumber: 2.3 Consensus size: 38
22407 TGGGCGCGTT
*
22417 GGCCTATTAGCCCGTTTTCGGCCCATTGGCCCGTTTTC
1 GGCCCATTAGCCCGTTTTCGGCCCATTGGCCCGTTTTC
*
22455 GGCCCATTGGCCCGTTTTCGGCCCATTGGCCCGTTTTC
1 GGCCCATTAGCCCGTTTTCGGCCCATTGGCCCGTTTTC
22493 GGCCCATTAAGCCC
1 GGCCCATT-AGCCC
22507 AAAAATACCG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 44 0.92
39 4 0.08
ACGTcount: A:0.09, C:0.37, G:0.24, T:0.30
Consensus pattern (38 bp):
GGCCCATTAGCCCGTTTTCGGCCCATTGGCCCGTTTTC
Found at i:22910 original size:27 final size:27
Alignment explanation
Indices: 22864--22949 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
22854 GGCAAAATGT
* * * * *
22864 TAATTTTACCCCACAAGGGTATCTCAG
1 TAATTCTACCCTACAGGGGTATTTCGG
*
22891 TAATTCTACCCTATAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGG
* *
22918 TATTTCTACCTTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGG
22945 TAATT
1 TAATT
22950 TTACAACTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGG
Found at i:30566 original size:64 final size:65
Alignment explanation
Indices: 30486--30666 Score: 181
Period size: 67 Copynumber: 2.8 Consensus size: 65
30476 AGACATTCTG
* *
30486 ATGTAGCTAGGTCGCATGGGTGATAC-GATGTGTACACCATGTAGACAAGAGAACTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACAGATGTGTACACCATGTAGACAAGAGAACTACGAGATAA
* * * * * * *
30550 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACAGATG-TGTACACCATGTAGACAAGAGAACTACGAGAT
30615 AA
64 AA
* * * * *
30617 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAG
1 ATGTAGCTAGGTCGCATGGGTGATACAGATGTGTACACCATGTAG-ACAAGAG
30667 GGCCAAACTA
Statistics
Matches: 94, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
62 1 0.01
63 16 0.17
64 21 0.22
65 7 0.07
66 18 0.19
67 31 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (65 bp):
ATGTAGCTAGGTCGCATGGGTGATACAGATGTGTACACCATGTAGACAAGAGAACTACGAGATAA
Done.