Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1856
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: 27140
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:933 original size:42 final size:43
Alignment explanation
Indices: 886--998 Score: 156
Period size: 43 Copynumber: 2.7 Consensus size: 43
876 TGAGTTATCG
* * *
886 TGTAAGACCACGTCTGGGACATTGGTATCG-TATTTGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTACA
* * *
928 TGTAAGACCTTGTCTGGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTACA
*
971 TGTAAGACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
999 TGTACGAGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 25 0.42
43 35 0.58
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTACA
Found at i:5049 original size:49 final size:49
Alignment explanation
Indices: 4887--5064 Score: 150
Period size: 48 Copynumber: 3.7 Consensus size: 49
4877 GTTATTTGAG
* * * * * ** *
4887 AGCCAGTGTAAGACCATATTTAGGACATGGCATCGACATTAAGATA--AG
1 AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTCGAGATATGAA
* * *
4935 AGCTAGTGTAAGACATGTCTGGCACAT-GCATCGGCCTCGAGATATGCA
1 AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGAA
* * * *
4983 AGCCAGTTTAAGACATGTCTGGGACATGGCGTCGGCCTCG-G-TTTTAA
1 AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGAA
*
5030 TAGTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 -AGCCAGTGTAAGA-CATGTCTGGGACATGGCATC
5065 AAATTGATGG
Statistics
Matches: 104, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
46 13 0.12
47 13 0.12
48 48 0.46
49 30 0.29
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (49 bp):
AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGATATGAA
Found at i:6831 original size:14 final size:14
Alignment explanation
Indices: 6812--6842 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6802 AAGTGTTAGC
6812 CACATAAGCTGAGA
1 CACATAAGCTGAGA
6826 CACATAAGCTGAGA
1 CACATAAGCTGAGA
6840 CAC
1 CAC
6843 GGCTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (14 bp):
CACATAAGCTGAGA
Found at i:15952 original size:24 final size:23
Alignment explanation
Indices: 15911--15982 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
15901 AAAGTCTGTC
*
15911 AGGAGAGGA-TTAGGAGTTGATAA
1 AGGATAGGATTTAGGAGTTGAT-A
15934 AGGATAGGATTTAGGAGTTGATA
1 AGGATAGGATTTAGGAGTTGATA
* **
15957 AGGATACGATTTAGGAGCAGATA
1 AGGATAGGATTTAGGAGTTGATA
15980 AGG
1 AGG
15983 GAGGAAATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 32 0.73
24 12 0.27
ACGTcount: A:0.38, C:0.03, G:0.36, T:0.24
Consensus pattern (23 bp):
AGGATAGGATTTAGGAGTTGATA
Found at i:18780 original size:39 final size:40
Alignment explanation
Indices: 18578--18796 Score: 250
Period size: 40 Copynumber: 5.5 Consensus size: 40
18568 TATTCGAATG
* * *
18578 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
18618 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
*
18658 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
18698 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * **
18737 ATATCCGGGCTAAGACCCGAAGAC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
18776 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
18797 ATACTTGGGT
Statistics
Matches: 153, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
37 1 0.01
38 13 0.08
39 51 0.33
40 86 0.56
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:20759 original size:27 final size:26
Alignment explanation
Indices: 20654--20765 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
20644 AGGAAGCATC
* **
20654 CTGGTGGCTATGCCACAATTATCTAAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
20681 CTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
20708 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
20736 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
20762 CTGG
1 CTGG
20766 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.68
28 17 0.23
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:20760 original size:54 final size:54
Alignment explanation
Indices: 20654--20765 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
20644 AGGAAGCATC
* *
20654 CTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATATATCTGTT
* * * *
20708 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCT-AATCTGGTGACTCTGCCACATATATCTGTT
20762 CTGG
1 CTGG
20766 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATATATCTGTT
Done.