Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3496
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: 41009
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Found at i:2850 original size:29 final size:29
Alignment explanation
Indices: 2809--2910 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
2799 GGTTACAGAA
*
2809 CTCGCATACACAGTGCCTCAACAATC-GAT
1 CTCGCACACACAGTGCCTCAACAA-CGGAT
* **** *
2838 CTCGCACATACAGTG-CTCGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACGGAT
*
2866 CTCGCACACACAGTGCCTCAACAACTGAT
1 CTCGCACACACAGTGCCTCAACAACGGAT
*
2895 CTCGCACACAGAGTGC
1 CTCGCACACACAGTGC
2911 TCAGTTACGA
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
27 1 0.02
28 20 0.36
29 35 0.62
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAACAACGGAT
Found at i:2851 original size:57 final size:55
Alignment explanation
Indices: 2754--2940 Score: 230
Period size: 57 Copynumber: 3.3 Consensus size: 55
2744 GATCTCATTT
* * *
2754 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACAGAACTCG
1 CACACAC--AGTGCCTCAACAA-CGATCTCGCACACACAGTGCTCGGTTAC-GAACTCG
* *
2813 CATACACAGTGCCTCAACAATCGATCTCGCACATACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAA-CGATCTCGCACACACAGTGCTCGGTTAC-GAACTCG
* * *
2870 CACACACAGTGCCTCAACAACTGATCTCGCACACAGAGTGCTCAGTTACGAAACTCA
1 CACACACAGTGCCTCAACAAC-GATCTCGCACACACAGTGCTCGGTTACG-AACTCG
2927 CACACACAGTGCCT
1 CACACACAGTGCCT
2941 ATGTTCACTT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
56 2 0.02
57 106 0.93
59 6 0.05
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (55 bp):
CACACACAGTGCCTCAACAACGATCTCGCACACACAGTGCTCGGTTACGAACTCG
Found at i:4827 original size:26 final size:27
Alignment explanation
Indices: 4785--4854 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
4775 TCGATATTTT
4785 GCACACTAAGTGCCATTCTCAATATCTC
1 GCACACTAAGT-CCATTCTCAATATCTC
*
4813 GCACACTAAGT-CATTCTCAATATTTC
1 GCACACTAAGTCCATTCTCAATATCTC
* *
4839 GTACACTGAGTACCAT
1 GCACACTAAGT-CCAT
4855 ATTTGATTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 23 0.62
28 14 0.38
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (27 bp):
GCACACTAAGTCCATTCTCAATATCTC
Found at i:9285 original size:68 final size:67
Alignment explanation
Indices: 9213--9360 Score: 176
Period size: 67 Copynumber: 2.2 Consensus size: 67
9203 CATCATGTGT
* * * *
9213 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
9275 ATGTAG
62 ATGTAG
* * *
9281 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
9346 AG
66 AG
9348 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
9361 GAGATAAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 3 0.04
67 27 0.39
68 13 0.19
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.22
Consensus pattern (67 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:13692 original size:68 final size:67
Alignment explanation
Indices: 13620--13769 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
13610 CATCATGTGT
* * * *
13620 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
13682 ATGTAG
62 ATGTAG
** * *
13688 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
13753 AG
66 AG
13755 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
13770 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:13725 original size:64 final size:64
Alignment explanation
Indices: 13644--13827 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
13634 AGACATTATG
* *
13644 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
13708 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
13773 AA
63 AA
* * * *
13775 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
13828 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:32074 original size:47 final size:46
Alignment explanation
Indices: 31923--32088 Score: 137
Period size: 47 Copynumber: 3.5 Consensus size: 46
31913 ATTTGGTGCG
* *
31923 GCCAGTGTAAGACATGTCTGGGACAATGC-TCGGCC-ACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGAC-ATGCATCGGCCGACATGA-GATA
* * *
31969 GCCAGTGTAAGACATGTTTGGGACATGGCATCAAGTACAAGA-ATGAG-T-
1 GCCAGTGTAAGACATGTCTGGGACAT-GCATC--G-GC-CGACATGAGATA
*
32017 GCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-C-CGACATGAGATA
* *
32064 GCCAGTGTAAGACGTGTCTAGGACA
1 GCCAGTGTAAGACATGTCTGGGACA
32089 CCATACGGCT
Statistics
Matches: 96, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
45 9 0.09
46 27 0.28
47 29 0.30
48 24 0.25
49 1 0.01
50 2 0.02
51 3 0.03
52 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCGACATGAGATA
Found at i:36496 original size:1 final size:1
Alignment explanation
Indices: 36490--36514 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
36480 CGAGTCTGAA
36490 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
36515 CCTATTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:40969 original size:41 final size:44
Alignment explanation
Indices: 40877--41001 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 44
40867 GTGTTTATCA
* * * **
40877 TGTAAGACCACGTCTGGGACATTGGCATCGACT-TATGATTTATT
1 TGTAAGACCATGTCTGGGACAGTGGCATCGA-TATTTGATTTACC
*
40921 TGTAAGACCATGTCTGGGACA-T-GCATC-ATATTTGATTTCCC
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTTACC
* *
40962 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATT
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATT
41002 AGCATGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.39
42 6 0.09
43 6 0.09
44 30 0.43
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTTACC
Done.