Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold48
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1102
ACGTcount: A:0.19, C:0.18, G:0.40, T:0.23
Found at i:105 original size:39 final size:39
Alignment explanation
Indices: 73--204 Score: 194
Period size: 39 Copynumber: 3.4 Consensus size: 39
63 CAGTGGTGGT
*
73 CAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTG
1 CAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTAGTGTG
*
112 CAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTAGTGTG
1 CAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTAGTGTG
* * *
151 CAGTGACGTAGTAGGCGTAGTCTGGGTACCAGT-GATGTG
1 CAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTAG-TGTG
*
190 CAGCGACGTAGTAGG
1 CAGCGACGTGGTAGG
205 ACCAGTAGAC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 84 0.99
ACGTcount: A:0.18, C:0.17, G:0.42, T:0.23
Consensus pattern (39 bp):
CAGCGACGTGGTAGGCGTAGTCTGGGTGCCAGTAGTGTG
Left flanking sequence: Indices 1 -- 72
AGTCTGGGTACCAGTGGTGTGCAGCGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAG
TGGTGGT
Right flanking sequence: Indices 205 -- 704
ACCAGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGTCAGCGACGTCGTAGGCGTAGTCTCAG
ATCCGGTGGTCGTCAGCGATGTGGTTTTAGACGTAGTGCTGGTGTTTGTGGTAGTCAGCTCAGAC
GTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCCACGTGGTGATAGT
CACTGTTATACACGACAGGGGTGGAGGTGTGGAGGTGGTGGAAGATTCTGATGTAGGACCGGTGG
ACGTAGTCAGAGTCGTAGGACCAGTGGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTA
GTGTGCAGCGACGTCGTAGGCGTATTCTGAGTACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGT
CTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTGCCAGTGGTGGTCAGCGACG
TCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAG
Found at i:210 original size:27 final size:26
Alignment explanation
Indices: 178--258 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
168 TAGTCTGGGT
178 ACCAGTGATGTGCAGCGACGTAGTAGG
1 ACCAGTGATGTGCAGCGACGT-GTAGG
*
205 ACCAGTAGACGTAGTCAGCGACGTG--GG
1 ACCAGT-GATGT-G-CAGCGACGTGTAGG
*
232 ACCAGTGGTAGT-CAGCGACGTCGTAGG
1 ACCAGTGAT-GTGCAGCGACGT-GTAGG
259 CGTAGTCTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
24 9 0.20
25 1 0.02
26 1 0.02
27 18 0.41
28 4 0.09
29 2 0.05
30 9 0.20
ACGTcount: A:0.25, C:0.21, G:0.37, T:0.17
Consensus pattern (26 bp):
ACCAGTGATGTGCAGCGACGTGTAGG
Left flanking sequence: Indices 1 -- 177
AGTCTGGGTACCAGTGGTGTGCAGCGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAG
TGGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGACGTGGTAGGCGTA
GTCTGAGTGCCAGTAGTGTGCAGTGACGTAGTAGGCGTAGTCTGGGT
Right flanking sequence: Indices 259 -- 758
CGTAGTCTCAGATCCGGTGGTCGTCAGCGATGTGGTTTTAGACGTAGTGCTGGTGTTTGTGGTAG
TCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCCAC
GTGGTGATAGTCACTGTTATACACGACAGGGGTGGAGGTGTGGAGGTGGTGGAAGATTCTGATGT
AGGACCGGTGGACGTAGTCAGAGTCGTAGGACCAGTGGTGGTCAGCGACGTGGTGGGCGTAGTCT
GGGTGCCAGTAGTGTGCAGCGACGTCGTAGGCGTATTCTGAGTACCAGTGGTGGTCAGCGACGTG
GTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGTGCCAGTGGT
GGTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCT
GAGTGCCAGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGTAC
Found at i:528 original size:39 final size:39
Alignment explanation
Indices: 484--1102 Score: 508
Period size: 39 Copynumber: 15.2 Consensus size: 39
474 GAGTCGTAGG
*
484 ACCAGTGGTG-GTCAGCGACGTGGTGGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
* * * * *
523 GCCAGTAGTGTGCAGCGACGTCGTAGGCGTATTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
562 ACCAGTGGTG-GTCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
* *
601 ACCAGTGGTGTGCAGCGACGTAGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
* *
640 GCCAGTGGTG-GTCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
*
679 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
* * *
718 GCCAGTAGTGTGCAGCGACGTCGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
757 ACCAGTGGTG-GTCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
* * * *
796 ACCAGTGGTGTGCAGCGACGTAGTGGGACCAGTAGAC-GTAGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGG--C-GTAGTCTG-GGT
* * * * *
838 -CAGAGTCGTAG-GACCAGTG--GTGGTCAGCGACGTGGT-AGGCGT
1 AC-CAGTGGT-GTG--CAGCGACGTGGT-AG-G-CGTAGTCTGG-GT
*
880 AGTCTGAGTGCCTGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
1 A--C-CA------GTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
* *
928 ACCAGTGGTGTGCAGCGTA-GTAGGACCAGTAGACGTAGTCAGAGTCGT
1 ACCAGTGGTGTGCAGCG-ACGT--G----GTAGGCGTAGTCTG-G--GT
* *
976 AGGACCAGTGGTG-GTCAGCGACGTGGTGGGCGTAGTCTGAGT
1 ---ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
* * *
1018 GCCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAGT
1 ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
1057 ACCAGTGGTG-GTCAGCGACGTGGTAGGCGTAGTCTGGGT
1 ACCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGGGT
1096 ACCAGTG
1 ACCAGTG
Statistics
Matches: 474, Mismatches: 57, Indels: 98
0.75 0.09 0.16
Matches are distributed among these distances:
38 4 0.01
39 348 0.73
40 6 0.01
41 4 0.01
42 25 0.05
43 3 0.01
44 5 0.01
45 27 0.06
46 2 0.00
48 10 0.02
49 8 0.02
50 5 0.01
51 27 0.06
ACGTcount: A:0.17, C:0.19, G:0.41, T:0.23
Consensus pattern (39 bp):
ACCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGT
Left flanking sequence: Indices 1 -- 483
AGTCTGGGTACCAGTGGTGTGCAGCGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAG
TGGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGACGTGGTAGGCGTA
GTCTGAGTGCCAGTAGTGTGCAGTGACGTAGTAGGCGTAGTCTGGGTACCAGTGATGTGCAGCGA
CGTAGTAGGACCAGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGTCAGCGACGTCGTAGGCG
TAGTCTCAGATCCGGTGGTCGTCAGCGATGTGGTTTTAGACGTAGTGCTGGTGTTTGTGGTAGTC
AGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCCACGT
GGTGATAGTCACTGTTATACACGACAGGGGTGGAGGTGTGGAGGTGGTGGAAGATTCTGATGTAG
GACCGGTGGACGTAGTCAGAGTCGTAGG
Right flanking sequence: None
Found at i:570 original size:78 final size:78
Alignment explanation
Indices: 484--1102 Score: 572
Period size: 78 Copynumber: 7.6 Consensus size: 78
474 GAGTCGTAGG
* * *
484 ACCAGTGGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGACGTCGTAG
1 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTCGTAG
*
549 GCGTATTCTGAGT
66 GCGTAGTCTGAGT
*
562 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTAGTAG
1 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTCGTAG
627 GCGTAGTCTGAGT
66 GCGTAGTCTGAGT
* * *
640 GCCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTGGTAG
1 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTCGTAG
705 GCGTAGTCTGAGT
66 GCGTAGTCTGAGT
* * * *
718 GCCAGTAGT-GTGCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTG-GTCAGCGACGTGGT
1 ACCAGTGGTGGT-CAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTG-CAGCGACGTCGT
*
781 AGGCGTAGTCTGGGT
64 AGGCGTAGTCTGAGT
* * * * * * *
796 ACCAGTGGT-GTGCAGCGACGTAGTGGGACCAGTAGAC-GTAGT-CAGAGTCGTAG-GACCAGTG
1 ACCAGTGGTGGT-CAGCGACGTGGTAGG--C-GTAGTCTG-GGTAC-CAGTGGT-GTG--CAGCG
* * ** *
857 --GTGGTCAGCGACGTGGTAGGCGT
57 ACGTCGT-AG-G-CGTAGTCTGAGT
*
880 AGTCTGAGTGCCTGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCG
1 A--C-CAGTG---GT-G-GT-CAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCG
* *
945 TA-GTAGGACCAGTAGACGTAGTCAGAGTCGTAGG
57 -ACGT-----C-GTAGGCGTAGTC----T-G-AGT
* * *
979 ACCAGTGGTGGTCAGCGACGTGGTGGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTCGTAG
1 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTCGTAG
1044 GCGTAGTCTGAGT
66 GCGTAGTCTGAGT
1057 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTG
1 ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTG
Statistics
Matches: 454, Mismatches: 48, Indels: 78
0.78 0.08 0.13
Matches are distributed among these distances:
77 3 0.01
78 287 0.63
79 1 0.00
80 4 0.01
81 17 0.04
82 4 0.01
83 5 0.01
84 20 0.04
85 1 0.00
86 1 0.00
87 4 0.01
88 4 0.01
89 2 0.00
90 60 0.13
91 5 0.01
92 1 0.00
93 23 0.05
95 2 0.00
96 6 0.01
97 1 0.00
98 1 0.00
99 2 0.00
ACGTcount: A:0.17, C:0.19, G:0.41, T:0.23
Consensus pattern (78 bp):
ACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGACGTCGTAG
GCGTAGTCTGAGT
Left flanking sequence: Indices 1 -- 483
AGTCTGGGTACCAGTGGTGTGCAGCGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAG
TGGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGACGTGGTAGGCGTA
GTCTGAGTGCCAGTAGTGTGCAGTGACGTAGTAGGCGTAGTCTGGGTACCAGTGATGTGCAGCGA
CGTAGTAGGACCAGTAGACGTAGTCAGCGACGTGGGACCAGTGGTAGTCAGCGACGTCGTAGGCG
TAGTCTCAGATCCGGTGGTCGTCAGCGATGTGGTTTTAGACGTAGTGCTGGTGTTTGTGGTAGTC
AGCTCAGACGTCGTGGGGGATGTCTCCGATGACGTAGACACGAAAACCGTCGGCGTAGTCCACGT
GGTGATAGTCACTGTTATACACGACAGGGGTGGAGGTGTGGAGGTGGTGGAAGATTCTGATGTAG
GACCGGTGGACGTAGTCAGAGTCGTAGG
Right flanking sequence: None
Found at i:897 original size:132 final size:132
Alignment explanation
Indices: 730--1083 Score: 574
Period size: 129 Copynumber: 2.7 Consensus size: 132
720 CAGTAGTGTG
* * *
730 CAGCGACGTCGTAGGCGTAGTCTGGGTACCAGTGGTG-GTCAGCGACGTGGTAGGCGTAGTCTGG
1 CAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGTGTG-CAGCGACGTGGTAGGCGTAGTCTGG
*
794 GTACCAGTGGTGTGCAGCGACGTAGTGGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGT
65 GTACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGT
859 GGT
130 GGT
*
862 CAGCGACGTGGTAGGCGTAGTCTGAGTGCCTGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGG
1 CAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGG
927 TACCAGTGGTGTGCA--G-CGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTG
66 TACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTG
989 GT
131 GT
* * *
991 CAGCGACGTGGTGGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTCGTAGGCGTAGTCTGAG
1 CAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGG
*
1056 TACCAGTGGTG-GTCAGCGACGTGGTAGG
66 TACCAGTGGTGTG-CAGCGACGTAGTAGG
1084 CGTAGTCTGG
Statistics
Matches: 207, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
128 1 0.00
129 121 0.58
130 1 0.00
131 1 0.00
132 82 0.40
133 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.22
Consensus pattern (132 bp):
CAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTGGTGTGCAGCGACGTGGTAGGCGTAGTCTGGG
TACCAGTGGTGTGCAGCGACGTAGTAGGACCAGTAGACGTAGTCAGAGTCGTAGGACCAGTGGTG
GT
Left flanking sequence: Indices 230 -- 729
GGACCAGTGGTAGTCAGCGACGTCGTAGGCGTAGTCTCAGATCCGGTGGTCGTCAGCGATGTGGT
TTTAGACGTAGTGCTGGTGTTTGTGGTAGTCAGCTCAGACGTCGTGGGGGATGTCTCCGATGACG
TAGACACGAAAACCGTCGGCGTAGTCCACGTGGTGATAGTCACTGTTATACACGACAGGGGTGGA
GGTGTGGAGGTGGTGGAAGATTCTGATGTAGGACCGGTGGACGTAGTCAGAGTCGTAGGACCAGT
GGTGGTCAGCGACGTGGTGGGCGTAGTCTGGGTGCCAGTAGTGTGCAGCGACGTCGTAGGCGTAT
TCTGAGTACCAGTGGTGGTCAGCGACGTGGTAGGCGTAGTCTGGGTACCAGTGGTGTGCAGCGAC
GTAGTAGGCGTAGTCTGAGTGCCAGTGGTGGTCAGCGACGTCGTAGGCGTAGTCTGGGTACCAGT
GGTGTGCAGCGACGTGGTAGGCGTAGTCTGAGTGCCAGTAGTGTG
Right flanking sequence: Indices 1084 -- 1102
CGTAGTCTGGGTACCAGTG
Done.