Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1849
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: 21894
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6438 original size:52 final size:51
Alignment explanation
Indices: 6360--6489 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 51
6350 CCGAAATATT
* *
6360 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
6412 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
*
6464 GCAAATTGCCTGCATGTATCGATACA
1 GAAAATTGCCTGCATGTATCGATACA
6490 AAGATCAGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:6504 original size:51 final size:50
Alignment explanation
Indices: 6360--6509 Score: 162
Period size: 52 Copynumber: 2.9 Consensus size: 50
6350 CCGAAATATT
* * *
6360 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGG
6412 GAAAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGG
* *
6464 GCAAA-TTGCCTGCATGTATCGATACAAAGATCAGTATATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
6510 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 32 0.37
52 46 0.53
53 1 0.01
54 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (50 bp):
GAAAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGG
Found at i:8169 original size:22 final size:21
Alignment explanation
Indices: 8121--8165 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
8111 ATTTTTTATC
*
8121 ATATA-AAAAATAAATATGTA
1 ATATATAAAAATAAATATATA
* *
8141 TTATATAAAAATAAATTTATA
1 ATATATAAAAATAAATATATA
8162 ATAT
1 ATAT
8166 TATAGTGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATATAAAAATAAATATATA
Found at i:9703 original size:25 final size:27
Alignment explanation
Indices: 9650--9704 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
9640 ATGTGTTTAC
*
9650 TTTTACTTATTTATATATTTAAAATAT
1 TTTTACTTATTTATATATTTAAAAAAT
9677 TTTTA-TT-TTTATAT-TTTAATAAAAT
1 TTTTACTTATTTATATATTTAA-AAAAT
9702 TTT
1 TTT
9705 AATTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 2 0.08
27 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTACTTATTTATATATTTAAAAAAT
Found at i:10902 original size:19 final size:19
Alignment explanation
Indices: 10856--10907 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
10846 TAAAATTTTT
* * *
10856 TATATATTAATTTAGCTAA
1 TATATCTTAATTTATCCAA
*
10875 T-TTTCTTAATTTATCCAA
1 TATATCTTAATTTATCCAA
10893 TATATCTTAATTTAT
1 TATATCTTAATTTAT
10908 TTGGTTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.54
Consensus pattern (19 bp):
TATATCTTAATTTATCCAA
Found at i:12031 original size:143 final size:140
Alignment explanation
Indices: 11764--12040 Score: 362
Period size: 143 Copynumber: 1.9 Consensus size: 140
11754 ATTTAAATAT
* *
11764 AAATGTGATATATATTAAAAATATTATATTGTATTAATCTTGTTTTTAGCAAATACATTATATTT
1 AAATATGATATATATTAAAAATATTATATTATATTAATCTTGTTTTTA-CAAATACATTATATTT
* * * * * * *
11829 ATATCATTTTTTTCAATTATCAAATATACTTGAGATAATAATTGTCCGACAGCTGTTTGAGTTTT
65 ATATCATTTTTTTCAATTATCAAATATACTTAAAATAATAATTATCCCACAACTATTTGAGCTTT
11894 AAAAAATTTTG
130 AAAAAATTTTG
*
11905 AAATATGATATATATTTAAAAATATTATATTATATTAATTTTGTTTTGT-CAAATACATTATATT
1 AAATATGATATATA-TTAAAAATATTATATTATATTAATCTTGTTTT-TACAAATACATTATA-T
* *
11969 TGTATTAT-ATTTTTTTCTATTATCAAATATACTTAAAATAATAATTATCCCA-ATATTATTTGA
63 T-TA-TATCATTTTTTTCAATTATCAAATATACTTAAAATAATAATTATCCCACA-ACTATTTGA
12032 GCTTTAAAA
125 GCTTTAAAA
12041 TTTTTTCATC
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
141 26 0.22
142 33 0.28
143 56 0.47
144 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (140 bp):
AAATATGATATATATTAAAAATATTATATTATATTAATCTTGTTTTTACAAATACATTATATTTA
TATCATTTTTTTCAATTATCAAATATACTTAAAATAATAATTATCCCACAACTATTTGAGCTTTA
AAAAATTTTG
Found at i:15737 original size:33 final size:33
Alignment explanation
Indices: 15695--15758 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
15685 ACAGAAGAAT
*
15695 AGGAACCACTTTCATTAGTCGTGAAAAACTGAC
1 AGGAACCACTTTCATTAGTAGTGAAAAACTGAC
*
15728 AGGAACCACTTTCATTAGTAGTGGAAAACTG
1 AGGAACCACTTTCATTAGTAGTGAAAAACTG
15759 GTTTTAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (33 bp):
AGGAACCACTTTCATTAGTAGTGAAAAACTGAC
Done.