Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold281
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: 12731
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:6194 original size:50 final size:50
Alignment explanation
Indices: 6084--6330 Score: 257
Period size: 50 Copynumber: 4.8 Consensus size: 50
6074 GATAATAACA
* * ** * *
6084 TGCCAAAGCCATGTCCCAGACAT-GTCTTACA-TGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
6133 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
6183 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
6233 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCT--C-TCATC-T-CGG
* *
6288 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
6331 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
49 22 0.13
50 96 0.57
51 3 0.02
52 1 0.01
53 4 0.02
54 2 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:6256 original size:100 final size:105
Alignment explanation
Indices: 6083--6330 Score: 332
Period size: 100 Copynumber: 2.4 Consensus size: 105
6073 TGATAATAAC
**
6083 ATGCCAAAGCCATGTCCCAGACAT-GTCTTACAT-GGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
6146 TCCCAGACATGGTCTTATAGGGGACCT-C-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCCATCATCTTAAGG
* *
6183 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
6246 TCCCAGACATGGTCTTACAGGGGACCTCCCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCT-CCATCATCTTAAGG
* *
6288 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
6331 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
99 23 0.18
100 56 0.43
101 3 0.02
102 1 0.01
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCCATCATCTTAAGG
Found at i:6446 original size:13 final size:13
Alignment explanation
Indices: 6425--6456 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6415 GCTTGGATCA
*
6425 TCATCAAATAAAT
1 TCATAAAATAAAT
6438 TCATAAAATAAAT
1 TCATAAAATAAAT
6451 TCATAA
1 TCATAA
6457 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:6702 original size:30 final size:30
Alignment explanation
Indices: 6667--6723 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
6657 CATCGACTCT
*
6667 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
6697 AACTTTTACATAATTATATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
6724 AAGGCTCGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:9472 original size:29 final size:30
Alignment explanation
Indices: 9413--9470 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9403 TCCGAGCCTT
*
9413 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
9443 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
9471 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:9700 original size:13 final size:13
Alignment explanation
Indices: 9682--9713 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9672 TTTCCAGCAA
9682 TTATGAATTTATT
1 TTATGAATTTATT
9695 TTATGAATTTATT
1 TTATGAATTTATT
*
9708 TGATGA
1 TTATGA
9714 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:9921 original size:50 final size:50
Alignment explanation
Indices: 9808--10049 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
9798 ATTTGGGTAA
* * *
9808 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
9864 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
9914 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
9964 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
10014 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
10050 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:9997 original size:100 final size:103
Alignment explanation
Indices: 9808--10057 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
9798 ATTTGGGTAA
9808 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
9873 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
9914 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
9976 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
10014 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
10058 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:12287 original size:17 final size:18
Alignment explanation
Indices: 12248--12288 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
12238 GTTCTGGTAG
12248 AAAGAGCTTGTAAAGTAA
1 AAAGAGCTTGTAAAGTAA
*
12266 GAAGA-CTTGTTAAAG-AA
1 AAAGAGCTTG-TAAAGTAA
12283 AAAGAG
1 AAAGAG
12289 AAGAGCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (18 bp):
AAAGAGCTTGTAAAGTAA
Done.