Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3760
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: 10286
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Found at i:1415 original size:50 final size:48
Alignment explanation
Indices: 1291--1479 Score: 222
Period size: 50 Copynumber: 3.9 Consensus size: 48
1281 GATAATAACA
* **
1291 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT--TGG
* * * *
1342 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-T-GG
*
1392 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA--TCTCGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTTGG
* *
1438 TGCCCATGCCATGTCCCAGACATGGTCTTATA-GGGACCTCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1480 TCATGATCTT
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
45 4 0.03
46 31 0.26
47 5 0.04
48 5 0.04
49 1 0.01
50 40 0.34
51 33 0.28
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTTGG
Found at i:1652 original size:13 final size:13
Alignment explanation
Indices: 1631--1662 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1621 GCTTGGATCA
*
1631 TCATCAAATAAAT
1 TCATAAAATAAAT
1644 TCATAAAATAAAT
1 TCATAAAATAAAT
1657 TCATAA
1 TCATAA
1663 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:1909 original size:30 final size:30
Alignment explanation
Indices: 1874--1931 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1864 CCTCGACTCT
*
1874 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1904 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1932 AAGGCTCGGA
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:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:8965 original size:50 final size:50
Alignment explanation
Indices: 8841--9089 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
8831 GATAATAACA
* * ** * *
8841 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
8892 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
8942 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
8992 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
9047 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
9090 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:9019 original size:100 final size:104
Alignment explanation
Indices: 8840--9089 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
8830 TGATAATAAC
**
8840 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
8905 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
8942 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
9005 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
9047 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
9090 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:9205 original size:13 final size:13
Alignment explanation
Indices: 9184--9215 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9174 GCTTGGATCA
*
9184 TCATCAAATAAAT
1 TCATAAAATAAAT
9197 TCATAAAATAAAT
1 TCATAAAATAAAT
9210 TCATAA
1 TCATAA
9216 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:9462 original size:30 final size:30
Alignment explanation
Indices: 9427--9484 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9417 CCTCGACTCT
*
9427 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9457 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9485 AAGGCTCGGA
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:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Done.