Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3609
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: 15301
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:1400 original size:50 final size:50
Alignment explanation
Indices: 1276--1523 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
1266 GATAATAACA
* * ** * *
1276 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
1327 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1377 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
1427 TGCC-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1481 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1524 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
49 37 0.22
50 56 0.33
51 33 0.19
52 2 0.01
53 1 0.01
54 2 0.01
55 4 0.02
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1465 original size:99 final size:104
Alignment explanation
Indices: 1275--1523 Score: 348
Period size: 99 Copynumber: 2.4 Consensus size: 104
1265 TGATAATAAC
**
1275 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1340 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1377 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTG-CCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
1439 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1481 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1524 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
99 40 0.30
100 10 0.08
101 36 0.27
102 3 0.02
103 1 0.01
104 2 0.02
105 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:1639 original size:13 final size:13
Alignment explanation
Indices: 1618--1649 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1608 GCTTGGATCA
*
1618 TCATCAAATAAAT
1 TCATAAAATAAAT
1631 TCATAAAATAAAT
1 TCATAAAATAAAT
1644 TCATAA
1 TCATAA
1650 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:1896 original size:30 final size:30
Alignment explanation
Indices: 1861--1918 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1851 CCTCGACTCT
*
1861 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1891 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1919 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:8880 original size:50 final size:50
Alignment explanation
Indices: 8802--8993 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
8792 GATAATAACA
* ** *
8802 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
8852 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
8902 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
8952 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
8994 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
49 7 0.05
50 122 0.95
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:9110 original size:13 final size:13
Alignment explanation
Indices: 9089--9120 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9079 GCTTGGATCA
*
9089 TCATCAAATAAAT
1 TCATAAAATAAAT
9102 TCATAAAATAAAT
1 TCATAAAATAAAT
9115 TCATAA
1 TCATAA
9121 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:9368 original size:30 final size:30
Alignment explanation
Indices: 9333--9390 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9323 CCTCGACTCT
*
9333 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9363 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9391 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.