Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3646
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: 13475
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Found at i:1598 original size:19 final size:20
Alignment explanation
Indices: 1574--1611 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1564 TGGTACACCA
1574 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
1593 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
1612 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:1953 original size:92 final size:92
Alignment explanation
Indices: 1839--2008 Score: 304
Period size: 92 Copynumber: 1.8 Consensus size: 92
1829 CCCCCTAAGT
* *
1839 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1904 CGAGTTCGGATGCCTAGTTACATTCAC
66 CGAGTTCGGATGCCTAGTTACATTCAC
* *
1931 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1996 CGAGTTCGGATGC
66 CGAGTTCGGATGC
2009 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTCAC
Found at i:2005 original size:46 final size:46
Alignment explanation
Indices: 1834--2005 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
1824 TAACCCCCCC
* * *
1834 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
1880 TAAATGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA
* *
1926 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1972 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2006 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 94 0.88
47 2 0.02
48 4 0.04
49 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:2024 original size:46 final size:46
Alignment explanation
Indices: 1836--2024 Score: 142
Period size: 46 Copynumber: 4.1 Consensus size: 46
1826 ACCCCCCCTA
* ** * *
1836 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
* *
1881 AAATGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
1929 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
1974 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
2020 AGTGA
1 AGTGA
2025 CATGTCACTT
Statistics
Matches: 115, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
44 9 0.08
45 2 0.02
46 94 0.82
47 1 0.01
48 4 0.03
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:9168 original size:19 final size:20
Alignment explanation
Indices: 9144--9181 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
9134 GGTACCACCA
9144 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
9163 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
9182 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:9510 original size:45 final size:45
Alignment explanation
Indices: 9403--9524 Score: 194
Period size: 45 Copynumber: 2.8 Consensus size: 45
9393 GTAACCCCCC
* * * *
9403 TAAGTGAACTCAGACTCAACTCAACGAGCTCGG-CGTTGCATCTA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
9447 TAA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
9491 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
9525 TGCTCAACCA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 27 0.38
44 15 0.21
45 30 0.42
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
Found at i:10898 original size:14 final size:14
Alignment explanation
Indices: 10876--10905 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10866 TTGAATCTCA
*
10876 TCTTTTTTTTGTTT
1 TCTTATTTTTGTTT
10890 TCTTATTTTTGTTT
1 TCTTATTTTTGTTT
10904 TC
1 TC
10906 GGTTTCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.10, G:0.07, T:0.80
Consensus pattern (14 bp):
TCTTATTTTTGTTT
Found at i:12949 original size:251 final size:253
Alignment explanation
Indices: 12487--12960 Score: 720
Period size: 251 Copynumber: 1.9 Consensus size: 253
12477 TTCAAAATAA
* *
12487 ATTTTCTAAATAAGGCAATATTTGGCGTTTGGAAATTTCGAGAAATCATGCCCTACGTGCTGGGT
1 ATTTTCTAAACAAGGCAATATTTGGCGTTTGGAAATTTCGAGAAATCATACCCTACGTGCTGGGT
* * * *
12552 TTCGATTTATCGTTTGACCGAACAACTTAATATCCTTTTTAAAATTTCAATGCATAAGTTTTGGG
66 TTCGATTTATCGTTTGACCAAACAACTGAATATCCTTTTTAAAATTTCAATGCATAAATTTTGGA
* *
12617 AATCATGAGATGATTTTGGTATTGAAGGTTTAAAATATCGTGTCCTACGTGCTGGATGTGATATT
131 AATCATGAGACGATTTTGGTATCGAAGGTTTAAAATATCGTGTCCTACGTGCTGGATGTGATATT
* * * *
12682 TTATTTCTTTGAAACAATATAATCTTAACTGTTTCAAACTATTGCATTTTTATTCGAG
196 GTATTTCTTCGAAACAAGAGAATCTTAACTGTTTCAAACTATTGCATTTTTATTCGAG
**
12740 ATTTT-TAAACAAGGCAATATTTGGCGTTTGGAAATTTCGAGAAATTGTACCCTACGTGCT-GGT
1 ATTTTCTAAACAAGGCAATATTTGGCGTTTGGAAATTTCGAGAAATCATACCCTACGTGCTGGGT
* * *
12803 TTTGATTTATCGTTTGACTAAACAA-TCGAATATCCTTTTTAAATTTTCAATGCATAAATTTTGG
66 TTCGATTTATCGTTTGACCAAACAACT-GAATATCCTTTTTAAAATTTCAATGCATAAATTTTGG
* * * * *
12867 AAATTATGAGACGATTTTGGTATCGAAGGTTTGAAATGTTGTGTCCTACGTGTTGGATGTGATAT
130 AAATCATGAGACGATTTTGGTATCGAAGGTTTAAAATATCGTGTCCTACGTGCTGGATGTGATAT
12932 TGTATTTCTTCGAAACAAGAGAATCTTAA
195 TGTATTTCTTCGAAACAAGAGAATCTTAA
12961 TATTCACTTC
Statistics
Matches: 198, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
250 1 0.01
251 141 0.71
252 51 0.26
253 5 0.03
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (253 bp):
ATTTTCTAAACAAGGCAATATTTGGCGTTTGGAAATTTCGAGAAATCATACCCTACGTGCTGGGT
TTCGATTTATCGTTTGACCAAACAACTGAATATCCTTTTTAAAATTTCAATGCATAAATTTTGGA
AATCATGAGACGATTTTGGTATCGAAGGTTTAAAATATCGTGTCCTACGTGCTGGATGTGATATT
GTATTTCTTCGAAACAAGAGAATCTTAACTGTTTCAAACTATTGCATTTTTATTCGAG
Done.