Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold656
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: 12921
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:794 original size:29 final size:29
Alignment explanation
Indices: 762--836 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
752 AAATGACCTC
*
762 TTTATAATTTTTATAATTTATT-TGAATTT
1 TTTATAATTTTTATAAGTTATTATG-ATTT
791 TTTAT-ATTCTTTATAAGTTATTATGATTT
1 TTTATAATT-TTTATAAGTTATTATGATTT
*
820 TTTATAAGTTATTATAA
1 TTTATAA-TTTTTATAA
837 AGTTCTAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 3 0.08
29 26 0.65
30 9 0.22
31 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTATAATTTTTATAAGTTATTATGATTT
Found at i:824 original size:10 final size:10
Alignment explanation
Indices: 762--836 Score: 57
Period size: 10 Copynumber: 7.7 Consensus size: 10
752 AAATGACCTC
762 TTTATAA-TT
1 TTTATAATTT
771 TTTATAATTT
1 TTTATAATTT
*
781 ATTT-GAATTT
1 -TTTATAATTT
*
791 TTTAT-ATTC
1 TTTATAATTT
*
800 TTTATAAGTT
1 TTTATAATTT
* *
810 ATTATGATTT
1 TTTATAATTT
*
820 TTTATAAGTT
1 TTTATAATTT
*
830 ATTATAA
1 TTTATAA
837 AGTTCTAAAC
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
9 18 0.36
10 29 0.58
11 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTATAATTT
Found at i:6705 original size:27 final size:27
Alignment explanation
Indices: 6656--6711 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
6646 GCACCTTTTG
* * *
6656 CCAAAGGTACCAGTGACAGAGGCGGCA
1 CCAAAGGTACCACTGACACAGGCGACA
* *
6683 CCAAAGGTGCCACTGCCACAGGCGACA
1 CCAAAGGTACCACTGACACAGGCGACA
6710 CC
1 CC
6712 TGTGCCATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.34, G:0.29, T:0.07
Consensus pattern (27 bp):
CCAAAGGTACCACTGACACAGGCGACA
Found at i:6900 original size:20 final size:21
Alignment explanation
Indices: 6858--6901 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
6848 AAAGAAAAAA
*
6858 AAAGAGAGAAAGAGAATAGAG
1 AAAGAGAGAAAGAGAAGAGAG
6879 AAAG-GAGAAAGA-AAGAGAAG
1 AAAGAGAGAAAGAGAAGAG-AG
6899 AAA
1 AAA
6902 AAAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (21 bp):
AAAGAGAGAAAGAGAAGAGAG
Found at i:9561 original size:17 final size:17
Alignment explanation
Indices: 9541--9579 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9531 ATTTCAATGT
*
9541 ATTTTTCTGATTTTCTG
1 ATTTTTCTGATTTTCGG
*
9558 ATTTTTCTTATTTTCGG
1 ATTTTTCTGATTTTCGG
9575 ATTTT
1 ATTTT
9580 ATTACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (17 bp):
ATTTTTCTGATTTTCGG
Found at i:9830 original size:158 final size:159
Alignment explanation
Indices: 9629--9929 Score: 518
Period size: 159 Copynumber: 1.9 Consensus size: 159
9619 TTTATATTAT
*
9629 TTTGAAATGTATTATTTTAGTGTGTGTTTTATATAAATTTAGT-AAAAACCCTTATTTTGGCTAT
1 TTTGAAATGTATTATTTTAGTGTGTGTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCAT
*
9693 TTATTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTA
66 TTATTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCAT-TTTTA
9758 TT-ATTTT-GTATTATTTTAGTACATAAAG
130 TTCATTTTCGTATTATTTTAGTACATAAAG
*
9786 TTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCA
1 TTTGAAATGTATTATTTTAGTGTG-TGTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCA
* *
9851 TTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCATTTTTA
65 TTTATTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCATTTTTA
9916 TTCATTTTCGTATT
130 TTCATTTTCGTATT
9930 TTATTTTTTC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
157 24 0.18
158 25 0.19
159 81 0.60
160 5 0.04
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (159 bp):
TTTGAAATGTATTATTTTAGTGTGTGTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCAT
TTATTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCATTTTTAT
TCATTTTCGTATTATTTTAGTACATAAAG
Found at i:9924 original size:16 final size:17
Alignment explanation
Indices: 9903--9942 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
9893 AAAATATACT
9903 ATTTTCAT-TTTTATTC
1 ATTTTCATATTTTATTC
*
9919 ATTTTCGTATTTTATT-
1 ATTTTCATATTTTATTC
9935 -TTTTCATA
1 ATTTTCATA
9943 AACATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTCATATTTTATTC
Found at i:10105 original size:30 final size:30
Alignment explanation
Indices: 10071--10179 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 30
10061 AAATAAAATA
10071 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
*
10101 AAATAATAAAATAATAAGACATAGTATGTACATAACAT
1 --A-AAT--AAT-A-AA-ACATAGAATGTACATAACAT
10139 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
10169 AAA-AATTAAAA
1 AAATAA-TAAAA
10180 TTAAATTATG
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
29 2 0.03
30 27 0.40
31 2 0.03
32 2 0.03
33 6 0.09
35 6 0.09
36 2 0.03
37 2 0.03
38 19 0.28
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:10123 original size:38 final size:38
Alignment explanation
Indices: 10067--10149 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
10057 AAATAAATAA
10067 AATAAAATAATAAAACATAGAATGTACATAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAAT
* *
10105 AATAAAATAATAAGACATAGTATGTACATAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAAT
10143 AATAAAA
1 AATAAAA
10150 CATAGAATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (38 bp):
AATAAAATAATAAAACATAGAATGTACATAACATAAAT
Found at i:10169 original size:16 final size:16
Alignment explanation
Indices: 10119--10169 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10109 AAATAATAAG
*
10119 ACATAGTATGTACATA
1 ACATAGAATGTACATA
*
10135 ACATA-AATAATA-A-A
1 ACATAGAAT-GTACATA
10149 ACATAGAATGTACATA
1 ACATAGAATGTACATA
10165 ACATA
1 ACATA
10170 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (16 bp):
ACATAGAATGTACATA
Found at i:10219 original size:68 final size:66
Alignment explanation
Indices: 10065--10221 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 66
10055 ACAAATAAAT
* *
10065 AAAATAAAAT-AATA-AAACATAGAATGTACATAACATAAATAATAAAATAATAAGACATAGTAT
1 AAAATAACATAAATATAAACATAGAATGTACATAACATAAATAATAAAATAATAAGACATAGAAT
10128 G
66 G
* * *
10129 TACATAACATAAATAATAAAACATAGAATGTACATAACATAAA-AATTAAAATTAAATTATGA-A
1 AAAATAACATAAAT-AT-AAACATAGAATGTACATAACATAAATAA-TAAAA-T-AA-TAAGACA
10192 T-GAATG
60 TAGAATG
*
10198 AAAATATAGATAAATATAAACATA
1 AAAATA-ACATAAATATAAACATA
10222 CCTTAATATC
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
64 7 0.09
65 3 0.04
66 1 0.01
67 2 0.03
68 37 0.49
69 11 0.14
70 11 0.14
71 4 0.05
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.25
Consensus pattern (66 bp):
AAAATAACATAAATATAAACATAGAATGTACATAACATAAATAATAAAATAATAAGACATAGAAT
G
Found at i:10449 original size:13 final size:14
Alignment explanation
Indices: 10418--10460 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
10408 CCCTCCCTCT
*
10418 TCTTTTTCTCCTTC
1 TCTTTTTCTTCTTC
*
10432 TCTTTTTCTTTTTC
1 TCTTTTTCTTCTTC
10446 -CTTTTTCTTCCTTC
1 TCTTTTTCTT-CTTC
10460 T
1 T
10461 GCGCCTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTTTCTTCTTC
Found at i:10482 original size:3 final size:3
Alignment explanation
Indices: 10474--10507 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
10464 CCTCCTTCCC
10474 CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
10508 CCTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Done.