Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold387
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: 361964
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 37635 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:266855 original size:27 final size:27
Alignment explanation
Indices: 266825--266876 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
266815 TATTTCTTTG
266825 AAGTTAAGATTAGATTTTTAA-ATTATT
1 AAGTTAA-ATTAGATTTTTAATATTATT
*
266852 AAGTTTAATTAGATTTTTAATATTA
1 AAGTTAAATTAGATTTTTAATATTA
266877 AATTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
AAGTTAAATTAGATTTTTAATATTATT
Found at i:267570 original size:18 final size:19
Alignment explanation
Indices: 267549--267584 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
267539 AAAAATTCAC
*
267549 ATAAA-TATTTTAATTGAA
1 ATAAAGTATTTAAATTGAA
267567 ATAAAGTATTTAAATTGA
1 ATAAAGTATTTAAATTGA
267585 GTTGAGGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
ATAAAGTATTTAAATTGAA
Found at i:271372 original size:35 final size:35
Alignment explanation
Indices: 271333--271404 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
271323 ATAAATGGTT
* * *
271333 TACTGGCTCTACGGAGCGACATCATGGAAATGATC
1 TACTGGCTCTACAGAGCGACACCATGAAAATGATC
* *
271368 TACTGGTTCTACAGAGCGACACCATGAAAATGGTC
1 TACTGGCTCTACAGAGCGACACCATGAAAATGATC
271403 TA
1 TA
271405 TTGACTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (35 bp):
TACTGGCTCTACAGAGCGACACCATGAAAATGATC
Found at i:273059 original size:25 final size:25
Alignment explanation
Indices: 273003--273050 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
272993 TTAACAATTT
273003 ATAGCTCGTGAGAGCATACCGATTC
1 ATAGCTCGTGAGAGCATACCGATTC
273028 ATAGCTCGTGAGAGCATACCGAT
1 ATAGCTCGTGAGAGCATACCGAT
273051 CTTCAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACCGATTC
Found at i:273090 original size:25 final size:25
Alignment explanation
Indices: 273005--273096 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
272995 AACAATTTAT
*
273005 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCATACCGATTCAC
*
273030 AGCTCGTGA-GAGCATACCGA-TCTTC
1 AGCTCGT-ATGAGCATACCGATTC-AC
**
273055 AGCTCAAATGAGCATACCGATTCAC
1 AGCTCGTATGAGCATACCGATTCAC
*
273080 AGGTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
273097 ATGTACATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.05
25 51 0.91
26 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTCAC
Found at i:279224 original size:7 final size:7
Alignment explanation
Indices: 279212--279262 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
279202 TAATTTGAAT
279212 CCTAAAC
1 CCTAAAC
279219 CCTAAAC
1 CCTAAAC
**
279226 TTTAAA-
1 CCTAAAC
279232 CCTAAAC
1 CCTAAAC
*
279239 CTTAAAC
1 CCTAAAC
279246 CCTAAAC
1 CCTAAAC
279253 CCTAAAC
1 CCTAAAC
279260 CCT
1 CCT
279263 GACCTTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
6 4 0.11
7 33 0.89
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:285205 original size:41 final size:40
Alignment explanation
Indices: 285131--285210 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 40
285121 TTGTAATATT
285131 ATTATTTATACTAAGTATTTAAAAGATAATTAAATATTTAG
1 ATTATTTATACTAAGTATTTAAAAGATAATTAAA-ATTTAG
* * * *
285172 ATTATTTTATATTAATTATTTACAA-ATATTTAAAATTTA
1 ATTA-TTTATACTAAGTATTTAAAAGATAATTAAAATTTA
285211 TATTTCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 5 0.15
41 12 0.35
42 17 0.50
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (40 bp):
ATTATTTATACTAAGTATTTAAAAGATAATTAAAATTTAG
Found at i:287846 original size:26 final size:26
Alignment explanation
Indices: 287810--287872 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
287800 TAGTGATTAT
287810 GTGATTATTTAGCAAGCTTTGAGCTG
1 GTGATTATTTAGCAAGCTTTGAGCTG
* *
287836 GTGATTTTTTAGCAAGCTTTGAGCCG
1 GTGATTATTTAGCAAGCTTTGAGCTG
*
287862 ATGATTATTTA
1 GTGATTATTTA
287873 ATAGGCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (26 bp):
GTGATTATTTAGCAAGCTTTGAGCTG
Found at i:289211 original size:21 final size:22
Alignment explanation
Indices: 289171--289218 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
289161 ACGGTTTGAG
* *
289171 CACACGGGCGTGTGGAGGTAGT
1 CACACGGGCATGTGGAGGTAGC
289193 CACACGGGCATGT-GAGGTAGC
1 CACACGGGCATGTGGAGGTAGC
289214 CACAC
1 CACAC
289219 AGGCTAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (22 bp):
CACACGGGCATGTGGAGGTAGC
Found at i:289760 original size:13 final size:13
Alignment explanation
Indices: 289742--289766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
289732 AACATATTTT
289742 TTTATTTGTGTAG
1 TTTATTTGTGTAG
289755 TTTATTTGTGTA
1 TTTATTTGTGTA
289767 ACACCCGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.20, T:0.64
Consensus pattern (13 bp):
TTTATTTGTGTAG
Found at i:297812 original size:18 final size:17
Alignment explanation
Indices: 297771--297813 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
297761 GTCGTTCGTG
297771 TTCAAAACGTTATTCAT
1 TTCAAAACGTTATTCAT
*
297788 TTACAAATCGTTATTCAAT
1 TT-CAAAACGTTATTC-AT
297807 TTCAAAA
1 TTCAAAA
297814 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (17 bp):
TTCAAAACGTTATTCAT
Found at i:301011 original size:39 final size:39
Alignment explanation
Indices: 300968--301046 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
300958 TTAACTTTTA
* * *
300968 CGGTTTAATCTTTTTTACTCAATTAAGTATCTAAATGTT
1 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
301007 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
1 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
301046 C
1 C
301047 AAATTTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44
Consensus pattern (39 bp):
CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
Found at i:305258 original size:37 final size:38
Alignment explanation
Indices: 305201--305276 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
305191 ATTTTTAACG
*
305201 TTAATTCTGTCCTATTATTTGCCCTAATTGACATAAAA
1 TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
305239 TTAATTCT-TCCCATTATTTGCCCTAATTGACATAAAA
1 TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
305276 T
1 T
305277 CCACCCTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (38 bp):
TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
Found at i:312992 original size:23 final size:23
Alignment explanation
Indices: 312915--313024 Score: 104
Period size: 23 Copynumber: 5.0 Consensus size: 23
312905 TCTGATCAGC
312915 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAT
****
312936 A-ACGACACACGGGGTGCCTG--
1 ATACGACACATAAAGTGCCTGAT
* *
312956 ATACGACATATAAAGTGCTTGAT
1 ATACGACACATAAAGTGCCTGAT
* *
312979 ATGCGACACGTAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAT
*
313002 GTACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAT
313025 CGGCAAGGCC
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
20 9 0.13
21 21 0.30
23 39 0.57
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAT
Found at i:314029 original size:13 final size:13
Alignment explanation
Indices: 314011--314040 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
314001 AACCTTTAGT
*
314011 TTTTCTTTTTTTC
1 TTTTCTTTCTTTC
314024 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
314037 TTTT
1 TTTT
314041 TCCTGCTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:323180 original size:25 final size:26
Alignment explanation
Indices: 323152--323266 Score: 73
Period size: 25 Copynumber: 4.6 Consensus size: 26
323142 CAAACCAAAC
323152 AAAGCCTATGTGACATA-TTATCTAG
1 AAAGCCTATGTGACATAGTTATCTAG
* * *
323177 AAAGCCTTTG-GGC-TAGTTAGCTA-
1 AAAGCCTATGTGACATAGTTATCTAG
* * *
323200 AAAGGCCTATGTGGCATA-TTATTTGG
1 AAA-GCCTATGTGACATAGTTATCTAG
** * *
323226 AAAAACTTTGTGACA-AGTTAT-TTG
1 AAAGCCTATGTGACATAGTTATCTAG
323250 AAATGCCTATGTGACAT
1 AAA-GCCTATGTGACAT
323267 TATTTTGGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
23 5 0.07
24 20 0.30
25 37 0.55
26 5 0.07
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (26 bp):
AAAGCCTATGTGACATAGTTATCTAG
Found at i:341750 original size:29 final size:31
Alignment explanation
Indices: 341702--341764 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
341692 GGGTCCAATT
* * *
341702 TTTTTAAAGTTGCTCGTAT-AGGAGTTAA-A
1 TTTTTAAAATTGATCATATAAGGAGTTAACA
*
341731 TTTTTAAAATTGATCATATAAGGATTTAACA
1 TTTTTAAAATTGATCATATAAGGAGTTAACA
341762 TTT
1 TTT
341765 ACAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 8 0.29
31 4 0.14
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (31 bp):
TTTTTAAAATTGATCATATAAGGAGTTAACA
Found at i:342699 original size:27 final size:27
Alignment explanation
Indices: 342669--342741 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
342659 ATAGGTGGTG
*
342669 CCTATCTGGTAGGCGCCACCGGTGACT
1 CCTATCTGATAGGCGCCACCGGTGACT
* *
342696 CCTATCTAATAGGCGCCACTGGTGACT
1 CCTATCTGATAGGCGCCACCGGTGACT
342723 CCTA-CTTGATAGGCGCCAC
1 CCTATC-TGATAGGCGCCAC
342742 TAGTGCTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (27 bp):
CCTATCTGATAGGCGCCACCGGTGACT
Found at i:344774 original size:62 final size:62
Alignment explanation
Indices: 344692--344852 Score: 198
Period size: 62 Copynumber: 2.6 Consensus size: 62
344682 CCGTGAGATT
* * **
344692 TTATACCACAAATAATGAGTTACACGACCAAGGCACACGCCTGTGTCCCTAGCCATGTGGTC
1 TTATACCACAAACAGTGAGTTACACGACCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
* * * * * *
344754 TTATACTATAAACAGTGAGTTATAC-AGCCAAAGCACACGCCCATGTCCCTGGCCGTGTGGTC
1 TTATACCACAAACAGTGAGTTACACGA-CCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
* *
344816 TTATACCACAAACAGTGAGTTACACGGCCATGGCACA
1 TTATACCACAAACAGTGAGTTACACGACCAAGGCACA
344853 TATTCGTGTG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 80 0.99
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (62 bp):
TTATACCACAAACAGTGAGTTACACGACCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
Found at i:344847 original size:49 final size:50
Alignment explanation
Indices: 344788--344889 Score: 116
Period size: 50 Copynumber: 2.1 Consensus size: 50
344778 CAGCCAAAGC
* * *
344788 ACACGCCCATGTC-CCTGGCCGTGTGGTCTTATACCACAAACAGTGAGTT
1 ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
* ** * * *
344837 ACACGGCCATGGCACATATTCGTGTGGTTTTATACCATAAACAGTGCGTT
1 ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
344887 ACA
1 ACA
344890 TTGCCAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
49 11 0.26
50 32 0.74
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (50 bp):
ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
Found at i:349907 original size:23 final size:21
Alignment explanation
Indices: 349850--349908 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
349840 ACGCACTCTC
* *
349850 TTTTCTTTATTTATTTTTTTA
1 TTTTTTTTATTTATTTTTATA
349871 TTTTTTGTTGATTTATTTTTCATA
1 TTTTTT-TT-ATTTATTTTT-ATA
349895 TTTTTATTTATTTA
1 TTTTT-TTTATTTA
349909 ATACTATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
23 15 0.47
24 9 0.28
25 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTTTTATTTATTTTTATA
Done.