Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2311
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: 43244
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:17004 original size:57 final size:57
Alignment explanation
Indices: 16854--17024 Score: 148
Period size: 57 Copynumber: 3.0 Consensus size: 57
16844 TTCCTATGTC
*** * * *
16854 ATGAAAAATGATTTAAATATTTTTAA-AATGTATGAAATTGCATTAAAGTCCTTAAATT
1 ATGAAAAATGATTTAAATAACCTCAACAAAG-ATGAAATTGCA-TAAAGTCCTTAGATT
* * * ** * * * *
16912 GTAAAAAATAAGCTAAATAACC-CTATCATACATGAATTTGCATAAAGTCCTTAGATT
1 ATGAAAAATGATTTAAATAACCTC-AACAAAGATGAAATTGCATAAAGTCCTTAGATT
*
16969 ATGAAAAATGATTTAAATAACCTCAACAAAGATGAAATTGCATAAATGTCATTAGA
1 ATGAAAAATGATTTAAATAACCTCAACAAAGATGAAATTGCATAAA-GTCCTTAGA
17025 ACATGACAAA
Statistics
Matches: 84, Mismatches: 25, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
57 49 0.58
58 34 0.40
59 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (57 bp):
ATGAAAAATGATTTAAATAACCTCAACAAAGATGAAATTGCATAAAGTCCTTAGATT
Found at i:19288 original size:55 final size:57
Alignment explanation
Indices: 19201--19494 Score: 214
Period size: 56 Copynumber: 5.3 Consensus size: 57
19191 TATTTTTGGA
** * * * * *
19201 CTTTTTCATTTTAATGCCAATTTCAA-TTGGAGCTATACCTATCAGTTACTCTTGGG
1 CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCTATACCTATCAGCTACTCTTAGG
* * **
19257 C-TTTTCAATTTGGTTCCAACTACAA-TAGGAGCTATACCTATTTGCTACTCTTAGG
1 CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCTATACCTATCAGCTACTCTTAGG
* * * * * **
19312 CTTTTTTATTTTGATTCTAATTTCAACTAGGA--TGAAACCTATGGGCTACTCTTAGG
1 CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCT-ATACCTATCAGCTACTCTTAGG
* *
19368 CTTTTTCATTTTGGTTCCAATTACAATTA-GAGCTATACCTATCTA-CGACT-TCTAGG
1 CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCTATACCTATC-AGCTACTCT-TAGG
* * ** * * * *
19424 CTTTTTCACTTTGGTTCTAATTTTAACT-GG-GATGAAACCTATTAGCTACTTTTAGG
1 CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCT-ATACCTATCAGCTACTCTTAGG
19480 CTTTCTT-ATTTTGGT
1 CTTT-TTCATTTTGGT
19495 GCAATTTCAG
Statistics
Matches: 187, Mismatches: 39, Indels: 24
0.75 0.16 0.10
Matches are distributed among these distances:
55 51 0.27
56 127 0.68
57 9 0.05
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (57 bp):
CTTTTTCATTTTGGTTCCAATTACAACTAGGAGCTATACCTATCAGCTACTCTTAGG
Found at i:19407 original size:112 final size:112
Alignment explanation
Indices: 19237--19494 Score: 317
Period size: 112 Copynumber: 2.3 Consensus size: 112
19227 TTGGAGCTAT
* * * * * *
19237 ACCTATCAGTTACTCTTGGGC-TTTTCAATTTGGTTCCAACTACAATAGGAGCTATACCTATTTG
1 ACCTATGAGCTACTCTTAGGCTTTTTCATTTTGGTTCCAACTACAATAGGAGCTATACCTATCTA
* * *
19301 CTAC-TCTTAGGCTTTTTTATTTTGATTCTAATTTCAACTAGGATGAA
66 CGACTTC-TAGGCTTTTTCACTTTGATTCTAATTTCAACTAGGATGAA
* *
19348 ACCTATGGGCTACTCTTAGGCTTTTTCATTTTGGTTCCAATTACAATTA-GAGCTATACCTATCT
1 ACCTATGAGCTACTCTTAGGCTTTTTCATTTTGGTTCCAACTACAA-TAGGAGCTATACCTATCT
* * *
19412 ACGACTTCTAGGCTTTTTCACTTTGGTTCTAATTTTAACTGGGATGAA
65 ACGACTTCTAGGCTTTTTCACTTTGATTCTAATTTCAACTAGGATGAA
* *
19460 ACCTATTAGCTACTTTTAGGCTTTCTT-ATTTTGGT
1 ACCTATGAGCTACTCTTAGGCTTT-TTCATTTTGGT
19495 GCAATTTCAG
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
111 17 0.13
112 103 0.82
113 6 0.05
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (112 bp):
ACCTATGAGCTACTCTTAGGCTTTTTCATTTTGGTTCCAACTACAATAGGAGCTATACCTATCTA
CGACTTCTAGGCTTTTTCACTTTGATTCTAATTTCAACTAGGATGAA
Found at i:25643 original size:16 final size:17
Alignment explanation
Indices: 25624--25656 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25614 TATTTTTATT
25624 TATATTA-ATTTATTTA
1 TATATTATATTTATTTA
*
25640 TATATTATATTTGTTTA
1 TATATTATATTTATTTA
25657 AATCATTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATATTATATTTATTTA
Found at i:26800 original size:282 final size:282
Alignment explanation
Indices: 26288--26854 Score: 902
Period size: 282 Copynumber: 2.0 Consensus size: 282
26278 TGCGCAATTA
* * * **
26288 CCTCCACATGGTATGCATGGTGAAAGATTGAAGAAGTTCAGTGGTGTAGACTTCAAATGGTGGCA
1 CCTCCACATGCTATGCATGGTGAAAGATTAAAGAAGTTAAGCAGTGTAGACTTCAAATGGTGGCA
* *
26353 ACAGAAGATGTTTATTTAACCACTTTTAATCTAGTATGGTTTTTAGTGGAAGAGGCATCGATTCT
66 ACAGAAGATGTTTATTTAACCACCTTCAATCTAGTATGGTTTTTAGTGGAAGAGGCATCGATTCT
26418 CAATGAAGGAAAAATGGATATTACCATGGTTACCTCAATGGATCCATGAAAACATTCAAAATTCC
131 CAATGAAGGAAAAATGGATATTACCATGGTTACCTCAATGGATCCATGAAAACATTCAAAATTCC
* * *
26483 TATGAAAGAACTAAAGCCTCAATAGACTGAATAATATTTTATACAATGCATAGAGTCTGATAAAG
196 TATGAAAGAACTAAAGCCTCAATAAACTAAATAATATTTTACACAATGCATAGAGTCTGATAAAG
*
26548 ACAGCGAAAAAGTTGTGGGAGT
261 ACAGCGAAAAAGCTGTGGGAGT
* *
26570 CCTCCACATGCTATGCATGGTGAGAGATTAAAGAAGTTAAGCAGTGTGGACTTCAAATGGTGGCA
1 CCTCCACATGCTATGCATGGTGAAAGATTAAAGAAGTTAAGCAGTGTAGACTTCAAATGGTGGCA
*
26635 ACATAAGATGTTTATTTAACCACCTTCAATCTAGTATGGTTTTTAGTGGAAGAGGCATCGATTCT
66 ACAGAAGATGTTTATTTAACCACCTTCAATCTAGTATGGTTTTTAGTGGAAGAGGCATCGATTCT
* * * *
26700 TAATGAA-GAAGAAATGGATATTACCATGGTTGCCTCAGTGGATCCATGAAAACATTCAAATTTC
131 CAATGAAGGAA-AAATGGATATTACCATGGTTACCTCAATGGATCCATGAAAACATTCAAAATTC
* * *
26764 CTATGAAAGAACTAAATCCTCAATAAACTAAATAATATTTTACATAATGCATATAGTCTGATAAA
195 CTATGAAAGAACTAAAGCCTCAATAAACTAAATAATATTTTACACAATGCATAGAGTCTGATAAA
* * *
26829 GATAGTGAAAGAGCTGTGGGAGT
260 GACAGCGAAAAAGCTGTGGGAGT
26852 CCT
1 CCT
26855 TAGATAAAAA
Statistics
Matches: 260, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
281 3 0.01
282 257 0.99
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (282 bp):
CCTCCACATGCTATGCATGGTGAAAGATTAAAGAAGTTAAGCAGTGTAGACTTCAAATGGTGGCA
ACAGAAGATGTTTATTTAACCACCTTCAATCTAGTATGGTTTTTAGTGGAAGAGGCATCGATTCT
CAATGAAGGAAAAATGGATATTACCATGGTTACCTCAATGGATCCATGAAAACATTCAAAATTCC
TATGAAAGAACTAAAGCCTCAATAAACTAAATAATATTTTACACAATGCATAGAGTCTGATAAAG
ACAGCGAAAAAGCTGTGGGAGT
Found at i:27761 original size:41 final size:41
Alignment explanation
Indices: 27716--27797 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
27706 AAGACCATCC
*
27716 TACAAATACTAAAAAATGTTGGTGTGCCTTGCTAAATATAA
1 TACAAATACTAAAAAATGTTGATGTGCCTTGCTAAATATAA
* * *
27757 TACAAATAGTTAAAAATGTTGATGTGTCTTGCTAAATATAA
1 TACAAATACTAAAAAATGTTGATGTGCCTTGCTAAATATAA
27798 GAAAAGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (41 bp):
TACAAATACTAAAAAATGTTGATGTGCCTTGCTAAATATAA
Found at i:41925 original size:17 final size:16
Alignment explanation
Indices: 41895--41930 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
41885 AGATATTTTC
41895 AATCAAAATAAAATTA
1 AATCAAAATAAAATTA
*
41911 AATCAAAAATTAAATTA
1 AATC-AAAATAAAATTA
41928 AAT
1 AAT
41931 TTGTCAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
AATCAAAATAAAATTA
Done.