Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_6492
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: 6967
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:1922 original size:17 final size:18
Alignment explanation
Indices: 1876--1937 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
1866 TAAGGGCAAT
1876 ATATATAATAATAATATATA
1 ATATATAA-AATAATAT-TA
*
1896 ATAAAGTAAAAT-ATATTA
1 ATATA-TAAAATAATATTA
*
1914 ATATATAAAAATAATGTTA
1 ATATAT-AAAATAATATTA
1933 ATATA
1 ATATA
1938 ATTTTGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 14 0.39
20 7 0.19
21 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATATAAAATAATATTA
Found at i:4243 original size:204 final size:206
Alignment explanation
Indices: 3669--4632 Score: 1374
Period size: 204 Copynumber: 4.7 Consensus size: 206
3659 TCCATTGAAT
* * * *
3669 GTGGAGATGCAGACTTC-ATTGTTCTC-GACAATACA-AAAAGA-AACATCAT-TTAGATTTGCT
1 GTGGAAATGCAGACTTCGATTGTTCTCTGACCATACAGAGACGACAA-ATCATCTTAGATTTGCT
* * * *
3729 TCATCGTAAACACGTGAAGGCCAAATCAGCTATATCTTCAATCTGCTCCCCGTCGAATACAGAAA
65 TCATCGTAAACACGTGAAAGCC-AATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGA
* * *
3794 GATAAGATCTGTCAT-ATGGATCTGCTTCAGTGT-AACATC-GAAGGTGAGATCCTGCTATGGGT
129 GATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGAT--TGCTATGTGT
3856 CTGCCTTCCATCAAA
192 CTGCCTTCCATCAAA
* * * * *
3871 GTGGAAATGCCAGACATAGATTGTTCTCTGACAATACAAAGGCGACAAATCATCTTAGATTTGCT
1 GTGGAAATG-CAGACTTCGATTGTTCTCTGACCATACAGAGACGACAAATCATCTTAGATTTGCT
* *
3936 TCATCGTAAACACGTGAAAGCCAAATTAGCCATATCTTCGATCTGCT--CCGCCGAATACAGAGA
65 TCATCGTAAACACGTGAAAGCC-AATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGA
3999 GATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGT-AGATCTGCTATGTGTC
129 GATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGAT-TGCTATGTGTC
4063 TGCCTTCCATCAAA
193 TGCCTTCCATCAAA
4077 GTGGAAATGCCAGACTTCGATTGTTCTCTGACCA-ACAGAGACGACAAAT-ATC-TAGA-TTGCT
1 GTGGAAATG-CAGACTTCGATTGTTCTCTGACCATACAGAGACGACAAATCATCTTAGATTTGCT
4138 TCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCCTGCTCCCCGCCGAATACAGAGA
65 TCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGAT-CTGCTCCCCGCCGAATACAGAGA
*
4203 GATAAGATCTGTCATCTTGGATCTGCTTCCAG-GTAAACATCTGAAGGTGAGATTTCTATGTGTC
129 GATAAGATCTGTCATCTTGGATCTGCTT-CAGCGTAAACATCTGAAGGTGAGATTGCTATGTGTC
4267 TGCCTTCCATCAAA
193 TGCCTTCCATCAAA
*
4281 GTGGAAATGCAGAC-TCGGATTTGTTCTCTGACCATAACAGAGACGA-AAATCATATTAGATTTG
1 GTGGAAATGCAGACTTC-GA-TTGTTCTCTGACCAT-ACAGAGACGACAAATCATCTTAGATTTG
*
4344 CTTCATCGTAAACACGTGAAAGCAAATCAGCTAATAT-TTCGATCTGCT-CCCGCCGAATACAGA
63 CTTCATCGTAAACACGTGAAAGCCAATCAGCT-ATATCTTCGATCTGCTCCCCGCCGAATACAGA
*
4407 GAGATAAGATCTGTCATCTTGGATC-GCTTCAGCGTAAACATCTGAAGGTGAGATTTCTATGTGT
127 GAGATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATTGCTATGTGT
4471 CTGCCTTCCATC-AA
192 CTGCCTTCCATCAAA
4485 GTGGAAATGCAGACTTCGATATGTTCT-T-ACCATACAGAGACGACAAATCATCTTAGA-TTGCT
1 GTGGAAATGCAGACTTCGAT-TGTTCTCTGACCATACAGAGACGACAAATCATCTTAGATTTGCT
*
4547 TCATCGTAAACACGTGAAAGCCAATCAGCTATA--TTCGATCTGCTCCCCG--GAATACAGAAAG
65 TCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAG
*
4608 ATAAGATTTGTCATCTTGGATCTGC
130 ATAAGATCTGTCATCTTGGATCTGC
4633 CTGATAATGG
Statistics
Matches: 705, Mismatches: 29, Indels: 59
0.89 0.04 0.07
Matches are distributed among these distances:
198 32 0.05
199 13 0.02
200 7 0.01
201 61 0.09
202 59 0.08
203 19 0.03
204 146 0.21
205 111 0.16
206 132 0.19
207 75 0.11
208 46 0.07
209 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (206 bp):
GTGGAAATGCAGACTTCGATTGTTCTCTGACCATACAGAGACGACAAATCATCTTAGATTTGCTT
CATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGA
TAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATTGCTATGTGTCTGC
CTTCCATCAAA
Found at i:4548 original size:409 final size:409
Alignment explanation
Indices: 3713--4632 Score: 1412
Period size: 409 Copynumber: 2.3 Consensus size: 409
3703 AAAAAGAAAC
* *
3713 ATCAT-TTAGATTTGCTTCATCGTAAACACGTGAAGGCCAAATCAGCTATATCTTCAATCTGCTC
1 ATCATCTTAGA-TTGCTTCATCGTAAACACGTGAAAGCC-AATCAGCTATATCTTCGATCTGCTC
*
3777 CCCGTCGAATACAGAAAGATAAGATCTGTCAT-ATGGATCTGCTTCAGTGTAACATCGAAGGTGA
64 CCCG-CGAATACAGAAAGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAACATCGAAGGTGA
3841 GATCCTGCTATGGGTCTGCCTTCCATCAAAGTGGAAATGCCAGACATAGATTGTTCTCTGACAAT
128 GAT-CTGCTATGGGTCTGCCTTCCATCAAAGTGGAAATGCCAGACATAGATTGTTCTCTGACAAT
* * * *
3906 ACAAAGGCGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATTAGCCATAT
192 ACAAAGACGACAAATCATATTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCAATAT
3971 CTTCGATCTGCTCCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAA
257 CTTCGATCTGCTCCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAA
4036 CATCTGAAGGTAGATCTGCTATGTGTCTGCCTTCCATCAAAGTGGAAATGCCAGACTTCGATTGT
322 CATCTGAAGGTAGATCTGCTATGTGTCTGCCTTCCATCAAAGTGGAAATGCCAGACTTCGATTGT
4101 TCTCTGACCAACAGAGACGACAA
387 TCTCTGACCAACAGAGACGACAA
4124 AT-ATC-TAGATTGCTTCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCCTGCTCC
1 ATCATCTTAGATTGCTTCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGAT-CTGCTCC
*
4187 CCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCTTCCAG-GTAAACATCTGAAGGT
65 CCG-CGAATACAGAAAGATAAGATCTGTCATCTTGGATCTGCTT-CAGTGT-AACATC-GAAGGT
* * *
4251 GAGAT-TTCTATGTGTCTGCCTTCCATCAAAGTGGAAATG-CAGAC-TCGGATTTGTTCTCTGAC
126 GAGATCTGCTATGGGTCTGCCTTCCATCAAAGTGGAAATGCCAGACAT-AGA-TTGTTCTCTGAC
* *
4313 CATAACAGAGACGA-AAATCATATTAGATTTGCTTCATCGTAAACACGTGAAAG-CAAATCAGCT
189 AAT-ACAAAGACGACAAATCATATTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGC-
4376 AATAT-TTCGATCTGCTCCCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATC-GCTTCAG
252 AATATCTTCGATCTGCT-CCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCTTCAG
*
4439 CGTAAACATCTGAAGGTGAGAT-TTCTATGTGTCTGCCTTCCATC-AAGTGGAAATG-CAGACTT
316 CGTAAACATCTGAAGGT-AGATCTGCTATGTGTCTGCCTTCCATCAAAGTGGAAATGCCAGACTT
4501 CGATATGTTCT-T-ACCATACAGAGACGACAA
380 CGAT-TGTTCTCTGACCA-ACAGAGACGACAA
4531 ATCATCTTAGATTGCTTCATCGTAAACACGTGAAAGCCAATCAGCTATA--TTCGATCTGCTCCC
1 ATCATCTTAGATTGCTTCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCTGCTCCC
*
4594 CG-GAATACAGAAAGATAAGATTTGTCATCTTGGATCTGC
66 CGCGAATACAGAAAGATAAGATCTGTCATCTTGGATCTGC
4633 CTGATAATGG
Statistics
Matches: 476, Mismatches: 17, Indels: 39
0.89 0.03 0.07
Matches are distributed among these distances:
404 35 0.07
406 14 0.03
407 33 0.07
408 39 0.08
409 175 0.37
410 150 0.32
411 19 0.04
412 11 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (409 bp):
ATCATCTTAGATTGCTTCATCGTAAACACGTGAAAGCCAATCAGCTATATCTTCGATCTGCTCCC
CGCGAATACAGAAAGATAAGATCTGTCATCTTGGATCTGCTTCAGTGTAACATCGAAGGTGAGAT
CTGCTATGGGTCTGCCTTCCATCAAAGTGGAAATGCCAGACATAGATTGTTCTCTGACAATACAA
AGACGACAAATCATATTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCAATATCTTC
GATCTGCTCCGCCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCTTCAGCGTAAACATC
TGAAGGTAGATCTGCTATGTGTCTGCCTTCCATCAAAGTGGAAATGCCAGACTTCGATTGTTCTC
TGACCAACAGAGACGACAA
Done.