Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold742
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: 7877
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3451 original size:44 final size:44
Alignment explanation
Indices: 3355--3911 Score: 257
Period size: 44 Copynumber: 12.8 Consensus size: 44
3345 ACTTGATGCG
* * * *
3355 ATCTGCTCTACTGCAACTTCAGAGAGATAGGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCTACTTCA
* * * * *
3399 ATCCGCTCCACTACAACCTCAGGGAGATAGGATTATCGACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCA
* * * *
3443 ATCTGCTCCACTGCAACCTCGGGGAGATAAGATT-TGCTTCCTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-CTACTTCA
* * *** * * * *
3487 GTCTGCCCCACTATGACTTCA-GAAGGATAAGACTTGTTTTC-TCA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTATCTACTTCA
* * * * * *
3531 GTCTGCTCCACTGCAACCTCAAGGAGATAAG---ACCTGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCT-ACTTCA
** * * *
3572 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCTACTTCA
* * * **
3616 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCA
* * * * *
3660 ATCTGCTCCACTGTAACTTCAGAGAGATACGATT-TGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCT-A-CTTCA
* * * * *
3705 ATCTGCCCCACTACAACTTCAGGGGGATAAGACCT-GCTTAC-TCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATC-TACTTCA
* * * ** * * *
3749 GTCTACTTCGTTGCAACTTCAGGGAGATAA-A--ACCTGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCT-ACTTCA
** * ** *
3790 ATCCACTCTACTGCAACTTCAAAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCTACTTCA
* * * **
3834 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCA
* * *
3878 ATCTGCTCCACTGTAACTTCAGAGAGATACGATT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
3912 TGTCATCTTC
Statistics
Matches: 376, Mismatches: 110, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
40 2 0.01
41 50 0.13
42 1 0.00
43 16 0.04
44 263 0.70
45 40 0.11
46 3 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCTACTTCA
Found at i:3818 original size:218 final size:218
Alignment explanation
Indices: 3348--3927 Score: 894
Period size: 218 Copynumber: 2.7 Consensus size: 218
3338 CGGCAAGACT
** *
3348 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAGGATCTATTACTTTAATCCGCTCCACTAC
1 TGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
* * * * * * *
3413 AACCTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCGGGGAGATAAGATTT
66 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
* * ** * * * *
3478 G-CTTCCTC-AGTCTGCCCCACTATGACTTCAGAAGGATAAGACTTGTTTTCTCAGTCTGCTCCA
131 GTCATCTTCGA-TCTGCCCCACTACAACTTCAGAAGGATAAGACCTGCTTACTCAGTCTACTCCA
*
3541 CTGCAACCTCAAGGAGATAAGACC
195 CTGCAACCTCAAGGAGATAAAACC
3565 TGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
1 TGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
3630 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
66 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
** * **
3695 GTCATCTTCGATCTGCCCCACTACAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTACTTCGT
131 GTCATCTTCGATCTGCCCCACTACAACTTCAGAAGGATAAGACCTGCTTACTCAGTCTACTCCAC
* *
3760 TGCAACTTCAGGGAGATAAAACC
196 TGCAACCTCAAGGAGATAAAACC
*
3783 TGATGCGATCCACTCTACTGCAACTTCAAAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
1 TGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
3848 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
66 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
3913 GTCATCTTCGATCTG
131 GTCATCTTCGATCTG
3928 AGAGACAAGA
Statistics
Matches: 334, Mismatches: 27, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
217 121 0.36
218 212 0.63
219 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (218 bp):
TGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTAC
AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGAGAGATACGATTT
GTCATCTTCGATCTGCCCCACTACAACTTCAGAAGGATAAGACCTGCTTACTCAGTCTACTCCAC
TGCAACCTCAAGGAGATAAAACC
Found at i:4157 original size:128 final size:128
Alignment explanation
Indices: 3929--4493 Score: 844
Period size: 128 Copynumber: 4.4 Consensus size: 128
3919 TTCGATCTGA
* * * *
3929 GAGACAAGATCTGTAATTTCCAACCTACTCCACTACTGACCAGGGACATTGGACTTGTGGCTTGA
1 GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
* * *
3994 ATCTGTTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTGCTCCGCTACTGCTTAAG
66 ATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
* * * *
4057 GAGACAAGATTTGTAATTTCCAACCTATTCTACTGCT-AGCTAGGGACATAGGACTTGTAGCTTA
1 GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGA-CCAGGGACATAGGACTTGTGGCTTA
* * * *
4121 AATTTACTTCCTTACACATAAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
65 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
* * ** *
4185 GAGACAAGATCTGTAATTTCCAACATATTCCACTGCTGACCAGAGACATATAACTTGTGGCTTGA
1 GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
* *
4250 ATTTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTGCTCCGCTACTGCTTAGG
66 ATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
* * * *
4313 GAGACAAGATTTGTAATTTCCAACCTATTCCACTACTGGCCAGGGATATAGGACTTGTGGCTTAA
1 GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
* *
4378 ATCTGCTTCCTTACACTTGAAGATAAGACTCGTCGTCTTCGATCTGCTCCGCTACTGCTTAGG
66 ATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
* *
4441 GAGACAAGATCTGTAATTTCCAACCTACTCCACTGCTGACCAGGGAGATAGGA
1 GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGA
4494 TTTGCAATTT
Statistics
Matches: 389, Mismatches: 46, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
127 1 0.00
128 387 0.99
129 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (128 bp):
GAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAA
ATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGG
Found at i:4503 original size:44 final size:43
Alignment explanation
Indices: 4455--4540 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
4445 CAAGATCTGT
4455 AATTTCCAACCTACTCCACTGCTGACCAGGGAGATAGGATTTGC
1 AATTTCCAACCTACTCCACTGCTGACCAGGGAGATAGG-TTTGC
* * ** *
4499 AATTTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGGTTTG
1 AATTTCCAACCTACTCCACTGCTGACCAGGGAGATAGGTTTG
4541 TGATTTCACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (43 bp):
AATTTCCAACCTACTCCACTGCTGACCAGGGAGATAGGTTTGC
Found at i:5766 original size:23 final size:24
Alignment explanation
Indices: 5743--5787 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
5733 ATTTTTACAT
5743 TTTCATTATTTT-TTATTTTT-CAT
1 TTTCATT-TTTTATTATTTTTACAT
*
5766 TTTCATTTTTTATTTTTTTTAC
1 TTTCATTTTTTATTATTTTTAC
5788 TTAAAGTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCATTTTTTATTATTTTTACAT
Done.