Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7665.1
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: 6404
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Found at i:198 original size:44 final size:44
Alignment explanation
Indices: 139--433 Score: 195
Period size: 44 Copynumber: 6.9 Consensus size: 44
129 TAGTGTCTTC
*
139 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
* * * * * * *
183 AATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGT-GT-CTTC
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTTATTTT
* *
226 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAATTCTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA-T-TTT
* * * **
272 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA-CGT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
* * * *
313 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAAATC-C----TTT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTTATTTT
* * * * * *
352 AATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-TAC-TATCCTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTTAT-TTT
*
396 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
434 GGCTTTAGTT
Statistics
Matches: 186, Mismatches: 47, Indels: 35
0.69 0.18 0.13
Matches are distributed among these distances:
39 24 0.13
40 3 0.02
41 26 0.14
42 3 0.02
43 31 0.17
44 64 0.34
45 3 0.02
46 32 0.17
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
Found at i:210 original size:87 final size:84
Alignment explanation
Indices: 56--433 Score: 353
Period size: 87 Copynumber: 4.5 Consensus size: 84
46 AGACTTGATG
* * * * * *
56 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-C-TTTAATCCACTCCACTGTAA-CTTCG
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATC-TCA
*
118 GGGAGATAGGATAGTGTCTT
65 GGGAGATAGGATACTGTCTT
138 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC---TTTTAATCCGCTCCACTGTAATC-
*
202 TCAGGGAGATAGGATAGTGTCTT
62 TCAGGGAGATAGGATACTGTCTT
** * *
225 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAATTCTTTGGTCTGTTCCACTGTAAT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC----T-TTTAATCCGCTCCACTGTAAT
* * * *
290 CTCAGGGAGATAAGA-CCTGACGT
61 CTCAGGGAGATAGGATACTGTCTT
* ** * * *
313 -GATCTTCTCTACTGTAA-CTTCAGAGAGATAAAATC-C-TTTAATCCGCTCCATTGTAATCTCA
1 CGATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATCTCA
* *
374 AGGAGATAGGATTACTATCCTT
65 GGGAGATAGGA-TACTGT-CTT
396 -GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
434 GGCTTTAGTT
Statistics
Matches: 242, Mismatches: 39, Indels: 27
0.79 0.13 0.09
Matches are distributed among these distances:
80 29 0.12
82 34 0.14
83 31 0.13
84 2 0.01
86 2 0.01
87 109 0.45
88 5 0.02
89 29 0.12
90 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (84 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATCTCAG
GGAGATAGGATACTGTCTT
Found at i:715 original size:86 final size:88
Alignment explanation
Indices: 613--954 Score: 410
Period size: 88 Copynumber: 3.9 Consensus size: 88
603 TGTAACCTTT
* * * * *
613 AACCAGCTCCAAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATG
1 AACCAGCTCC-ATCACAACCGAAGGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* *
675 CAGGAAGGCAAGATCTGCT-TCTTT
64 CAGGAAGGCAAGATCTGTTGTCTTC
* * * * * * *
699 AACTAGCTCCA-CTGCAATCGATGGATGCAAAGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATG
1 AACCAGCTCCATC-ACAACCGAAGGAGGC-AAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* *
761 TAGGAAGGCAAGATCTTTTGTCTTC
64 CAGGAAGGCAAGATCTGTTGTCTTC
* *
786 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
* * *
851 GAAAAGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTGTTGTCTTC
874 AACCAGCTCCATCACAACCGAAGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
939 GGAAGGCAAGATCTGT
66 GGAAGGCAAGATCTGT
955 AACTTCATTG
Statistics
Matches: 222, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
85 1 0.00
86 73 0.33
87 27 0.12
88 121 0.55
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAAGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
GGAAGGCAAGATCTGTTGTCTTC
Found at i:816 original size:44 final size:44
Alignment explanation
Indices: 766--904 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
756 TAATGTAGGA
766 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
* * * * * * * *
810 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCA-ATGCAGAAA-
1 AGGCAAGATCTTTTGTCTTCAACCAGC-T--CTATCACA-ACCGAAAG
* *
855 A-GCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAGG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
898 AGGCAAG
1 AGGCAAG
905 GTTTGTGTCT
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 8 0.12
43 15 0.22
44 21 0.30
45 15 0.22
46 10 0.14
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
Found at i:828 original size:43 final size:43
Alignment explanation
Indices: 779--916 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
769 CAAGATCTTT
779 TGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
* * * * * * * *
822 TGTCTTCGATCTGCTTCGCTGTCA-ATGCAGAAA-A-GCAAGATCTTT
1 TGTCTTCAACCAGC-T--CTATCACA-ACCGAAAGAGGCAAGGT-TTG
* *
867 TGTCTTCAACCAGCTCCATCACAACCGAAGGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
910 TGTCTTC
1 TGTCTTC
917 GATCTGCTTC
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 8 0.12
43 22 0.32
44 14 0.20
45 15 0.22
46 10 0.14
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
Found at i:946 original size:44 final size:44
Alignment explanation
Indices: 810--948 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
800 CAACCGAAAG
*
810 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * * ** * *
854 AAGCAAGATCTTTTGTCTTCAACCAGC-TC-CATCACAACCGAAGG-
1 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGC-TGTCAA-TGCAGGA
898 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
942 AGGCAAG
1 AGGCAAG
949 ATCTGTAACT
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
43 18 0.26
44 33 0.49
45 17 0.25
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
Found at i:5327 original size:19 final size:20
Alignment explanation
Indices: 5298--5346 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5288 CACTTCGTGA
* *
5298 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5317 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5337 AAATG-AATGC
1 AAATGTAATGC
5347 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Done.