Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3469
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: 39917
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2431 original size:51 final size:50
Alignment explanation
Indices: 2272--2428 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
2262 ACTTCTGATC
* *
2272 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
2323 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
2373 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
2424 AGTGA
1 AGTGA
2429 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:10200 original size:51 final size:50
Alignment explanation
Indices: 10041--10197 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
10031 ACTTCTGATC
* *
10041 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
10092 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
10142 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
10193 AGTGA
1 AGTGA
10198 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:12120 original size:17 final size:17
Alignment explanation
Indices: 12098--12131 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12088 GAATGAAAAC
*
12098 AATTATAACATTTTTAA
1 AATTATAAAATTTTTAA
12115 AATTATAAAATTTTTAA
1 AATTATAAAATTTTTAA
12132 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATAAAATTTTTAA
Found at i:16747 original size:30 final size:33
Alignment explanation
Indices: 16670--16747 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
16660 AAATACAATT
*
16670 AAATATAAAAAG-ATATATATAGACATAAACTA
1 AAATATATAAAGTATATATATAGACATAAACTA
* *
16702 AAATATATATA-TATATATATA-A-ATTAAC-A
1 AAATATATAAAGTATATATATAGACATAAACTA
16731 AAATATATAAAGTATAT
1 AAATATATAAAGTATAT
16748 TTAAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.28
30 10 0.25
31 1 0.03
32 18 0.45
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (33 bp):
AAATATATAAAGTATATATATAGACATAAACTA
Found at i:16752 original size:11 final size:10
Alignment explanation
Indices: 16702--16758 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
16692 ACATAAACTA
16702 AAATATATAT
1 AAATATATAT
*
16712 ATATATATAT
1 AAATATATAT
*
16722 AAAT-TA-AC
1 AAATATATAT
16730 AAA-ATATAT
1 AAATATATAT
*
16739 AAAGTATATTT
1 AAA-TATATAT
16750 AAATATATA
1 AAATATATA
16759 AAAGAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 6 0.16
9 6 0.16
10 17 0.46
11 8 0.22
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAATATATAT
Found at i:18886 original size:87 final size:85
Alignment explanation
Indices: 18770--19101 Score: 248
Period size: 87 Copynumber: 3.9 Consensus size: 85
18760 AGACTTGATG
* *
18770 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTGCTCCGCTGTAACCTCAGAGAGATAAGATCC--TATTTTAATCCGCTCCACTGTAATC-
*
18834 TCAGGGAGATAGGATAGTGTCTT
63 TCAGGGAGATAGGATACTGTCTT
* ** * *
18857 CGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCACTGTAA
1 CGATCTGCTCCGCTGTAACCTCAGAGAGATAAGATCCT---A-T-TTTAATCCGCTCCACTGTAA
* * * *
18921 TCTCAGGGAAATAAGA-CCTGAT-GT
61 TCTCAGGGAGATAGGATACTG-TCTT
* ** * *
18945 -GATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC---TTTAATCCGCTCCATTGTAATCTCA
1 CGATCTGCTCCGCTGTAACCTCAGAGAGATAAGATCCTATTTTAATCCGCTCCACTGTAATCTCA
* *
19006 AGGAGATAGGATTACTATCTT
66 GGGAGATAGGA-TACTGTCTT
* * * ** * * * *
19027 TGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCT
1 CGATCTGCTCCGCTGTAACCTCAGAGAGATAAGATC-CT-ATTTTAATCCGCTCCACTGTAATCT
19092 CAGGGAGATA
64 CAGGGAGATA
19102 AGATCTGAAA
Statistics
Matches: 188, Mismatches: 40, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
80 28 0.15
81 1 0.01
82 3 0.02
83 29 0.15
84 2 0.01
86 1 0.01
87 62 0.33
88 32 0.17
89 29 0.15
90 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (85 bp):
CGATCTGCTCCGCTGTAACCTCAGAGAGATAAGATCCTATTTTAATCCGCTCCACTGTAATCTCA
GGGAGATAGGATACTGTCTT
Found at i:18926 original size:46 final size:43
Alignment explanation
Indices: 18782--19150 Score: 215
Period size: 44 Copynumber: 8.5 Consensus size: 43
18772 ATCTACTCTG
* * * * *
18782 CTGTAACCTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT-CTATT-CTTTGATCTGCTCCA
* * *
18826 CTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTA-T-TCTTTGATCTGCTCCA
* * *
18869 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATTCTTTGATCTGCTCCA
* * * * *
18915 CTGTAATCTCAGGGAAATAAGACCTGA---TGTGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCT-ATTCTTTGATCTGCTCCA
* * *
18956 CTGTAA-CTTCAGAGAGATAAGATC----CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTATTCTTTGATCTGCTCCA
* * * *
18995 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTA-T-TCTTTGATCTGCTCCA
* * ** *
19039 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTAT-TCTTTGATCTGCTCCA
* * * *
19083 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCC
1 CTGTAATCTCAGGGAGATAAGATCT---ATTCTTTGATCTGCTCCA
19129 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
19151 CCTGTATAAT
Statistics
Matches: 249, Mismatches: 53, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
39 26 0.10
40 2 0.01
41 29 0.12
43 31 0.12
44 91 0.37
45 2 0.01
46 65 0.26
47 2 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTGTAATCTCAGGGAGATAAGATCTATTCTTTGATCTGCTCCA
Found at i:28973 original size:23 final size:23
Alignment explanation
Indices: 28947--29043 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
28937 ATAAGTGCCA
28947 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28970 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28993 CACTG--ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29014 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29037 CACTGAT
1 CACTGAT
29044 CAATAACACT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
21 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29012 original size:44 final size:44
Alignment explanation
Indices: 28954--29043 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
28944 CCACACTGAT
* *
28954 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
28998 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
29042 AT
1 AT
29044 CAATAACACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (44 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Found at i:36333 original size:23 final size:23
Alignment explanation
Indices: 36307--36403 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
36297 ATAAGTGCCA
36307 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
36330 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
36353 CACTG--ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
36374 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
36397 CACTGAT
1 CACTGAT
36404 CAATAACACT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
21 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:36372 original size:44 final size:44
Alignment explanation
Indices: 36314--36403 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
36304 CCACACTGAT
* *
36314 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
36358 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
36402 AT
1 AT
36404 CAATAACACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (44 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Found at i:38377 original size:10 final size:10
Alignment explanation
Indices: 38362--38391 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
38352 GAAAGAAGAC
38362 ATATATACAT
1 ATATATACAT
38372 ATATATACAT
1 ATATATACAT
*
38382 ATAAATACAT
1 ATATATACAT
38392 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (10 bp):
ATATATACAT
Done.