Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01786.P4
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: 14444
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Found at i:2295 original size:35 final size:34
Alignment explanation
Indices: 2226--2374 Score: 174
Period size: 35 Copynumber: 4.3 Consensus size: 34
2216 AAGTATGCCT
* * *
2226 CCTTGAAGGCTATGT-TTAAGAAGATGCAGTATG
1 CCTTGAAGGCTAAGTGTTAAGAAGACGAAGTATG
*
2259 CCTTGAAGGCTAAGTGTTATAGAAGACGAAGCATG
1 CCTTGAAGGCTAAGTGTTA-AGAAGACGAAGTATG
* * * *
2294 CCTTGAAGGCTAAGTATTTGAGAAGATGAAGTTTG
1 CCTTGAAGGCTAAGT-GTTAAGAAGACGAAGTATG
* *
2329 CCTTAAAGGCTAAGTGTTGAAGAAGACAAAGTATG
1 CCTTGAAGGCTAAGTGTT-AAGAAGACGAAGTATG
2364 CCTTGAAGGCT
1 CCTTGAAGGCT
2375 GTGTCTAAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
33 14 0.15
34 5 0.05
35 75 0.78
36 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (34 bp):
CCTTGAAGGCTAAGTGTTAAGAAGACGAAGTATG
Found at i:2331 original size:70 final size:68
Alignment explanation
Indices: 2226--2374 Score: 201
Period size: 70 Copynumber: 2.2 Consensus size: 68
2216 AAGTATGCCT
* * * *
2226 CCTTGAAGGCTATGTTTAAGAAGATGCAGTATGCCTTGAAGGCTAAGTGTT-ATAGAAGACGAAG
1 CCTTGAAGGCTATATTTAAGAAGATGAAGTATGCCTTAAAGGCTAAGTGTTGA-AGAAGACAAAG
2290 CATG
65 CATG
* *
2294 CCTTGAAGGCTAAGTATTTGAGAAGATGAAGTTTGCCTTAAAGGCTAAGTGTTGAAGAAGACAAA
1 CCTTGAAGGCT-A-TATTTAAGAAGATGAAGTATGCCTTAAAGGCTAAGTGTTGAAGAAGACAAA
*
2359 GTATG
64 GCATG
2364 CCTTGAAGGCT
1 CCTTGAAGGCT
2375 GTGTCTAAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
68 11 0.15
69 1 0.01
70 58 0.82
71 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (68 bp):
CCTTGAAGGCTATATTTAAGAAGATGAAGTATGCCTTAAAGGCTAAGTGTTGAAGAAGACAAAGC
ATG
Found at i:3762 original size:62 final size:58
Alignment explanation
Indices: 3668--3845 Score: 191
Period size: 56 Copynumber: 3.0 Consensus size: 58
3658 TGTGTATATA
* *
3668 TATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATTTGCATGTATATATATCTT
1 TATTCTGTTGATAAATTTGCATGCATCCGTAAGTGAAATTTGCATGTATATATATCTT
* * * * *
3726 TCTATCTGTT-ATAAATTTTGCATCATGCATCTGTAAGTGAAATGTG--TGTATATATATATA
1 TAT-TCTGTTGATAAA-TTTG---CATGCATCCGTAAGTGAAATTTGCATGTATATATATCTT
* * *
3786 TATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATTTGCATCTATATATATTCTT
1 TATTCTGTTGATAAATTTGCATGCATCCGTAAGTGAAATTTGCATGTATATATA-TCTT
3845 T
1 T
3846 TGATATACTC
Statistics
Matches: 96, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
56 21 0.22
58 15 0.16
59 21 0.22
60 18 0.19
62 21 0.22
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (58 bp):
TATTCTGTTGATAAATTTGCATGCATCCGTAAGTGAAATTTGCATGTATATATATCTT
Found at i:3810 original size:56 final size:55
Alignment explanation
Indices: 3662--3852 Score: 201
Period size: 52 Copynumber: 3.4 Consensus size: 55
3652 GTGAAATGTG
* *
3662 TATATATATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATT-TGCATGTA
1 TATATATATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATTGTGTATATA
* * * *
3716 TATATATCTTTCTATCTGTTATAAATTTTGCATCATGCATCTGTAAGTGAAATGTGTGTATATA
1 TATATAT-ATTCT-T-T-TGATATA-TTTG---CATGCATCCGTAAGTGAAAT-TGTGTATATA
* *
3780 TATATATATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATT-TG--CATC
1 TATATATATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATTGTGTATATA
3832 TATATATATTCTTTTGATATA
1 TATATATATTCTTTTGATATA
3853 CTCTTTCTAT
Statistics
Matches: 115, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
52 23 0.20
54 9 0.08
55 5 0.04
56 20 0.17
57 1 0.01
58 5 0.04
59 8 0.07
60 5 0.04
61 1 0.01
62 20 0.17
63 5 0.04
64 13 0.11
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (55 bp):
TATATATATTCTTTTGATATATTTGCATGCATCCGTAAGTGAAATTGTGTATATA
Found at i:3901 original size:29 final size:28
Alignment explanation
Indices: 3848--3915 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
3838 TATTCTTTTG
* * *
3848 ATATAC-TCTTTCTATCTATTTGTGTAT
1 ATATACTTTTTTCTATCTATGTGTGTAC
*
3875 ATATA-TTTTTTCTATCTGTATGTGTGTGC
1 ATATACTTTTTTCTATC--TATGTGTGTAC
3904 ATATACTTTTTT
1 ATATACTTTTTT
3916 TATATAATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 14 0.42
29 13 0.39
30 6 0.18
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (28 bp):
ATATACTTTTTTCTATCTATGTGTGTAC
Found at i:10824 original size:22 final size:22
Alignment explanation
Indices: 10796--10837 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10786 GGGAGTGTAA
10796 GAATATTCTGTAAATATTTTAG
1 GAATATTCTGTAAATATTTTAG
* *
10818 GAATATTTTGTAGATATTTT
1 GAATATTCTGTAAATATTTT
10838 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
GAATATTCTGTAAATATTTTAG
Found at i:14206 original size:41 final size:41
Alignment explanation
Indices: 14161--14289 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
14151 GTGGGGCACC
*
14161 GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTGAGGAG
1 GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTGAAGAG
* *
14202 GCATACTTGTTTGGTACATTGTTGGTAAAGACTGTGAAGAG
1 GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTGAAGAG
*
14243 GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTAAAGAG
1 GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTGAAGAG
*
14284 GAATAC
1 GCATAC
14290 ATAGTTGCTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (41 bp):
GCATACCTGTTTGGTACATTGTTGGAAAAGACTGTGAAGAG
Done.