Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00001.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: 23842
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4424 original size:2 final size:2
Alignment explanation
Indices: 4417--4447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4407 TTCTGAGATA
4417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4448 ACGACCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12923 original size:43 final size:43
Alignment explanation
Indices: 12822--12947 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
12812 AATTAATAAT
* * * *
12822 ATTATCCAAATGCATAATTAGTATTAC-ACTACATGATAACAACAAC
1 ATTATCCAAGTGCATAACTAATATTACAAC-ACAT--T-ATAACAAC
12868 ATTATCCAAGTGCATAACTAATATTACAACACATTATAACAAC
1 ATTATCCAAGTGCATAACTAATATTACAACACATTATAACAAC
* *
12911 ATTGTCCAAGTGCATAACTAATATTACACCACATTAT
1 ATTATCCAAGTGCATAACTAATATTACAACACATTAT
12948 CAATATCTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
43 42 0.58
44 1 0.01
46 28 0.38
47 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (43 bp):
ATTATCCAAGTGCATAACTAATATTACAACACATTATAACAAC
Found at i:15221 original size:897 final size:896
Alignment explanation
Indices: 13664--15456 Score: 3424
Period size: 897 Copynumber: 2.0 Consensus size: 896
13654 GATTTTCCCA
*
13664 AAAATGGTTCATCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
1 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
13729 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
66 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
* *
13794 CTCTTTTAAATGATATCGAATACCATGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
131 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
13859 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
196 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
13924 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
261 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
*
13989 GTGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
326 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
14054 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
391 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
*
14119 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATTTAATGCTCCAAT
456 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
*
14184 ACAATCTTTAAAATAAGGATTAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
521 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
*
14249 GTAATTTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
586 GTAATCTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
14314 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCACTCGAAACCTTACATTATGACCAATTAT
651 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCA-TCGAAACCTTACATTATGACCAATTAT
*
14379 ATGTAAAAATATAACTACTTGCTCCCTAATATTCACTGATTTAGTTGATTGTAACAAATTATTTC
715 ATGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTC
* *
14444 TACTAAGAATATCACACAAATTAAAAAATGCAACCGGTCGCATCCTTATCATATCAATACAATGC
780 TACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCGCATCCTTATCATATCAATACAATGC
14509 CGGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
845 CGGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
*
14561 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCTAAAAACACGTTCAATAGTG
1 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
*
14626 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCTTGAGCACTAAA
66 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
14691 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
131 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
*
14756 CATCAGCAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
196 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
14821 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
261 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
14886 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
326 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
*
14951 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCTCCCCTTTACGGCTA
391 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
15016 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
456 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
15081 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
521 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
*
15146 GTAATCTAATAACTAGTTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
586 GTAATCTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
15211 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCATCGAAACCTTACATTATGACCAATTATA
651 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCATCGAAACCTTACATTATGACCAATTATA
15276 TGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTCT
716 TGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTCT
*
15341 ACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCTCATCCTTATCATATCAATACAATGCC
781 ACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCGCATCCTTATCATATCAATACAATGCC
*
15406 GGTCACCACTATATAAAATATTATTAATATAATTTTCTCTTTCATAATCTC
846 GGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
15457 GATTTACATG
Statistics
Matches: 879, Mismatches: 17, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
896 204 0.23
897 675 0.77
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (896 bp):
AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
GTAATCTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCATCGAAACCTTACATTATGACCAATTATA
TGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTCT
ACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCGCATCCTTATCATATCAATACAATGCC
GGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
Found at i:15692 original size:2 final size:2
Alignment explanation
Indices: 15685--15713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15675 AAGTGCATAC
15685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15714 AGTTTCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16194 original size:2 final size:2
Alignment explanation
Indices: 16183--16212 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16173 GAACCTTTAC
16183 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16213 GGTTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18855 original size:46 final size:46
Alignment explanation
Indices: 18805--18980 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
18795 TGGTTGAGCA
18805 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
18851 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
18896 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
18944 CCCGAGCTCGTTGATTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18981 GCGGGTTATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:18963 original size:93 final size:93
Alignment explanation
Indices: 18802--18973 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
18792 GGATGGTTGA
* *
18802 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
18867 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
18895 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
18960 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
18974 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20333 original size:18 final size:18
Alignment explanation
Indices: 20312--20358 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20302 TTAAATTGTT
20312 TAAATTTAAAAAATTAT-A
1 TAAATTTAAAAAA-TATCA
* *
20330 TAAAATTATAAAATATCA
1 TAAATTTAAAAAATATCA
20348 TCAAATTTAAA
1 T-AAATTTAAA
20359 TTTAAAATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTTAAAAAATATCA
Found at i:20733 original size:55 final size:55
Alignment explanation
Indices: 20645--20750 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
20635 AAGGAGGTGC
* *
20645 TTTTACACCTAGAAGGATAACTGATTTTGGGGGTCAAAATTACGGTGAAAAATTG
1 TTTTACACCGAGAAGGATAACTGATTTTGGGGGTCAAAATTAAGGTGAAAAATTG
*
20700 TTTTACACCGAGAAGGATAACTGATTTTTGGGGTCAAAATTAAGGTGAAAA
1 TTTTACACCGAGAAGGATAACTGATTTTGGGGGTCAAAATTAAGGTGAAAA
20751 TTTATTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (55 bp):
TTTTACACCGAGAAGGATAACTGATTTTGGGGGTCAAAATTAAGGTGAAAAATTG
Found at i:20934 original size:31 final size:31
Alignment explanation
Indices: 20894--20985 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
20884 TATTTTGTAC
20894 CATTATATTAAATTATTTAAATATAATTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
*
20925 CATTGTATTAAATTATTT-AATATAATTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
* * * *
20955 TATTATATTTAATTTTTTAAA-ATATTTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
20985 C
1 C
20986 TATCATTAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 34 0.64
31 19 0.36
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (31 bp):
CATTATATTAAATTATTTAAATATAATTTAT
Found at i:21003 original size:28 final size:27
Alignment explanation
Indices: 20939--21011 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 27
20929 GTATTAAATT
*
20939 ATTTAATATAAT-TTATTATTATATTTA
1 ATTTAATAAAATATT-TTATTATATTTA
**
20966 ATTTTTTAAAATATTTTATCTATCA-TTA
1 ATTTAATAAAATATTTTAT-TAT-ATTTA
*
20994 ATTTAAT-AAATACTTTAT
1 ATTTAATAAAATATTTTAT
21012 ATTAATTACT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 23 0.62
28 13 0.35
29 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTAATAAAATATTTTATTATATTTA
Done.