Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00001.P3
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: 23759
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4341 original size:2 final size:2
Alignment explanation
Indices: 4334--4364 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4324 TTCTGAGATA
4334 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
4365 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:12840 original size:43 final size:43
Alignment explanation
Indices: 12739--12864 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
12729 AATTAATAAT
* * * *
12739 ATTATCCAAATGCATAATTAGTATTAC-ACTACATGATAACAACAAC
1 ATTATCCAAGTGCATAACTAATATTACAAC-ACAT--T-ATAACAAC
12785 ATTATCCAAGTGCATAACTAATATTACAACACATTATAACAAC
1 ATTATCCAAGTGCATAACTAATATTACAACACATTATAACAAC
* *
12828 ATTGTCCAAGTGCATAACTAATATTACACCACATTAT
1 ATTATCCAAGTGCATAACTAATATTACAACACATTAT
12865 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:15138 original size:897 final size:896
Alignment explanation
Indices: 13581--15373 Score: 3424
Period size: 897 Copynumber: 2.0 Consensus size: 896
13571 GATTTTCCCA
*
13581 AAAATGGTTCATCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
1 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
13646 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
66 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
* *
13711 CTCTTTTAAATGATATCGAATACCATGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
131 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
13776 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
196 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
13841 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
261 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
*
13906 GTGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
326 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
13971 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
391 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
*
14036 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATTTAATGCTCCAAT
456 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
*
14101 ACAATCTTTAAAATAAGGATTAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
521 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
*
14166 GTAATTTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
586 GTAATCTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
14231 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCACTCGAAACCTTACATTATGACCAATTAT
651 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCA-TCGAAACCTTACATTATGACCAATTAT
*
14296 ATGTAAAAATATAACTACTTGCTCCCTAATATTCACTGATTTAGTTGATTGTAACAAATTATTTC
715 ATGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTC
* *
14361 TACTAAGAATATCACACAAATTAAAAAATGCAACCGGTCGCATCCTTATCATATCAATACAATGC
780 TACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCGCATCCTTATCATATCAATACAATGC
14426 CGGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
845 CGGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
*
14478 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCTAAAAACACGTTCAATAGTG
1 AAAATGGTTCAGCATCTAATACACGAAACCGTTTCTTCAAAATCCCAAAAACACGTTCAATAGTG
*
14543 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCTTGAGCACTAAA
66 ATTCGCAATGATGAATGACGAAGATTAAAGAGTTCCTTTTCATTTTCAGGCCCCTGAGCACTAAA
14608 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
131 CTCTTTTAAATGATATCGAACACCACGATATGGGGTAATATATCCATTACGGATGCCATATCCAG
*
14673 CATCAGCAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
196 CATCAACAAGATAATATTTACCTACAATTTGACAAAACATAATTATTACTAATAAATTATGAGCT
14738 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
261 TAGTAGAACTATTTGGTATTTAATGTTTTATAATTCTTACCTTCCGGAATTTTTAATCCTCTTGG
14803 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
326 GCGTGAAAGTGCATCACTTAAAATACGAGAATCATGTGCACTACCTTCCCAACCAGCTAGAACAT
*
14868 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCTCCCCTTTACGGCTA
391 AGGAAAATTTCAAATCAAATGTAATGGCAGCCAATACATTTTGTGTCGTCCCCCCTTTACGGCTA
14933 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
456 CGAAATCTTCCTTGAATGTTAAGTGGAACGGATGCACGAACATGAGTTCCATCTAATGCTCCAAT
14998 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
521 ACAATCTTTAAAATAAGGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAG
*
15063 GTAATCTAATAACTAGTTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
586 GTAATCTAATAACTAGCTTATACAATTTCAAAACAGCTCTCAATACAACCCTAAAGTAACGGTGA
15128 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCATCGAAACCTTACATTATGACCAATTATA
651 ATTGTCTCAGTTGATCTATAATATCTAGATCCTATCATCGAAACCTTACATTATGACCAATTATA
15193 TGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTCT
716 TGTAAAAATATAACTACTTGCTCCCTAATATTCACCGATTTAGTTGATTGTAACAAATTATTTCT
*
15258 ACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCTCATCCTTATCATATCAATACAATGCC
781 ACAAAGAATATCACACAAATTAAAAAATGCAACAGGTCGCATCCTTATCATATCAATACAATGCC
*
15323 GGTCACCACTATATAAAATATTATTAATATAATTTTCTCTTTCATAATCTC
846 GGTCACCACTATATAAAATACTATTAATATAATTTTCTCTTTCATAATCTC
15374 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:15609 original size:2 final size:2
Alignment explanation
Indices: 15602--15630 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15592 AAGTGCATAC
15602 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
15631 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:16111 original size:2 final size:2
Alignment explanation
Indices: 16100--16129 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16090 GAACCTTTAC
16100 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
16130 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:18772 original size:46 final size:46
Alignment explanation
Indices: 18722--18897 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
18712 TGGTTGAGCA
18722 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
18768 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
18813 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
18861 CCCGAGCTCGTTGATTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18898 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:18880 original size:93 final size:93
Alignment explanation
Indices: 18719--18890 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
18709 GGATGGTTGA
* *
18719 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
18784 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
18812 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
18877 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
18891 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:20250 original size:18 final size:18
Alignment explanation
Indices: 20229--20275 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20219 TTAAATTGTT
20229 TAAATTTAAAAAATTAT-A
1 TAAATTTAAAAAA-TATCA
* *
20247 TAAAATTATAAAATATCA
1 TAAATTTAAAAAATATCA
20265 TCAAATTTAAA
1 T-AAATTTAAA
20276 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:20650 original size:55 final size:55
Alignment explanation
Indices: 20562--20667 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
20552 AAGGAGGTGC
* *
20562 TTTTACACCTAGAAGGATAACTGATTTTGGGGGTCAAAATTACGGTGAAAAATTG
1 TTTTACACCGAGAAGGATAACTGATTTTGGGGGTCAAAATTAAGGTGAAAAATTG
*
20617 TTTTACACCGAGAAGGATAACTGATTTTTGGGGTCAAAATTAAGGTGAAAA
1 TTTTACACCGAGAAGGATAACTGATTTTGGGGGTCAAAATTAAGGTGAAAA
20668 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:20851 original size:31 final size:31
Alignment explanation
Indices: 20811--20902 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
20801 TATTTTGTAC
20811 CATTATATTAAATTATTTAAATATAATTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
*
20842 CATTGTATTAAATTATTT-AATATAATTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
* * * *
20872 TATTATATTTAATTTTTTAAA-ATATTTTAT
1 CATTATATTAAATTATTTAAATATAATTTAT
20902 C
1 C
20903 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:20920 original size:28 final size:27
Alignment explanation
Indices: 20856--20928 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 27
20846 GTATTAAATT
*
20856 ATTTAATATAAT-TTATTATTATATTTA
1 ATTTAATAAAATATT-TTATTATATTTA
**
20883 ATTTTTTAAAATATTTTATCTATCA-TTA
1 ATTTAATAAAATATTTTAT-TAT-ATTTA
*
20911 ATTTAAT-AAATACTTTAT
1 ATTTAATAAAATATTTTAT
20929 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.