Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03832.F1
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, 954
Length: 1591
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Found at i:452 original size:228 final size:227
Alignment explanation
Indices: 55--1391 Score: 1119
Period size: 228 Copynumber: 5.9 Consensus size: 227
45 CTCCCAGAAG
* * * * * * * * *
55 ATGCAGATCTTTGTGAAGACCCTTACTGGTAAGACCATCACCCTTGAGGTAGAAAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * * * * *
120 TATCGATAATGTCAAGGCTAAAATCCAAGACAAAGAAGGGATCCCTCCTGACCAACAAAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGG-TTG
* * * * * * *
184 ATCTTTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTGCCGACTACAATATCCAAAAGGAGTC
130 ATTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTC
* * * **
249 CACCCTCCACCTAGTGCTTCGTCTAAGGGGTGGC
194 CACCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
* * * * * * *
283 ATGCAGATATTCGTGAAAACTCTTACTGGCAAGACCATCACCCTCGAGGTGGAAAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
*
348 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAACAGAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGG-TTG
* * *
412 ATCTTTGCCGGTAAACAGCTTGAAGATGGCCGAACTCTTGCGGATTACAACATCCAGAAA-GAGT
130 ATTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCA-AAAGGAGT
* * * * *
476 CTACCCTCCACCTT-GTCCTTCGTCTTAGGGGTGGG
193 CCACCCTCCA-CTTGGTGCTTCGACTTCGGGGTGGC
* * * * * ** *
511 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATTACGTTGGAGGTGGAGAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * *
576 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGA
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
* * * * * * *
641 TTTTTGCTGGAAAGCAGCTTGAAGATGGCCGAACTCTTGCTGATTATAACATTCAGAAGGAATCG
131 TTTTTGCTGGAAA-CAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTCC
* * *
706 ACCCTCCATTTGGTG-TTACGACTCCGTGGTGGC
195 ACCCTCCACTTGGTGCTT-CGACTTCGGGGTGGC
* * * * * * * ** * *
739 ATGCAAATTTTTGTGAAGACTCTCACCGGAAAGACTATTACTTTGGAAGTTGAGAGTTCTGACAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * * * *
804 CATTGACAATGTAAAAGCTAAGATCCAGGACAAGGAAGGGATTCCACCAGATCAGCAGAGGTTGA
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
** * * *
869 TTTTTGCTGGCAAACAGCTCGAAGATGGTAGGACACTTGCAGATTACAACATCCAGAAA-GAGTC
131 TTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCA-AAAGGAGTC
* * * * * *
933 TACCCTTCACTTGGTGCTCCGACTGCGTGGTGGA
194 CACCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
* ** * *
967 ATGCAGATTTTTGTGAAAACT-TTGACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACA
1 ATGCAGATTTTTGTGAAAACTCTT-ACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACA
* * *
1031 CAATTGATAATGTGAAGGCCAAGATCCAAGATAAGG-AGGGTATCCCACCTGACCAGCAGAGGTT
65 CAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGG-ATCCCACCAGACCAGCAGAGGTT
* ** * * * *
1095 GATTTTTGCTGGAAAGCAGCTCGAGGATGGGAGGACCCTTGCGGATTATAACATCCAAAAGGAAT
129 GATTTTTGCTGGAAA-CAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGT
* * * * * * *
1160 CGACCCTGCATTTGGT-TTTGCGACTTCGAGGAGGG
193 CCACCCTCCACTTGGTGCTT-CGACTTCGGGGTGGC
* * * * * * * *
1195 ATGCAGATATTCGTGAAGAC-CTTGACCGGTAAAACCATCACCCTGGAGGTCGAGAGCTCGGACA
1 ATGCAGATTTTTGTGAAAACTCTT-ACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACA
* * * * * * * *
1259 CCATTGACAATGTGAAAGCCAAGATTCAGGACAAGGAGGGGATTCCACCAGACCAGCAGAGGTTG
65 CAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTG
* * * * * * * * * * *
1324 ATATTTGCTGGGAAGCAGTTGGAGGATGGTCGAACTCTAGCTGACTACAATATCCAGAAGGAGTC
130 ATTTTTGCT-GGAAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTC
1389 CAC
194 CAC
1392 ACTGCATCTT
Statistics
Matches: 922, Mismatches: 169, Indels: 36
0.82 0.15 0.03
Matches are distributed among these distances:
227 23 0.02
228 881 0.96
229 18 0.02
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (227 bp):
ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
TTTTTGCTGGAAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTCCA
CCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
Found at i:1420 original size:456 final size:452
Alignment explanation
Indices: 124--1421 Score: 1326
Period size: 456 Copynumber: 2.8 Consensus size: 452
114 TGATACTATC
* * * * * * * * * *
124 GATAATGTCAAGGCTAAAATCCAAGACAAAGAAGGGATCCCTCCTGACCAACAAAGGCTT-ATCT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGG-TTGATTT
* * * * * * * * * * * *
188 TTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTGCCGACTACAATATCCAAAAGGAGTCCACC
65 TTGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
** * * ** * * * * *
253 CTCCACCTAGTGCTT-CGTCTAAGGGGTGGCATGCAGATATTCGTGAAAACTCTTACTGGCAAGA
130 CTCCATTTGGTG-TTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGAC-CTTACCGG-AAAA
* * * * * * * * *
317 CCATCACCCTCGAGGTGGAAAGTTCTGATACAATTGATAATGTCAAGGCCAAGATCCAAGACAAG
192 CCATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAG
* * * * * *
382 GAAGGGATCCCACCAGACCAACAGAGGCTT-ATCTTTGCCGGTAAACAGCTTGAAGATGGCCGAA
257 GAAGGGATTCCACCAGACCAGCAGAGG-TTGATATTTGCTGGCAAACAG-TTGAAGATGGTCGAA
* * ** * *
446 CTCTTGCGGATTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTTAGGGGTGGG
320 CTCTTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGACTCCGTGGTGGA
* * * * *
511 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATTACGTTGGAGGTGGAGAGTTCTGATAC
384 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACAC
*
576 GATT
449 AATT
* * *
580 GATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
* * * * * *
645 TGCTGGAAAGCAGCTTGAAGATGGCCGAACTCTTGCTGATTATAACATTCAGAAGGAATCGACCC
66 TGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACCC
* * * * * * *
710 TCCATTTGGTGTTACGACTCCGTGGTGGCATGCAAATTTTTGTGAAGACTCTCACCGGAAAGACT
131 TCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGAC-CTTACCGGAAA-ACC
* ** * * *
775 ATTACTTTGGAAGTTGAGAGTTCTGACACCATTGACAATGTAAAAGCTAAGATCCAGGACAAGGA
194 ATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGGA
* * * * * *
840 AGGGATTCCACCAGATCAGCAGAGGTTGATTTTTGCTGGCAAACAGCTCGAAGATGGTAGGACAC
259 AGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAG-TTGAAGATGGTCGAACTC
* * * *
905 TTGCAGATTACAACATCCAGAAAGAGTCTACCCTTCACTTGGTGCTCCGACTGCGTGGTGGAATG
323 TTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCACTT-GTCCTTCGACTCCGTGGTGGAATG
* ** *
970 CAGATTTTTGTGAAAACTTTGACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAAT
387 CAGATTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAAT
1035 T
452 T
*
1036 GATAATGTGAAGGCCAAGATCCAAGATAAGG-AGGGTATCCCACCTGACCAGCAGAGGTTGATTT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGG-ATCCCACCGGACCAGCAGAGGTTGATTT
* * *
1100 TTGCTGGAAAGCAGCTCGAGGATGGGAGGACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
65 TTGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
* * * * *
1165 CTGCATTTGGTTTTGCGACTTCGAGGAGGGATGCAGATATTCGTGAAGACCTTGACCGGTAAAAC
130 CTCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGACCTT-ACCGG-AAAAC
* * * *
1230 CATCACCCTGGAGGTCGAGAGCTCGGACACCATTGACAATGTGAAAGCCAAGATTCAGGACAAGG
193 CATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGG
* * * *
1295 AGGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGGAAGCAGTTGGAGGATGGTCGAACT
258 AAGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAGTT-GAAGATGGTCGAACT
* * * * * * * * *
1360 CTAGCTGACTACAATATCCAGAAGGAGTCCACACTGCATCTTGTCCTTCGCCTCCGTGGTGG
322 CTTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGACTCCGTGGTGG
1422 TTTCTAATTG
Statistics
Matches: 691, Mismatches: 141, Indels: 20
0.81 0.17 0.02
Matches are distributed among these distances:
455 18 0.03
456 667 0.97
457 6 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (452 bp):
GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
TGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACCC
TCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGACCTTACCGGAAAACCAT
CACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGGAAG
GGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAGTTGAAGATGGTCGAACTCTTG
CAGATTACAACATCCAGAAAGAGTCTACCCTCCACTTGTCCTTCGACTCCGTGGTGGAATGCAGA
TTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAATT
Done.