Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00768.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, 994
Length: 1657
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Found at i:460 original size:228 final size:227
Alignment explanation
Indices: 52--1400 Score: 1092
Period size: 228 Copynumber: 5.9 Consensus size: 227
42 AATCTTCAAG
* * * * *
52 ATGCAAATTTTTGTCAAGACCCTGACCGGCAAGACTATCACCCTT-GAGGTGGAAAGCTCCGACA
1 ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCA-CCTTGGAGGTTGAAAGCTCAGACA
* * * * * *
116 CCATCGATAATGTCAAGGCAAAGATCCAAGATAAAGAAGGAATCCCACCAAATCAACAGAGGCTT
65 CCATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGGATCCC-CCAGACCAACAGAGG-TT
** * * * * * * * *
181 -ATCTTTGCTAGTAAGCAGCTAGAATATGGTCGTACACTTGCTGACTACAACATTCAGAAGGAGT
128 GATCTTTGCCGGTAAGCAACTAGAAGATGGCCGCACACTGGCTGACTACAACATCCAAAAGGAAT
* *
245 CCACCCTGCACTTGGTCCTTCGT-TTGAGGAGTGGT
193 CCACCCTCCATTTGGTCCTTCGTCTTGAGG-GTGGT
* * * * * *
280 ATGCAAATCTTTGTTAAGACCCTCACCGGCAAGACTATCACCCTT-GAGGTGGAAAGCTCGGACA
1 ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCA-CCTTGGAGGTTGAAAGCTCAGACA
* * * *
344 CCATTGATAATGTCAAGGCCAAGATCCAAGACAAATAAGGGATCCCTCCAGACCAGCAGAGGCTT
65 CCATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGGATCCC-CCAGACCAACAGAGG-TT
* * * * *
409 -ATCTTTGCCGGTAAGCAACTAGAAGATGGTCGTACCCTGGCTGATTACAACATCCAAAAGGATT
128 GATCTTTGCCGGTAAGCAACTAGAAGATGGCCGCACACTGGCTGACTACAACATCCAAAAGGAAT
* * * * * *
473 CCACCCTCCATTTGGTGCTCCGCCTTCG-TGGAGGA
193 CCACCCTCCATTTGGTCCTTCGTCTT-GAGGGTGGT
* * * * * * * * *
508 ATGCAAATCTTTGTTAAGACCTTGACAGGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATAC
1 ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCACCTTGGAGGTTGAAAGCTCAGACAC
* * * ** *
573 CATTGACAATGTCAAGGCTAAGATCCAGGAT-AAGGAGGGTATTCGGCCAGACCAGCAGAGGTTG
66 CATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGG-A-TCCCCCAGACCAACAGAGGTTG
* * *
637 ATCTTTGCTGGTAAGCAACTAGAAGATGGCCGCACCCTGGCTGACTACATCATCCAAAAGGAATC
129 ATCTTTGCCGGTAAGCAACTAGAAGATGGCCGCACACTGGCTGACTACAACATCCAAAAGGAATC
* *
702 CACCCTCTATTTGGTGCTTCGTCTCCGTGGTGGTATGCAAATGTGGTGGT
194 CACCCTCCATTTGGT-C--C-T-T-C---GT-CT-TG---A-G-GGTGGT
* * * * * * * * *
752 ATGCAAATATTTGTTAAGACTCTTACCGGAAAGACCATTACTTTGGAGGTTGAGAGTTCAGATAC
1 ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCACCTTGGAGGTTGAAAGCTCAGACAC
* * *
817 CATTGACAATGTCAAGGCTAAGATCCAGGACAAAG-AGGGTATTCCCCCAGACCAACAGAGGTTG
66 CATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGG-A-TCCCCCAGACCAACAGAGGTTG
* * * *
881 ATCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACTCTCGCTGATTACAACATCCAAAAGGAATC
129 ATCTTTGCCGGTAAGCAACTAGAAGATGGCCGCACACTGGCTGACTACAACATCCAAAAGGAATC
* * ***
946 CACCCTCCACTTGGTGCTTCGTCTTTTTGGTGGT
194 CACCCTCCATTTGGTCCTTCGTCTTGAGGGTGGT
* * * * * * *
980 ATGCAGATTTTTGTGAAGACTCTTACCAGGAAA-ACGATCACCTTGGAAGTTGAGAGCTCTGACA
1 ATGCAAATTTTTGTTAAGACCCTGACC-GGAAAGACGATCACCTTGGAGGTTGAAAGCTCAGACA
* * * * *
1044 CTATTGACAATGTCAAGGCCAAAATCCAGGATAAGGAAGGTATCCCTCCAGACCAACAGAGGTTG
65 CCATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGGATCCC-CCAGACCAACAGAGGTTG
* * * * * * *
1109 AT-TTT-CACGGGTAAGCAGCTTG-AGAATGGCAGGACACTTGCAGACTACAACAT-TAAAAGGA
129 ATCTTTGC-C-GGTAAGCAACTAGAAG-ATGGCCGCACACTGGCTGACTACAACATCCAAAAGGA
* * * *
1170 ATCGACCCTCCATTTGGTTCTTCGTCTTCG-TGGTGGG
191 ATCCACCCTCCATTTGGTCCTTCGTCTT-GAGGGTGGT
* ** * * * * *
1207 ATGCAAATTTTTGTGAAGACATTGACAGGAAAGACGATCACTTTGGAAGTTGAAAGCTCGGACAT
1 ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCACCTTGGAGGTTGAAAGCTCAGACAC
* * * * * *
1272 TATTGATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGAATCCCCCTAGACCAGCAGAGGTTGA
66 CATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGGATCCCCC-AGACCAACAGAGGTTGA
* * * ** * *
1337 TCTTTGCAGGGAAGCAACTTGAAGATGGAAGGAC-CTTGGCAGACTACAACATCCAGAAA-GAAT
130 TCTTTGCCGGTAAGCAACTAGAAGATGGCCGCACAC-TGGCTGACTACAACATCCA-AAAGGAAT
1400 C
193 C
1401 GACTCTGCAC
Statistics
Matches: 944, Mismatches: 138, Indels: 78
0.81 0.12 0.07
Matches are distributed among these distances:
226 9 0.01
227 201 0.21
228 507 0.54
229 17 0.02
230 1 0.00
231 1 0.00
232 1 0.00
233 1 0.00
234 2 0.00
235 2 0.00
237 1 0.00
238 3 0.00
239 2 0.00
240 1 0.00
241 1 0.00
244 191 0.20
245 3 0.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (227 bp):
ATGCAAATTTTTGTTAAGACCCTGACCGGAAAGACGATCACCTTGGAGGTTGAAAGCTCAGACAC
CATTGACAATGTCAAGGCCAAGATCCAAGATAAAGAAGGGATCCCCCAGACCAACAGAGGTTGAT
CTTTGCCGGTAAGCAACTAGAAGATGGCCGCACACTGGCTGACTACAACATCCAAAAGGAATCCA
CCCTCCATTTGGTCCTTCGTCTTGAGGGTGGT
Found at i:747 original size:16 final size:16
Alignment explanation
Indices: 728--759 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
718 CTTCGTCTCC
728 GTGGTGGTATGCAAAT
1 GTGGTGGTATGCAAAT
744 GTGGTGGTATGCAAAT
1 GTGGTGGTATGCAAAT
760 ATTTGTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (16 bp):
GTGGTGGTATGCAAAT
Found at i:937 original size:244 final size:242
Alignment explanation
Indices: 508--1215 Score: 828
Period size: 244 Copynumber: 3.0 Consensus size: 242
498 TCGTGGAGGA
* *
508 ATGCAAATCTTTGTTAAGAC-CTTGACAGGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATA
1 ATGCAAATATTTGTTAAGACTCTT-ACCGGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATA
** *
572 CCATTGACAATGTCAAGGCTAAGATCCAGGATAAGGAGGGTATTCGGCCAGACCAGCAGAGGTTG
65 CCATTGACAATGTCAAGGCTAAGATCCAGGATAAGGAGGGTATTCCCCCAGACCAACAGAGGTTG
* * * * *
637 ATCTTTGCTGGTAAGCAACTAGAAGATGGCCGCACCCTGGCTGACTACATCATCCAAAAGGAATC
130 ATCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACACTCGCTGACTACAACATCCAAAAGGAATC
*
702 CACCCTCTATTTGGTGCTTCGTCTCCGTGGTGGTATGCAAATGTGGTGGT
195 CACCCTCCATTTGGTGCTTCGTCT-CGTGGTGGTATGCAAAT-TGGTGGT
*
752 ATGCAAATATTTGTTAAGACTCTTACCGGAAAGACCATTACTTTGGAGGTTGAGAGTTCAGATAC
1 ATGCAAATATTTGTTAAGACTCTTACCGGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATAC
* *
817 CATTGACAATGTCAAGGCTAAGATCCAGGACAAAGAGGGTATTCCCCCAGACCAACAGAGGTTGA
66 CATTGACAATGTCAAGGCTAAGATCCAGGATAAGGAGGGTATTCCCCCAGACCAACAGAGGTTGA
* *
882 TCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACTCTCGCTGATTACAACATCCAAAAGGAATCC
131 TCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACACTCGCTGACTACAACATCCAAAAGGAATCC
*
947 ACCCTCCACTTGGTGCTTCG--TC----T--T-T-----TTGGTGGT
196 ACCCTCCATTTGGTGCTTCGTCTCGTGGTGGTATGCAAATTGGTGGT
* * * * * * * * * *
980 ATGCAGATTTTTGTGAAGACTCTTACCAGGAAA-ACGATCACCTTGGAAGTTGAGAGCTCTGACA
1 ATGCAAATATTTGTTAAGACTCTTACC-GGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATA
* * * *
1044 CTATTGACAATGTCAAGGCCAAAATCCAGGATAAGGAAGGTA-TCCCTCCAGACCAACAGAGGTT
65 CCATTGACAATGTCAAGGCTAAGATCCAGGATAAGGAGGGTATTCCC-CCAGACCAACAGAGGTT
* * * * * *
1108 GAT-TTT-CACGGGTAAGCAGCTTG-AGAATGGCAGGACACTTGCAGACTACAACAT-TAAAAGG
129 GATCTTTGC-C-GGTAAGCAACTTGAAG-ATGGCCGCACACTCGCTGACTACAACATCCAAAAGG
* * *
1169 AATCGACCCTCCATTTGGTTCTTCGTCTTCGTGGTGGGATGCAAATT
191 AATCCACCCTCCATTTGGTGCTTCGTC-TCGTGGTGGTATGCAAATT
1216 TTTGTGAAGA
Statistics
Matches: 399, Mismatches: 44, Indels: 44
0.82 0.09 0.09
Matches are distributed among these distances:
226 1 0.00
227 38 0.10
228 145 0.36
229 6 0.02
230 2 0.01
234 2 0.01
235 1 0.00
237 2 0.01
241 1 0.00
242 3 0.01
244 195 0.49
245 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (242 bp):
ATGCAAATATTTGTTAAGACTCTTACCGGAAAGACAATTACTTTGGAGGTTGAGAGTTCAGATAC
CATTGACAATGTCAAGGCTAAGATCCAGGATAAGGAGGGTATTCCCCCAGACCAACAGAGGTTGA
TCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACACTCGCTGACTACAACATCCAAAAGGAATCC
ACCCTCCATTTGGTGCTTCGTCTCGTGGTGGTATGCAAATTGGTGGT
Found at i:1291 original size:227 final size:228
Alignment explanation
Indices: 744--1400 Score: 787
Period size: 227 Copynumber: 2.9 Consensus size: 228
734 GTATGCAAAT
* * * * * * *
744 GTGGTGGTATGCAAATATTTGTTAAGACTCTTACCGGAAAGACCATTACTTTGGAGGTTGAGAGT
1 GTGGTGGTATGCAAATTTTTGTGAAGACTCTTACAGGAAAGACGATCACTTTGGAAGTTGAGAGC
* * * * * *
809 TCAGATACCATTGACAATGTCAAGGCTAAGATCCAGGACAAAGAGGGTATTCCCCCAGACCAACA
66 TCAGACACTATTGACAATGTCAAGGCCAAGATCCAGGATAAGGAAGGTA-TCCCCCAGACCAACA
* * * * *
874 GAGGTTGATCTTTGC-C-GGTAAGCAACTTGAAGATGGCCGCACTCTCGCTGATTACAACATCCA
130 GAGGTTGATCTTTGCACGGGTAAGCAACTTGAAGATGGCAGGAC-CTTGCAGACTACAACATCCA
*
937 AAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTT
194 AAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTC
* * *
972 TTGGTGGTATGCAGATTTTTGTGAAGACTCTTACCAGGAAA-ACGATCACCTTGGAAGTTGAGAG
1 GTGGTGGTATGCAAATTTTTGTGAAGACTCTTA-CAGGAAAGACGATCACTTTGGAAGTTGAGAG
* *
1036 CTCTGACACTATTGACAATGTCAAGGCCAAAATCCAGGATAAGGAAGGTATCCCTCCAGACCAAC
65 CTCAGACACTATTGACAATGTCAAGGCCAAGATCCAGGATAAGGAAGGTATCCC-CCAGACCAAC
*
1101 AGAGGTTGAT-TTT-CACGGGTAAGCAGCTTG-AGAATGGCAGGACACTTGCAGACTACAACAT-
129 AGAGGTTGATCTTTGCACGGGTAAGCAACTTGAAG-ATGGCAGGAC-CTTGCAGACTACAACATC
* * * *
1162 TAAAAGGAATCGACCCTCCATTTGGTTCTTCGTCTTC
192 CAAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTC
* * *
1199 GTGGTGGGATGCAAATTTTTGTGAAGACAT-TGACAGGAAAGACGATCACTTTGGAAGTTGAAAG
1 GTGGTGGTATGCAAATTTTTGTGAAGAC-TCTTACAGGAAAGACGATCACTTTGGAAGTTGAGAG
* * * * * * *
1263 CTCGGACATTATTGATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGAATCCCCCTAGACCAGC
65 CTCAGACACTATTGACAATGTCAAGGCCAAGATCCAGGATAAGGAAGGTATCCCCC-AGACCAAC
*
1328 AGAGGTTGATCTTTGCA-GGG-AAGCAACTTGAAGATGGAAGGACCTTGGCAGACTACAACATCC
129 AGAGGTTGATCTTTGCACGGGTAAGCAACTTGAAGATGGCAGGACCTT-GCAGACTACAACATCC
1391 AGAAA-GAATC
193 A-AAAGGAATC
1401 GACTCTGCAC
Statistics
Matches: 368, Mismatches: 47, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
226 13 0.04
227 186 0.51
228 158 0.43
229 11 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (228 bp):
GTGGTGGTATGCAAATTTTTGTGAAGACTCTTACAGGAAAGACGATCACTTTGGAAGTTGAGAGC
TCAGACACTATTGACAATGTCAAGGCCAAGATCCAGGATAAGGAAGGTATCCCCCAGACCAACAG
AGGTTGATCTTTGCACGGGTAAGCAACTTGAAGATGGCAGGACCTTGCAGACTACAACATCCAAA
AGGAATCCACCCTCCACTTGGTGCTTCGTCTTC
Done.