Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01821.R2
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: 3392
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Found at i:416 original size:96 final size:96
Alignment explanation
Indices: 252--454 Score: 264
Period size: 96 Copynumber: 2.1 Consensus size: 96
242 AATACAGCGA
* * * *
252 AGAGTTAGTCCAAGGTTTCAAAATCTACCAAACGGTGGTAAATCGAACATTGAGAAGATATGGAA
1 AGAGTTAGCCCAAGGTTTCAAAATCTACCAAACGGTGGGAAATCAAACATTGAGAAGATAAGGAA
*
317 TGCAACAAAATCAAGAAA-AACATTAAATACT
66 TGCAACAAAATCAAGAAAGAA-ATCAAATACT
* * * *
348 AGAGTTAGCCCAAGGTTTCAAAATCTACTAAATGTTGGGAACTCAAACATTGAGAAGATAAGGAA
1 AGAGTTAGCCCAAGGTTTCAAAATCTACCAAACGGTGGGAAATCAAACATTGAGAAGATAAGGAA
** * *
413 TGCAACTGACTCAGGAAAGAAATCAAATACT
66 TGCAACAAAATCAAGAAAGAAATCAAATACT
*
444 AGAGCTAGCCC
1 AGAGTTAGCCC
455 TAACTCAAAG
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 90 0.98
97 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.21
Consensus pattern (96 bp):
AGAGTTAGCCCAAGGTTTCAAAATCTACCAAACGGTGGGAAATCAAACATTGAGAAGATAAGGAA
TGCAACAAAATCAAGAAAGAAATCAAATACT
Found at i:474 original size:69 final size:69
Alignment explanation
Indices: 387--523 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
377 AAATGTTGGG
* *
387 AACTCAAACATTGAGAAGATAAGGAATGCAACTGACTC-AGGAAAGAAATCAAATACTAGAGCTA
1 AACTCAAACATTGAGAAGATAAGGAATGAAACTGACTCGA-CAAAGAAATCAAATACTAGAGCTA
451 GCCCT
65 GCCCT
* * * * *
456 AACTCAAAGATTGTGAAGATACGGAATGAAACTGACTCGACAAAGATATCAAATACTAGAGTTAG
1 AACTCAAACATTGAGAAGATAAGGAATGAAACTGACTCGACAAAGAAATCAAATACTAGAGCTAG
521 CCC
66 CCC
524 GAGGTTCCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 59 0.98
70 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (69 bp):
AACTCAAACATTGAGAAGATAAGGAATGAAACTGACTCGACAAAGAAATCAAATACTAGAGCTAG
CCCT
Found at i:780 original size:81 final size:81
Alignment explanation
Indices: 678--973 Score: 217
Period size: 81 Copynumber: 3.5 Consensus size: 81
668 CTCAACAAAG
* *
678 ACATCAAATACTAGTGCTAGCCCAAGGTTCCAAAATCTACCAAATATTGAGAAGATATGGAATGC
1 ACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAATATTGAGAAGATATGGAATGC
743 AACCGACTCAAGAACA
66 AACCGACTCAAGAACA
* * ** * *
759 ACATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTAATGGTG-GTAACTCCAACAATG
1 ACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAATATTGAG-AA----GA-TATG
* ** ***
823 AGAA-GAAAAGGGA-TGCAACTCCCTCA
60 -GAATG-CAACCGACT-CAA---GAACA
* *
849 ACA-AAGACATCAAATAGAGTTAGCCCAAGGTTCCAAAATCTACCAAA-ATTTGAGAAGATATGG
1 ACATCA-A-AT--ACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAATA-TTGAGAAGATATGG
* *
912 GATGCAACCGACCCAAGAA-A
61 AATGCAACCGACTCAAGAACA
*
932 GAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACC
1 -ACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACC
974 TAATGGTGAT
Statistics
Matches: 160, Mismatches: 33, Indels: 44
0.68 0.14 0.19
Matches are distributed among these distances:
80 1 0.01
81 76 0.47
83 3 0.02
84 3 0.02
85 2 0.01
86 5 0.03
87 19 0.12
88 4 0.03
89 2 0.01
90 6 0.04
91 2 0.01
93 36 0.22
94 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (81 bp):
ACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAATATTGAGAAGATATGGAATGC
AACCGACTCAAGAACA
Found at i:791 original size:177 final size:177
Alignment explanation
Indices: 495--1194 Score: 935
Period size: 177 Copynumber: 3.9 Consensus size: 177
485 AACTGACTCG
* * **
495 ACAAAGATATCAAATACTAGAGTTAGCCCGAGGTTCCAAAATCTACCAAAATTTGAGAAGATGCG
1 ACAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATATG
* * *
560 GGATGCAGCTGACACAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTA
66 GGATGCAACCGACTCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTA
* *
625 ATGGTGGTAACTCCAACAATGAGAAGAAAAGGGATGCAGCTCTCTCA
131 ATGGTGATAACTCCAACAATGAGAAGAAAAGGGATGCAACTCTCTCA
* *
672 ACAAAGACATCAAATACTAGTGCTAGCCCAAGGTTCCAAAATCTACC-AAATATTGAGAAGATAT
1 ACAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAAT-TTGAGAAGATAT
* *
736 GGAATGCAACCGACTCAAGAACA-ACATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACC
65 GGGATGCAACCGACTCAAGAA-AGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACC
* *
800 TAATGGTGGTAACTCCAACAATGAGAAGAAAAGGGATGCAACTCCCTCA
129 TAATGGTGATAACTCCAACAATGAGAAGAAAAGGGATGCAACTCTCTCA
849 ACAAAGACATC-AA-A-TAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATATG
1 ACAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATATG
* *
911 GGATGCAACCGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCTA
66 GGATGCAACCGACTCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTA
* *
976 ATGGTGATAACTCCAATAATGAGAA-ATTAAGGGATGCAACTCTCTCA
131 ATGGTGATAACTCCAACAATGAGAAGA-AAAGGGATGCAACTCTCTCA
* *
1023 ATAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATGTACCAAATGTTGATAACGCAAA
1 ACAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAA-----AT--------
* * ** *
1088 CATTGAGAAGACATGGGATGCAACTGACTCAAGAAAGACGTTAAATACTAGAGTTAGCCCAAGGT
53 --TTGAGAAGATATGGGATGCAACCGACTCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGT
* * *
1153 TTCAAAATCTACCAAATGGTGATAACTCAAACATTGAGAAGA
116 TTCAAAATCTACCTAATGGTGATAACTCCAACAATGAGAAGA
1195 TACAGAATGT
Statistics
Matches: 463, Mismatches: 36, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
173 2 0.00
174 151 0.33
175 7 0.02
176 7 0.02
177 200 0.43
178 1 0.00
182 2 0.00
192 92 0.20
193 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (177 bp):
ACAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATATG
GGATGCAACCGACTCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTA
ATGGTGATAACTCCAACAATGAGAAGAAAAGGGATGCAACTCTCTCA
Found at i:940 original size:351 final size:356
Alignment explanation
Indices: 512--1194 Score: 993
Period size: 351 Copynumber: 1.9 Consensus size: 356
502 TATCAAATAC
* * * *
512 TAGAGTTAGCCCGAGGTTCCAAAATCTACCAAAATTTGAGAAGATGCGGGATGCAGCTGACACAA
1 TAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATACGGGATGCAACCGACACAA
* *
577 GAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTAATGGTGGTAACTCCAAC
66 GAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCTAATGGTGATAACTCCAAC
* *
642 AATGAGAAGA-AAAGGGATGCAGCTCTCTCAACAAAGACATCAAATACTAGTGCTAGCCCAAGGT
131 AATGAGAA-ATAAAGGGATGCAACTCTCTCAACAAAGACATCAAATACTAGAGCTAGCCCAAGGT
* *
706 TCCAAAA-T-C-T-AC-CAAATATTGAGAAGATATGGAATGCAACCGACTCAAGAACA-ACATCA
195 TCCAAAAGTACATAACGCAAACATTGAGAAGACATGGAATGCAACCGACTCAAGAA-AGACATCA
* * *
765 AATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCTAATGGTGGTAACTCCAACAATGAGAAGAA
259 AATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCAAATGGTGATAACTCAAACAATGAGAAGAA
830 AAGGGATGCAACTCCCTCAACAAAGACATCAAA
324 AAGGGATGCAACTCCCTCAACAAAGACATCAAA
* *
863 TAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATATGGGATGCAACCGACCCAA
1 TAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATACGGGATGCAACCGACACAA
*
928 GAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCTAATGGTGATAACTCCAAT
66 GAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCTAATGGTGATAACTCCAAC
* * *
993 AATGAGAAATTAAGGGATGCAACTCTCTCAATAAAGACATCAAATACTAGAGTTAGCCCAAGGTT
131 AATGAGAAATAAAGGGATGCAACTCTCTCAACAAAGACATCAAATACTAGAGCTAGCCCAAGGTT
* *
1058 CCAAAATGTACCAAATGTTGATAACGCAAACATTGAGAAGACATGGGATGCAACTGACTCAAGAA
196 CCAAAA-GTA-C--------ATAACGCAAACATTGAGAAGACATGGAATGCAACCGACTCAAGAA
* * *
1123 AGACGTTAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCAAATGGTGATAACTCAAACATT
251 AGACATCAAATACTAGAGTTAGCCCAAGGTTTCAAAATCTACCAAATGGTGATAACTCAAACAAT
1188 GAGAAGA
316 GAGAAGA
1195 TACAGAATGT
Statistics
Matches: 291, Mismatches: 24, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
350 1 0.00
351 185 0.64
353 1 0.00
355 1 0.00
364 1 0.00
365 3 0.01
366 99 0.34
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (356 bp):
TAGAGTTAGCCCAAGGTTCCAAAATCTACCAAAATTTGAGAAGATACGGGATGCAACCGACACAA
GAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATCTACCTAATGGTGATAACTCCAAC
AATGAGAAATAAAGGGATGCAACTCTCTCAACAAAGACATCAAATACTAGAGCTAGCCCAAGGTT
CCAAAAGTACATAACGCAAACATTGAGAAGACATGGAATGCAACCGACTCAAGAAAGACATCAAA
TACTAGAGTTAGCCCAAGGTTTCAAAATCTACCAAATGGTGATAACTCAAACAATGAGAAGAAAA
GGGATGCAACTCCCTCAACAAAGACATCAAA
Found at i:1063 original size:96 final size:96
Alignment explanation
Indices: 899--1243 Score: 392
Period size: 96 Copynumber: 3.6 Consensus size: 96
889 TACCAAAATT
* * * *
899 TGAGAAGATATGGGATGCAAC-CGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTC
1 TGAGAAGACAAGGGATGCAACTC-ACTCAAGAAAGACATCAAATACTAGAGTTAGCCCAAGGTTC
* * *
963 CAAAATCTACCTAATGGTGATAACTCCAATAA
65 CAAAATCTACCAAATGGTGATAACTCAAACAA
* * *
995 TGAGAA-ATTAAGGGATGCAACTCTCTCAATAAAGACATCAAATACTAGAGTTAGCCCAAGGTTC
1 TGAGAAGA-CAAGGGATGCAACTCACTCAAGAAAGACATCAAATACTAGAGTTAGCCCAAGGTTC
* * * *
1059 CAAAATGTACCAAATGTTGATAACGCAAACAT
65 CAAAATCTACCAAATGGTGATAACTCAAACAA
* * * * *
1091 TGAGAAGACATGGGATGCAACTGACTCAAGAAAGACGTTAAATACTAGAGTTAGCCCAAGGTTTC
1 TGAGAAGACAAGGGATGCAACTCACTCAAGAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCC
*
1156 AAAATCTACCAAATGGTGATAACTCAAACAT
66 AAAATCTACCAAATGGTGATAACTCAAACAA
* * * * * *
1187 TGAGAAGATACA-GAATG-TACCCGATTCAAGAAAGACACCAAATACTAGAGTTAGCCC
1 TGAGAAGACA-AGGGATGCAACTC-ACTCAAGAAAGACATCAAATACTAGAGTTAGCCC
1244 CAGACTCCAA
Statistics
Matches: 211, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
95 3 0.01
96 206 0.98
97 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (96 bp):
TGAGAAGACAAGGGATGCAACTCACTCAAGAAAGACATCAAATACTAGAGTTAGCCCAAGGTTCC
AAAATCTACCAAATGGTGATAACTCAAACAA
Found at i:1231 original size:192 final size:192
Alignment explanation
Indices: 898--1243 Score: 484
Period size: 192 Copynumber: 1.8 Consensus size: 192
888 CTACCAAAAT
*
898 TTGAGAAGATATGGGATGCAACCGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTC
1 TTGAGAAGACATGGGATGCAACCGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTC
* * * * * *
963 CAAAATCTACCTAATGGTGATAACTCCAATAATGAGAAATTAAGGGATGCAACTCTCTCAATAAA
66 CAAAATCTACCAAATGGTGATAACTCAAACAATGAGAAATTAAGGAATGCAACCCTCTCAAGAAA
*
1028 GACATCAAATACTAGAGTTAGCCCAAGGTTCCAAAATGTACCAAATGTTGATAACGCAAACA
131 GACACCAAATACTAGAGTTAGCCCAAGGTTCCAAAATGTACCAAATGTTGATAACGCAAACA
* * ** * *
1090 TTGAGAAGACATGGGATGCAACTGACTCAAGAAAGACGTTAAATACTAGAGTTAGCCCAAGGTTT
1 TTGAGAAGACATGGGATGCAACCGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTC
* *
1155 CAAAATCTACCAAATGGTGATAACTCAAACATTGAGAAGA-TACA-GAATG-TACCCGAT-TCAA
66 CAAAATCTACCAAATGGTGATAACTCAAACAATGAGAA-ATTA-AGGAATGCAACCC--TCTCAA
1216 GAAAGACACCAAATACTAGAGTTAGCCC
127 GAAAGACACCAAATACTAGAGTTAGCCC
1244 CAGACTCCAA
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
191 3 0.02
192 128 0.96
193 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (192 bp):
TTGAGAAGACATGGGATGCAACCGACCCAAGAAAGAAATCAAATACTAGAGTTAGCCCAAGGTTC
CAAAATCTACCAAATGGTGATAACTCAAACAATGAGAAATTAAGGAATGCAACCCTCTCAAGAAA
GACACCAAATACTAGAGTTAGCCCAAGGTTCCAAAATGTACCAAATGTTGATAACGCAAACA
Done.