Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g01005.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, 1000
Length: 4814
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:2435 original size:33 final size:32
Alignment explanation
Indices: 2331--2451 Score: 111
Period size: 33 Copynumber: 3.7 Consensus size: 32
2321 TAAGTAGAAC
* * * *
2331 GGATGATGCTCCTATAAGTAGTCCTAGTAGTAG
1 GGATGATGCCCCTATAAGCAGGCCTAGTAG-CG
* * *
2364 GGATGATGCCCCTGTGAGCA--CCTCAAGTACCTG
1 GGATGATGCCCCTATAAGCAGGCCT--AGTAGC-G
*
2397 GGATGATGCTCCTATAAGCAGGCCTAGTAGCG
1 GGATGATGCCCCTATAAGCAGGCCTAGTAGCG
2429 GTGATGATGCCCCTATAAGCAGG
1 G-GATGATGCCCCTATAAGCAGG
2452 TTAAGTATGG
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
31 3 0.04
32 2 0.03
33 63 0.89
35 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (32 bp):
GGATGATGCCCCTATAAGCAGGCCTAGTAGCG
Found at i:2537 original size:98 final size:100
Alignment explanation
Indices: 2413--2638 Score: 343
Period size: 98 Copynumber: 2.3 Consensus size: 100
2403 TGCTCCTATA
* ** *
2413 AGCAGGCCTAGTAGCGGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCTCCTGT
1 AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT
2478 AAGTGGACCAACTGCTGGTGAAGATT-ACCC-TTT
66 AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT
* *
2511 AGCAGGCCAAGTAGAAGTGTTGATGCCCCTATAAGCAGGTTAAGTATTGGGGAAAATGCCCCTGT
1 AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT
*
2576 AAGTGGACCAACTGCTGGTGAAGATTGTCCCGTTT
66 AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT
*
2611 -GCAGGCCAAGTAGCAA-TAATGATGCCCC
1 AGCAGGCCAAGTAG-AAGTGATGATGCCCC
2639 CATGAGCTGT
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
98 85 0.73
99 26 0.22
100 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (100 bp):
AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT
AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT
Found at i:4082 original size:390 final size:398
Alignment explanation
Indices: 3553--4329 Score: 910
Period size: 402 Copynumber: 2.0 Consensus size: 398
3543 TCTGGTGTAG
* ** * * *
3553 AAGAAATGGATATTAGGAACTCCATCTCCTCATCTCCTGAACTGATAGATGTTATGAGGGATGAA
1 AAGAAATGGATATTAGGAACTCCATCTCCTCATCTCCAGAACCCACAAATGTTACGAGGGATGAA
** * * * * *
3618 TTGGATATGAGAAACACGACTAGTCCAGTGACCAATACATTAAGTTTCTGTGGAGCTTTAAGTTC
66 TTGGATACAAGAAACACGACTAGTCCAGTGACCAATACATCAAGCTGCTCTGAAGCTTTAAGTTC
* * * *
3683 AACACCAAATATTTCGGATTATTCTGGTGTCGAAG-AA-A-TGT-CCA-T-TAT-CTCT-GGTGT
131 AACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAAGATTGTACAACTCCATGCCCTAGGTGT
* * * * * *
3740 TCAAGAAATGGATATTGTG-AACT-CTATTTCCTCGTCTCCAGAACCCATGAATGTTGTGAGGGA
196 TAAAGAAATGGATATCG-GCAACTCCT-TTTCCCCATCTCCAGAACCCATCAATGTTGTGAGAGA
**
3803 TGAATTAGATATAAGAAACAGGATTAGTCAAGTGACCCTTGCAGCAAGCTGCTATGAAGCTTTAA
259 TGAATTAGATATAAGAAACAGGACAAGTCAAGTGACCCTTGCAGCAAGCTGCTATGAAGCTTTAA
* * * * * *
3868 GTTCAACATCAAATGCTTCATATTATTCTTGTGTTAAAG-AGGTGGATGTTAGGAACTCAATGCG
324 GTTCAACACCAAATGCTTCAGATTATTCTGGTGGTAAAGAAAG-GGATATTAGGAACTCAATGCG
3932 CTCCACTTTTA
388 CTCCACTTTTA
* * *
3943 AAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCACAAATGTTGCGAGGGATGAA
1 AAGAAATGGATATTAGGAACTCCATCTCCTCATCTCCAGAACCCACAAATGTTACGAGGGATGAA
* * * ** *
4008 TTGGATGCAAGAAACATGACTAGTTCAGTGACCCTTGCATCAAGCTGCTCTGAAGCTTTAAGTTC
66 TTGGATACAAGAAACACGACTAGTCCAGTGACCAATACATCAAGCTGCTCTGAAGCTTTAAGTTC
* * * *
4073 AACACCAAATGTTTTGGATTATTCTGGTGTTAAAGAAATGGATTGTAGGAACTCCATGCCCTACG
131 AACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAA--GATTGTA-CAACTCCATGCCCTA-G
*
4138 TTGTTAAAGAAATGGATATCGGCAACTCCTTTTCCCCATCTCCAGAACCCATCAATGTTGTGAGA
192 GTGTTAAAGAAATGGATATCGGCAACTCCTTTTCCCCATCTCCAGAACCCATCAATGTTGTGAGA
* * * ** * * *
4203 GATGAATTGGATATGAGAAACATGACAAGTCCGGTGACCCTTGCATCAAGTTGCTCTGAAGCTTT
257 GATGAATTAGATATAAGAAACAGGACAAGTCAAGTGACCCTTGCAGCAAGCTGCTATGAAGCTTT
* * *
4268 AATTTCAACACCAAATGTTTCAGATTATTGTGGTGGTAAAGAAAGGGATATTAGGAACTCAA
322 AAGTTCAACACCAAATGCTTCAGATTATTCTGGTGGTAAAGAAAGGGATATTAGGAACTCAA
4330 CTTCCTCCCC
Statistics
Matches: 316, Mismatches: 56, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
390 139 0.44
391 2 0.01
394 1 0.00
395 3 0.01
397 1 0.00
398 1 0.00
399 2 0.01
400 3 0.01
401 1 0.00
402 159 0.50
403 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (398 bp):
AAGAAATGGATATTAGGAACTCCATCTCCTCATCTCCAGAACCCACAAATGTTACGAGGGATGAA
TTGGATACAAGAAACACGACTAGTCCAGTGACCAATACATCAAGCTGCTCTGAAGCTTTAAGTTC
AACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAAGATTGTACAACTCCATGCCCTAGGTGT
TAAAGAAATGGATATCGGCAACTCCTTTTCCCCATCTCCAGAACCCATCAATGTTGTGAGAGATG
AATTAGATATAAGAAACAGGACAAGTCAAGTGACCCTTGCAGCAAGCTGCTATGAAGCTTTAAGT
TCAACACCAAATGCTTCAGATTATTCTGGTGGTAAAGAAAGGGATATTAGGAACTCAATGCGCTC
CACTTTTA
Found at i:4096 original size:201 final size:199
Alignment explanation
Indices: 3737--4329 Score: 744
Period size: 201 Copynumber: 2.9 Consensus size: 199
3727 TTATCTCTGG
* * * * *
3737 TGTTCAAGAAATGGATATTGTGAACTCTATTTCCTCGTCTCCAGAACCCATGAATGTTGTGAGGG
1 TGTTAAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCA-CAATGTTGTGAGGG
* * * * *
3802 ATGAATTAGATATAAGAAACAGGATTAG-TCAAGTGACCCTTGCAGCAAGCTGCTATGAAGCTTT
65 ATGAATTGGATATAAGAAACATGACTAGTTC-AGTGACCCTTGCATCAAGCTGCTCTGAAGCTTT
* * * * *
3866 AAGTTCAACATCAAATGCTTCATATTATTCTTGTGTTAAAGAGGTGGATGTTAGGAACTCAATGC
129 AAGTTCAACACCAAATGTTTCAGATTATTCTGGTGTTAAAGAAGTGGAT-TTAGGAACTCAATGC
3931 GCTCCAC-T
193 -C-CCACGT
*
3939 T-TTAAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCACAAATGTTGCGAGGG
1 TGTTAAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCAC-AATGTTGTGAGGG
**
4003 ATGAATTGGATGCAAGAAACATGACTAGTTCAGTGACCCTTGCATCAAGCTGCTCTGAAGCTTTA
65 ATGAATTGGATATAAGAAACATGACTAGTTCAGTGACCCTTGCATCAAGCTGCTCTGAAGCTTTA
** * *
4068 AGTTCAACACCAAATGTTTTGGATTATTCTGGTGTTAAAGAAATGGATTGTAGGAACTCCATGCC
130 AGTTCAACACCAAATGTTTCAGATTATTCTGGTGTTAAAGAAGTGGATT-TAGGAACTCAATGCC
*
4133 CTACGT
194 CCACGT
* * * * *
4139 TGTTAAAGAAATGGATATCGGCAACTCCTTTTCCCCATCTCCAGAACCCATCAATGTTGTGAGAG
1 TGTTAAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCA-CAATGTTGTGAGGG
* * * * *
4204 ATGAATTGGATATGAGAAACATGACAAGTCCGGTGACCCTTGCATCAAGTTGCTCTGAAGCTTTA
65 ATGAATTGGATATAAGAAACATGACTAGTTCAGTGACCCTTGCATCAAGCTGCTCTGAAGCTTTA
* * *
4269 ATTTCAACACCAAATGTTTCAGATTATTGTGGTGGTAAAGAAAG-GGATATTAGGAACTCAA
130 AGTTCAACACCAAATGTTTCAGATTATTCTGGTGTTAAAG-AAGTGGAT-TTAGGAACTCAA
4330 CTTCCTCCCC
Statistics
Matches: 340, Mismatches: 43, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
199 3 0.01
200 4 0.01
201 326 0.96
202 7 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (199 bp):
TGTTAAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCACAATGTTGTGAGGGA
TGAATTGGATATAAGAAACATGACTAGTTCAGTGACCCTTGCATCAAGCTGCTCTGAAGCTTTAA
GTTCAACACCAAATGTTTCAGATTATTCTGGTGTTAAAGAAGTGGATTTAGGAACTCAATGCCCC
ACGT
Done.