Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_504 ID=scaffold_504-JGI_221_v2.0
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: 6330
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Found at i:3814 original size:339 final size:338
Alignment explanation
Indices: 3195--3891 Score: 911
Period size: 339 Copynumber: 2.1 Consensus size: 338
3185 AATCGGTCAA
* * * *
3195 GGGTCAATTCCAAGCGAGCTTACTTGGTTCCGACCCTATCGGCGAAATTTCCATTTTGACCCGAA
1 GGGTCAATTCCAAGCGAGCTTACTTGATTCCGACCCGATCAGCGAAATATCCATTTTGACCCGAA
* * * * *
3260 ACATTTAGTCCATGTTATCCGTGTCGATTTTTCTCGATTTGGGACGGAGAAAAATATTCGAGATT
66 ACATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACGGAGAAAAAAATTCAAGATT
* * * * * *
3325 TCAGTCGCATCCTACGTTGCTGGAAGCGTAGAATCGATACCGCACGGTCCCGACTCTCGGGGAGG
131 TCAGTCGCATCCTACATAGCTGGAAGCATAGAATCGATACCGCACGCTCCCGACACTCGGCGAGG
3390 CTTCCTGAGCCGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTC
196 CTTCCTGAGCCGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTC
* * * *
3455 TTTCTCTAGAGCGTTTTCAGCGGCTAGCTCGAAGCAAGGGATTTGCGGAGCTATTT-CGACT-GA
261 TTTCTCTAGAGCGTTTTCAGCGGATAGCTCGAAGCAAGGGACTCGCGGAGCT-TTTCCAACTCG-
* * * *
3518 AAAATTGCACTCGGC
324 AAAATCGAACACAGC
* * * * *
3533 GGGTCAATTCCAAGCGAGCTTACTTGAATT-CGGCCCGATCAGCGAACTATCGATTTTGACGCTA
1 GGGTCAATTCCAAGCGAGCTTACTTG-ATTCCGACCCGATCAGCGAAATATCCATTTTGACCCGA
*
3597 ATA-ATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAGAAAAAAATTTCAAG
65 A-ACATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACGGAGAAAAAAA-TTCAAG
* ** * *
3661 ATTTCAGTCGCATCCTATATAG-TCGGTGGCATAGAATCGGTTCCGCACGCTCCCGACACTCGGC
128 ATTTCAGTCGCATCCTACATAGCT-GGAAGCATAGAATCGATACCGCACGCTCCCGACACTCGGC
* * *
3725 GAGGCTTCCTGAGTCGAGAAACAGTCAA-AAGCTGGTCAAAAAGGAGCTTTTCTGACCACTTTTT
192 GAGGCTTCCTGAGCCGAGAAACAGT-AAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTT
* * * *
3789 GCCTGTTTCTCTGGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTTCCAAC
256 GACTCTTTCTCTAGAGCGTTTTCAGCGGATAGCTCGAAGCAAGGGACTCGCGGAGCTTTTCCAAC
3854 TCGAAAATCGAACACAGC
321 TCGAAAATCGAACACAGC
*
3872 GGGTCAATTCCATGCGAGCT
1 GGGTCAATTCCAAGCGAGCT
3892 CAGATCCAAA
Statistics
Matches: 310, Mismatches: 42, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
338 106 0.34
339 201 0.65
340 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (338 bp):
GGGTCAATTCCAAGCGAGCTTACTTGATTCCGACCCGATCAGCGAAATATCCATTTTGACCCGAA
ACATTTAGTCCATGTAACCCCTGTCGATTTTTCTCGATTTGGGACGGAGAAAAAAATTCAAGATT
TCAGTCGCATCCTACATAGCTGGAAGCATAGAATCGATACCGCACGCTCCCGACACTCGGCGAGG
CTTCCTGAGCCGAGAAACAGTAAGAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTC
TTTCTCTAGAGCGTTTTCAGCGGATAGCTCGAAGCAAGGGACTCGCGGAGCTTTTCCAACTCGAA
AATCGAACACAGC
Found at i:5434 original size:197 final size:197
Alignment explanation
Indices: 5043--5434 Score: 428
Period size: 197 Copynumber: 2.0 Consensus size: 197
5033 GAGGCTCCCT
* * * * *
5043 GAGCCGAGAAACATTCAGAAACTGGTCAAAAACGAGCATTTCTGACTCCTTTTTGAATCTTTCTC
1 GAGCCGAGAAACAGTCAAAAACAGGTAAAAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTC
* * ** * * * *
5108 TGGAGCGTTTTCAGCGGATAGCTTTAAGCGAGGGAGTCGCGAACCTTTACCGACTCGAAAATCGC
66 TAGAGCGTTTTCAGCAGATAGCTCGAAGCAAGGGACTCACGAACCTATACCGACTCGAAAATCGC
* ** ** * * ** * *
5173 ACTCGGCGGGTCAATTCCAAGTTACCTTACTTGGTGCCGGTCCGATTGGCGAAATTTTGATTTTG
131 ACTCAGCGGGTCAATTCCAAGGGACCTTACCCGGTGCCAGCCCGAACGGAGAAATTTCGATTTTG
5238 TC
196 TC
* *
5240 GAGCCGAGAACCAGTCAAAAACAGGTAAAAAACGAGCATTTCTGAC-CACTTTTTGACCCTTTCT
1 GAGCCGAGAAACAGTCAAAAACAGGTAAAAAACGAGCATTTCTGACTC-CTTTTTGAACCTTTCT
* * * * *
5304 CTAGAGCGTTTTCAGCAGATAGCTCGAAGCAAGGGACTTACGGAGCTATACCGACTGGAAAATTG
65 CTAGAGCGTTTTCAGCAGATAGCTCGAAGCAAGGGACTCACGAACCTATACCGACTCGAAAATCG
* * ** *
5369 CACTCAGCGGGTCATTTCCAAGGGGA-CTTGCCCGGTTTCAGCCCGAACGGAGAACTTTCGATTT
130 CACTCAGCGGGTCAATTCCAA-GGGACCTTACCCGGTGCCAGCCCGAACGGAGAAATTTCGATTT
5433 TG
194 TG
5435 ACCCCGAAAT
Statistics
Matches: 157, Mismatches: 36, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
196 1 0.01
197 154 0.98
198 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (197 bp):
GAGCCGAGAAACAGTCAAAAACAGGTAAAAAACGAGCATTTCTGACTCCTTTTTGAACCTTTCTC
TAGAGCGTTTTCAGCAGATAGCTCGAAGCAAGGGACTCACGAACCTATACCGACTCGAAAATCGC
ACTCAGCGGGTCAATTCCAAGGGACCTTACCCGGTGCCAGCCCGAACGGAGAAATTTCGATTTTG
TC
Done.