Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1037 ID=scaffold_1037-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: 2852
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.16
Warning! 1479 characters in sequence are not A, C, G, or T
Found at i:330 original size:194 final size:195
Alignment explanation
Indices: 1--549 Score: 859
Period size: 194 Copynumber: 2.8 Consensus size: 195
* *
1 AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTCGAGTCACTATTTGTAAAATGAATTAAGCTT
1 AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTT
* * *
66 CTTTGATGGTGATGATGCATGTGCATATAACATGGTTTCAATGCCCTAAGACTCAAACATGTCTT
66 CTTTGATGGTGATGATACATGTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTT
* *
131 ATGACCTTCAATAATAAGTTGGTAATAATTTTCATAGGCAGCCTTCTAGGGGTGTAAACAAGT-C
131 ATGACCTTCAATAATAAGTTGCTAATAATTTTCATAGGCAGCCTTCTAAGGGTGTAAACAAGTCC
**
195 AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTGGAGTCACTGTACGTAAAATGAATTAAGCTT
1 AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTT
* *
260 CTTTGATGGTGATGATACATGTGCATATAACATGGTTTCAATGCCCCAAGAGTTAAACTTGTCTT
66 CTTTGATGGTGATGATACATGTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTT
** * * * *
325 ATGACCTTCAATGGTAAATTGCAAATAATTTTCTTAGGCAGTCTTCTAAGGGTGTAAACAAGTCC
131 ATGACCTTCAATAATAAGTTGCTAATAATTTTCATAGGCAGCCTTCTAAGGGTGTAAACAAGTCC
* * * * *
390 AA-TTCCATGTGACCTAGTTCGGCTCGCTATAGTGGAATCACTGTTTGTAAAATGAATTAAGTTT
1 AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTT
* *
454 CTTTGATGGTGATGATACATGTACAGATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTT
66 CTTTGATGGTGATGATACATGTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTT
*
519 ATGACCTTCAATAACAAGTTGCTAATAATTT
131 ATGACCTTCAATAATAAGTTGCTAATAATTT
550 NNNNNNNNNN
Statistics
Matches: 321, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
194 318 0.99
195 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (195 bp):
AAGTTACATGTGAGCTAGTTGGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTT
CTTTGATGGTGATGATACATGTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTT
ATGACCTTCAATAATAAGTTGCTAATAATTTTCATAGGCAGCCTTCTAAGGGTGTAAACAAGTCC
Found at i:2579 original size:193 final size:194
Alignment explanation
Indices: 2029--2766 Score: 957
Period size: 194 Copynumber: 3.8 Consensus size: 194
2019 NNNNNNNNNN
* * *
2029 GTGCATATAACATGGTTTCAATGCCCCAAGGCTCGAACTTGTCCTATGACCTTCAATAATAAGTT
1 GTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTTATGACCTTCAATAATAAGTT
*
2094 GCTAATAA-TTTCTTTAGGCAGCCTTCTAAGGGTGTAAACAAGTCAAGTTCCATGTGAGCTAGTT
66 GCTAATAATTTTCGTTAGGCAGCCTTCT-AGGGTGTAAACAAGTCAAGTTCCATGTGAGCTAGTT
* * *
2158 GGGCTTGCTATAGTGGAGTCACTGTTTGTAAATTGAATTAAGCTTCTTTGATGGTGATGATACAT
130 GGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTTCTTTGATGGAGATGATACAT
* *
2223 GTGCATATAGCATGGTTTCAATGCCCCAAGACTCAAACTTGTCTTATGGCCTTCAATAATAAGTT
1 GTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTTATGACCTTCAATAATAAGTT
* * * *
2288 GCTAAAAATTTTC-TTAGGCAGTCTTCTAGGGGTGTAAACAAGTCAATTTACATGTGAGCTAGTT
66 GCTAATAATTTTCGTTAGGCAGCCTTCTA-GGGTGTAAACAAGTCAAGTTCCATGTGAGCTAGTT
* * * * *
2352 GGGCTCGTTATAGTGGAGTCAATGATTGTAAAATGAATTAAGGC-TCTTAGATGCAGATGATACA
130 GGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAA-GCTTCTTTGATGGAGATGATACA
2416 T
194 T
* * *
2417 GTGCATATAACATGGATTCAATGCCGCAAGACTCAAACTTGTCTTATGACCTTC-ACAATAAGTT
1 GTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTTATGACCTTCAATAATAAGTT
* *
2481 GCTAATAATTTTC-TTAGGCAGCCTTCTAGGGATGTAAATAAGCCAAGTTCCATGTGAGCTAGTT
66 GCTAATAATTTTCGTTAGGCAGCCTTCTAGGG-TGTAAACAAGTCAAGTTCCATGTGAGCTAGTT
* * * * *
2545 GGACTCGCTATAGTGTAGTCACTGTTTCTAAAATGAATTAAGCTTCTTTGATGGGGATGATACTT
130 GGGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTTCTTTGATGGAGATGATACAT
* * * * *
2610 TTGCCTATAACATGGTTTTCAATGCCCCAAGAGTCAAACTTGTTTGTATGACGCTTTAAT-ATAA
1 GTGCATATAACATGG-TTTCAATGCCCCAAGACTCAAACTTGTCT-TATGAC-CTTCAATAATAA
* * *
2674 GTTGGCAAATAATTTTTCGTTAGGCAGCCCTTTCTATAGGTTGGAAACAAAGTCAATGTTCCATG
63 GTT-GCTAATAA-TTTTCGTTAGGCAG-CC-TTC--TAGGGTGTAAAC-AAGTCAA-GTTCCATG
*
2739 TGAGCTAGTTGCGCTCGCTATAAGTGGA
120 TGAGCTAGTTGGGCTCGCTAT-AGTGGA
2767 AGCTCAGATG
Statistics
Matches: 471, Mismatches: 54, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
192 5 0.01
193 129 0.27
194 242 0.51
195 12 0.03
196 10 0.02
197 8 0.02
198 5 0.01
199 8 0.02
200 2 0.00
201 3 0.01
202 5 0.01
203 10 0.02
204 27 0.06
205 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (194 bp):
GTGCATATAACATGGTTTCAATGCCCCAAGACTCAAACTTGTCTTATGACCTTCAATAATAAGTT
GCTAATAATTTTCGTTAGGCAGCCTTCTAGGGTGTAAACAAGTCAAGTTCCATGTGAGCTAGTTG
GGCTCGCTATAGTGGAGTCACTGTTTGTAAAATGAATTAAGCTTCTTTGATGGAGATGATACAT
Done.