Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_598 ID=scaffold_598-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: 5458
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2353 original size:327 final size:330
Alignment explanation
Indices: 1636--2606 Score: 1009
Period size: 327 Copynumber: 2.9 Consensus size: 330
1626 TCCATTCTCA
* * * * * * *
1636 CCCTGTCGATTTATCTTGATTTTGGA-GGAGAAAAAAAATTTCGAG--CTGAGTGTCGGATCTTA
1 CCCTGTCGATTTTTCTCGA-TTTGGACTGAGAAAAAAAATTTCGAGATTTCAGTCTC-GATCCTA
* * * * *
1698 CATAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTAACTCTCGGCGAGGCTCCCTGAGCCGAG
64 CGTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGAGTCTCTGCGAGGCTTCCTGAGCCGAG
* * * *
1763 AAACATTCAGAAACTGGTCAAAAACGAGCATTTCTG-ACTCCTTTTTGAATCTTTCTCTGGAGCA
129 AAA-A--C----A--GGTCAAAAACGAGCATTTCTGAAC-ACTTTTTGACTCTTTCTC-AGAGCG
* *
1827 TTTTCAGCAGATAGCTCTAAGCGAGGGACTTGCGGAGCTTTTCGGACTCGAAAATCGCACTCAGC
183 TTTTCAGCAGATAGCTCTAAGCGAGGGACTAGCGGAGCTTTTCGGACTCGAAAATCGCACTTAGC
** * * * * * *
1892 GAGTCTTTTCAAAGCGAGCTTACTTGGTTTTGGCCTGATGGGCGAACTTTCGATTTCGACCCGAA
248 GAGTCAATTCCAAGCGAGCTAACTTGCTTTCGGCCTGATCGGCGAACTATCGATTTCGACCCGAA
1957 AAATTTAGTCCATGTAAC
313 AAATTTAGTCCATGTAAC
* * * ** *
1975 CCATGTCAATTTTTCTCCAGTTTGGACTGAGAAAAAACGTTT-GAAATTTCAGT-TCGATCCTAC
1 CCCTGTCGATTTTTCTCGA-TTTGGACTGAGAAAAAAAATTTCGAGATTTCAGTCTCGATCCTAC
* * *
2038 GTAGTTGGAGGCGTAGAATTGATTCCGCACGGTCTCGAGTCTCTGCGAGACTTCCTGAGCCGAG-
65 GTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGAGTCTCTGCGAGGCTTCCTGAGCCGAGA
*
2102 AAACA-GTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCCGTAGCGTTTTCAGCAGA
130 AAACAGGTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCAG-AGCGTTTTCAGCAGA
*
2166 TAGCTCTAAGCGAGGGACTAGCGGAGC-TTTCGGACTCGAAAATCGCACTTAGCGGGTCAATTCC
194 TAGCTCTAAGCGAGGGACTAGCGGAGCTTTTCGGACTCGAAAATCGCACTTAGCGAGTCAATTCC
* * * *
2230 AAGCG-GCCTAACTTGCTTTCGG-CTCGATCGGCGAACTATCGATTTTGACGCTAAAAGTTTAGT
259 AAGCGAG-CTAACTTGCTTTCGGCCT-GATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGT
2293 CCATGTAAC
322 CCATGTAAC
2302 CCCTGTCGATTTTTCTCGATTTGGGACTGA-AAAAAAAATTTCGAGATTTCAGTCTC-ATCCTAC
1 CCCTGTCGATTTTTCTCGATTT-GGACTGAGAAAAAAAATTTCGAGATTTCAGTCTCGATCCTAC
* * *
2365 GCAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTG-GCGCTCTGCGAGGCTTCCTTAGCCGAA
65 GTAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGAG-TCTCTGCGAGGCTTCCTGAGCCG--
* * *
2429 AAACAGTCAAAAACAGGTCAAAAACGAGCTTTTCTGACCAATTTTTGACTCTTTGGCT-AGAGCG
127 ----AG---AAAACAGGTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTT--CTCAGAGCG
* * * * * * * *
2493 TTTTCAGCGGACAGCCCGAAGCGAGGGACTCGCGGAGCTTTTCAGACTGGAGAATCGCACTTAGC
183 TTTTCAGCAGATAGCTCTAAGCGAGGGACTAGCGGAGCTTTTCGGACTCGAAAATCGCACTTAGC
* ** * * *
2558 GTGTCAATTCCAAGCGAGCTTCCTCGGTTTCAGCCTGGATCGGCGAACT
248 GAGTCAATTCCAAGCGAGCTAACTTGCTTTCGGCCT-GATCGGCGAACT
2607 TTNNNNNNNN
Statistics
Matches: 534, Mismatches: 71, Indels: 53
0.81 0.11 0.08
Matches are distributed among these distances:
326 16 0.03
327 185 0.35
328 78 0.15
329 2 0.00
331 1 0.00
333 2 0.00
335 1 0.00
337 6 0.01
338 74 0.14
339 134 0.25
340 31 0.06
341 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (330 bp):
CCCTGTCGATTTTTCTCGATTTGGACTGAGAAAAAAAATTTCGAGATTTCAGTCTCGATCCTACG
TAGTTGGAGGCGTAGAATCGATTCCGCACGGTCTTGAGTCTCTGCGAGGCTTCCTGAGCCGAGAA
AACAGGTCAAAAACGAGCATTTCTGAACACTTTTTGACTCTTTCTCAGAGCGTTTTCAGCAGATA
GCTCTAAGCGAGGGACTAGCGGAGCTTTTCGGACTCGAAAATCGCACTTAGCGAGTCAATTCCAA
GCGAGCTAACTTGCTTTCGGCCTGATCGGCGAACTATCGATTTCGACCCGAAAAATTTAGTCCAT
GTAAC
Found at i:4946 original size:1 final size:1
Alignment explanation
Indices: 4940--4971 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
4930 CATGAAATCG
4940 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4972 TTTACCATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5403 original size:13 final size:13
Alignment explanation
Indices: 5387--5414 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5377 ATGTACCCAA
5387 AAATGGTTTGCTC
1 AAATGGTTTGCTC
5400 AAATGGTTTGCTC
1 AAATGGTTTGCTC
5413 AA
1 AA
5415 GGTAAGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (13 bp):
AAATGGTTTGCTC
Done.