Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1004 ID=scaffold_1004-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: 3771
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.12
Warning! 2223 characters in sequence are not A, C, G, or T
Found at i:215 original size:114 final size:114
Alignment explanation
Indices: 11--799 Score: 1321
Period size: 114 Copynumber: 6.9 Consensus size: 114
1 ATAGTGGCAG
*
11 TAGCGGCGTTTGTTTGTAAGCGCCGC-AACAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
75 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
124 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* ** *
189 ATAGTAGAATTGGTGGCGTTTTTGTAAAAACGCTACTGAAGTGTATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* * *
238 TAGCGGCGTTT-TTTTTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCATACAAGTTTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* *
302 ATAGCAGAATTGGTGGCGTTTCTGTAAAAACACCGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
351 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCATACAGGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
*
416 ATAGTAGAATTGGTGGCGTTTCCGTAAAAACGCCGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
465 TAGCAGCGTTTGCTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* * *
530 ATAGTAGAATTAGTGGCATTTCTGTAAAAACGCCGCTGAAGTGTATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
579 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAACGTACAAGACTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* * * * *
644 ATAGTTGAATTTGTGGCGTTTCTATAGAAACGCAGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
693 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGG
1 TAGCGGCGTTTGTTTGTAAGCGCCGC-AAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGG
*
758 TATAGTAGAATTGGTGGCGTTTCTATAAAAACGCCGCTGAAG
65 TATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAG
800 CACATTATTA
Statistics
Matches: 628, Mismatches: 45, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
113 130 0.21
114 424 0.68
115 74 0.12
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (114 bp):
TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
Found at i:1088 original size:114 final size:114
Alignment explanation
Indices: 961--1176 Score: 267
Period size: 114 Copynumber: 1.9 Consensus size: 114
951 TGTGAAGCCG
* ** *
961 AAACGCAACGTTTCGTCTTGA-GCTATAG-CGCATTTACTGGCGCTTATCCGTAAACGCCGCTGA
1 AAACGCAACGTTTCGACTACACG-TATAGACGCA-TTACTGGCGCTTATCCGGAAACGCCGCTG-
* *
1024 ATATCAGCTTTTAGTGGCGCTTATG-TTTAAGCGCCGCAACATTTCTTAGGA
63 ATATCAGCTTTTAGTGGCGCTTATGATTAAAACGCCGCAACATTTCTTAGGA
* ** * **
1075 AAACGCATCGTTTCGACTACACGTATAGATTCATTAGTGGCGCTTATTTGGAAACGCCGCTGATA
1 AAACGCAACGTTTCGACTACACGTATAGACGCATTACTGGCGCTTATCCGGAAACGCCGCTGATA
*
1140 TCAGCTTTTAGTGGCGCTTTTGATTAAAACGCCGCAA
66 TCAGCTTTTAGTGGCGCTTATGATTAAAACGCCGCAA
1177 GAANNNNNNN
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
113 24 0.28
114 59 0.69
115 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (114 bp):
AAACGCAACGTTTCGACTACACGTATAGACGCATTACTGGCGCTTATCCGGAAACGCCGCTGATA
TCAGCTTTTAGTGGCGCTTATGATTAAAACGCCGCAACATTTCTTAGGA
Found at i:3554 original size:24 final size:24
Alignment explanation
Indices: 3522--3572 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3512 GGTTCCTAGT
3522 TGTCTATATGTGCAGATATATGTG
1 TGTCTATATGTGCAGATATATGTG
*
3546 TGTCTATATGTGCAGATATGTGTG
1 TGTCTATATGTGCAGATATATGTG
3570 TGT
1 TGT
3573 GTTAGTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (24 bp):
TGTCTATATGTGCAGATATATGTG
Done.