Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_848 ID=scaffold_848-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: 3250
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.31
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:701 original size:44 final size:44
Alignment explanation
Indices: 653--1079 Score: 222
Period size: 44 Copynumber: 9.9 Consensus size: 44
643 TGAAATCTTC
653 AGTCTGC-CTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
1 AGTCTGCTC-CACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
* * *
697 AGTCTGCTCCACTGCAACTTCAGGGGGATAAGACTAG-ATAC--
1 AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
* ** * *
738 AATCTGCT-TTCTGCAACTTCA-GAGAGATAAGATCTGAGGTT--TT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGA-CT-TGCTTACTT
* * * *
781 AATCCGCTCCACTGCAACTTCAAGGA-GATAGGATTATCGGC-T--TT
1 AGTCTGCTCCACTGCAACTTC-AGGAGGATAAGACT-T--GCTTACTT
* * * *
825 AATCTGCTCCTCTGTAACTTCAGG-GAGATAAGACTTGC-CATCTT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTTA-CTT
* *
869 CAGTCTGCCCCGCTGCAACTTCAGGAGGATAAGACTTGCTTACTT
1 -AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
* * * *
914 AGTCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAG-ATGC-G
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTTGCTTACTT
* * *
956 A-TCTGCT-CTCTGCAACTTCA-GAGAGATAAGATTTGAGGTT--TT
1 AGTCTGCTCCACTGCAACTTCAGGAG-GATAAGACTT--GCTTACTT
* * * * *
998 AATCCGCTCCAATGCAACTTCAAGGA-GATAGGATTATCGGC-T--TT
1 AGTCTGCTCCACTGCAACTTC-AGGAGGATAAGACT-T--GCTTACTT
*
1042 AATCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGC
1 AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGC
1080 CATCTTCGAT
Statistics
Matches: 302, Mismatches: 49, Indels: 67
0.72 0.12 0.16
Matches are distributed among these distances:
39 3 0.01
40 40 0.13
41 19 0.06
42 5 0.02
43 30 0.10
44 158 0.52
45 41 0.14
46 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTCTGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
Found at i:767 original size:84 final size:85
Alignment explanation
Indices: 664--948 Score: 222
Period size: 89 Copynumber: 3.3 Consensus size: 85
654 GTCTGCCTCA
664 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGGGATAAG
1 CTGCAACTTCAGGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGGGATAAG
*
729 ACTA-GATACAATCTGCT-TT
65 ACTACGATACAATCTGCTCCT
* * * * * *
748 CTGCAACTTCAGAGAGATAAGATCTGAGGTT--TTAATCCGCTCCACTGCAACTTCAAGGAGATA
1 CTGCAACTTCAG-GAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGGGATA
* * * **
811 GGATTATCGGCTTTAATCTGCTCCT
63 AGACTA-C-GATACAATCTGCTCCT
* * * * *
836 CTGTAACTTCAGGGAGATAAGACTTGC-CATCTTCAGTCTGCCCCGCTGCAACTTCAGGAGGATA
1 CTGCAACTTCA-GGAGATAAGACTTGCTTA-CTT-AGTCTGCTCCACTGCAACTTCAGGGGGATA
* * * *
900 AGACT-TGCTTACTTAGTCTGCTCCA
63 AGACTACG-ATAC--AATCTGCTCCT
925 CTGCAACTTCAGGGAGATAAGACT
1 CTGCAACTTCA-GGAGATAAGACT
949 AGATGCGATC
Statistics
Matches: 154, Mismatches: 32, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
84 51 0.33
85 4 0.03
86 5 0.03
87 13 0.08
88 22 0.14
89 59 0.38
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (85 bp):
CTGCAACTTCAGGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGGGATAAGA
CTACGATACAATCTGCTCCT
Found at i:870 original size:217 final size:217
Alignment explanation
Indices: 605--1086 Score: 781
Period size: 217 Copynumber: 2.2 Consensus size: 217
595 AATCCGCCAT
* * ** ** *
605 CTTTGATCTGCTCCACTACTGCTT-AGGGAGATAAGA-TCTGAAATCTTCAGTCTGCCTCACTGC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCCATCTTCAGTCTGCCCCACTGC
*
668 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGGGATAAGACTA
65 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
733 GATACAATCTGCTTTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAA
130 GATACAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAA
798 CTTCAAGGAGATAGGATTATCGG
195 CTTCAAGGAGATAGGATTATCGG
* * *
821 CTTTAATCTGCTCCTCTGTAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCGCTGCA
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCA
886 ACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG
66 ACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG
* * *
951 ATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATTTGAGGTTTTAATCCGCTCCAATGCAAC
131 ATACAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAAC
1016 TTCAAGGAGATAGGATTATCGG
196 TTCAAGGAGATAGGATTATCGG
1038 CTTTAATCTGCTCCACTGCAACTTCA-GGAGGATAAGACTTGCCATCTTC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCCATCTTC
1087 GATTTGCTCC
Statistics
Matches: 245, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
216 21 0.09
217 223 0.91
218 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (217 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCA
ACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG
ATACAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAAC
TTCAAGGAGATAGGATTATCGG
Done.