Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010993.1 Kokia drynarioides strain JFW-HI SEQ_125963, whole genome shotgun sequence
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: 4975
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:4264 original size:144 final size:144
Alignment explanation
Indices: 4001--4294 Score: 439
Period size: 144 Copynumber: 2.0 Consensus size: 144
3991 CTTACGCTCA
*
4001 AAGCGAGCAAAATTGTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAA
1 AAGCGAGCAAAATTGTCAAAACCCAGCTTCCTGATGAGACACCGAGAAGCAGGTGGAAGCAATAA
* *
4066 ATGGTTAGCTCCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAG
66 ATGGTTAGCTCCCTGATAAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAG
4131 AAGCGGATTGAAAC
131 AAGCGGATTGAAAC
* * * * *
4145 AAGCGAGCAAAATCT-TCGAACCCCAGCTTCCTGATGAGATACCGAGAAGCAGTTTGAAGCAATA
1 AAGCGAGCAAAAT-TGTCAAAACCCAGCTTCCTGATGAGACACCGAGAAGCAGGTGGAAGCAATA
* * * *
4209 GATGGTTAGCTTCCTGATAAGATACAT-AGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAG
65 AATGGTTAGCTCCCTGATAAGATA-ATGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAG
*
4273 AGAAGCGGATTGAAAT
129 AGAAGCGGATTGAAAC
4289 AAGCGA
1 AAGCGA
4295 TGTGGTCATT
Statistics
Matches: 135, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
144 133 0.99
145 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (144 bp):
AAGCGAGCAAAATTGTCAAAACCCAGCTTCCTGATGAGACACCGAGAAGCAGGTGGAAGCAATAA
ATGGTTAGCTCCCTGATAAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAG
AAGCGGATTGAAAC
Found at i:4598 original size:202 final size:200
Alignment explanation
Indices: 4145--4732 Score: 867
Period size: 202 Copynumber: 2.9 Consensus size: 200
4135 GGATTGAAAC
* * * *
4145 AAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACCGAGAAGCAGTTTGAAGCAATAG
1 AAGCGAGCAAAATCTTC-AAACTCAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAG
4210 ATGGTTAGCTTCCTGATAAGATAC-ATAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGA
65 ATGGTTAGCTTCCTGATAAGATACGA-AGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGA
*
4274 GAAGCGGATTGAAATAAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAGACCCAAATG
129 GAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAGACCCAAATG
4339 AGGCTCA
194 AGGCTCA
*
4346 AAGCGAGCAAAATCTTCGAACTCCAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAG
1 AAGCGAGCAAAATCTTCAAACT-CAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAG
* * *
4411 ACGGTTAGCTTCCTTATAAGATACGAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
65 ATGGTTAGCTTCCTGATAAGATACGAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAG
4476 AAGCGGATTGAAACAAAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAGACCCAAATG
130 AAGCGGATTGAAAC-AAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAGACCCAAATG
*
4541 AGGCTTGA
194 AGGC-TCA
* * * * * * *
4549 AA-CGAGCGAAATCTTCAAAACTCAGCTTCTTGATGAGACACTGAGAAGCAAGTGGAAGCAATAA
1 AAGCGAGCAAAATCTTC-AAACTCAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAG
* * * *
4613 ATAGTTAGCTCCCTGATGAGATATTG-AGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGA
65 ATGGTTAGCTTCCTGATAAGATA-CGAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGA
* * * *
4677 GAAGCGGATTGAAACAAGCGACGCGGTCATTTTCCTGATGAGATACTGAGAAGAAG
129 GAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAG
4733 GTCAAGTCAA
Statistics
Matches: 352, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
200 2 0.01
201 167 0.47
202 174 0.49
203 9 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (200 bp):
AAGCGAGCAAAATCTTCAAACTCAGCTTCCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAGA
TGGTTAGCTTCCTGATAAGATACGAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGA
AGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATAAGACACTGAGAAGAAGACCCAAATGAG
GCTCA
Done.