Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000085.1 Kokia drynarioides strain JFW-HI SEQ_110709, 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, 804
Length: 1340
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:943 original size:29 final size:28
Alignment explanation
Indices: 886--1247 Score: 354
Period size: 29 Copynumber: 12.2 Consensus size: 28
876 AAGGTCCCTA
* *
886 AACTTCCAAAAAATCCCATTTTAAACCCCT
1 AACTTCC-AAAAATCCCATTTT-TACCCCG
* *
916 AACCTTCCAAAAATTACCA-TTTTACCCCCA
1 AA-CTTCCAAAAA-TCCCATTTTTA-CCCCG
946 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
* *
975 AACCTTACAAAAATTACCA-TTTTACCCCCG
1 AA-CTTCCAAAAA-TCCCATTTTTA-CCCCG
1005 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
**
1034 AACTTCCAAAAATCCCATTTTTAACCCTA
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
*
1063 AACTTCCAAAAATCTCATTTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
* *
1092 AACCTTCCAAAAATTACCA-TTTTACCCCAA
1 AA-CTTCCAAAAA-TCCCATTTTTACCCC-G
1122 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
* *
1151 AACTTCCAAAAAGTCCCATTTTTTATCCCA
1 AACTTCCAAAAA-TCCCA-TTTTTACCCCG
*
1181 AACCTTCCAAAAATTACCA-TTTTACCCCCG
1 AA-CTTCCAAAAA-TCCCATTTTTA-CCCCG
*
1211 AACTTCCAAAAATCCCATTTTTGACGCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCG
1240 AACCTTCC
1 AA-CTTCC
1248 CCAAAACTTC
Statistics
Matches: 283, Mismatches: 27, Indels: 44
0.80 0.08 0.12
Matches are distributed among these distances:
28 16 0.06
29 151 0.53
30 81 0.29
31 35 0.12
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (28 bp):
AACTTCCAAAAATCCCATTTTTACCCCG
Found at i:1094 original size:117 final size:117
Alignment explanation
Indices: 885--1231 Score: 472
Period size: 117 Copynumber: 2.9 Consensus size: 117
875 GAAGGTCCCT
* * * * *
885 AAACTTCCAAAAAATCCCATTTTAAACCCCTAACCTTCCAAAAATTACCA-TTTTACCCCCAAAC
1 AAACTTCC-AAAAATCCCATTTTTAACCCCGAA-CTTCCAAAAAGTCCCATTTTTA-ACCCAAAC
* * *
949 TTCCAAAAATCCCATTTTTAACCCCGAACCTTACAAAAATTACCATTTTACCCCC
63 TTCCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
*
1004 GAACTTCCAAAAATCCCATTTTTAACCCCGAACTTCCAAAAA-TCCCATTTTTAACCCTAAACTT
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACTTCCAAAAAGTCCCATTTTTAACCC-AAACTT
1068 CCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
65 CCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
*
1121 AAACTTCCAAAAATCCCATTTTTAACCCCGAACTTCCAAAAAGTCCCATTTTTTATCCCAAACCT
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACTTCCAAAAAGTCCCA-TTTTTAACCCAAA-CT
* *
1186 TCCAAAAAT-TACCA-TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTT
64 TCCAAAAATCT--CATTTTTAACCCCGAACCTTCCAAAAATTACCATTTT
1232 TGACGCCGAA
Statistics
Matches: 209, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
116 7 0.03
117 120 0.57
118 41 0.20
119 39 0.19
120 2 0.01
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (117 bp):
AAACTTCCAAAAATCCCATTTTTAACCCCGAACTTCCAAAAAGTCCCATTTTTAACCCAAACTTC
CAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
Found at i:1247 original size:59 final size:59
Alignment explanation
Indices: 885--1231 Score: 454
Period size: 59 Copynumber: 5.9 Consensus size: 59
875 GAAGGTCCCT
* * *
885 AAACTTCCAAAAAATCCCATTTTAAACCCCTAACCTTCCAAAAATTACCATTTTACCCCC
1 AAACTTCC-AAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
* *
945 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTACAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
* * * *
1004 GAACTTCCAAAAATCCCATTTTTAACCCCGAA-CTTCCAAAAA-TCCCATTTTTAACCCT
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCA-TTTTACCCCA
*
1062 AAACTTCCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
* * *
1121 AAACTTCCAAAAATCCCATTTTTAACCCCGAA-CTTCCAAAAAGTCCCATTTTTTATCCCA
1 AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCA--TTTTACCCCA
* * * *
1181 AACCTTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTT
1 AAACTTCCAAAAA-TCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTT
1232 TGACGCCGAA
Statistics
Matches: 261, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
57 8 0.03
58 61 0.23
59 133 0.51
60 55 0.21
61 4 0.02
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCA
Done.