Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010428.1 Kokia drynarioides strain JFW-HI SEQ_125318, 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: 7334
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:964 original size:30 final size:29
Alignment explanation
Indices: 928--1127 Score: 133
Period size: 30 Copynumber: 6.8 Consensus size: 29
918 CAAAACTGTC
*
928 CAAAAATTCCATTTTCACCCTCGAACTTCT
1 CAAAAATTCCATTTTAACCCTCGAACTT-T
* * * * *
958 AAAAAATTCCATTTTTGACCCCCAAAACTTC
1 CAAAAATTCCA-TTTTAACCCTC-GAACTTT
*
989 CAAAAATTCCATTTT-CCCCT-GAACTTT
1 CAAAAATTCCATTTTAACCCTCGAACTTT
* **
1016 CAAAAATCCCATTTTTAACCCTAAAACTTT
1 CAAAAATTCCA-TTTTAACCCTCGAACTTT
* * *
1046 TAAAAATTCCATTTTTACCC-CTAAACTTT
1 CAAAAATTCCATTTTAACCCTC-GAACTTT
** *
1075 TGAAAATCCCATTTTTAACCC-CGAAAC-TT
1 CAAAAATTCCA-TTTTAACCCTCG-AACTTT
1104 CTAAAAATTACCATTTT-ACCCTCG
1 C-AAAAATT-CCATTTTAACCCTCG
1128 GATGTCCAAA
Statistics
Matches: 135, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
27 15 0.11
28 4 0.03
29 37 0.27
30 52 0.39
31 22 0.16
32 5 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTAACCCTCGAACTTT
Found at i:1086 original size:59 final size:58
Alignment explanation
Indices: 916--1124 Score: 242
Period size: 59 Copynumber: 3.5 Consensus size: 58
906 CCCTGAAGGT
* * *
916 CCCAAAACTGTCCAAAAATTCCATTTT-CACCCTCGAACTTCTAAAAAATTCCATTTTTGACC
1 CCCAAAACT-TCTAAAAATTCCATTTTAC-CCCT-GAACTT-TAAAAAATCCCATTTTT-AAC
* *
978 CCCAAAACTTCCAAAAATTCCATTTT-CCCCTGAACTTTCAAAAATCCCATTTTTAAC
1 CCCAAAACTTCTAAAAATTCCATTTTACCCCTGAACTTTAAAAAATCCCATTTTTAAC
* * * **
1035 CCTAAAACTTTTAAAAATTCCATTTTTACCCCTAAACTTTTGAAAATCCCATTTTTAAC
1 CCCAAAACTTCTAAAAATTCCA-TTTTACCCCTGAACTTTAAAAAATCCCATTTTTAAC
*
1094 CCCGAAACTTCTAAAAATTACCATTTTACCC
1 CCCAAAACTTCTAAAAATT-CCATTTTACCC
1125 TCGGATGTCC
Statistics
Matches: 132, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
57 21 0.16
58 19 0.14
59 58 0.44
60 7 0.05
61 18 0.14
62 9 0.07
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
CCCAAAACTTCTAAAAATTCCATTTTACCCCTGAACTTTAAAAAATCCCATTTTTAAC
Found at i:1146 original size:59 final size:58
Alignment explanation
Indices: 916--1237 Score: 212
Period size: 59 Copynumber: 5.4 Consensus size: 58
906 CCCTGAAGGT
* * *
916 CCCAAAACTGTCCAAAAATTCCATTTTCACCCTCGAACTTCTAAAAAATTCCATTTTTGACC
1 CCCAAAACT-TCCAAAAATTCCATTTT-ACCCTCGAACTTC-CAAAAACTCCATTTTT-AAC
* *
978 CCCAAAACTTCCAAAAATTCCATTTTCCCCT-GAACTTTCAAAAA-TCCCATTTTTAAC
1 CCCAAAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAACT-CCATTTTTAAC
* ** * ***
1035 CCTAAAACTTTTAAAAATTCCATTTTTACCC-CTAAACTTTTGAAAA-TCCCATTTTTAAC
1 CCCAAAACTTCCAAAAATTCCA-TTTTACCCTC-GAACTTCCAAAAACT-CCATTTTTAAC
* * * *
1094 CCCGAAACTTCTAAAAATTACCATTTTACCCTCGGA-TGTCCAAAAACTCCATTTTTGAC
1 CCCAAAACTTCCAAAAATT-CCATTTTACCCTCGAACT-TCCAAAAACTCCATTTTTAAC
* * * * * * * * *
1153 CTCGAAACTAT-C-AAAATTACCCTTTTACCC-CTAAATGTCTAAAGATTCCATTCTTAA-
1 CCCAAAACT-TCCAAAAATT-CCATTTTACCCTCGAACT-TCCAAAAACTCCATTTTTAAC
*
1210 CCCAAAACTTTCCCAAAATTACCATTTT
1 CCCAAAAC-TTCCAAAAATT-CCATTTT
1238 GCCCCCGGGT
Statistics
Matches: 214, Mismatches: 33, Indels: 29
0.78 0.12 0.11
Matches are distributed among these distances:
57 31 0.14
58 57 0.27
59 90 0.42
60 10 0.05
61 17 0.08
62 9 0.04
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
CCCAAAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAACTCCATTTTTAAC
Done.