Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003494.1 Kokia drynarioides strain JFW-HI SEQ_116321, 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: 1998
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Found at i:988 original size:79 final size:78
Alignment explanation
Indices: 866--1213 Score: 475
Period size: 79 Copynumber: 4.4 Consensus size: 78
856 TAAATAATTA
* * * * * *
866 GATTGCTTCAATCTGTCCCATGATCG-GGATAAGAGATCGGATGGTCTTCAATTTGCTCTCTAGT
1 GATTGCTTCAATTTG-CCCATGGTCGAGG-TAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGT
930 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
** *
945 GATTGCTTCAATTTGCCCAATGGTCGAGGTAAGAGATAAGATGGTCTAT-AATCTGCCCTCTGTT
1 GATTGCTTCAATTTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCT-TCAATCTGCCCTCTGGT
1009 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
* * *
1024 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTGGATGGTCTTCAATCTGCACTCTGGTT
1 GATTGCTTCAATTTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
1089 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
* *
1103 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGGTT
1 GATTGCTTCAATTTG-CCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
1168 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
* *
1182 GATTGCTTCAATTGGCCCCATGGTCGGGGTAA
1 GATTGCTTCAATTTG-CCCATGGTCGAGGTAA
1214 AATACTCGGG
Statistics
Matches: 240, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
78 4 0.02
79 230 0.96
80 6 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (78 bp):
GATTGCTTCAATTTGCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
GGGTAAAAGATTG
Found at i:1016 original size:40 final size:40
Alignment explanation
Indices: 899--1193 Score: 264
Period size: 40 Copynumber: 7.5 Consensus size: 40
889 TCGGGATAAG
* * * *
899 AGATCGGATGGTCTTCAATTTGCTCTCTAGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* * ** * *
939 AGATTGGATTG-CTTCAATTTGCCCAATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAG-GGTAAA
** *
978 AGATAAGATGGTCTAT-AATCTGCCCTCTGTTTAGGGTAAA
1 AGATTGGATGGTCT-TCAATCTGCCCTCTGGTTAGGGTAAA
* * ** *
1018 AGATTGGATTG-CTTCAATCTGCCCTATGGTCGGGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
1057 AGATTGGATGGTCTTCAATCTGCACTCTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* * * * *
1097 AGATTGGAT-TTCTTCAATTTGTCCC-ATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTG-CCCTCTGGTTAG-GGTAAA
*
1136 AGATTGGATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
1176 AGATTGGATTG-CTTCAAT
1 AGATTGGATGGTCTTCAAT
1194 TGGCCCCATG
Statistics
Matches: 201, Mismatches: 43, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
38 5 0.02
39 95 0.47
40 96 0.48
41 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (40 bp):
AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
Found at i:1212 original size:39 final size:39
Alignment explanation
Indices: 866--1215 Score: 251
Period size: 39 Copynumber: 8.9 Consensus size: 39
856 TAAATAATTA
* * * * *
866 GATTGCTTCAATCTGTCCCATGATCGGGATAAGAGATCG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * * * **
905 GATGGTCTTCAATTTGCTCTC-TAGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * * **
945 GATTGCTTCAATTTGCCCAATGGTCGAGGTAAGAGATAA
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
984 GATGGTCTAT-AATCTGCCCTC-TGTTTAGGGTAAAAGATTG
1 GATTG-CT-TCAATCTGCCC-CATGGTCGGGGTAAAAGATTG
* *
1024 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
1063 GATGGTCTTCAATCTGCACTC-TGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * * *
1103 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* ** **
1142 GATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
1182 GATTGCTTCAAT-TGGCCCCATGGTCGGGGTAAAA
1 GATTGCTTCAATCT-GCCCCATGGTCGGGGTAAAA
1216 TACTCGGGGT
Statistics
Matches: 231, Mismatches: 67, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
38 5 0.02
39 111 0.48
40 111 0.48
41 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (39 bp):
GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
Found at i:1415 original size:50 final size:50
Alignment explanation
Indices: 1288--1418 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
1278 TTAATATGCT
* * *
1288 CCTCTACAGCTTTAGGTGAATGAGATTCGTCATTGCGGCTTCAATCTGCC
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* * **
1338 CCTTTACAGCTTTAGGTGTATGAGATTTTTCATTGCAGCTTCAATCTGTT
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* *
1388 TCTCTACAGCTTTAGGGGTAT-AGGATTTGTC
1 CCTCTACAGCTTTAGGTGTATGA-GATTTGTC
1419 GTTCTATTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (50 bp):
CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
Done.