Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010067.1 Kokia drynarioides strain JFW-HI SEQ_124843, 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: 5380
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.22
Warning! 186 characters in sequence are not A, C, G, or T
Found at i:2752 original size:139 final size:139
Alignment explanation
Indices: 2566--3541 Score: 1410
Period size: 139 Copynumber: 7.1 Consensus size: 139
2556 ATCCACAAAG
* *
2566 CAGATTCGTCTTCCTGATGAGATACAGAGAAATGGATCGAAACAGTGATGGGATTATCTTCCTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
* * * * *
2631 TGAGACACTGAAAAGAAAACCCAAACAAGGCTCGAAATGAGCAAATCTTTCTGATGAGATACAGA
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
2696 GAAGTGAAC
131 GAAGTGAAC
* * * *
2705 CAGATTCGTATTCCTGATTAGATACAGAGAAACGGATCGAAATAGTGATGGGATCATCTTCTTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
* * *
2770 TGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCCGATGAGATACGAA
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
2835 GAAGTGAAC
131 GAAGTGAAC
* * * *
2844 TAGATTCGTATTCCTGATGAGATACAGAGAAACGGATTGAAGCAGTGATGGGATCATCTTCCTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
2909 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
2974 GAAGTGAAC
131 GAAGTGAAC
* * **
2983 CAGATTCGTCTTCCTGTTGAGATACAGAGAAACGGGTCGAAACAGCAATGGGATCATCTTCCTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
* *
3048 TGAGACGCTGAGAAGAAAACCCAAACGAGGCTCGAAGA-GAGCAAATCTTCCTGATAAGATACGG
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAA-ACGAGCAAATCTTCCTGATGAGATACGG
3112 AGAAGTGAAC
130 AGAAGTGAAC
* *
3122 CAGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCTTGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
3187 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
*
3252 GAACTGAAC
131 GAAGTGAAC
* *
3261 CAGATTCGTCTTCCTGATGAGATACAGAGAAAC-GAGTCGAAACAGCGATGAGATCATCTTCCTG
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGA-TCGAAACAGTGATGGGATCATCTTCCTG
* * *
3325 ATGGGACACTGAGAAGAAAATCCAAACGACGCTCGAAGA-GAGCAAATCTTCCTGATGAGATACG
65 ATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAA-ACGAGCAAATCTTCCTGATGAGATACG
3389 GAGAAGTGAAC
129 GAGAAGTGAAC
* * * * * *
3400 CAGATTCATCTTCCTAATAAGATACAGAGAAACAGATTGAAACAGTGA---G--CATCTTCCCGA
1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
** * * * ** * * * *
3460 TGAGACGTTGAGAAGGAGACCCAAACGAGGCTTGAAGTGAGCAGATCTTCCAAGATGAGGTACTG
66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCC-TGATGAGATACGG
3525 AGAAGTGAAC
130 AGAAGTGAAC
*
3535 CAAATTC
1 CAGATTC
3542 ATAAGCGAAT
Statistics
Matches: 762, Mismatches: 68, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
134 50 0.07
135 26 0.03
136 1 0.00
138 3 0.00
139 678 0.89
140 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (139 bp):
CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGTGATGGGATCATCTTCCTGA
TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
GAAGTGAAC
Found at i:4029 original size:17 final size:17
Alignment explanation
Indices: 4007--4052 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
3997 TTGGAAATTG
* *
4007 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
4024 AATTTAATTTTATTATA
1 AATTTAAATTTATTATA
*
4041 AAATTAAATTTA
1 AATTTAAATTTA
4053 GAAAAGTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:4106 original size:15 final size:15
Alignment explanation
Indices: 4086--4167 Score: 94
Period size: 15 Copynumber: 5.5 Consensus size: 15
4076 TCCAAAACAA
4086 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
** *
4101 ATGGCCCAAATACAA
1 ATGGCCCAGTTACAG
4116 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
** *
4131 ATGGCCCAAATACAA
1 ATGGCCCAGTTACAG
*
4146 ATGGGCC-GTTACAG
1 ATGGCCCAGTTACAG
4160 ATGGCCCA
1 ATGGCCCA
4168 AATACAAATT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 10 0.19
15 42 0.81
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (15 bp):
ATGGCCCAGTTACAG
Found at i:4116 original size:30 final size:30
Alignment explanation
Indices: 4077--4176 Score: 177
Period size: 30 Copynumber: 3.4 Consensus size: 30
4067 CAAAAAAAAT
4077 CCAAA-ACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
4106 CCAAATACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
*
4136 CCAAATACAAATGGGCC-GTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
4165 CCAAATACAAAT
1 CCAAATACAAAT
4177 TGTCCAATTG
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 29 0.42
30 40 0.58
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (30 bp):
CCAAATACAAATGGCCCAGTTACAGATGGC
Found at i:4544 original size:139 final size:134
Alignment explanation
Indices: 4286--4645 Score: 454
Period size: 139 Copynumber: 2.6 Consensus size: 134
4276 NNNNNNNNNN
4286 TGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAA-ACGAGCAAATCTTCCTGATGAGATA
1 TGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGA-GAGCAAATCTTCCTGATGAGATA
* * * *
4350 CGGAGAACTGAACCAGATTCGTCTTCCTGATGAGATACAGAGAAACGAGTCGAAACAGCGATGAG
65 CGGAGAAGTGAACCAGATTCATCTTCCTAATAAGATACAGAGAAACGAGTCGAAACA--G-TGAG
4415 ATCATCTTCC
127 --CATCTTCC
* * *
4425 TGATGGGACACTGAGAAGAAAATCCAAACGACGCTCGAAGAGAGCAAATCTTCCTGATGAGATAC
1 TGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAAATCTTCCTGATGAGATAC
*
4490 GGAGAAGTGAACCAGATTCATCTTCCTAATAAGATACAGAGAAAC-AGATTGAAACAGTGAGCAT
66 GGAGAAGTGAACCAGATTCATCTTCCTAATAAGATACAGAGAAACGAG-TCGAAACAGTGAGCAT
4554 CTTCC
130 CTTCC
* ** * * * * * * *
4559 CGATGAGACGTTGAGAAGGAGACCCAAACGAGGCTTGAAGTGAGCAGATCTTCCAAGATGAGGTA
1 TGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAAATCTTCC-TGATGAGATA
* *
4624 CTGAGAAGTGAACCAAATTCAT
65 CGGAGAAGTGAACCAGATTCAT
4646 AAGCGAATTG
Statistics
Matches: 195, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
134 51 0.26
135 28 0.14
136 4 0.02
137 1 0.01
138 2 0.01
139 108 0.55
140 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (134 bp):
TGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAGAGAGCAAATCTTCCTGATGAGATAC
GGAGAAGTGAACCAGATTCATCTTCCTAATAAGATACAGAGAAACGAGTCGAAACAGTGAGCATC
TTCC
Found at i:5131 original size:17 final size:17
Alignment explanation
Indices: 5109--5154 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5099 TTGGAAATTG
* *
5109 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
5126 AATTTAATTTTATTATA
1 AATTTAAATTTATTATA
*
5143 AAATTAAATTTA
1 AATTTAAATTTA
5155 GAAAAGTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:5208 original size:15 final size:15
Alignment explanation
Indices: 5188--5269 Score: 94
Period size: 15 Copynumber: 5.5 Consensus size: 15
5178 TCCAAAACAA
5188 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
** *
5203 ATGGCCCAAATACAA
1 ATGGCCCAGTTACAG
5218 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
** *
5233 ATGGCCCAAATACAA
1 ATGGCCCAGTTACAG
*
5248 ATGGGCC-GTTACAG
1 ATGGCCCAGTTACAG
5262 ATGGCCCA
1 ATGGCCCA
5270 AATACAAATT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 10 0.19
15 42 0.81
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (15 bp):
ATGGCCCAGTTACAG
Found at i:5218 original size:30 final size:30
Alignment explanation
Indices: 5179--5278 Score: 177
Period size: 30 Copynumber: 3.4 Consensus size: 30
5169 CAAAAAAAAT
5179 CCAAA-ACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
5208 CCAAATACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
*
5238 CCAAATACAAATGGGCC-GTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
5267 CCAAATACAAAT
1 CCAAATACAAAT
5279 TGTCCAATTG
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 29 0.42
30 40 0.58
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (30 bp):
CCAAATACAAATGGCCCAGTTACAGATGGC
Done.