Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012209.1 Kokia drynarioides strain JFW-HI SEQ_127210, 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: 6878
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3487 original size:208 final size:208
Alignment explanation
Indices: 3111--3656 Score: 796
Period size: 208 Copynumber: 2.6 Consensus size: 208
3101 TCGATTACGA
* * *
3111 TCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCAATAAAGCGAAGCTCAATACGAATGAG
1 TCATCTTCCTGATGAGATACAGAGAAGTAGAACAAATCAATGAAGCGAAGCTCAATACGAATGAG
* * *
3176 GCTTCAAACCCCATCTTCCTAATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGTGGTCATCTT
66 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGAGGTCATCTT
* * *
3241 CTTAATGAGATACAGAGAAGTGAACTAAATCCGCCTTCCTGATGAGATACAAAGAGGTGCATTAA
131 CTTAATGAGATACAGAGAAGGGAACTAAATCCGCCTTCCTAATGAGATACAAAGAAGTGCATTAA
3306 ATCAATGAAGCGG
196 ATCAATGAAGCGG
*
3319 TCATCTTCCTGATGACATACAGAGAAGTAGAACAAATCAATGAAGCGAAGCTCAATACGAATGAG
1 TCATCTTCCTGATGAGATACAGAGAAGTAGAACAAATCAATGAAGCGAAGCTCAATACGAATGAG
* *
3384 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTT
66 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGAGGTCATCTT
* * * * * *
3449 CTTGATGAGATACAGA-AAGGGGGAGC-AAATCTGCCTTCCTAATGAGATACAGATAAGTGGATT
131 CTTAATGAGATACAGAGAA--GGGAACTAAATCCGCCTTCCTAATGAGATACAAAGAAGTGCATT
* *
3512 GAATCTATGAAGCGG
194 AAATCAATGAAGCGG
* * * *
3527 TCATCTTCCTGATGAGATACATAGAAGTAG-ACTTAATTAATGAAGTGAAGCTCAATACGAATGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGAAC-AAATCAATGAAGCGAAGCTCAATACGAATGA
*
3591 GACTTCAAACCCCATCTTCC-GATGAGATACAGAGAAGTGGG-CTAAAGTAATAAAGAGGTCATC
65 GACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTC-AAAGAAATAAAGAGGTCATC
3654 TTC
129 TTC
3657 CCAATTAATT
Statistics
Matches: 308, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
206 1 0.00
207 46 0.15
208 257 0.83
209 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (208 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGAACAAATCAATGAAGCGAAGCTCAATACGAATGAG
ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAGAGGTCATCTT
CTTAATGAGATACAGAGAAGGGAACTAAATCCGCCTTCCTAATGAGATACAAAGAAGTGCATTAA
ATCAATGAAGCGG
Found at i:3816 original size:13 final size:13
Alignment explanation
Indices: 3791--3839 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3781 AACCTAATAC
3791 CACTAAA-CCAAA
1 CACTAAACCCAAA
3803 CACTAAACCCAAA
1 CACTAAACCCAAA
3816 CTCAC-AAACCCTAAA
1 --CACTAAACCC-AAA
3831 -ACTAAACCC
1 CACTAAACCC
3840 TGACCTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.28
13 11 0.34
14 6 0.19
15 6 0.19
ACGTcount: A:0.51, C:0.39, G:0.00, T:0.10
Consensus pattern (13 bp):
CACTAAACCCAAA
Found at i:5317 original size:208 final size:207
Alignment explanation
Indices: 4956--5524 Score: 863
Period size: 208 Copynumber: 2.7 Consensus size: 207
4946 GATCATCTTT
* * *
4956 TTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTAAATACGAGTAAGGCTTCAAA
1 TTGATGAGATACAGAGAAGTAGA-CAAATCAATGAAGCGAAGCTAAATACGAATGAGACTTCAAA
* * * * *
5021 CCCCATCTTCCTAATGAGATACAGAGAAGTGGGTCAAAGA-ATTAAAGTGGCCATCTTCTTAATG
65 CCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAA-ACAATAAAGTGGTCATCTTCCTGATG
* *
5085 AGATACAA-AGAAGTGGACCAAATCCGCGTTCCTGATGAGATACAGAGAAGTGAATTGAATCAAT
129 AGATA-AAGAGAAGTGGAGCAAATCCGCGTTCCTGATGAGATACAGAGAAGTGAATTAAATCAAT
5149 GAAGCGGTCATCCTC
193 GAAGCGGTCATCCTC
5164 TTGATGAGATACAGAGAAGTAGAGCAAATCAATGAAGCGAAGCTAAATACGAATGAGACTTCAAA
1 TTGATGAGATACAGAGAAGTAGA-CAAATCAATGAAGCGAAGCTAAATACGAATGAGACTTCAAA
*
5229 CCGCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCTGATGA
65 CCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCTGATGA
* * *
5294 GATAAAGAGAAGTGAAGCAAATCCGCGTTCCTGATGAGATACAGAGAAGTGGATTAAATCTATGA
130 GATAAAGAGAAGTGGAGCAAATCCGCGTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGA
*
5359 AGCGGTCATCTTC
195 AGCGGTCATCCTC
* * * * * *
5372 CTGATGAGATACAGAGAAGTAGACTGAATCAATAAAGTGAAGCTCAATACGAATGAGACATCAAA
1 TTGATGAGATACAGAGAAGTAGAC-AAATCAATGAAGCGAAGCTAAATACGAATGAGACTTCAAA
* *
5437 CCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCGGTCATCTTCCTGATGA
65 CCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCTGATGA
*
5502 GATACAGAGAAGTGGAGCAAATC
130 GATAAAGAGAAGTGGAGCAAATC
5525 AATGAAGCAA
Statistics
Matches: 331, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
207 4 0.01
208 327 0.99
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (207 bp):
TTGATGAGATACAGAGAAGTAGACAAATCAATGAAGCGAAGCTAAATACGAATGAGACTTCAAAC
CCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCTGATGAG
ATAAAGAGAAGTGGAGCAAATCCGCGTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAA
GCGGTCATCCTC
Found at i:5379 original size:85 final size:85
Alignment explanation
Indices: 5236--5391 Score: 249
Period size: 85 Copynumber: 1.8 Consensus size: 85
5226 AAACCGCATC
* *
5236 TTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCTGATGAGATAAAG
1 TTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATCTTCCTGATGAGATAAAG
5301 AGAAGTGAAGCAAATCCGCG
66 AGAAGTGAAGCAAATCCGCG
* * * * *
5321 TTCCTGATGAGATACAGAGAAGTGGATTAAATCTATGAAGCGGTCATCTTCCTGATGAGATACAG
1 TTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATCTTCCTGATGAGATAAAG
5386 AGAAGT
66 AGAAGT
5392 AGACTGAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.24
Consensus pattern (85 bp):
TTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATCTTCCTGATGAGATAAAG
AGAAGTGAAGCAAATCCGCG
Found at i:5542 original size:123 final size:124
Alignment explanation
Indices: 5321--5629 Score: 379
Period size: 123 Copynumber: 2.5 Consensus size: 124
5311 CAAATCCGCG
* * * *
5321 TTCCTGATGAGATACAGAGAAGTGGATTAAATCTATGAAGCGGTCATCTTCCTGATGAGATACAG
1 TTCCTGATGAGATACAGAGAAGTGGGTTAAAACAATAAAGCGGTCATCTTCCTGATGAGATACAG
* ** *
5386 AGAAGTAGACTGAATCAATAAAGTGAAGCTCAATACGAATGAGACATCAAACCCC-ATC
66 AGAAGTAGACTAAATCAATAAAGCAAAGCTCAATACGAATGAAACATCAAACCCCTATC
* *
5444 TTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCGGTCATCTTCCTGATGAGATACAG
1 TTCCTGATGAGATACAGAGAAGTGGGTTAAAACAATAAAGCGGTCATCTTCCTGATGAGATACAG
* * * * * * *
5509 AGAAGTGGAGC-AAATCAATGAAGCAAAGTTCAATGCGAGTGAAACTTCAAACCCCTATT
66 AGAAGTAGA-CTAAATCAATAAAGCAAAGCTCAATACGAATGAAACATCAAACCCCTATC
* * * * ** *
5568 TTCTTGATGAGGTACAGAGAAGTGAGTTGAAGTAATAAAGCGATCATCTTCCTGATGAGATA
1 TTCCTGATGAGATACAGAGAAGTGGGTTAAAACAATAAAGCGGTCATCTTCCTGATGAGATA
5630 TGAGATACAG
Statistics
Matches: 158, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
123 102 0.65
124 56 0.35
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (124 bp):
TTCCTGATGAGATACAGAGAAGTGGGTTAAAACAATAAAGCGGTCATCTTCCTGATGAGATACAG
AGAAGTAGACTAAATCAATAAAGCAAAGCTCAATACGAATGAAACATCAAACCCCTATC
Found at i:6064 original size:18 final size:18
Alignment explanation
Indices: 6043--6113 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 18
6033 ATAAAACAAA
6043 TTTTAAATTTAAATTTAC
1 TTTTAAATTTAAATTTAC
*
6061 TTTTAATTTTAAATGTCCAATAC
1 TTTTAAATTTAAAT-T----TAC
6084 ATTTTAAATTTAAATTT--
1 -TTTTAAATTTAAATTTAC
*
6101 GTTTAAATTTAAA
1 TTTTAAATTTAAA
6114 AGTCAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
16 12 0.27
18 13 0.30
19 2 0.05
23 4 0.09
24 13 0.30
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTTAAATTTAAATTTAC
Found at i:6126 original size:42 final size:41
Alignment explanation
Indices: 6042--6120 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
6032 TATAAAACAA
* * * *
6042 ATTTTAAATTTAAATTTACTTTTAATTTTAAATGTCCAATAC
1 ATTTTAAATTTAAATTTA-GTTTAAATTTAAAAGTCAAATAC
6084 ATTTTAAATTTAAATTT-GTTTAAATTTAAAAGTCAAA
1 ATTTTAAATTTAAATTTAGTTTAAATTTAAAAGTCAAA
6121 AATACAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.48
42 17 0.52
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (41 bp):
ATTTTAAATTTAAATTTAGTTTAAATTTAAAAGTCAAATAC
Found at i:6184 original size:21 final size:21
Alignment explanation
Indices: 6146--6185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6136 ACCACTAAAC
* *
6146 CAAACGCTAAACCCAAACCCA
1 CAAACCCTAAAACCAAACCCA
*
6167 CAAACCCTAAAACTAAACC
1 CAAACCCTAAAACCAAACC
6186 TTAACCAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.40, G:0.03, T:0.07
Consensus pattern (21 bp):
CAAACCCTAAAACCAAACCCA
Done.