Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014523.1 Kokia drynarioides strain JFW-HI SEQ_129562, 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: 54933
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7130 original size:91 final size:90
Alignment explanation
Indices: 6975--7155 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 90
6965 TATGCACCGA
6975 CAATATTATTTGTTGCTACGTCCCTGAAGAAGAAATGCTCTATATCTTGAAGCATTGCCATGATG
1 CAATATTATTTGTTGCTACGTCCCTGAAGAAGAAATGCTCTATATCTTGAAGCATTGCCATGATG
*
7040 CACCTTATGACGGTCATTTTGGTGG
66 CACCTTATGACGATCATTTTGGTGG
7065 NCAATATTATTTGTTGCTACGTCCCTGAAGAAGAAATGCTCTATATCTTGAAGCATTGCCATGAT
1 -CAATATTATTTGTTGCTACGTCCCTGAAGAAGAAATGCTCTATATCTTGAAGCATTGCCATGAT
7130 GCACCTTATGACGATCATTTTGGTGG
65 GCACCTTATGACGATCATTTTGGTGG
7156 TGTTAGGACT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (90 bp):
CAATATTATTTGTTGCTACGTCCCTGAAGAAGAAATGCTCTATATCTTGAAGCATTGCCATGATG
CACCTTATGACGATCATTTTGGTGG
Found at i:9422 original size:15 final size:15
Alignment explanation
Indices: 9387--9429 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
9377 GGTATCAAGG
*
9387 AGAAGAAGGAAGAGAA
1 AGAAGAA-GAAAAGAA
9403 AGAAGAAGAAAAGAA
1 AGAAGAAGAAAAGAA
*
9418 GGAAGAAGAAAA
1 AGAAGAAGAAAA
9430 CGAGGAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAGAA
Found at i:21987 original size:2 final size:2
Alignment explanation
Indices: 21967--22007 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
21957 CAACATTTAT
*
21967 TA TA TA -A TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22007 T
1 T
22008 TTCTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:23111 original size:15 final size:15
Alignment explanation
Indices: 23061--23111 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
23051 ATCGGGACAA
23061 CTTCTTTT-TTTTC-
1 CTTCTTTTCTTTTCT
*
23074 CTTCTCTTCTTTTTCTT
1 CTTCTTTTC-TTTTC-T
23091 CTTCTTTTCTTTTCT
1 CTTCTTTTCTTTTCT
23106 CTTCTT
1 CTTCTT
23112 GTATTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 7 0.22
15 12 0.38
16 5 0.16
17 8 0.25
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTCTTTTCTTTTCT
Found at i:34304 original size:3 final size:3
Alignment explanation
Indices: 34296--34391 Score: 129
Period size: 3 Copynumber: 32.0 Consensus size: 3
34286 AATTACACAT
34296 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
34344 ATA ATA ATA ATA ATA AAA ATG ACA ATG ACA ATA ACA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34392 GGGTTAAATG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:34889 original size:18 final size:18
Alignment explanation
Indices: 34852--34887 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34842 GCAAATCGAG
*
34852 TTATTCGAGTTAATCAAA
1 TTATTCGAGTCAATCAAA
34870 TTATTCGAGTCAACTCAA
1 TTATTCGAGTCAA-TCAA
34888 TTTTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
TTATTCGAGTCAATCAAA
Found at i:35310 original size:18 final size:18
Alignment explanation
Indices: 35287--35347 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
35277 ACTCTCCCTG
35287 TTTACTTTCCCTAAAAAT
1 TTTACTTTCCCTAAAAAT
*
35305 TTTAC--TCCCTAAAACTT
1 TTTACTTTCCCTAAAA-AT
* *
35322 TTTA-TTTCCCCCAAAACT
1 TTTACTTT-CCCTAAAAAT
35340 TTTACTTT
1 TTTACTTT
35348 TCACCCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 9 0.26
17 5 0.14
18 11 0.31
19 10 0.29
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTACTTTCCCTAAAAAT
Found at i:38465 original size:28 final size:28
Alignment explanation
Indices: 38425--38641 Score: 222
Period size: 28 Copynumber: 7.8 Consensus size: 28
38415 ATAACTACTT
* ** *
38425 TGATTATGGCTCAAAAAGAGTGATATTC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
** *
38453 TGATTCTGGCTCAAAAAGAGCAATATTC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
*
38481 TAATTCTGGCTCGGAAAGAGCGATATTC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
* * * *
38509 TGATTCTAGCTCGAAAAGAGTGATAATC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
* *
38537 TGATTCTAGCTCGGAAAGAGTGATATTC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
** * * *
38565 AT-ATTAAGACTTGGAAAGAACGATATTC
1 -TGATTCTGGCTCGGAAAGAGCGATATTC
*
38593 TGATTCTGGCTCAGAAAGAGCGATATTC
1 TGATTCTGGCTCGGAAAGAGCGATATTC
*
38621 TGTTTCTGGCTC-GAAAGAGCG
1 TGATTCTGGCTCGGAAAGAGCG
38642 TTGTTTTGTT
Statistics
Matches: 159, Mismatches: 28, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
27 10 0.06
28 148 0.93
29 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (28 bp):
TGATTCTGGCTCGGAAAGAGCGATATTC
Found at i:38651 original size:27 final size:27
Alignment explanation
Indices: 38439--38701 Score: 172
Period size: 28 Copynumber: 9.5 Consensus size: 27
38429 TATGGCTCAA
* * *
38439 AAAGAGTGATATTCTGATTCTGGCTCAA
1 AAAGAGCGATATTCTGTTTCTGGCTC-G
* **
38467 AAAGAGCAATATTCTAATTCTGGCTCGG
1 AAAGAGCGATATTCTGTTTCTGGCTC-G
* *
38495 AAAGAGCGATATTCTGATTCTAGCTCG
1 AAAGAGCGATATTCTGTTTCTGGCTCG
* * * *
38522 AAAAGAGTGATAATCTGATTCTAGCTCGG
1 -AAAGAGCGATATTCTGTTTCTGGCTC-G
* * ** * *
38551 AAAGAGTGATATTCAT-ATTAAGACTTGG
1 AAAGAGCGATATTC-TGTTTCTGGC-TCG
* *
38579 AAAGAACGATATTCTGATTCTGGCTCAG
1 AAAGAGCGATATTCTGTTTCTGGCTC-G
38607 AAAGAGCGATATTCTGTTTCTGGCTCG
1 AAAGAGCGATATTCTGTTTCTGGCTCG
* * * *
38634 AAAGAGCGTTGTTTTGTTTCTAGCTCG
1 AAAGAGCGATATTCTGTTTCTGGCTCG
*
38661 AAAGAAGC-ATTACTCTG-TTCTGGGCTCG
1 AAAG-AGCGA-TATTCTGTTTCT-GGCTCG
* *
38689 AATGAGCTATATT
1 AAAGAGCGATATT
38702 TCTATAATAG
Statistics
Matches: 190, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
27 41 0.22
28 146 0.77
29 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (27 bp):
AAAGAGCGATATTCTGTTTCTGGCTCG
Found at i:44799 original size:13 final size:13
Alignment explanation
Indices: 44781--44805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44771 ACATTGTAGC
44781 GATAAATTTGTCT
1 GATAAATTTGTCT
44794 GATAAATTTGTC
1 GATAAATTTGTC
44806 GTCGCACCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GATAAATTTGTCT
Found at i:50075 original size:20 final size:20
Alignment explanation
Indices: 50050--50161 Score: 95
Period size: 20 Copynumber: 5.6 Consensus size: 20
50040 GTATATCTTG
50050 CACAAAGCCT-ATTACACCGA
1 CACAAAGCCTGA-TACACCGA
50070 CACAAAGCCTGATACACCGA
1 CACAAAGCCTGATACACCGA
* *
50090 CACAAAGCCTGA-ATCCCCGG
1 CACAAAGCCTGATA-CACCGA
* * * * *
50110 TATAAAGCTTGATACTCCGG
1 CACAAAGCCTGATACACCGA
*
50130 TACAAAGCCTGA-ATCACCGA
1 CACAAAGCCTGATA-CACCGA
*
50150 CATAAAGCCTGA
1 CACAAAGCCTGA
50162 ATCACTGGCA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 72 0.95
21 2 0.03
ACGTcount: A:0.37, C:0.31, G:0.16, T:0.16
Consensus pattern (20 bp):
CACAAAGCCTGATACACCGA
Found at i:50117 original size:40 final size:40
Alignment explanation
Indices: 50050--50205 Score: 129
Period size: 40 Copynumber: 3.9 Consensus size: 40
50040 GTATATCTTG
* *
50050 CACAAAGCCT-ATTACACCGACACAAAGCCTGATACACCGA
1 CACAAAGCCTGAAT-CACCGACATAAAGCCTGATACACCGA
* ** * * *
50090 CACAAAGCCTGAATCCCCGGTATAAAGCTTGATACTCCGG
1 CACAAAGCCTGAATCACCGACATAAAGCCTGATACACCGA
* * *
50130 TACAAAGCCTGAATCACCGACATAAAGCCTGA-ATCACTGG
1 CACAAAGCCTGAATCACCGACATAAAGCCTGATA-CACCGA
* * * * *
50170 CATAAAGGCTGATTTACCGGCATAAAGCCTGA-ACAC
1 CACAAAGCCTGAATCACCGACATAAAGCCTGATACAC
50206 TTAGGTATAA
Statistics
Matches: 93, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 4 0.04
40 87 0.94
41 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.17
Consensus pattern (40 bp):
CACAAAGCCTGAATCACCGACATAAAGCCTGATACACCGA
Found at i:50162 original size:20 final size:20
Alignment explanation
Indices: 50073--50202 Score: 111
Period size: 20 Copynumber: 6.5 Consensus size: 20
50063 ACACCGACAC
* *
50073 AAAGCCTG-ATACACCGACAC
1 AAAGCCTGAAT-CACCGGCAT
* *
50093 AAAGCCTGAATCCCCGGTAT
1 AAAGCCTGAATCACCGGCAT
* * * *
50113 AAAGCTTG-ATACTCCGGTAC
1 AAAGCCTGAAT-CACCGGCAT
*
50133 AAAGCCTGAATCACCGACAT
1 AAAGCCTGAATCACCGGCAT
*
50153 AAAGCCTGAATCACTGGCAT
1 AAAGCCTGAATCACCGGCAT
* * *
50173 AAAGGCTGATTTACCGGCAT
1 AAAGCCTGAATCACCGGCAT
50193 AAAGCCTGAA
1 AAAGCCTGAA
50203 CACTTAGGTA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.93
21 4 0.05
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AAAGCCTGAATCACCGGCAT
Found at i:50197 original size:60 final size:61
Alignment explanation
Indices: 50070--50202 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 61
50060 ATTACACCGA
* *
50070 CACAAAGCCTG-ATACACCGACACAAAGCCTGAATCCCCGGTATAAAGCTTGATACTCCGG
1 CACAAAGCCTGAATACACCGACACAAAGCCTGAATCACCGGCATAAAGCTTGATACTCCGG
* * * *
50130 TACAAAGCCTGAAT-CACCGACATAAAGCCTGAATCACTGGCATAAAGGC-TGAT-TTACCGG
1 CACAAAGCCTGAATACACCGACACAAAGCCTGAATCACCGGCATAAA-GCTTGATACT-CCGG
*
50190 CATAAAGCCTGAA
1 CACAAAGCCTGAA
50203 CACTTAGGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
59 1 0.02
60 57 0.92
61 4 0.06
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (61 bp):
CACAAAGCCTGAATACACCGACACAAAGCCTGAATCACCGGCATAAAGCTTGATACTCCGG
Found at i:54497 original size:81 final size:81
Alignment explanation
Indices: 54353--54545 Score: 269
Period size: 81 Copynumber: 2.4 Consensus size: 81
54343 TGAGTGATTT
** * * * *
54353 ACGATGCTGCTTGCATAAGTTGATGAGAATCCACAACATATGTGAGACCTCAGCTATCGCTACGG
1 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
54418 TCTATATCACCCGCTC
66 TCTATATCACCCGCTC
* * *
54434 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATTTGAGACCTCAACCATCTCTACGT
1 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
* * *
54499 TTTATATCACTCGCTT
66 TCTATATCACCCGCTC
*
54515 ACGATGCTGCTCACACAAGCTAATGAGAATC
1 ACGATGCTGCTCACACAAGCTGATGAGAATC
54546 TGCAACGTAT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 99 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (81 bp):
ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
TCTATATCACCCGCTC
Done.