Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009152.1 Kokia drynarioides strain JFW-HI SEQ_123856, 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: 23839
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:44 original size:17 final size:17
Alignment explanation
Indices: 22--101 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
12 TGGACTTTTC
* *
22 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
39 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
56 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
73 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
90 TAAACTTAAATT
1 TAAATTTAAATT
102 CAATTTCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:73 original size:7 final size:6
Alignment explanation
Indices: 22--101 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
12 TGGACTTTTC
*
22 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* * * *
68 TAAA-A TAAACT TAAATT TAAA-A TAAACT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
102 CAATTTCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
4 5 0.09
5 11 0.19
6 38 0.66
7 4 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:710 original size:9 final size:9
Alignment explanation
Indices: 693--780 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
683 TTAATTTTTT
*
693 AAATATAAA
1 AAATTTAAA
702 AAATTTAAA
1 AAATTTAAA
*
711 AAATATAAA
1 AAATTTAAA
*
720 AAGTATTAAA
1 AAAT-TTAAA
*
730 AACTTT-AA
1 AAATTTAAA
*
738 AAA-CTACAA
1 AAATTTA-AA
*
747 AGATTATAAAA
1 AAATT-T-AAA
*
758 AAATTTTAA
1 AAATTTAAA
*
767 AATTTTAAA
1 AAATTTAAA
776 AAATT
1 AAATT
781 AATTAATTGT
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
9 38 0.64
10 8 0.14
11 7 0.12
12 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
AAATTTAAA
Found at i:714 original size:18 final size:19
Alignment explanation
Indices: 693--731 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
683 TTAATTTTTT
693 AAATATAAAAAAT-TTAAA
1 AAATATAAAAAATATTAAA
*
711 AAATATAAAAAGTATTAAA
1 AAATATAAAAAATATTAAA
730 AA
1 AA
732 CTTTAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
AAATATAAAAAATATTAAA
Found at i:729 original size:28 final size:28
Alignment explanation
Indices: 698--777 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
688 TTTTTAAATA
698 TAAAAAATTTAAAAAATATAAAAAGTAT
1 TAAAAAATTTAAAAAATATAAAAAGTAT
* * * * *
726 TAAAAACTTTAAAAACTACAAAGATTAT
1 TAAAAAATTTAAAAAATATAAAAAGTAT
* * * *
754 AAAAAAATTTTAAAATTTTAAAAA
1 TAAAAAATTTAAAAAATATAAAAA
778 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAAAAATTTAAAAAATATAAAAAGTAT
Found at i:7997 original size:172 final size:171
Alignment explanation
Indices: 7616--8118 Score: 888
Period size: 172 Copynumber: 3.0 Consensus size: 171
7606 ATTAAATTGC
*
7616 GTTTATGATTAAATGATGATATATAGCGTGTGAAATACAA---TTTAAATAAAGAGGAAAAATAA
1 GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
** *
7678 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTAATTAATCATAG-TT
66 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTAATCGATGATAGTTT
7742 TGAGTTTTGGGTATTATATTAAATGGTATCAGATAAATTTT
131 TGAGTTTTGGGTATTATATTAAATGGTATCAGATAAATTTT
7783 GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
1 GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
*
7848 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTGATCGATGATAGTTT
66 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTAATCGATGATAG-TT
*
7913 TTGAGCTTTGGGTATTATATTAAATGGTATCAGATAAATTTT
130 TTGAGTTTTGGGTATTATATTAAATGGTATCAGATAAATTTT
7955 GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
1 GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
*
8020 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCTTAATCGATGATAGCTT
66 TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTAATCGATGATAG-TT
*
8085 TTGAGTTTTGGGTATTATATTTAATGGTATCAGA
130 TTGAGTTTTGGGTATTATATTAAATGGTATCAGA
8119 GCTTATGATT
Statistics
Matches: 320, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
167 39 0.12
170 80 0.25
172 201 0.63
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (171 bp):
GTTTATGATTAAATGATGATATATAGCGTGTGAAGTACAATTCTTTAAATAAAGAGGAAAAATAA
TGATGTTAAAGATGAACTGTGATAAATGAATAGTAAGGCACTGAAACCCTAATCGATGATAGTTT
TGAGTTTTGGGTATTATATTAAATGGTATCAGATAAATTTT
Found at i:14751 original size:19 final size:19
Alignment explanation
Indices: 14707--14757 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
14697 ACCATGTGTC
* *
14707 CCAAATACAACTTCTTACA
1 CCAAATGCAATTTCTTACA
14726 CCAAATGCAATTTCTTACA
1 CCAAATGCAATTTCTTACA
14745 CCAAATGCAATTT
1 CCAAATGCAATTT
14758 AAACTCAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (19 bp):
CCAAATGCAATTTCTTACA
Found at i:15211 original size:20 final size:20
Alignment explanation
Indices: 15188--15331 Score: 112
Period size: 20 Copynumber: 7.2 Consensus size: 20
15178 TAAAGCTTGC
*
15188 TACACCGGCAGAAAGCCTAA
1 TACACCGGCATAAAGCCTAA
*
15208 TACACCGGCATAAAGCCTGA
1 TACACCGGCATAAAGCCTAA
* * * *
15228 TACACCGACATAATGTCTGA
1 TACACCGGCATAAAGCCTAA
*
15248 TACACCGGCACAAAGCCTGAA
1 TACACCGGCATAAAGCCT-AA
* *
15269 -CCACCGGCAAAAAGCCTAA
1 TACACCGGCATAAAGCCTAA
** *
15288 -ATCATTGGCATAAAGCCTGA
1 TA-CACCGGCATAAAGCCTAA
** *
15308 TTTATCGGCATAAAGCCTGAA
1 TACACCGGCATAAAGCCT-AA
15329 TAC
1 TAC
15332 TTAGGTATAA
Statistics
Matches: 97, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.02
20 92 0.95
21 3 0.03
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (20 bp):
TACACCGGCATAAAGCCTAA
Found at i:15232 original size:40 final size:40
Alignment explanation
Indices: 15175--15331 Score: 147
Period size: 40 Copynumber: 3.9 Consensus size: 40
15165 TGTATATCCT
* * *
15175 GCATAAAGCTTGCTACACCGGCAGAAAGCCTAATACACCG
1 GCATAAAGCCTGATACACCGGCATAAAGCCTAATACACCG
* * * *
15215 GCATAAAGCCTGATACACCGACATAATGTCTGATACACCG
1 GCATAAAGCCTGATACACCGGCATAAAGCCTAATACACCG
* * **
15255 GCACAAAGCCTGA-ACCACCGGCAAAAAGCCTAA-ATCATTG
1 GCATAAAGCCTGATA-CACCGGCATAAAGCCTAATA-CACCG
** *
15295 GCATAAAGCCTGATTTATCGGCATAAAGCCTGAATAC
1 GCATAAAGCCTGATACACCGGCATAAAGCCT-AATAC
15332 TTAGGTATAA
Statistics
Matches: 92, Mismatches: 20, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.93
41 3 0.03
42 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (40 bp):
GCATAAAGCCTGATACACCGGCATAAAGCCTAATACACCG
Found at i:15300 original size:60 final size:61
Alignment explanation
Indices: 15176--15331 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 61
15166 GTATATCCTG
* * * * *
15176 CATAAAGCTTGCTACACCGGCAGAAAGCCT-AATACACCGGCATAAAGCCTGATACACCGA
1 CATAAAGCCTGATACACCGGCACAAAGCCTGAATACACCGGCAAAAAGCCTAATACACCGA
* * * ** *
15236 CATAATGTCTGATACACCGGCACAAAGCCTGAA-CCACCGGCAAAAAGCCTAA-ATCATTGG
1 CATAAAGCCTGATACACCGGCACAAAGCCTGAATACACCGGCAAAAAGCCTAATA-CACCGA
** * *
15296 CATAAAGCCTGATTTATCGGCATAAAGCCTGAATAC
1 CATAAAGCCTGATACACCGGCACAAAGCCTGAATAC
15332 TTAGGTATAA
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
59 1 0.01
60 71 0.95
61 3 0.04
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.18
Consensus pattern (61 bp):
CATAAAGCCTGATACACCGGCACAAAGCCTGAATACACCGGCAAAAAGCCTAATACACCGA
Found at i:22903 original size:41 final size:41
Alignment explanation
Indices: 22857--22952 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
22847 TTAGCGGCGT
* *
22857 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTGCTGCA
1 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
* * * *
22898 TTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTTCCGGCG
1 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
22939 TTTTCTCATAAACG
1 TTTTCTCATAAACG
22953 TCGTTATTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (41 bp):
TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
Found at i:22972 original size:41 final size:40
Alignment explanation
Indices: 22851--22981 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 40
22841 TAACCTTTAG
* * *
22851 CGGCGTTTTTCTCATAAACGCCACTAATGCTCTTACCTTTTG
1 CGGCG-TTTTCTCATAAACGCCGCTAGTGCTCTTA-CTTTTC
* *
22893 CTGCATTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTTC
1 CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTAC-TTTTC
* * * * * *
22934 CGGCGTTTTCTCATAAACGTCGTTATTGCTTTTCCTTTTG
1 CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTC
22974 CGGCGTTT
1 CGGCGTTT
22982 ATGAAAAAAC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 13 0.17
41 59 0.79
42 3 0.04
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (40 bp):
CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTC
Done.