Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004022.1 Kokia drynarioides strain JFW-HI SEQ_117144, 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, 696
Length: 1161
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Found at i:663 original size:30 final size:29
Alignment explanation
Indices: 607--850 Score: 149
Period size: 30 Copynumber: 8.5 Consensus size: 29
597 AGTTCGAGGT
*
607 TAAAAGATGGAATTTTTAGACA-TTTAGGGG
1 TAAAA-ATGGAATTTTTAGA-AGTTTTGGGG
* *
637 TAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 TAAAAATGGAATTTTTAGAAGTTTT-GGGG
* * *
667 TAAAAAAGGAATTTTTGGACA--TTCGAGGG
1 TAAAAATGGAATTTTTAGA-AGTTTTG-GGG
* *
696 -CAAAATGGTAATTTTT-GAAAGTTTTGGGAT
1 TAAAAATGG-AATTTTTAG-AAGTTTTGGG-G
726 TAAAAATGGAA----T-----TTTTGGGG
1 TAAAAATGGAATTTTTAGAAGTTTTGGGG
746 TCAAAAATGGAATTTTTAGAAGTTTTGGGG
1 T-AAAAATGGAATTTTTAGAAGTTTTGGGG
* *
776 TCGAAAATGGAATTTTTAGAAGTTTTGAGG
1 T-AAAAATGGAATTTTTAGAAGTTTTGGGG
* *
806 TCGAAAATGGAATTTTTTGAAG-TTTGGGG
1 T-AAAAATGGAATTTTTAGAAGTTTTGGGG
* *
835 TTGAAAATGTAATTTT
1 -TAAAAATGGAATTTT
851 CGAACAGTTT
Statistics
Matches: 176, Mismatches: 17, Indels: 43
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.01
21 17 0.10
25 1 0.01
26 1 0.01
28 10 0.06
29 49 0.28
30 89 0.51
31 8 0.05
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
TAAAAATGGAATTTTTAGAAGTTTTGGGG
Found at i:668 original size:60 final size:57
Alignment explanation
Indices: 604--850 Score: 208
Period size: 59 Copynumber: 4.3 Consensus size: 57
594 GGAAGTTCGA
604 GGTTAAAAGATGGAATTTTTAGACATTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTTAG
1 GGTTAAAA-ATGGAATTTTTAGA-ATTT-GGGGTCAAAAATGGAATTTTTGGAAGTTTT-G
* * * *
664 GGTTAAAAAAGGAATTTTTGGACATTCGAGGG-C-AAAATGGTAATTTTTGAAAGTTTTG
1 GGTTAAAAATGGAATTTTTAGA-ATTTG-GGGTCAAAAATGG-AATTTTTGGAAGTTTTG
*
722 GGATTAAAAATGGAA---TT----TTTGGGGTCAAAAATGGAATTTTTAGAAGTTTTGG
1 GG-TTAAAAATGGAATTTTTAGAATTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT-G
** * * * *
774 GGTCGAAAATGGAATTTTTAGAAGTTTTGAGGTCGAAAATGGAATTTTTTGAAGTTTGG
1 GGTTAAAAATGGAATTTTTAGAA--TTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTG
* *
833 GGTTGAAAATGTAATTTT
1 GGTTAAAAATGGAATTTT
851 CGAACAGTTT
Statistics
Matches: 155, Mismatches: 16, Indels: 33
0.76 0.08 0.16
Matches are distributed among these distances:
50 3 0.02
51 28 0.18
52 10 0.06
54 2 0.01
56 2 0.01
58 11 0.07
59 62 0.40
60 37 0.24
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (57 bp):
GGTTAAAAATGGAATTTTTAGAATTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTG
Found at i:742 original size:59 final size:58
Alignment explanation
Indices: 561--850 Score: 194
Period size: 59 Copynumber: 5.1 Consensus size: 58
551 AAAATGCTAA
* * * *
561 TTTTGGACTTTCG-GGGCAAGATGGTAATTTTGGGGAAG-TTCGAGGTTAAAAGATGGAAT
1 TTTTGGACATTCGAGGGCAAAATGGTAATTTT-TGGAAGTTTTG-GGTTAAAA-ATGGAAT
* * * *
620 TTTTAGACATT-TAGGGGTAAAAATGG-AATTTTTGGAAGTTTTAGGGTTAAAAAAGGAAT
1 TTTTGGACATTCGA-GGG-CAAAATGGTAATTTTTGGAAGTTTT-GGGTTAAAAATGGAAT
*
679 TTTTGGACATTCGAGGGCAAAATGGTAATTTTTGAAAGTTTTGGGATTAAAAATGGAAT
1 TTTTGGACATTCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGGG-TTAAAAATGGAAT
** * **
738 TTTTGG--GGTC-A----AAAATGG-AATTTTTAGAAGTTTTGGGGTCGAAAATGGAAT
1 TTTTGGACATTCGAGGGCAAAATGGTAATTTTTGGAAGTTTT-GGGTTAAAAATGGAAT
* * * * * * *
789 TTTTAGA-AGTTTTGAGGTCGAAAATGG-AATTTTTTGAAGTTTGGGGTTGAAAATGTAAT
1 TTTTGGACA--TTCGAGGGC-AAAATGGTAATTTTTGGAAGTTTTGGGTTAAAAATGGAAT
848 TTT
1 TTT
851 CGAACAGTTT
Statistics
Matches: 186, Mismatches: 27, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
51 30 0.16
52 10 0.05
54 1 0.01
55 1 0.01
56 1 0.01
57 2 0.01
58 10 0.05
59 83 0.45
60 41 0.22
61 7 0.04
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.37
Consensus pattern (58 bp):
TTTTGGACATTCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGGGTTAAAAATGGAAT
Found at i:762 original size:22 final size:21
Alignment explanation
Indices: 717--762 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
707 TTTTTGAAAG
*
717 TTTTGGGATTAAAAATGGAAT
1 TTTTGGGATCAAAAATGGAAT
*
738 TTTTGGGGTCAAAAATGGAAT
1 TTTTGGGATCAAAAATGGAAT
759 TTTT
1 TTTT
763 AGAAGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
TTTTGGGATCAAAAATGGAAT
Found at i:832 original size:110 final size:109
Alignment explanation
Indices: 633--850 Score: 264
Period size: 110 Copynumber: 2.0 Consensus size: 109
623 TAGACATTTA
* * *
633 GGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAAAGGAATTTTTGGACATTCGAGGGCA
1 GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAAAGGAATTTTTAGACATTCGAGGGCA
698 AAATGGTAATTTTTGAAAGTTTTGGGATTAAAAATGGAATTTTT
66 AAATGGTAATTTTTGAAAGTTTTGGGATTAAAAATGGAATTTTT
* * * *
742 GGGGTCAAAAATGGAATTTTTAGAAGTTTTGGGGTCGAAAATGGAATTTTTAGA-AGTTTTGAGG
1 GGGGT-AAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAAAGGAATTTTTAGACA--TTCGAGG
* * * *
806 TCGAAAATGG-AATTTTTTG-AAG-TTTGGGGTTGAAAATGTAATTTT
63 GC-AAAATGGTAA-TTTTTGAAAGTTTTGGGATTAAAAATGGAATTTT
851 CGAACAGTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
109 6 0.06
110 62 0.67
111 12 0.13
112 13 0.14
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (109 bp):
GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAAAGGAATTTTTAGACATTCGAGGGCA
AAATGGTAATTTTTGAAAGTTTTGGGATTAAAAATGGAATTTTT
Found at i:860 original size:60 final size:60
Alignment explanation
Indices: 738--850 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
728 AAAATGGAAT
* *
738 TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTTGGGGTCGAAAATGGAATTTTTAGAAG
1 TTTTGAGGTCAAAAATGGAATTTTTAGAAGTTTTGGGGTCGAAAATGGAATTTTGAGAAG
* * * *
798 TTTTGAGGTCGAAAATGGAATTTTTTGAAG-TTTGGGGTTGAAAATGTAATTTT
1 TTTTGAGGTCAAAAATGGAATTTTTAGAAGTTTTGGGGTCGAAAATGGAATTTT
851 CGAACAGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 21 0.44
60 27 0.56
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.40
Consensus pattern (60 bp):
TTTTGAGGTCAAAAATGGAATTTTTAGAAGTTTTGGGGTCGAAAATGGAATTTTGAGAAG
Done.