Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005489.1 Kokia drynarioides strain JFW-HI SEQ_119550, 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, 876
Length: 1461
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Found at i:584 original size:59 final size:59
Alignment explanation
Indices: 521--683 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 59
511 GCTTTAGGAA
* * *
521 TAAAATGGTAATTTTTGGAAGGTTCGAGGTTTAAAAA-GGAATTTTTAGATATTCGGGGG
1 TAAAATGGTAATTTTTGGAAGGTTCG-GGATAAAAAATGGAATTTTTAGACATTCGGGGG
* * *
580 TAAAATGGAAATTTTTGGAAGGCTCGGGATAAAAAATGGTATTTTTAGACATTCGGGGG
1 TAAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAATTTTTAGACATTCGGGGG
* * *
639 TAAAATTGTAATTTTT-GAAAGTTCGTGGA-AAAAAATGTAATTTTT
1 TAAAATGGTAATTTTTGGAAGGTTCG-GGATAAAAAATGGAATTTTT
684 GGAAAATTTG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 29 0.32
59 61 0.68
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (59 bp):
TAAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAATTTTTAGACATTCGGGGG
Found at i:612 original size:29 final size:28
Alignment explanation
Indices: 520--687 Score: 76
Period size: 29 Copynumber: 5.7 Consensus size: 28
510 TGCTTTAGGA
520 ATAAAATGGTAATTTTTGGAAGGTTCGAGG
1 ATAAAATGG-AATTTTTGGAAGGTTCG-GG
* * *
550 TTTAAAAAGGAATTTTTAGATA--TTCGGGG
1 -ATAAAATGGAATTTTTGGA-AGGTTC-GGG
* *
579 GTAAAATGGAAATTTTTGGAAGGCTCGGG
1 ATAAAATGG-AATTTTTGGAAGGTTCGGG
* *
608 ATAAAAAATGGTATTTTTAGACA--TTCGGGG
1 AT--AAAATGGAATTTTTGGA-AGGTTC-GGG
* * *
638 GTAAAATTGTAATTTTT-GAAAGTTCGTGG
1 ATAAAA-TGGAATTTTTGGAAGGTTCG-GG
* *
667 AAAAAAATGTAATTTTTGGAA
1 -ATAAAATGGAATTTTTGGAA
688 AATTTGGGGT
Statistics
Matches: 106, Mismatches: 16, Indels: 31
0.69 0.10 0.20
Matches are distributed among these distances:
27 1 0.01
28 15 0.14
29 43 0.41
30 31 0.29
31 16 0.15
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
ATAAAATGGAATTTTTGGAAGGTTCGGG
Found at i:711 original size:30 final size:30
Alignment explanation
Indices: 669--934 Score: 132
Period size: 29 Copynumber: 9.1 Consensus size: 30
659 GTTCGTGGAA
*
669 AAAAATGTAATTTTTGGAAAATTTGGGGTC
1 AAAAATGAAATTTTTGGAAAATTTGGGGTC
699 AAAAATGAAA-TTTT-GAAAAGTTTGGTGG-C
1 AAAAATGAAATTTTTGGAAAA-TTTGG-GGTC
* * * * * *
728 AAAAATG-TATTTTTTGAAAACTCGAGGTT
1 AAAAATGAAATTTTTGGAAAATTTGGGGTC
* * * *
757 AAAAATGAGA-TTTTAGAAAGTTCGAGGG-C
1 AAAAATGAAATTTTTGGAAAATTTG-GGGTC
* ** *
786 AAAAATGTAATTTTTGGAAAATTCAGTGTC
1 AAAAATGAAATTTTTGGAAAATTTGGGGTC
* * *
816 AAAAATGGAA-TTTTGGAAATTTTTGGTGT-
1 AAAAATGAAATTTTTGGAAA-ATTTGGGGTC
* *
845 -AAAATGTAATTTTTGGAAAATTTGAGGT-
1 AAAAATGAAATTTTTGGAAAATTTGGGGTC
* *
873 TAAAATGGAA-TTTT-G-AAATGTTCAGGGGT-
1 AAAAATGAAATTTTTGGAAAAT-TT--GGGGTC
*
902 AAAAAT-ATAATTTTTGGAGAATTAT-GGGTC
1 AAAAATGA-AATTTTTGGAAAATT-TGGGGTC
932 AAA
1 AAA
935 CTAACAATTT
Statistics
Matches: 184, Mismatches: 31, Indels: 42
0.72 0.12 0.16
Matches are distributed among these distances:
26 4 0.02
27 3 0.02
28 26 0.14
29 92 0.50
30 53 0.29
31 2 0.01
32 4 0.02
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAAATGAAATTTTTGGAAAATTTGGGGTC
Found at i:713 original size:58 final size:58
Alignment explanation
Indices: 651--934 Score: 240
Period size: 58 Copynumber: 4.9 Consensus size: 58
641 AAATTGTAAT
**
651 TTTTGAAAGTTCGTGGAAAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
1 TTTTGAAAGTTCGTGGGCAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
* * * * * * *
709 TTTTGAAAAGTTTG-GTGGCAAAAATGT-ATTTTTTGAAAACTCGAGGTTAAAAATGAGA
1 TTTTG-AAAGTTCGTG-GGCAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
* ** * *
767 TTTTAGAAAGTTCGAGGGCAAAAATGTAATTTTTGGAAAATTCAGTGTCAAAAATGGAA
1 TTTT-GAAAGTTCGTGGGCAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
** * * * *
826 TTTTGGAAA-TTTTTGGTG-TAAAATGTAATTTTTGGAAAATTTGAGGT-TAAAATGGAA
1 TTTT-GAAAGTTCGTGG-GCAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
* * *
883 TTTTGAAATGTTCAG-GGGTAAAAATATAATTTTTGGAGAATTAT-GGGTCAAA
1 TTTTGAAA-GTTC-GTGGGCAAAAATGTAATTTTTGGAAAATT-TGGGGTCAAA
935 CTAACAATTT
Statistics
Matches: 179, Mismatches: 35, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
56 4 0.02
57 14 0.08
58 108 0.60
59 53 0.30
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (58 bp):
TTTTGAAAGTTCGTGGGCAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAA
Found at i:742 original size:117 final size:117
Alignment explanation
Indices: 611--830 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 117
601 GCTCGGGATA
* * * * * *
611 AAAAATGGTATTTTT-AGACATTCGGGGGTAAAATTGTA-ATTTTTGAAAGTTCGTGGAAAAAAA
1 AAAAATGGTATTTTTGA-AAACTCGAGGGTAAAAATG-AGATTTTAGAAAGTTCGAGGAAAAAAA
**
674 TGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAATTTTGAAAAGTTTGGTGGC
64 TGTAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTTGAAAAGTTTGGTGGC
* **
728 AAAAAT-GTATTTTTTGAAAACTCGAGGTTAAAAATGAGATTTTAGAAAGTTCGAGGGCAAAAAT
1 AAAAATGGTA-TTTTTGAAAACTCGAGGGTAAAAATGAGATTTTAGAAAGTTCGAGGAAAAAAAT
* *
792 GTAATTTTTGGAAAATTCAGTGTCAAAAATGGAATTTTG
65 GTAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTTG
831 GAAATTTTTG
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 4 0.05
117 82 0.94
118 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (117 bp):
AAAAATGGTATTTTTGAAAACTCGAGGGTAAAAATGAGATTTTAGAAAGTTCGAGGAAAAAAATG
TAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTTGAAAAGTTTGGTGGC
Found at i:857 original size:117 final size:115
Alignment explanation
Indices: 651--934 Score: 317
Period size: 117 Copynumber: 2.4 Consensus size: 115
641 AAATTGTAAT
* * **
651 TTTTGAAAGTTCGTGGAAAAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAATGAAATTTTGAA
1 TTTTGAAAGTTCGAGGGAAAAAATGTAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTTGAA
*
716 AAGTTTGGTGGCAAAAATGTATTTTTTGAAAACTCGAGGTTAAAAAT-GAGA
66 AAGTTTGGTGGCAAAAATGTATTTTTGGAAAACTCGAGGTT-AAAATGGA-A
* * *
767 TTTTAGAAAGTTCGAGGGCAAAAATGTAATTTTTGGAAAATTCAGTGTCAAAAATGGAATTTTGG
1 TTTT-GAAAGTTCGAGGGAAAAAATGTAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTT-G
** * * *
832 AAATTTTTGGT-G-TAAAATGTAATTTTTGGAAAATTTGAGGTTAAAATGGAA
64 AAAAGTTTGGTGGCAAAAATGT-ATTTTTGGAAAACTCGAGGTTAAAATGGAA
* * *
883 TTTTGAAATGTTC-AGGGGTAAAAATATAATTTTTGGAGAATT-ATGGGTCAAA
1 TTTTGAAA-GTTCGA-GGGAAAAAATGTAATTTTTGGAAAATTCA-GGGTCAAA
935 CTAACAATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
115 6 0.04
116 56 0.39
117 72 0.50
118 10 0.07
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (115 bp):
TTTTGAAAGTTCGAGGGAAAAAATGTAATTTTTGGAAAATTCAGGGTCAAAAATGAAATTTTGAA
AAGTTTGGTGGCAAAAATGTATTTTTGGAAAACTCGAGGTTAAAATGGAA
Found at i:904 original size:28 final size:28
Alignment explanation
Indices: 817--905 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
807 TTCAGTGTCA
** *
817 AAAATGGAATTTTGGAAATTTTTGGTGT
1 AAAATGGAATTTTGGAAATTTCAGGGGT
* * *
845 AAAATGTAATTTTTGGAAAATTTGA-GGTT
1 AAAATGGAA-TTTTGG-AAATTTCAGGGGT
874 AAAATGGAATTTT-GAAATGTTCAGGGGT
1 AAAATGGAATTTTGGAAAT-TTCAGGGGT
902 AAAA
1 AAAA
906 ATATAATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
26 4 0.08
27 4 0.08
28 19 0.39
29 16 0.33
30 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAATTTCAGGGGT
Done.