Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010171.1 Kokia drynarioides strain JFW-HI SEQ_124976, 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: 5570
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2772 original size:28 final size:28
Alignment explanation
Indices: 2741--2808 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 28
2731 TGGAAATTTA
* * *
2741 AGGGCAAAATCATAATTTTTGGATGTTC
1 AGGGCAAAATCATAATTTTGGGAAGATC
* **
2769 AGGGGTAAAATGGTAATTTTGGGAAGATC
1 A-GGGCAAAATCATAATTTTGGGAAGATC
2798 AGGGTCAAAAT
1 AGGG-CAAAAT
2809 GTGTTTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.29
Consensus pattern (28 bp):
AGGGCAAAATCATAATTTTGGGAAGATC
Found at i:2778 original size:29 final size:29
Alignment explanation
Indices: 2753--3006 Score: 118
Period size: 29 Copynumber: 8.7 Consensus size: 29
2743 GGCAAAATCA
*
2753 TAATTTTTGGATGTTCAGGGGTAAAATGG
1 TAATTTTTGGAAGTTCAGGGGTAAAATGG
* *
2782 TAATTTTGGGAAGATCA-GGGTCAAAATGTG
1 TAATTTTTGGAAGTTCAGGGGT-AAAATG-G
*
2812 T--TTTTTGGAAGTTTTAGGGGTAAAATGG
1 TAATTTTTGGAAG-TTCAGGGGTAAAATGG
* * * * *
2840 TAATTTTTGGATGTTAAAGGGCAAAACGG
1 TAATTTTTGGAAGTTCAGGGGTAAAATGG
2869 TAA-TTTTGGAAAAG-TCTA-GGGTCAAAAAT-G
1 TAATTTTTGG--AAGTTC-AGGGGT--AAAATGG
*
2899 TAATTTTTGAGAAGTT-TGGGGTAAAAAT-G
1 TAATTTTTG-GAAGTTCAGGGGT-AAAATGG
** * * *
2928 TGCTTTTTGAAAGTT-TGGGGCCAAAAAT-G
1 TAATTTTTGGAAGTTCAGGGG--TAAAATGG
* **
2957 TATTTTTTGGAAGTTCAAGGGAAAAAAT-G
1 TAATTTTTGGAAGTTC-AGGGGTAAAATGG
* *
2986 TGATTTTTGGTAAATTCAGGG
1 TAATTTTTGG-AAGTTCAGGG
3007 ACCTTCTAGG
Statistics
Matches: 177, Mismatches: 28, Indels: 40
0.72 0.11 0.16
Matches are distributed among these distances:
28 31 0.18
29 98 0.55
30 34 0.19
31 13 0.07
32 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
TAATTTTTGGAAGTTCAGGGGTAAAATGG
Found at i:2837 original size:87 final size:88
Alignment explanation
Indices: 2721--2924 Score: 236
Period size: 87 Copynumber: 2.3 Consensus size: 88
2711 AAGTTAGAAG
* * * * * * *
2721 TGTGATTTTTTGGAAATTTAAGGGCAAAATCATAATTTTTGGATGTTCAGGGGTAAAATGGTAAT
1 TGTG-TTTTTTGGAAGTTTAGGGGTAAAATCATAATTTTTGGATGTTAAAGGGCAAAACGGTAAT
*
2786 TTTGG-GAAGATC-AGGGTC-AAAA
65 TTTGGAAAAG-TCTAGGGTCAAAAA
**
2808 TGTGTTTTTTGGAAGTTTTAGGGGTAAAATGGTAATTTTTGGATGTTAAAGGGCAAAACGGTAAT
1 TGTGTTTTTTGGAAG-TTTAGGGGTAAAATCATAATTTTTGGATGTTAAAGGGCAAAACGGTAAT
2873 TTTGGAAAAGTCTAGGGTCAAAAA
65 TTTGGAAAAGTCTAGGGTCAAAAA
**
2897 TGTAATTTTTGAGAAGTTT-GGGGTAAAA
1 TGTGTTTTTTG-GAAGTTTAGGGGTAAAA
2925 ATGTGCTTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
86 10 0.10
87 52 0.52
88 18 0.18
89 16 0.16
90 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (88 bp):
TGTGTTTTTTGGAAGTTTAGGGGTAAAATCATAATTTTTGGATGTTAAAGGGCAAAACGGTAATT
TTGGAAAAGTCTAGGGTCAAAAA
Found at i:2876 original size:58 final size:58
Alignment explanation
Indices: 2769--2879 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
2759 TTGGATGTTC
* * *
2769 AGGGGTAAAATGGTAATTTTGGGAAGATCAGGGTCAAAATGTGTTTTTTGGAAGTTTT
1 AGGGGTAAAATGGTAATTTTGGGAAGATAAGGGTCAAAACGTGTATTTTGGAAGTTTT
* * *
2827 AGGGGTAAAATGGTAATTTTTGGATGTTAAAGGG-CAAAACG-GTAATTTTGGAA
1 AGGGGTAAAATGGTAATTTTGGGAAGAT-AAGGGTCAAAACGTGT-ATTTTGGAA
2880 AAGTCTAGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.04
58 39 0.87
59 4 0.09
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
AGGGGTAAAATGGTAATTTTGGGAAGATAAGGGTCAAAACGTGTATTTTGGAAGTTTT
Found at i:5275 original size:59 final size:59
Alignment explanation
Indices: 5200--5535 Score: 355
Period size: 58 Copynumber: 5.8 Consensus size: 59
5190 TTGGATCAAT
* *
5200 AATTTTTGGACGTTCGGGGGTAAAATAGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * *
5259 AATTTTTGGACATTCGGGGATAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * * * * *
5318 GA-TTTTGGAAATTTGGGGGTAAAATGGTAATTTTAGGAAAATTCGAGATCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * *
5376 ATTTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGG-AAGTT-TAGGGTCAAAAATGA
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGA-GGTCAAAAATGG
* * * * * * * *
5434 AATTTTGGGACATCCGTGGATAAAATGATAATTTTGGGAAAATTC-AGAGTTAAAAAT-T
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAG-GTCAAAAATGG
* * *
5492 AGA-TTTTGGA-AATCTGAGGGTAAAATGGTAATTTTGTG-AAGTTC
1 A-ATTTTTGGACATTC-GGGGGTAAAATGGTAATTTTGGGAAAGTTC
5536 AGGGGCGATA
Statistics
Matches: 230, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
57 8 0.03
58 121 0.53
59 101 0.44
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
Found at i:5409 original size:117 final size:116
Alignment explanation
Indices: 5214--5539 Score: 390
Period size: 117 Copynumber: 2.8 Consensus size: 116
5204 TTTGGACGTT
* * * *
5214 CGGGGGTAAAATAGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGACATTCGGGGA
1 CGGGGGTAAAATGGTAATTTTGGGAAAATTCGAGATCAAAAATGG-ATTTTTGGACATTCGGGGG
* ** *
5279 TAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGGGATTTT-GGAAATT
65 TAAAATGGTAATTTTGGG-AAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
* *
5331 TGGGGGTAAAATGGTAATTTTAGGAAAATTCGAGATCAAAAATGGATTTTTTGGACATTCGGGGG
1 CGGGGGTAAAATGGTAATTTTGGGAAAATTCGAGATCAAAAATGGA-TTTTTGGACATTCGGGGG
*
5396 TAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGACATC
65 TAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
* * * * * * *
5448 CGTGGATAAAATGATAATTTTGGGAAAATTC-AGAGTTAAAAATTAGA-TTTTGGA-AATCTGAG
1 CGGGGGTAAAATGGTAATTTTGGGAAAATTCGAGA-TCAAAAA-TGGATTTTTGGACATTC-GGG
* *
5510 GGTAAAATGGTAATTTTGTGAAGTTCAGGG
63 GGTAAAATGGTAATTTTGGGAAGTTTAGGG
5540 GCGATAATGT
Statistics
Matches: 182, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
115 3 0.02
116 64 0.35
117 112 0.62
118 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (116 bp):
CGGGGGTAAAATGGTAATTTTGGGAAAATTCGAGATCAAAAATGGATTTTTGGACATTCGGGGGT
AAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
Done.