Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006666.1 Kokia drynarioides strain JFW-HI SEQ_121258, 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: 10095
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2417 original size:29 final size:29
Alignment explanation
Indices: 2339--2418 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
2329 TTTTTAGAGG
*
2339 TTCGAGGGTAAAATAA-TAATTTTGGACAC
1 TTCGAGGG-AAAAAAAGTAATTTTGGACAC
** ** *
2368 TTTAAGGGAAAAATGGAAATTTTGGACAC
1 TTCGAGGGAAAAAAAGTAATTTTGGACAC
2397 -TCGAGGGCAAAAAAAGTAATTT
1 TTCGAGGG-AAAAAAAGTAATTT
2419 CTAGAAGCTT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
28 9 0.24
29 29 0.76
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.28
Consensus pattern (29 bp):
TTCGAGGGAAAAAAAGTAATTTTGGACAC
Found at i:2470 original size:30 final size:30
Alignment explanation
Indices: 2431--2595 Score: 142
Period size: 30 Copynumber: 5.6 Consensus size: 30
2421 AGAAGCTTGG
2431 GGGTAAAATGGTAATTTTTAGAAAATTCAA
1 GGGTAAAATGGTAATTTTTAGAAAATTCAA
* * * * * **
2461 TGTTAAAATGAT-A-TTTTCGAAAGTTCGG
1 GGGTAAAATGGTAATTTTTAGAAAATTCAA
* **
2489 GGGTAAAATGGTAATTTTTAGAAAGTTCGG
1 GGGTAAAATGGTAATTTTTAGAAAATTCAA
*
2519 GGGTTAATAATGG-AATTTTT-GGAAATTCAA
1 GGG-TAA-AATGGTAATTTTTAGAAAATTCAA
* * *
2549 GGGTAAAATGGT-ATTTTTTGGACATTCAA
1 GGGTAAAATGGTAATTTTTAGAAAATTCAA
*
2578 GGGTAACATGGTAATTTT
1 GGGTAAAATGGTAATTTT
2596 CAAAAAGTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
28 31 0.28
29 25 0.23
30 40 0.36
31 10 0.09
32 5 0.05
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTAGAAAATTCAA
Found at i:2505 original size:29 final size:29
Alignment explanation
Indices: 2412--2710 Score: 129
Period size: 29 Copynumber: 10.3 Consensus size: 29
2402 GGCAAAAAAA
2412 GTAATTTCTAG-AAGCTT-GGGGGTAAAATG
1 GTAATTT-TAGAAAG-TTCGGGGGTAAAATG
* *** *
2441 GTAATTTTTAGAAAATTCAATGTTAAAATG
1 GTAA-TTTTAGAAAGTTCGGGGGTAAAATG
* *
2471 AT-ATTTTCGAAAGTTCGGGGGTAAAATG
1 GTAATTTTAGAAAGTTCGGGGGTAAAATG
2499 GTAATTTTTAGAAAGTTCGGGGGTTAATAATG
1 GTAA-TTTTAGAAAGTTCGGGGG-TAA-AATG
* **
2531 G-AATTTTTGGAAA-TTCAAGGGTAAAATG
1 GTAA-TTTTAGAAAGTTCGGGGGTAAAATG
* * * ** *
2559 GTATTTTTTGGACA-TTCAAGGGTAACATG
1 GTA-ATTTTAGAAAGTTCGGGGGTAAAATG
* **
2588 GTAATTTTCAAAAAGTT-TAGGGTCAAGAATG
1 GTAATTTT-AGAAAGTTCGGGGGT-AA-AATG
* *
2619 AT-A-TTTATGGAAGTTCGGGGGTAAAATG
1 GTAATTTTA-GAAAGTTCGGGGGTAAAATG
* * * *
2647 GTAATTTTTGGAAGTTTGGGGGCAAAAATG
1 GTAATTTTAGAAAGTTCGGGGG-TAAAATG
* **
2677 TGT-TTTTTAG-AAGTT-AAGGGTAAAAT-
1 -GTAATTTTAGAAAGTTCGGGGGTAAAATG
2703 GTAATTTT
1 GTAATTTT
2711 TGGAATTTTG
Statistics
Matches: 209, Mismatches: 41, Indels: 43
0.71 0.14 0.15
Matches are distributed among these distances:
25 2 0.01
26 4 0.02
27 5 0.02
28 38 0.18
29 75 0.36
30 60 0.29
31 20 0.10
32 5 0.02
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
GTAATTTTAGAAAGTTCGGGGGTAAAATG
Found at i:2630 original size:88 final size:89
Alignment explanation
Indices: 2489--2658 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 89
2479 GAAAGTTCGG
* * * * * *
2489 GGGTAAAATGGTAATTTTTAGAAAGTTCGGGGGTTAATAATGGAATTTTTGGAAATTCAAGGGTA
1 GGGTAAAATGGTAATTTTCAAAAAGTTCGAGGGTCAAGAATGGAATTTATGGAAATTCAAGGGTA
*
2554 AAATGGTATTTTTTGGACATTCAA
66 AAATGGTAATTTTTGGACATTCAA
* * * **
2578 GGGTAACATGGTAATTTTCAAAAAGTT-TAGGGTCAAGAAT-GATATTTATGGAAGTTCGGGGGT
1 GGGTAAAATGGTAATTTTCAAAAAGTTCGAGGGTCAAGAATGGA-ATTTATGGAAATTCAAGGGT
2641 AAAATGGTAATTTTTGGA
65 AAAATGGTAATTTTTGGA
2659 AGTTTGGGGG
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
87 2 0.03
88 42 0.62
89 24 0.35
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (89 bp):
GGGTAAAATGGTAATTTTCAAAAAGTTCGAGGGTCAAGAATGGAATTTATGGAAATTCAAGGGTA
AAATGGTAATTTTTGGACATTCAA
Found at i:2747 original size:57 final size:56
Alignment explanation
Indices: 2637--2776 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 56
2627 GGAAGTTCGG
* * *
2637 GGGTAAAATGGTAATTTTTGGAAGTTTGGGGGCAAAAATGTGTTTTTTAGAAGTTAA
1 GGGTAAAAT-GTAATTTTTGGAAGTTTGAGGGCAAAAATATATTTTTTAGAAGTTAA
* **
2694 GGGTAAAATGTAATTTTTGGAATTTTGAGGGCAAAAATATAATTTTTGT-GAAGTTGG
1 GGGTAAAATGTAATTTTTGGAAGTTTGAGGGCAAAAATAT-ATTTTT-TAGAAGTTAA
* *
2751 GGGCAAAATGTAATATTTGTGAAGTT
1 GGGTAAAATGTAATTTTTG-GAAGTT
2777 AGGGGTTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
56 28 0.39
57 37 0.52
58 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (56 bp):
GGGTAAAATGTAATTTTTGGAAGTTTGAGGGCAAAAATATATTTTTTAGAAGTTAA
Found at i:2781 original size:28 final size:28
Alignment explanation
Indices: 2636--2781 Score: 120
Period size: 28 Copynumber: 5.1 Consensus size: 28
2626 TGGAAGTTCG
* *
2636 GGGGTAAAATGGTAATTTTTG-GAAGTTTG
1 GGGGCAAAAT-GTAATTTTTGTGAAG-TTA
*
2665 GGGGCAAAAATGT-GTTTTT-TAGAAGTTA
1 GGGGC-AAAATGTAATTTTTGT-GAAGTTA
* * * *
2693 AGGGTAAAATGTAATTTTTG-GAATTTT
1 GGGGCAAAATGTAATTTTTGTGAAGTTA
* *
2720 GAGGGCAAAAATATAATTTTTGTGAAGTTG
1 G-GGGC-AAAATGTAATTTTTGTGAAGTTA
*
2750 GGGGCAAAATGTAATATTTGTGAAGTTA
1 GGGGCAAAATGTAATTTTTGTGAAGTTA
2778 GGGG
1 GGGG
2782 TTAAAATATG
Statistics
Matches: 93, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
27 12 0.13
28 42 0.45
29 28 0.30
30 11 0.12
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
GGGGCAAAATGTAATTTTTGTGAAGTTA
Found at i:2781 original size:29 final size:29
Alignment explanation
Indices: 2628--2781 Score: 131
Period size: 29 Copynumber: 5.4 Consensus size: 29
2618 GATATTTATG
* *
2628 GAAGTTCGGGGGTAAAATGGTAATTTTTG-
1 GAAGTTAGGGGGCAAAAT-GTAATTTTTGT
* *
2657 GAAGTTTGGGGGCAAAAATGT-GTTTTT-T
1 GAAGTTAGGGGGC-AAAATGTAATTTTTGT
* *
2685 AGAAGTTA-AGGGTAAAATGTAATTTTTG-
1 -GAAGTTAGGGGGCAAAATGTAATTTTTGT
* * * *
2713 GAATTTTGAGGGCAAAAATATAATTTTTGT
1 GAAGTTAGGGGGC-AAAATGTAATTTTTGT
*
2743 GAAGTT-GGGGGCAAAATGTAATATTTGT
1 GAAGTTAGGGGGCAAAATGTAATTTTTGT
2771 GAAGTTAGGGG
1 GAAGTTAGGGG
2782 TTAAAATATG
Statistics
Matches: 101, Mismatches: 15, Indels: 18
0.75 0.11 0.13
Matches are distributed among these distances:
27 12 0.12
28 37 0.37
29 42 0.42
30 10 0.10
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
GAAGTTAGGGGGCAAAATGTAATTTTTGT
Found at i:2797 original size:28 final size:27
Alignment explanation
Indices: 2722--2797 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
2712 GGAATTTTGA
2722 GGGCAAAAATATAATTTTTGTGAAGTTGG
1 GGGC-AAAATATAA-TTTTGTGAAGTTGG
*
2751 GGGCAAAATGTAATATTTGTGAAGTTAGG
1 GGGCAAAATATAAT-TTTGTGAAGTT-GG
** *
2780 GGTTAAAATATGATTTTG
1 GGGCAAAATATAATTTTG
2798 GAAAAGTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 23 0.57
29 16 0.40
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (27 bp):
GGGCAAAATATAATTTTGTGAAGTTGG
Found at i:9147 original size:25 final size:23
Alignment explanation
Indices: 9119--9164 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
9109 GTTGGATCCA
9119 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
9144 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
9165 CCGTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Done.