Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007744.1 Kokia drynarioides strain JFW-HI SEQ_122377, 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: 2953
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Found at i:2390 original size:29 final size:29
Alignment explanation
Indices: 2305--2633 Score: 154
Period size: 30 Copynumber: 11.3 Consensus size: 29
2295 ACACTCGTGG
** *
2305 GGTAATTTTGGGAAAGTTCGAGGTAAAAAAC
1 GGTAATTTTTAGAAAGTTCG-GGT-AAAAAT
* * *
2336 GG-ATTTTTTAGACA-TCCGAGGT-AAAAT
1 GGTAATTTTTAGAAAGTTCG-GGTAAAAAT
*
2363 GGTAATTTTTTGAAAGTTCGGGTCAAAAAT
1 GGTAATTTTTAGAAAGTTCGGGT-AAAAAT
* *
2393 GG-AA-TTTTAGGAAGTTTGAGGGT-AAAAT
1 GGTAATTTTTAGAAAG-TT-CGGGTAAAAAT
* *
2421 GGTAATTTTTGGAAAAATT-GAGGTAAAAAT
1 GGTAATTTTTAG-AAAGTTCG-GGTAAAAAT
* *
2451 GG-AA-TTTT-GGAAGTTCGAGGT-AAAAC
1 GGTAATTTTTAGAAAGTTCG-GGTAAAAAT
* * *
2477 GGTAATTTTTGGAAAAATTAGGGTTAAAAAT
1 GGTAATTTTTAG-AAAGTTCGGG-TAAAAAT
* *
2508 GG-AATTTTT-GGAAGTTCAAGGT-AAAAT
1 GGTAATTTTTAGAAAGTTC-GGGTAAAAAT
* **
2535 GGTAATTTTTAAAAAAATCGAGGTTAAAAAT
1 GGTAATTTTTAGAAAGTTCG-GG-TAAAAAT
*
2566 GG-AA-TTTTGGAAAGTTCGAGGGTAAAAAT
1 GGTAATTTTTAGAAAGTTC--GGGTAAAAAT
*
2595 -GTAATTTTTAGAAAGTTTAGGGTCAAAAAAT
1 GGTAATTTTTAGAAAG-TTCGGGT--AAAAAT
2626 GG-AATTTT
1 GGTAATTTT
2634 GGAAAAGTTT
Statistics
Matches: 228, Mismatches: 38, Indels: 64
0.69 0.12 0.19
Matches are distributed among these distances:
26 10 0.04
27 21 0.09
28 49 0.21
29 55 0.24
30 60 0.26
31 32 0.14
32 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
GGTAATTTTTAGAAAGTTCGGGTAAAAAT
Found at i:2392 original size:30 final size:28
Alignment explanation
Indices: 2316--2633 Score: 154
Period size: 29 Copynumber: 10.9 Consensus size: 28
2306 GTAATTTTGG
* *
2316 GAAAGTTCGAGGTAAAAAACGGATTTTTTA
1 GAAAGTTCG-GGT-AAAAATGGAATTTTTA
* * *
2346 GACA-TCCGAGGT-AAAATGGTAATTTTTT
1 GAAAGTTCG-GGTAAAAATGG-AATTTTTA
2374 GAAAGTTCGGGTCAAAAATGGAA-TTTTA
1 GAAAGTTCGGGT-AAAAATGGAATTTTTA
* * *
2402 GGAAGTTTGAGGGT-AAAATGGTAATTTTTG
1 GAAAG-TT-CGGGTAAAAATGG-AATTTTTA
*
2432 GAAAAATT-GAGGTAAAAATGGAA-TTTT-
1 G-AAAGTTCG-GGTAAAAATGGAATTTTTA
* * *
2459 GGAAGTTCGAGGT-AAAACGGTAATTTTTG
1 GAAAGTTCG-GGTAAAAATGG-AATTTTTA
* *
2488 GAAAAATTAGGGTTAAAAATGGAATTTTT-
1 G-AAAGTTCGGG-TAAAAATGGAATTTTTA
* *
2517 GGAAGTTCAAGGT-AAAATGGTAATTTTTA
1 GAAAGTTC-GGGTAAAAATGG-AATTTTTA
* ** *
2546 AAAAAATCGAGGTTAAAAATGGAA-TTTTG
1 GAAAGTTCG-GG-TAAAAATGGAATTTTTA
*
2575 GAAAGTTCGAGGGTAAAAATGTAATTTTTA
1 GAAAGTTC--GGGTAAAAATGGAATTTTTA
*
2605 GAAAGTTTAGGGTCAAAAAATGGAATTTT
1 GAAAG-TTCGGGT--AAAAATGGAATTTT
2634 GGAAAAGTTT
Statistics
Matches: 221, Mismatches: 37, Indels: 59
0.70 0.12 0.19
Matches are distributed among these distances:
26 10 0.05
27 21 0.10
28 48 0.22
29 56 0.25
30 55 0.25
31 31 0.14
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (28 bp):
GAAAGTTCGGGTAAAAATGGAATTTTTA
Found at i:2400 original size:58 final size:57
Alignment explanation
Indices: 2305--2637 Score: 320
Period size: 58 Copynumber: 5.8 Consensus size: 57
2295 ACACTCGTGG
* * * * * * *
2305 GGTAATTTTGGGAAAGTTCGAGGTAAAAAACGGATTTTTTAGACA-TCCGAGGTAAAAT
1 GGTAATTTTTGGAAAATTCGAGGTCAAAAATGGA-ATTTTGGA-AGTTCGAGGTAAAAT
* * *
2363 GGTAATTTTTTGAAAGTTCG-GGTCAAAAATGGAATTTTAGGAAGTTTGAGGGTAAAAT
1 GGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTT-GGAAGTTCGA-GGTAAAAT
*
2421 GGTAATTTTTGGAAAAATT-GAGGT-AAAAATGGAATTTTGGAAGTTCGAGGTAAAAC
1 GGTAATTTTTGG-AAAATTCGAGGTCAAAAATGGAATTTTGGAAGTTCGAGGTAAAAT
* * *
2477 GGTAATTTTTGGAAAAATTAG-GGTTAAAAATGGAATTTTTGGAAGTTCAAGGTAAAAT
1 GGTAATTTTTGG-AAAATTCGAGGTCAAAAATGGAA-TTTTGGAAGTTCGAGGTAAAAT
** * *
2535 GGTAATTTTTAAAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAAT
1 GGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGG-AAGTTCGA-GGT-AAAAT
* * *
2595 -GTAATTTTTAGAAAGTT-TAGGGTCAAAAAATGGAATTTTGGAA
1 GGTAATTTTTGGAAAATTCGA-GGTC-AAAAATGGAATTTTGGAA
2638 AAGTTTAGGG
Statistics
Matches: 237, Mismatches: 24, Indels: 27
0.82 0.08 0.09
Matches are distributed among these distances:
56 34 0.14
57 48 0.20
58 104 0.44
59 30 0.13
60 21 0.09
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (57 bp):
GGTAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAGTTCGAGGTAAAAT
Found at i:2632 original size:31 final size:28
Alignment explanation
Indices: 2358--2647 Score: 157
Period size: 30 Copynumber: 9.9 Consensus size: 28
2348 CATCCGAGGT
* *
2358 AAAATGGTAATTTTTTGAAAG-TTCGGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTTAGGGT-A
2388 AAAATGGAATTTTAGG-AAGTTTGAGGGT-
1 AAAATGGAATTTT-GGAAAGTTT-AGGGTA
**
2416 AAAATGGTAATTTTTGGAAAAATT-GAGGTA
1 AAAATGG-AA-TTTTGGAAAGTTTAG-GGTA
*
2446 AAAATGGAATTTTGG-AAG-TTCGAGGT-
1 AAAATGGAATTTTGGAAAGTTTAG-GGTA
* **
2472 AAAACGGTAATTTTTGGAAAAATTAGGGTTA
1 AAAATGG-AA-TTTTGGAAAGTTTAGGG-TA
* *
2503 AAAATGGAATTTTTGG-AAGTTCAAGGT-
1 AAAATGGAA-TTTTGGAAAGTTTAGGGTA
** * ** *
2530 AAAATGGTAATTTTTAAAAAAATCGAGGTTA
1 AAAATGG-AA-TTTT-GGAAAGTTTAGGGTA
*
2561 AAAATGGAATTTTGGAAAGTTCGAGGGTA
1 AAAATGGAATTTTGGAAAGTT-TAGGGTA
* *
2590 AAAATGTAATTTTTAGAAAGTTTAGGGTCAA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGT--A
2621 AAAATGGAATTTTGGAAAAGTTTAGGG
1 AAAATGGAATTTTGG-AAAGTTTAGGG
2648 GTCATAATAT
Statistics
Matches: 206, Mismatches: 30, Indels: 47
0.73 0.11 0.17
Matches are distributed among these distances:
26 8 0.04
27 16 0.08
28 39 0.19
29 47 0.23
30 63 0.31
31 33 0.16
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTA
Found at i:2673 original size:30 final size:31
Alignment explanation
Indices: 2560--2676 Score: 100
Period size: 30 Copynumber: 3.8 Consensus size: 31
2550 AATCGAGGTT
* *
2560 AAAAATGGAATTTTGGAAAG-TTCGAGGGT--
1 AAAAATGGATTTTTGGAAAGTTTAG-GGGTCA
* *
2589 AAAAATGTAATTTTTAGAAAGTTTA-GGGTCA
1 AAAAATG-GATTTTTGGAAAGTTTAGGGGTCA
*
2620 AAAAATGGAATTTTGGAAAAGTTTAGGGGTCA
1 AAAAATGGATTTTTGG-AAAGTTTAGGGGTCA
* * *
2652 TAATAT-GATTTTTGGATAGTTTAGG
1 AAAAATGGATTTTTGGAAAGTTTAGG
2677 AACCTTCAGG
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
29 11 0.15
30 25 0.35
31 25 0.35
32 10 0.14
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (31 bp):
AAAAATGGATTTTTGGAAAGTTTAGGGGTCA
Found at i:2675 original size:61 final size:60
Alignment explanation
Indices: 2365--2676 Score: 172
Period size: 58 Copynumber: 5.3 Consensus size: 60
2355 GGTAAAATGG
* * * *
2365 TAATTTTTTGAAAG-TTCGGGTC-AAAAATGGAATTTTAGG-AAGTTTGAGGGT-AAAATGG
1 TAATTTTTAGAAAGTTTAGGGTCAAAAAATGGAATTTT-GGAAAGTTAGAGGGTAAAAAT-A
* ** * ***
2423 TAATTTTTGGAAAAATT-GAGGT--AAAAATGGAATTTTGG-AAGTTCGA-GGTAAAACGG
1 TAATTTTTAGAAAGTTTAG-GGTCAAAAAATGGAATTTTGGAAAGTTAGAGGGTAAAAATA
* ** * *
2479 TAATTTTTGGAAAAATTAGGGT-TAAAAATGGAATTTTTGG-AAGTTCA-A-GGT-AAAATGG
1 TAATTTTTAGAAAGTTTAGGGTCAAAAAATGGAA-TTTTGGAAAGTT-AGAGGGTAAAAAT-A
*** * * * *
2537 TAATTTTTA-AAAAAATCGAGGT-TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATG
1 TAATTTTTAGAAAGTTTAG-GGTCAAAAAATGGAATTTTGGAAAGTTAGAGGGTAAAAATA
* *
2596 TAATTTTTAGAAAGTTTAGGGTCAAAAAATGGAATTTTGGAAAAGTTTAG-GGGTCATAATA
1 TAATTTTTAGAAAGTTTAGGGTCAAAAAATGGAATTTTGG-AAAG-TTAGAGGGTAAAAATA
* * *
2657 TGATTTTTGGATAGTTTAGG
1 TAATTTTTAGAAAGTTTAGG
2677 AACCTTCAGG
Statistics
Matches: 213, Mismatches: 24, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
56 24 0.11
57 39 0.18
58 71 0.33
59 21 0.10
60 26 0.12
61 29 0.14
62 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (60 bp):
TAATTTTTAGAAAGTTTAGGGTCAAAAAATGGAATTTTGGAAAGTTAGAGGGTAAAAATA
Found at i:2754 original size:12 final size:11
Alignment explanation
Indices: 2729--2771 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2719 TAAATAAGCC
2729 AAATTAAAACA
1 AAATTAAAACA
2740 AAATTAAAGACA
1 AAATTAAA-ACA
*
2752 AAATTGAAACGA
1 AAATTAAAAC-A
2764 AAA-TAAAA
1 AAATTAAAA
2772 GGGGAAGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (11 bp):
AAATTAAAACA
Done.