Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003564.1 Kokia drynarioides strain JFW-HI SEQ_116427, 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: 28311
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:459 original size:28 final size:28
Alignment explanation
Indices: 427--489 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
417 GTAAAGGGAT
427 AATTTT-GAGAGTTTT-AGGGGTAAAATGG
1 AATTTTGGA-AGTTTTGA-GGGTAAAATGG
*
455 AATTTCTGGAAGTTTTGAGGTTAAAATGG
1 AATTT-TGGAAGTTTTGAGGGTAAAATGG
484 AATTTT
1 AATTTT
490 TGGGGTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 6 0.19
29 22 0.71
30 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.40
Consensus pattern (28 bp):
AATTTTGGAAGTTTTGAGGGTAAAATGG
Found at i:490 original size:20 final size:21
Alignment explanation
Indices: 461--511 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
451 ATGGAATTTC
*
461 TGGAAGTTTTGAGGTT-AAAA
1 TGGAATTTTTGAGGTTAAAAA
*
481 TGGAATTTTTGGGGTTAAAAA
1 TGGAATTTTTGAGGTTAAAAA
*
502 TGGGATTTTT
1 TGGAATTTTT
512 AGAAGTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (21 bp):
TGGAATTTTTGAGGTTAAAAA
Found at i:517 original size:50 final size:51
Alignment explanation
Indices: 448--543 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 51
438 TTTTAGGGGT
* *
448 AAAATGGAATTTCTGGAAGTTTTGAGGT-TAAAATGGAATTTTTGGGGTTA
1 AAAATGGAATTTCTAGAAGTTTTGAGGTCAAAAATGGAATTTTTGGGGTTA
* * *
498 AAAATGGGATTTTTAGAAGTTTTGAGGTCAAAAATGGGATTTTTGG
1 AAAATGGAATTTCTAGAAGTTTTGAGGTCAAAAATGGAATTTTTGG
544 AAGTTCGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 25 0.62
51 15 0.38
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (51 bp):
AAAATGGAATTTCTAGAAGTTTTGAGGTCAAAAATGGAATTTTTGGGGTTA
Found at i:553 original size:29 final size:30
Alignment explanation
Indices: 497--608 Score: 138
Period size: 30 Copynumber: 3.8 Consensus size: 30
487 TTTTGGGGTT
* * *
497 AAAAATGGGATTTTTAGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
527 AAAAATGGGATTTTTGGAAG-TTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* *
556 AAAAATGGAATTTTTGGTAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
586 AAAAATGGAATTTTTGGATGTTT
1 AAAAATGGAATTTTTGGAAGTTT
609 AGGATCTCCA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
29 25 0.35
30 47 0.65
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.37
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:1637 original size:3 final size:3
Alignment explanation
Indices: 1631--1678 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1621 TTTCTTTTTT
* * *
1631 TTA TTA TTA TTA ATG CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1679 ATTAATGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2428 original size:17 final size:17
Alignment explanation
Indices: 2403--2511 Score: 69
Period size: 17 Copynumber: 6.3 Consensus size: 17
2393 GGACTTTTAA
* **
2403 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
2420 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
* **
2437 TTAAATTTAAAAGGAAT
1 TTAAATTTTAAATAAAT
*
2454 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
2473 TTAAA-TTTAAATTTAAAA
1 TTAAATTTTAAA--TAAAT
* *
2491 ATAAA-TTTGAATAAAT
1 TTAAATTTTAAATAAAT
2507 TTAAA
1 TTAAA
2512 CCCAATAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
16 9 0.12
17 36 0.50
18 18 0.25
19 9 0.12
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:2432 original size:6 final size:6
Alignment explanation
Indices: 2418--2511 Score: 70
Period size: 6 Copynumber: 16.2 Consensus size: 6
2408 TTTTAAATCC
* ***
2418 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-AGGA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** ** *
2465 AGATAA ATTTAA ATTTAA ATTTAA AAATAA ATTTGA A--TAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
2511 A
1 A
2512 CCCAATAAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
4 3 0.05
5 6 0.09
6 52 0.80
7 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:14099 original size:3 final size:3
Alignment explanation
Indices: 14091--14118 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14081 CGTATTATGA
14091 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14119 CAAAGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17592 original size:2 final size:2
Alignment explanation
Indices: 17587--17647 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
17577 AAGAAATACC
*
17587 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17629 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
17648 ATTTATATGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22887 original size:49 final size:49
Alignment explanation
Indices: 22821--22929 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
22811 ATAATACTTT
* ** ***
22821 AACCCGTGACCACATAACTACTGTCAACTAGGCTTCCGAGTTATACTCC
1 AACCCGTGACCACATAACCACCATCAACTAGGAGCCCGAGTTATACTCC
* * *
22870 AACCCGTGACCATATAACCACCATCAACTAGGAGCCCTAGTTATACTTC
1 AACCCGTGACCACATAACCACCATCAACTAGGAGCCCGAGTTATACTCC
*
22919 AACCTGTGACC
1 AACCCGTGACC
22930 GTATTAGCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (49 bp):
AACCCGTGACCACATAACCACCATCAACTAGGAGCCCGAGTTATACTCC
Found at i:23709 original size:20 final size:21
Alignment explanation
Indices: 23672--23711 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23662 AAAAATAACC
* *
23672 AAAAAATCTATTTTTTATAAA
1 AAAAAATATATTTATTATAAA
23693 AAAAAATATA-TTATTATAA
1 AAAAAATATATTTATTATAA
23712 TGATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATATATTTATTATAAA
Done.