Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010978.1 Kokia drynarioides strain JFW-HI SEQ_125948, 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: 1908
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.29
Warning! 106 characters in sequence are not A, C, G, or T
Found at i:290 original size:96 final size:96
Alignment explanation
Indices: 124--297 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
114 TTGATTATCC
* * * * *
124 CGATTTGATGAAAGATTGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATCTAAGATAAGGAAA
1 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGATAAAGAAA
189 CATTGCCTCGATTAAGGGTATTCGATTATTT
66 CATTGCCTCGATTAAGGGTATTCGATTATTT
* * *
220 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGTAAATTTT-TGAAACTCGAA-ATAAA-A
1 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCAG-AA-TCGAAGATAAAGA
*
282 GAATATTGCCTCGATT
64 -AACATTGCCTCGATT
298 TTAAAGTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 60 0.91
97 4 0.06
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGATAAAGAAA
CATTGCCTCGATTAAGGGTATTCGATTATTT
Found at i:679 original size:59 final size:57
Alignment explanation
Indices: 611--844 Score: 195
Period size: 59 Copynumber: 4.0 Consensus size: 57
601 AGAGTTTCGA
611 GGTCAAAAATGGAGTTTTTGGACA-TCCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGG
1 GGTCAAAAATGGAGTTTTTGGA-AGT-CGAGGGCAAAATGG-AATTTTTGGAAGTTTTGG
*** ** * * *
670 GGTCAAAAATGG-GATTTTCAAAAGTTTAGGGGTAAAAATGGAATTTTTGAAAGTTTTAG
1 GGTCAAAAATGGAG-TTTTTGGAAGTCGA-GGG-CAAAATGGAATTTTTGGAAGTTTTGG
** ** *
729 GGTTTAAAAT-GAGATTTTTGGAAGTTTAGGGGAAAATGGAATTTTTGGAAGTTTTGGG
1 GGTCAAAAATGGAG-TTTTTGGAAGTCGAGGGCAAAATGGAATTTTTGGAAGTTTT-GG
* * * *
787 GGTCAAAAATGTAATTTTTAGAAGTTCGAGGGTGAAAATGGAATTTTTGGACAGTTTT
1 GGTCAAAAATGGAGTTTTTGGAAG-TCGAGGG-CAAAATGGAATTTTTGGA-AGTTTT
845 AGGACCTTCA
Statistics
Matches: 142, Mismatches: 23, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
57 22 0.15
58 25 0.18
59 64 0.45
60 25 0.18
61 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (57 bp):
GGTCAAAAATGGAGTTTTTGGAAGTCGAGGGCAAAATGGAATTTTTGGAAGTTTTGG
Found at i:687 original size:30 final size:29
Alignment explanation
Indices: 644--844 Score: 185
Period size: 30 Copynumber: 6.8 Consensus size: 29
634 ATCCGAGGGC
644 AAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGT-A
* *** *
675 AAAATGGGATTTTCAAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* * *
704 AAAATGGAATTTTTGAAAGTTTTAGGGTTT
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTA
*
734 AAAAT-GAGATTTTTGGAAGTTTAGGGG--
1 AAAATGGA-ATTTTTGGAAGTTTTGGGGTA
761 AAAATGGAATTTTTGGAAGTTTTGGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTT-GGGGT-A
* * * *
792 AAAATGTAATTTTTAGAAG-TTCGAGGGTG
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
821 AAAATGGAATTTTTGGACAGTTTT
1 AAAATGGAATTTTTGGA-AGTTTT
845 AGGACCTTCA
Statistics
Matches: 138, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
27 19 0.14
28 6 0.04
29 41 0.30
30 46 0.33
31 26 0.19
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:715 original size:117 final size:114
Alignment explanation
Indices: 498--833 Score: 299
Period size: 117 Copynumber: 2.9 Consensus size: 114
488 ATCAAAGTTG
* * * * * *
498 AAAATGAGACTTTTTGGATACCCGGGGGCAAAATGGTAATTTTGGGAAAGTTTT-GGGTTAAGAA
1 AAAATG-GAGTTTTTGGA-ATCCGAGGGCAAAATGGTAATTTTTGG-AAGTTTTGGGGTCAAAAA
* * *
562 TGGAATCTTTAGACA-TTTAGGGGTAAAAGGGTAATTTTGAGAGTTTCGA-GGTCA
63 TGGAAT-TTTA-AAAGTTTAGGGGTAAAATGG-AATTTTGAAAGTTT-GAGGGTCA
616 AAAATGGAGTTTTTGGACATCCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATG
1 AAAATGGAGTTTTTGGA-ATCCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATG
* * **
681 GGATTTTCAAAAGTTTAGGGGTAAAAATGGAATTTTTGAAAGTTTTAGGGTTT
65 GAATTTT-AAAAGTTTAGGGGT-AAAATGGAA-TTTTGAAAGTTTGAGGGTCA
** *
734 AAAAT-GAGATTTTTGGAAGT-TTAGGGGAAAATGG-AATTTTTGGAAGTTTTGGGGGTCAAAAA
1 AAAATGGAG-TTTTTGGAA-TCCGAGGGCAAAATGGTAATTTTTGGAAGTTTT-GGGGTCAAAAA
* * *
796 TGTAATTTTTAGAAG-TTCGAGGGTGAAAATGGAATTTT
63 TGGAA-TTTTAAAAGTTTAG-GGGT-AAAATGGAATTTT
834 TGGACAGTTT
Statistics
Matches: 185, Mismatches: 22, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
116 35 0.19
117 106 0.57
118 44 0.24
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (114 bp):
AAAATGGAGTTTTTGGAATCCGAGGGCAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
AATTTTAAAAGTTTAGGGGTAAAATGGAATTTTGAAAGTTTGAGGGTCA
Done.