Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004879.1 Kokia drynarioides strain JFW-HI SEQ_118557, 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: 2721
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:415 original size:96 final size:96
Alignment explanation
Indices: 231--424 Score: 232
Period size: 96 Copynumber: 2.0 Consensus size: 96
221 TCTTTGCGAA
* ** *
231 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAATATTTCG
* * *
296 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAACCGAAGATAAAGAAACATTGCCTCGATT
* * *
327 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAATA-TTTC
* *
391 GAAACCCGAA-ATGAAAG-AATATTGCCTTGATT
65 GAAA-CCGAAGAT-AAAGAAACATTGCCTCGATT
423 AA
1 AA
425 AGTTTTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 1 0.01
96 75 0.90
97 7 0.08
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:809 original size:30 final size:30
Alignment explanation
Indices: 736--1057 Score: 435
Period size: 30 Copynumber: 10.8 Consensus size: 30
726 TTTTGGAAAA
* *
736 TTTTGGGGTAAAAAAATGGGATTTTTAGGAG
1 TTTTGGGGT-TAAAAATGGGATTTTTAGAAG
* *
767 -TTTGAGGG-TAAAAATGGAACTTTTCA-AAG
1 TTTTG-GGGTTAAAAATGGGA-TTTTTAGAAG
796 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
* *
826 -TTTGGGGGTAATAAATGGGATTTTTGGAAG
1 TTTTGGGGTTAA-AAATGGGATTTTTAGAAG
856 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
*
886 TTTTAGGGTTAAAAATGGGATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
916 -TTTGGGGTT-AAAATGGGATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
*
944 TTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
*
974 TTTTGGGGTTAAAAATAGGATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTAGAAG
*
1004 -TTT-GGGTGTAAAAATGGGATTTTTGGAAG
1 TTTTGGGGT-TAAAAATGGGATTTTTAGAAG
* *
1033 TTTCGAGGTTAAAAATGGGATTTTT
1 TTTTGGGGTTAAAAATGGGATTTTT
1058 GAACAATTTA
Statistics
Matches: 260, Mismatches: 19, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
28 23 0.09
29 68 0.26
30 153 0.59
31 16 0.06
ACGTcount: A:0.30, C:0.01, G:0.30, T:0.39
Consensus pattern (30 bp):
TTTTGGGGTTAAAAATGGGATTTTTAGAAG
Found at i:810 original size:59 final size:58
Alignment explanation
Indices: 717--1057 Score: 452
Period size: 59 Copynumber: 5.7 Consensus size: 58
707 TTCCCGGATG
* * * * *
717 AAATGGTAATTTTGGAAAATTTTGGGGTAAAAAAATGGGATTTTTAGGAGTTTGAGGGTAA
1 AAATGGGATTTTTGG-AAGTTTTGGGGT-TAAAAATGGGATTTTTAGAAGTTTG-GGGTAA
* * **
778 AAATGGAACTTTTCAAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAA
1 AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTT-GGGGTAA
*
837 TAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTTAGGGTTAA
1 -AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG-TTT-GGGGTAA
*
898 AAATGGGATTTTTAGAAG-TTTGGGGTT-AAAATGGGATTTTTAGAAGTTTTGGGGTTAA
1 AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG-TTTGGGG-TAA
*
956 AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATAGGATTTTTAGAAGTTTGGGTGTAA
1 AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTGGG-GTAA
* *
1015 AAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTT
1 AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTT
1058 GAACAATTTA
Statistics
Matches: 253, Mismatches: 20, Indels: 16
0.88 0.07 0.06
Matches are distributed among these distances:
57 3 0.01
58 43 0.17
59 95 0.38
60 92 0.36
61 20 0.08
ACGTcount: A:0.31, C:0.01, G:0.30, T:0.38
Consensus pattern (58 bp):
AAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTGGGGTAA
Found at i:2150 original size:3 final size:3
Alignment explanation
Indices: 2142--2189 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
2132 ATCATTAAAA
* * *
2142 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
2188 AT
1 AT
2190 ATAAATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Done.