Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000651.1 Kokia drynarioides strain JFW-HI SEQ_111629, 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, 792
Length: 1321
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Found at i:771 original size:97 final size:97
Alignment explanation
Indices: 597--778 Score: 242
Period size: 97 Copynumber: 1.9 Consensus size: 97
587 AGGATGTTCA
* *
597 ATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAGAATCAGAGAT
1 ATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAATCAGAAAT
662 AAAGAAACATTGCCTCGATTGAAGGGTATTCG
66 AAAGAAACATTGCCTCGATTGAAGGGTATTCG
* * ** * *
694 ATTATTTCGATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAATTCA-AAA
1 ATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAA-TCAGAAA
* *
758 TAAA-AGAATATTGCCTTGATT
65 TAAAGA-AACATTGCCTCGATT
779 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.01
97 69 0.95
98 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (97 bp):
ATTATCTCGATTTAAAGAAAAGTCGCACCTAGTAAGTTAAGACACAAAATTTCAAAATCAGAAAT
AAAGAAACATTGCCTCGATTGAAGGGTATTCG
Found at i:1084 original size:58 final size:58
Alignment explanation
Indices: 994--1321 Score: 392
Period size: 58 Copynumber: 5.6 Consensus size: 58
984 TGAAAACAAG
* * * * * * *
994 ATTTTTGGATACTCGGGGGCAAAATGGTAATTTTGGGAAAGTTGAGGGTCAAAATGGA
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAATTCAGGGTAAAAATGGA
* * * * *
1052 ATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAAATTCAAGGTCGAAAAATAGA
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAATTCAGGGT--AAAAATGGA
*
1112 ATTTTT-GAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAATT-AGGGTAAAAAATGGA
1 ATTTTTGGAAA-TTCGAGGGTAAAATGGTAATTTTGGGAAAATTCAGGGT-AAAAATGGA
* *
1170 ATTTTTGGAAATTTGAGGGTAAAATGGTAATTTT-GGAAAAATCAGGGTAAAAAATGGA
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAATTCAGGGT-AAAAATGGA
* * * *
1228 ATTTTTGGAAATTCGAGGGTGAAATGGTAATTTTTGGAAAAAATCGGGGTTAAAAATGGA
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAA-TTTTGGGAAAATTCAGGG-TAAAAATGGA
*
1288 ATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTT
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTT
Statistics
Matches: 239, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
57 7 0.03
58 119 0.50
59 19 0.08
60 93 0.39
61 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (58 bp):
ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAATTCAGGGTAAAAATGGA
Found at i:1202 original size:118 final size:116
Alignment explanation
Indices: 994--1321 Score: 417
Period size: 118 Copynumber: 2.8 Consensus size: 116
984 TGAAAACAAG
* * * * * * * *
994 ATTTTTGGATACTCGGGGGCAAAATGGTAATTTTGGGAAAGTTGAGGGTCAAAATGGAATTTTTA
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAATT-AGGGTAAAAATGGAATTTTTG
* * *
1059 GACATTCGAGGGTAAAATGGTAATTTTTGGAAAATTCAAGGTCGAAAAATAGA
65 GAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAAGGT-AAAAAATAGA
1112 ATTTTT-GAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAATTAGGGTAAAAAATGGAATTTTT
1 ATTTTTGGAAA-TTCGAGGGTAAAATGGTAATTTTTGGAAAATTAGGGT-AAAAATGGAATTTTT
* * *
1176 GGAAATTTGAGGGTAAAATGGTAA-TTTTGGAAAAATCAGGGTAAAAAATGGA
64 GGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATAGA
* **
1228 ATTTTTGGAAATTCGAGGGTGAAATGGTAATTTTTGGAAAAAATCGGGGTTAAAAATGGAATTTT
1 ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGG--AAAATTAGGG-TAAAAATGGAATTTT
*
1293 TGGAAGTTCGAGGGTAAAATGGTAATTTT
63 TGGAAATTCGAGGGTAAAATGGTAATTTT
Statistics
Matches: 184, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
116 39 0.21
117 28 0.15
118 113 0.61
119 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (116 bp):
ATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAATTAGGGTAAAAATGGAATTTTTGG
AAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTAAAAAATAGA
Done.