Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014006.1 Kokia drynarioides strain JFW-HI SEQ_129037, 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: 8008
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:6365 original size:96 final size:96
Alignment explanation
Indices: 6188--6372 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
6178 GAAAAGGATG
* *
6188 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGATAAGGCGCAAATTTTCAGAATCGA
*
6253 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
*
6284 TTCGATTATTTCGATTTGAAGAGAA-ATTGCACCTAGTAAGATAAGGCGCAAATTTTC-GAAACT
1 TTCGATTATCTCGATTTGAAGA-AAGATTGCACCTAGTAAGATAAGGCGCAAATTTTCAG-AA-T
*
6347 CGAA-ATAAA-AGAATATTGCCTCGATT
63 CGAAGATAAAGA-AACATTGCCTCGATT
6373 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
95 2 0.03
96 71 0.89
97 7 0.09
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGATAAGGCGCAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:6759 original size:29 final size:28
Alignment explanation
Indices: 6599--6820 Score: 78
Period size: 29 Copynumber: 7.7 Consensus size: 28
6589 TGGATACCCA
6599 GGGGTAAAATGGTAA-TTTTGGAC-TCG
1 GGGGTAAAATGGTAATTTTTGGACATCG
* * ** * *
6625 AGGGAAAAACCGTAATTTTGGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGACA--TCG
* * *
6655 GGGTTAAAAATGG-AATTTTTAGACACTTG
1 GGGGT-AAAATGGTAATTTTTGGACA-TCG
* * * * *
6684 GGGGTAAAA-GGATAACTTTTGAAAAAACC
1 GGGGTAAAATGG-TAATTTTTG-GACATCG
* ** *
6713 GGGATCAAAAACGAAATTTTTGGACATCCG
1 GGGGT-AAAATGGTAATTTTTGGACAT-CG
* *
6743 GGGGTAAAATGGTAATTTTCAGGAAAATC-
1 GGGGTAAAATGGTAATTTT-TGG-ACATCG
* *
6772 GGGATCAAAATGG-AATTTTTGGACATTTG
1 GGGGT-AAAATGGTAATTTTTGGACA-TCG
* *
6801 GGGGTGAAATAGTAATTTTT
1 GGGGTAAAATGGTAATTTTT
6821 AAAAGTTTGG
Statistics
Matches: 134, Mismatches: 45, Indels: 31
0.64 0.21 0.15
Matches are distributed among these distances:
26 11 0.08
27 10 0.07
28 12 0.09
29 50 0.37
30 42 0.31
31 9 0.07
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGGACATCG
Found at i:6816 original size:58 final size:57
Alignment explanation
Indices: 6660--6824 Score: 163
Period size: 58 Copynumber: 2.8 Consensus size: 57
6650 GTTCGGGGTT
* * *
6660 AAAAATGGAATTTTTAGACACTTGGGGGTAAA-AGGATAACTTTTGAAAAAACCGGGATC
1 AAAAATGGAATTTTTGGACATTTGGGGGTAAATA-G-TAA-TTTTCAAAAAACCGGGATC
* * ** * * *
6719 AAAAACGAAATTTTTGGACATCCGGGGGTAAAATGGTAATTTTCAGGAAAATCGGGATC
1 AAAAATGGAATTTTTGGACATTTGGGGGT-AAATAGTAATTTTCA-AAAAACCGGGATC
*
6778 -AAAATGGAATTTTTGGACATTTGGGGGTGAAATAGTAATTTTTAAAA
1 AAAAATGGAATTTTTGGACATTTGGGGGT-AAATAGTAATTTTCAAAA
6825 GTTTGGGGGT
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
57 2 0.02
58 42 0.49
59 37 0.44
60 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGACATTTGGGGGTAAATAGTAATTTTCAAAAAACCGGGATC
Found at i:6883 original size:29 final size:29
Alignment explanation
Indices: 6778--6946 Score: 132
Period size: 29 Copynumber: 5.8 Consensus size: 29
6768 AATCGGGATC
*
6778 AAAATGGAATTTTTGGACA-TTT-GGGGGT
1 AAAATGGAATTTTTGGA-AGTTTCGGGGTT
* * ** * *
6806 GAAATAGTAATTTTTAAAAGTTTGGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTCGGGGTT
*
6836 AAAATGTAATTTTTGGAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTT
* *
6865 AAAATGGAATTTTTTGAAG-TTCGAGGTAAT
1 AAAATGGAATTTTTGGAAGTTTCGGGGT--T
*
6895 AAATAT-G-ATTTTTGGAAGTTTTGGGGTT
1 AAA-ATGGAATTTTTGGAAGTTTCGGGGTT
*
6923 AAAAATGGATTTTTTGGATAGTTT
1 -AAAATGGAATTTTTGGA-AGTTT
6947 AGAGGCCTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
28 15 0.13
29 63 0.56
30 27 0.24
31 7 0.06
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTT
Found at i:7909 original size:3 final size:3
Alignment explanation
Indices: 7891--7943 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
7881 CTTTCCTTTT
* * *
7891 TTA TTA CTA TTTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA ATA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7936 TTAA TTA T
1 TT-A TTA T
7944 AGTTGCCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Done.