Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002912.1 Kokia drynarioides strain JFW-HI SEQ_115341, 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: 1732
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Found at i:300 original size:96 final size:96
Alignment explanation
Indices: 124--305 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
114 AAGGATGTTT
** *
124 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGAGCAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAATTTCCAGAATCGAAGA
* * *
189 TAAGGAAACATTGCCTGGATTAAGGGTATTC
66 TAAAGAAACACTGCCTCGATTAAGGGTATTC
* *
220 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTCC-GAAACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAATTTCCAG-AA-TCGAA
284 -ATAAAAGAAA-ACTGCCTCGATT
64 GAT-AAAGAAACACTGCCTCGATT
306 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 1 0.01
96 63 0.84
97 11 0.15
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAATTTCCAGAATCGAAGA
TAAAGAAACACTGCCTCGATTAAGGGTATTC
Found at i:553 original size:29 final size:29
Alignment explanation
Indices: 521--612 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 29
511 AAAATGAGAG
521 TTTTTGGATAATCGGGGGTAAAATGGTAA
1 TTTTTGGATAATCGGGGGTAAAATGGTAA
** * *
550 -TTTTGGATTCTCAGGGGCAAAATGGTAA
1 TTTTTGGATAATCGGGGGTAAAATGGTAA
* *
578 TTTTGGGA-AAGTTCGGGGTTAAAAATGG-AA
1 TTTTTGGATAA--TCGGGGGT-AAAATGGTAA
608 TTTTT
1 TTTTT
613 AGACACCTGG
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
28 24 0.50
29 6 0.12
30 11 0.23
31 7 0.15
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (29 bp):
TTTTTGGATAATCGGGGGTAAAATGGTAA
Found at i:635 original size:58 final size:58
Alignment explanation
Indices: 563--905 Score: 231
Period size: 59 Copynumber: 5.9 Consensus size: 58
553 TGGATTCTCA
*
563 GGGGCAAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACA-CCT
1 GGGGTAAAATGGTAATTTT-GGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATCCT
* * * ** * * *
621 GGGGTAAAACGGTAACTTT-AAAAAATCGGGATAAAAAACGGAATTTTTAGACATCC-
1 GGGGTAAAATGGTAATTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATCCT
* * * * ** * * *
677 GAGGGTAAAATGGTACTTTTTAGGAAA-ATCGAGATCGAAAATGGAATTTTTGGACATTCA
1 G-GGGTAAAATGGTA-ATTTT-GGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATCCT
* * * * *
737 GGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGTAATTTTTGGACATCCT
1 GGGGTAAAATGGTAATTTTGGAAAG-TTCGGGGTTAAAAATGGAATTTTTAGACATCCT
* * * * *
796 GGGGCAAAATGGTAATTTTTGG-AAGTTTTGGGG-TCAAAATGGAATTTTTGGA-AGT-TT
1 GGGGTAAAATGGTAA-TTTTGGAAAG-TTCGGGGTTAAAAATGGAATTTTTAGACA-TCCT
* *
853 AAGGGTAAAAAT-GTAATTTTTGG-AAGTTCGAGGG-TAAAAATGCAATTTTTAGA
1 -GGGGT-AAAATGGTAA-TTTTGGAAAGTTCG-GGGTTAAAAATGGAATTTTTAGA
906 AGTTCGAGGG
Statistics
Matches: 229, Mismatches: 43, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
56 29 0.13
57 23 0.10
58 77 0.34
59 91 0.40
60 9 0.04
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTTAGACATCCT
Found at i:753 original size:29 final size:29
Alignment explanation
Indices: 737--1081 Score: 227
Period size: 29 Copynumber: 11.8 Consensus size: 29
727 TGGACATTCA
* *
737 GGGGTAAAAGGGTAATTTTTGAAAGTTTT
1 GGGGTAAAAAGGTAATTTTTGGAAGTTTT
* **
766 GGGGTTAAAAATGTAATTTTTGGACA-TCCT
1 GGGG-TAAAAAGGTAATTTTTGGA-AGTTTT
* *
796 GGGGCAAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAAGGTAATTTTTGGAAGTTTT
* *
825 GGGGTCAAAATGG-AATTTTTGGAAGTTTA
1 GGGGT-AAAAAGGTAATTTTTGGAAGTTTT
* * *
854 AGGGTAAAAATGTAATTTTTGGAAG-TTC
1 GGGGTAAAAAGGTAATTTTTGGAAGTTTT
* * * *
882 GAGGGTAAAAATGCAATTTTTAGAAG-TTC
1 G-GGGTAAAAAGGTAATTTTTGGAAGTTTT
* * **
911 GAGGGTAAAAATGCAATTTTCAGAAGTTTT
1 G-GGGTAAAAAGGTAATTTTTGGAAGTTTT
* * *
941 GGGTTAAAAATGG-AAGTTTTGGAAG-TTC
1 GGGGTAAAAA-GGTAATTTTTGGAAGTTTT
* *** * *
969 GAGGATAAAATTATATTTTTTAGAAGTTTT
1 G-GGGTAAAAAGGTAATTTTTGGAAGTTTT
* *
999 GAGGTCAAAAATGG-AATTTTTGGAAGTTTA
1 GGGGT-AAAAA-GGTAATTTTTGGAAGTTTT
** *
1029 GGGGTAAAAATATAATTTTTGAAAGTTTT
1 GGGGTAAAAAGGTAATTTTTGGAAGTTTT
**
1058 GGGGTAAAAAATTGAATTTTTGGA
1 GGGGTAAAAAGGT-AATTTTTGGA
1082 CAATTTAGGT
Statistics
Matches: 250, Mismatches: 51, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.04
29 172 0.69
30 66 0.26
31 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAAGGTAATTTTTGGAAGTTTT
Found at i:908 original size:58 final size:58
Alignment explanation
Indices: 714--1081 Score: 357
Period size: 58 Copynumber: 6.3 Consensus size: 58
704 ATCGAGATCG
* ** *
714 AAAATGGAATTTTTGGACA-TTCAGGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGA-AGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGG-TA
* ** ** *
773 AAAATGTAATTTTTGGACA--TCCTGGGGCAAAATGGTAATTTTTGGAAGTTTTGGGGTC
1 AAAATGGAATTTTTGGA-AGTTCAAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTA
* *
831 AAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTG-GGGTA
* * * * ** *
889 AAAATGCAATTTTTAGAAGTTCGAGGGTAAAAATGCAATTTTCAGAAGTTTTGGGTTA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTA
* * * * * * * *
947 AAAATGGAAGTTTTGGAAGTTCGAGGATAAAATTATATTTTTTAGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGT-A
* * * *
1006 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTTGAAAGTTTTGGGGTAA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGT-A
*
1065 AAAATTGAATTTTTGGA
1 AAAATGGAATTTTTGGA
1082 CAATTTAGGT
Statistics
Matches: 254, Mismatches: 49, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
57 4 0.02
58 134 0.53
59 116 0.46
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTA
Found at i:908 original size:87 final size:88
Alignment explanation
Indices: 737--1055 Score: 321
Period size: 87 Copynumber: 3.6 Consensus size: 88
727 TGGACATTCA
* * * *
737 GGGGT-AAAAGGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGTAATTTTTGGACA-TCCTG-GG
1 GGGGTCAAAATGG-AATTTTTGGAAGTTTAGGGGTTAAAAATGTAATTTTTGGA-AGTTC-GAGG
* *
799 G-CAAAATGGTAATTTTTGGAAGTTTT
63 GTAAAAAT-GTAATTTTTAGAAGTTTT
*
825 GGGGTCAAAATGGAATTTTTGGAAGTTTAAGGG-TAAAAATGTAATTTTTGGAAGTTCGAGGGTA
1 GGGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTTAAAAATGTAATTTTTGGAAGTTCGAGGGTA
* *
889 AAAATGCAATTTTTAGAAG-TTC
66 AAAATGTAATTTTTAGAAGTTTT
* * ** * * * *
911 GAGGGTAAAAATGCAATTTTCAGAAGTTT-TGGGTTAAAAATGGAAGTTTTGGAAGTTCGAGGAT
1 G-GGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTTAAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
975 AAAATTATATTTTTTAGAAGTTTT
65 AAAAATGTAATTTTTAGAAGTTTT
* * *
999 GAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGG-TAAAAATATAATTTTTGAAAGTT
1 GGGGTC-AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAAATGTAATTTTTGGAAGTT
1056 TTGGGGTAAA
Statistics
Matches: 190, Mismatches: 32, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
86 8 0.04
87 105 0.55
88 68 0.36
89 9 0.05
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (88 bp):
GGGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTTAAAAATGTAATTTTTGGAAGTTCGAGGGTA
AAAATGTAATTTTTAGAAGTTTT
Done.