Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000329.1 Kokia drynarioides strain JFW-HI SEQ_111099, 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: 1784
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Found at i:514 original size:96 final size:96
Alignment explanation
Indices: 325--516 Score: 264
Period size: 96 Copynumber: 2.0 Consensus size: 96
315 AATTTTGGAA
**
325 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
390 GAATCGAACATAAGGAAACATTGTCTCGATT
66 GAATCGAACATAAAGAAACATTGCCTCGATT
* * *
421 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAATGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
*
486 -AATCTCGAA-ATAAA-AGAATATTGCCTCGATT
66 GAA--TCGAACATAAAGA-AACATTGCCTCGATT
517 GTAAAGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 3 0.04
96 77 0.91
97 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
GAATCGAACATAAAGAAACATTGCCTCGATT
Found at i:889 original size:29 final size:29
Alignment explanation
Indices: 857--1169 Score: 141
Period size: 30 Copynumber: 10.7 Consensus size: 29
847 GAAGTTTGGG
857 GGGT-AAAATGGTAATTTTTGGAAAAATTA
1 GGGTAAAAATGG-AATTTTTGGAAAAATTA
* * *
886 GGGTAAAAAATAGAATTTGTGG--AAGTTCGA
1 GGGT-AAAAATGGAATTTTTGGAAAAATT--A
* * * **
916 GAGT-AAAATGAAAATTTTGGAAAAATCG
1 GGGTAAAAATGGAATTTTTGGAAAAATTA
*
944 GGGTCAAAAATGGAATTTTTGG--AAGTTCA
1 GGGT-AAAAATGGAATTTTTGGAAAAATT-A
* *
973 GGGGTAAAACGAT--AATTTTTGGAGAGATTA
1 -GGGTAAAA--ATGGAATTTTTGGAAAAATTA
* *
1003 AGGTCAAAAATGGAA-TTTTGG-AAAGTTA
1 GGGT-AAAAATGGAATTTTTGGAAAAATTA
* **
1031 GGGGTAAAAATGTAATTTTTGGAAAAATCG
1 -GGGTAAAAATGGAATTTTTGGAAAAATTA
*
1061 GGGTCAAAAATGGAA-TTTTGGAAAATTTA
1 GGGT-AAAAATGGAATTTTTGGAAAAATTA
* ** *
1090 GGGGTAAGAATATAA-TTTT-CAAAAAGTTTA
1 -GGGTAAAAATGGAATTTTTGGAAAAA--TTA
* * **
1120 AGGTCGAAAATGGAA-TTTTGGAAAGTTTGA
1 GGGT-AAAAATGGAATTTTTGGAAAAATT-A
*
1150 GGGTAAAAATGTAATTTTTG
1 GGGTAAAAATGGAATTTTTG
1170 TACAATTTAG
Statistics
Matches: 208, Mismatches: 48, Indels: 55
0.67 0.15 0.18
Matches are distributed among these distances:
28 41 0.20
29 74 0.36
30 79 0.38
31 14 0.07
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAAAATTA
Found at i:953 original size:58 final size:57
Alignment explanation
Indices: 811--1083 Score: 253
Period size: 58 Copynumber: 4.6 Consensus size: 57
801 AAAATGGTAA
* * * * * * *
811 TTTTGGGAAAATCGAGGTTAAAAAATGGATTTTTTGGAAGTTTGGGGGGTAAAATGGTAAT
1 TTTTGGAAAAATCG-GGGTCAAAAATGGA-ATTTTGGAAG-TTCGAGGGTAAAAT-GAAAT
** * * * *
872 TTTTGGAAAAATTAGGGTAAAAAATAGAATTTGTGGAAGTTCGAGAGTAAAATGAAAA
1 TTTTGGAAAAATCGGGGTCAAAAATGGAATTT-TGGAAGTTCGAGGGTAAAATGAAAT
*
930 TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTC-AGGGGTAAAACGATAAT
1 TTTTGGAAAAATCGGGGTCAAAAATGGAA-TTTTGGAAGTTCGA-GGGTAAAATGA-AAT
* * *** * *
989 TTTTGGAGAGATTAAGGTCAAAAATGGAATTTTGGAAAGTTAG-GGGTAAAAATGTAAT
1 TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTGG-AAGTTCGAGGGT-AAAATGAAAT
1047 TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTGGAA
1 TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTGGAA
1084 AATTTAGGGG
Statistics
Matches: 174, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.02
58 89 0.51
59 53 0.30
60 18 0.10
61 11 0.06
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (57 bp):
TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGAAAT
Found at i:1012 original size:117 final size:117
Alignment explanation
Indices: 800--1146 Score: 348
Period size: 117 Copynumber: 3.0 Consensus size: 117
790 GACATCCGAA
** * * * * **
800 TAAAATGGTAATTTTGGGAAAATCGAGGTTAAAAAATGGATTTTTTGGAAGTTTGGGGGGTAAAA
1 TAAAATGAAAATTTTGGAAAAATCG-GGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGGTAAAA
* * * *
865 TGGTAATTTTTGGAAAAATTAGGGTAAAAAATAGAATTTGTGG-AAGTTCGAGAG
65 CGATAATTTTTGGAAAAATTAAGGTAAAAAATAGAATTT-TGGAAAGTTAG-GAG
919 TAAAATGAAAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAG-TTCAGGGGTAAAAC
1 TAAAATGAAAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGGTAAAAC
* * * * *
983 GATAATTTTTGGAGAGATTAAGGTCAAAAATGGAATTTTGGAAAGTTAGGGG
66 GATAATTTTTGGAAAAATTAAGGTAAAAAATAGAATTTTGGAAAGTTAGGAG
* * *
1035 TAAAAATGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAA-TTTTGGAAAATTT-AGGGGTAAG
1 T-AAAATGAAAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGG-AAGTTTCAGGGGTAA-
* * ** *
1098 AA-TATAA-TTTT-CAAAAAGTTTAAGGTCGAAAATGGAATTTTGGAAAGTT
63 AACGATAATTTTTGGAAAAA--TTAAGGTAAAAAATAGAATTTTGGAAAGTT
1147 TGAGGGTAAA
Statistics
Matches: 196, Mismatches: 25, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
115 3 0.02
116 16 0.08
117 129 0.66
118 26 0.13
119 22 0.11
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (117 bp):
TAAAATGAAAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTTCAGGGGTAAAAC
GATAATTTTTGGAAAAATTAAGGTAAAAAATAGAATTTTGGAAAGTTAGGAG
Found at i:1130 original size:59 final size:58
Alignment explanation
Indices: 945--1167 Score: 213
Period size: 59 Copynumber: 3.8 Consensus size: 58
935 GAAAAATCGG
* * * * * *
945 GGTCAAAAATGGAATTTTTGG-AAGTTCAGGGGT-AAAACGATAATTTTTGGAGAGATTAA
1 GGTCAAAAATGGAA-TTTTGGAAAATTTAGGGGTAAAAATG-TAA-TTTTGCAAAAATTAA
* * ***
1004 GGTCAAAAATGGAATTTTGG-AAAGTTAGGGGTAAAAATGTAATTTTTGGAAAAATCGG
1 GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAAAATGTAA-TTTTGCAAAAATTAA
* *
1062 GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAGAATATAATTTT-CAAAAAGTTTAA
1 GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAAAATGTAATTTTGCAAAAA--TTAA
* *
1121 GGTCGAAAATGGAATTTTGGAAAGTTT-GAGGGTAAAAATGTAATTTT
1 GGTCAAAAATGGAATTTTGGAAAATTTAG-GGGTAAAAATGTAATTTT
1168 TGTACAATTT
Statistics
Matches: 139, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 5 0.04
58 54 0.39
59 80 0.58
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAAAATGTAATTTTGCAAAAATTAA
Done.