Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010966.1 Kokia drynarioides strain JFW-HI SEQ_125934, 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: 8233
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:5502 original size:59 final size:59
Alignment explanation
Indices: 5430--5828 Score: 522
Period size: 59 Copynumber: 6.8 Consensus size: 59
5420 ATGTTCGGAA
*
5430 TCAAAAATAGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
*
5489 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * *
5548 TCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAA-AGTC-AGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGA-GG
* * * * * * * *
5606 TTAAAAATGAGAATTTTGGAAGTT-TAGGGATAAAACGGTAATTTTTAAAAGGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTTAGAAGATTCGAGG
*
5665 TCAAAAATGGGATTTTTGGAAGTTCG-GGAGTAAAATGGTAATTTTTGGAA-AGTTCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATGGTAATTTTTAGAAGA-TTCGAGG
* * * * *
5724 TCAAAAATGAGATTTTTGGAAGTT-TAGAGATAAAATGGTAATTTTTAGAAGGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTTAGAAGATTCGAGG
* *
5783 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
5829 GGAAAGTTCA
Statistics
Matches: 295, Mismatches: 34, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
57 5 0.02
58 43 0.15
59 244 0.83
60 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
Found at i:5740 original size:176 final size:176
Alignment explanation
Indices: 5430--5828 Score: 563
Period size: 176 Copynumber: 2.3 Consensus size: 176
5420 ATGTTCGGAA
* *
5430 TCAAAAAT-AGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGTCAAA
1 TCAAAAATGA-GAATTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAAAAGATTCGAGGTCAAA
* *
5494 AATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGGTCAAAAATGGG
64 AATGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTAGAAGATTCGAGGTCAAAAATGAG
* *
5559 ATTTTTGGAAGTTCAAG-GGTAAAATGGTAATTTTTGGAAAG-TCAGGG
129 ATTTTTGGAAGTT-AAGAGATAAAATGGTAATTTTTAGAAAGTTCAGGG
* * * * *
5606 TTAAAAATGAGAATTTTGGAAGTTTAGGGATAAAACGGTAATTTTTAAAAGGTTCGGGGTCAAAA
1 TCAAAAATGAGAATTTTGGAAGTTCAGGG-TAAAATGGTAATTTTTAAAAGATTCGAGGTCAAAA
*
5671 ATGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAA-AGTTCGAGGTCAAAAATGAG
65 ATGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTAGAAGA-TTCGAGGTCAAAAATGAG
* * *
5735 ATTTTTGGAAGTTTAGAGATAAAATGGTAATTTTTAGAAGGTTCGGGG
129 ATTTTTGGAAGTTAAGAGATAAAATGGTAATTTTTAGAAAGTTCAGGG
* *
5783 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT
1 TCAAAAATGAGAATTTTGGAAGTTC-AGGGTAAAATGGTAATTTTT
5829 GGAAAGTTCA
Statistics
Matches: 197, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
175 7 0.04
176 144 0.73
177 43 0.22
178 3 0.02
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (176 bp):
TCAAAAATGAGAATTTTGGAAGTTCAGGGTAAAATGGTAATTTTTAAAAGATTCGAGGTCAAAAA
TGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTAGAAGATTCGAGGTCAAAAATGAGAT
TTTTGGAAGTTAAGAGATAAAATGGTAATTTTTAGAAAGTTCAGGG
Found at i:5785 original size:118 final size:117
Alignment explanation
Indices: 5430--5837 Score: 606
Period size: 118 Copynumber: 3.5 Consensus size: 117
5420 ATGTTCGGAA
* *
5430 TCAAAAATAGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAG-AAGATTCGAGGTCAAA
1 TCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTGGAAAG-TTCGAGGTCAAA
* ** * * *
5494 AATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
64 AATGAGATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTAGAAGGTTCGGGG
* *
5548 TCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAG-TC-AGGGTTAAA
1 TCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGGAAAGTTCGA-GGTCAAA
* * *
5611 AATGAGAATTTTGGAAGTTTAGGGATAAAACGGTAATTTTTAAAAGGTTCGGGG
64 AATGAGATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTAGAAGGTTCGGGG
5665 TCAAAAATGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGGG-GTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAA
*
5730 ATGAGATTTTTGGAAGTTTAGAGATAAAATGGTAATTTTTAGAAGGTTCGGGG
65 ATGAGATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTAGAAGGTTCGGGG
*
5783 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTC
1 TCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGGAAAGTTC
5838 AAGGACCTCC
Statistics
Matches: 263, Mismatches: 20, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
116 3 0.01
117 101 0.38
118 152 0.58
119 7 0.03
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (117 bp):
TCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAA
TGAGATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTAGAAGGTTCGGGG
Found at i:6957 original size:7 final size:7
Alignment explanation
Indices: 6945--6989 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
6935 CTTCGTTTTT
6945 TTATTAA
1 TTATTAA
6952 TTATTAA
1 TTATTAA
*
6959 TTAATAA
1 TTATTAA
6966 TTATTAA
1 TTATTAA
6973 -TATT-A
1 TTATTAA
6978 TTATT-A
1 TTATTAA
6984 TTATTA
1 TTATTA
6990 TCAAAACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 1 0.03
6 14 0.41
7 19 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATTAA
Found at i:6990 original size:21 final size:21
Alignment explanation
Indices: 6951--7020 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 21
6941 TTTTTTATTA
*
6951 ATTATTAATTAATAATTATTAAT
1 ATTATT-ATT-ATTATTATTAAT
*
6974 ATTATTATTATTATTATCAA-
1 ATTATTATTATTATTATTAAT
**
6994 AACA-T-TTATTATTATTAAT
1 ATTATTATTATTATTATTAAT
7013 GATTATTA
1 -ATTATTA
7021 AGAAAAACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
18 12 0.33
19 1 0.03
20 4 0.11
21 10 0.28
22 3 0.08
23 6 0.17
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTATTATTATTATTATTAAT
Found at i:8144 original size:7 final size:7
Alignment explanation
Indices: 8132--8176 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
8122 CTTCGTTTTT
8132 TTATTAA
1 TTATTAA
8139 TTATTAA
1 TTATTAA
*
8146 TTAATAA
1 TTATTAA
8153 TTATTAA
1 TTATTAA
8160 -TATT-A
1 TTATTAA
8165 TTATT-A
1 TTATTAA
8171 TTATTA
1 TTATTA
8177 TCAAAACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 1 0.03
6 14 0.41
7 19 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATTAA
Found at i:8177 original size:21 final size:21
Alignment explanation
Indices: 8138--8207 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 21
8128 TTTTTTATTA
*
8138 ATTATTAATTAATAATTATTAAT
1 ATTATT-ATT-ATTATTATTAAT
*
8161 ATTATTATTATTATTATCAA-
1 ATTATTATTATTATTATTAAT
**
8181 AACA-T-TTATTATTATTAAT
1 ATTATTATTATTATTATTAAT
8200 GATTATTA
1 -ATTATTA
8208 AGAAAAACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
18 12 0.33
19 1 0.03
20 4 0.11
21 10 0.28
22 3 0.08
23 6 0.17
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTATTATTATTATTATTAAT
Done.