Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013711.1 Kokia drynarioides strain JFW-HI SEQ_128739, 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: 7428
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:611 original size:51 final size:51
Alignment explanation
Indices: 535--638 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
525 TTCGCCTGCT
*
535 TAGAAAGCGTAACCCGGGGGTATGGGACGATGAATGTCAGGAAACCTTCAA
1 TAGAAAGCGTAACCAGGGGGTATGGGACGATGAATGTCAGGAAACCTTCAA
*
586 TAGAAAGCGTAACCAGGGGGTATGGGACGATGAATGTCATGAAACCTTCAA
1 TAGAAAGCGTAACCAGGGGGTATGGGACGATGAATGTCAGGAAACCTTCAA
637 TA
1 TA
639 AGGTCAAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (51 bp):
TAGAAAGCGTAACCAGGGGGTATGGGACGATGAATGTCAGGAAACCTTCAA
Found at i:4120 original size:206 final size:206
Alignment explanation
Indices: 3761--4424 Score: 887
Period size: 206 Copynumber: 3.2 Consensus size: 206
3751 TGCGATACCC
* * *
3761 ACAAACGATGCGGTCATCTTCCT-AGTGAGATACTGAGAAGAAGACAAAATCAGGCCCATGCTCA
1 ACAAGCGATGCGGTCATCTTCCTGA-TGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCA
* * * * *
3825 AAGCGAGCAAAATTTTCTAACCCAAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAA
65 AAGCGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGATACCGAGAAGCAGGTCGAAGCAATAA
*
3890 ACAGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
130 ACGGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
3955 AAGCTGATTGAA
195 AAGCTGATTGAA
3967 ACAAGCGATGCGGTCATCTTCCT-AGTGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCA
1 ACAAGCGATGCGGTCATCTTCCTGA-TGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCA
*
4031 AAGCGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGATACCGAGAAGTAGGTCGAAGCAATAA
65 AAGCGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGATACCGAGAAGCAGGTCGAAGCAATAA
4096 ACGGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
130 ACGGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
*
4161 AAGCGGATTGAA
195 AAGCTGATTGAA
* * * **
4173 ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCGAACCAAACCCACG--C--
1 ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCAA
* * * *
4234 A-CGATGAATAAACCTTCGAACCCCAGCTTCTTGAT-AGAATACTGAGAAGCAGGTCGAAGTAAT
66 AGCGA-GCA-AAATCTTCGAACCCCAGCTTCTTGATGAG-ATACCGAGAAGCAGGTCGAAGCAAT
* * * ** * * *
4297 AAAACGGATAGCTCCCTGATGAGATACGGAGGAGTGAACCAAATTCGTCTTCCTGATGAAACACA
128 -AAACGGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACA
* * **
4362 CAGAA-ATGGATCAAA
192 GAGAAGCT-GATTGAA
* * *
4377 ACAAGTGATGCGGCCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
1 ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
4425 GTCAACGAAA
Statistics
Matches: 415, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
201 3 0.01
202 5 0.01
203 47 0.11
204 111 0.27
206 248 0.60
207 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (206 bp):
ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAGGCCCACGCTCAA
AGCGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAA
CGGTTAGCTTCCAGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
AGCTGATTGAA
Found at i:4804 original size:6 final size:6
Alignment explanation
Indices: 4793--4856 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
4783 ATTTGTGTAG
* *
4793 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
4839 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
4857 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 9 0.19
6 31 0.65
7 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:4815 original size:17 final size:16
Alignment explanation
Indices: 4793--4888 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 16
4783 ATTTGTGTAG
4793 AAATTTAAATTTATATT
1 AAATTTAAATTTAT-TT
4810 AAATTTAAATTTATTT
1 AAATTTAAATTTATTT
*
4826 CGAATTTAAATTTAATTT
1 -AAATTTAAATTT-ATTT
*
4844 AAGTTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
4861 CCAAATTTAAGA-TTATTAT
1 --AAATTTAA-ATTTATT-T
4880 AAATTTAAA
1 AAATTTAAA
4889 ATGAATAAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 4 0.06
17 46 0.68
18 6 0.09
19 11 0.16
20 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:4837 original size:34 final size:34
Alignment explanation
Indices: 4794--4859 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
4784 TTTGTGTAGA
4794 AATTTAAATTT-ATATTAAATTTAAATTTATTTCG
1 AATTTAAATTTAAT-TTAAATTTAAATTTATTTCG
*
4828 AATTTAAATTTAATTTAAGTTTAAATTTATTT
1 AATTTAAATTTAATTTAAATTTAAATTTATTT
4860 TCCAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
AATTTAAATTTAATTTAAATTTAAATTTATTTCG
Found at i:5613 original size:6 final size:6
Alignment explanation
Indices: 5602--5650 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
5592 NNNNNNNNNA
* *
5602 TTAAAT TTAAAT TT--AT TTCGAAT TTAAAT TT-AAT TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT
5648 TTA
1 TTA
5651 TTTTCCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 23 0.64
7 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:5627 original size:17 final size:15
Alignment explanation
Indices: 5605--5653 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 15
5595 NNNNNNATTA
5605 AATTTAAATTTATTT
1 AATTTAAATTTATTT
5620 CGAATTTAAATTTAATTT
1 --AATTTAAATTT-ATTT
5638 AAGTTTAAATTTATTT
1 AA-TTTAAATTTATTT
5654 TCCAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.20
17 20 0.67
18 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (15 bp):
AATTTAAATTTATTT
Found at i:5636 original size:11 final size:12
Alignment explanation
Indices: 5602--5650 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
5592 NNNNNNNNNA
5602 TTAAATTTAAAT
1 TTAAATTTAAAT
*
5614 TT--ATTTCGAAT
1 TTAAATTT-AAAT
5625 TTAAATTT-AAT
1 TTAAATTTAAAT
*
5636 TTAAGTTTAAAT
1 TTAAATTTAAAT
5648 TTA
1 TTA
5651 TTTTCCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 15 0.48
12 8 0.26
13 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (12 bp):
TTAAATTTAAAT
Done.