Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010765.1 Kokia drynarioides strain JFW-HI SEQ_125726, 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: 82672
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:202 original size:13 final size:13
Alignment explanation
Indices: 184--218 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
174 TGGGTGTCAG
184 GTATTTTTTTGTC
1 GTATTTTTTTGTC
197 GTA--TTTTTGTC
1 GTATTTTTTTGTC
208 GTATTTTTTTG
1 GTATTTTTTTG
219 AAAAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.69
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:6781 original size:73 final size:73
Alignment explanation
Indices: 6688--6860 Score: 294
Period size: 73 Copynumber: 2.4 Consensus size: 73
6678 TATTTTCTTT
** * *
6688 TCTCT-CACTTTTCTTCCCAACCAAGCAAACTCAAAATTTATTTTCTTTTCACTTTTGCACTCTC
1 TCTCTCCACTTTTCCACCCAACCAAGCAAACTCAAAATTTATTTTCTTTTCACTTTTCCACACTC
6752 TCCTCCCA
66 TCCTCCCA
*
6760 TCTCTCCACTTTTCCACCCAACCAAGCAGACTCAAAATTTATTTTCTTTTCACTTTTCCACACTC
1 TCTCTCCACTTTTCCACCCAACCAAGCAAACTCAAAATTTATTTTCTTTTCACTTTTCCACACTC
6825 TCCTCCCA
66 TCCTCCCA
6833 TCTCTCCACTTTTCCACCCAACCAAGCA
1 TCTCTCCACTTTTCCACCCAACCAAGCA
6861 CACCCAAAGA
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 5 0.05
73 90 0.95
ACGTcount: A:0.23, C:0.38, G:0.03, T:0.36
Consensus pattern (73 bp):
TCTCTCCACTTTTCCACCCAACCAAGCAAACTCAAAATTTATTTTCTTTTCACTTTTCCACACTC
TCCTCCCA
Found at i:8193 original size:52 final size:52
Alignment explanation
Indices: 8115--8216 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
8105 TTTACCCTAA
*
8115 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGATACACTTGGCCT
1 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGCCT
* *
8167 CCTTTTTTCTATAAGACCAGAACCTATATTATCACAAAGACACATTTGGC
1 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGC
8217 TTTATCGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (52 bp):
CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGCCT
Found at i:10802 original size:25 final size:24
Alignment explanation
Indices: 10773--10820 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
10763 CCACCTTTTA
*
10773 TAATTGATTGATTGTTATTTTTAAT
1 TAATTGATTGATT-TAATTTTTAAT
* *
10798 TAATTTATTTATTTAATTTTTAA
1 TAATTGATTGATTTAATTTTTAA
10821 ACATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
TAATTGATTGATTTAATTTTTAAT
Found at i:12627 original size:7 final size:7
Alignment explanation
Indices: 12617--12650 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12607 TCTAAAATTT
12617 AAAAAAG
1 AAAAAAG
12624 AAAAAAG
1 AAAAAAG
12631 AAAAAAG
1 AAAAAAG
**
12638 GGAAAAG
1 AAAAAAG
12645 AAAAAA
1 AAAAAA
12651 TATATTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12762 original size:3 final size:3
Alignment explanation
Indices: 12756--12793 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
12746 TAGAAAAGTG
*
12756 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12794 AAAGAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18782 original size:6 final size:6
Alignment explanation
Indices: 18773--18803 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
18763 ATATATAAAC
*
18773 ACACAT ACACAT ACACAT ACACGT ACACAT A
1 ACACAT ACACAT ACACAT ACACAT ACACAT A
18804 TACTTCAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.32, G:0.03, T:0.16
Consensus pattern (6 bp):
ACACAT
Found at i:29671 original size:6 final size:6
Alignment explanation
Indices: 29660--29689 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29650 TATATAAACA
29660 GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG
1 GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG
29690 AAAGGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
GCAGAG
Found at i:30669 original size:21 final size:20
Alignment explanation
Indices: 30643--30686 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30633 GTTATTTGAT
30643 AAAAATACAAATATAAAAGTA
1 AAAAATACAAAT-TAAAAGTA
* *
30664 AAAAATATAAATTAAAATTA
1 AAAAATACAAATTAAAAGTA
30684 AAA
1 AAA
30687 TTAAGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATACAAATTAAAAGTA
Found at i:31487 original size:15 final size:13
Alignment explanation
Indices: 31446--31489 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
31436 ATATTTTTCA
*
31446 TTTTCTTCTTTA-
1 TTTTCTTTTTTAT
31458 TTTTCTTTTTTAT
1 TTTTCTTTTTTAT
31471 TTTTCTTTTAGTTAT
1 TTTTCTTTT--TTAT
31486 TTTT
1 TTTT
31490 GTTGTCTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.39
13 9 0.32
15 8 0.29
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTAT
Found at i:38681 original size:30 final size:30
Alignment explanation
Indices: 38622--38691 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
38612 GTTACAAAAA
38622 TAATCATTTAATTATATTTTTGTTCTATTT
1 TAATCATTTAATTATATTTTTGTTCTATTT
*
38652 TAATTATTTAATTATTAATTTTT-TT-TA-TT
1 TAATCATTTAATTA-T-ATTTTTGTTCTATTT
*
38681 TAATCACTTAA
1 TAATCATTTAA
38692 CTTTTCGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.31
30 15 0.43
31 3 0.09
32 6 0.17
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (30 bp):
TAATCATTTAATTATATTTTTGTTCTATTT
Found at i:38696 original size:21 final size:21
Alignment explanation
Indices: 38655--38696 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38645 TCTATTTTAA
* *
38655 TTATTTAATTATTAATTTTTT
1 TTATTTAATCATTAATCTTTT
38676 TTATTTAATCACTTAA-CTTTT
1 TTATTTAATCA-TTAATCTTTT
38697 CGAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTAATCATTAATCTTTT
Found at i:48757 original size:47 final size:47
Alignment explanation
Indices: 48703--48796 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
48693 CATCATCCAA
48703 GAGTAATGTTCTCTTCTTATCTACTGAGAAGTCTTTTTGGGTTTCTT
1 GAGTAATGTTCTCTTCTTATCTACTGAGAAGTCTTTTTGGGTTTCTT
48750 GAGTAATGTTCTCTTCTTATCTACTGAGAAGTCTTTTTGGGTTTCTT
1 GAGTAATGTTCTCTTCTTATCTACTGAGAAGTCTTTTTGGGTTTCTT
48797 TCTTTCTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (47 bp):
GAGTAATGTTCTCTTCTTATCTACTGAGAAGTCTTTTTGGGTTTCTT
Found at i:48777 original size:25 final size:25
Alignment explanation
Indices: 48703--48777 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
48693 CATCATCCAA
48703 GAGTAATGTTCTCTTCTTATCTACT
1 GAGTAATGTTCTCTTCTTATCTACT
* *
48728 GAG-AA-G-TCT-TT-TTGGGT-TTCTT
1 GAGTAATGTTCTCTTCTT--ATCTAC-T
48750 GAGTAATGTTCTCTTCTTATCTACT
1 GAGTAATGTTCTCTTCTTATCTACT
48775 GAG
1 GAG
48778 AAGTCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 8 0.22
23 3 0.08
24 3 0.08
25 11 0.30
26 4 0.11
27 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (25 bp):
GAGTAATGTTCTCTTCTTATCTACT
Found at i:70249 original size:25 final size:26
Alignment explanation
Indices: 70206--70266 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
70196 TAAATTTAAA
70206 AATTATTTAAATAAATTTTATA-TTTTT
1 AATT-TTT-AATAAATTTTATACTTTTT
*
70233 AATTTTTAATAATTTTTATACTTTTT
1 AATTTTTAATAAATTTTATACTTTTT
*
70259 TATTTTTA
1 AATTTTTA
70267 TATGCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 12 0.39
26 15 0.48
27 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
AATTTTTAATAAATTTTATACTTTTT
Done.