Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004202.1 Kokia drynarioides strain JFW-HI SEQ_117444, 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: 46457
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2238 original size:31 final size:31
Alignment explanation
Indices: 2203--2263 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
2193 TTTAAATTTT
2203 AATTTTAAT-TTT-AATACTTTTATTTTTTCCA
1 AATTTTAATATTTCAATA-TTTT-TTTTTTCCA
2234 AATTTTAATAATTTCAATATTTTTTTTTTC
1 AATTTTAAT-ATTTCAATATTTTTTTTTTC
2264 ATTTATATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 9 0.33
32 7 0.26
33 7 0.26
34 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (31 bp):
AATTTTAATATTTCAATATTTTTTTTTTCCA
Found at i:4536 original size:17 final size:17
Alignment explanation
Indices: 4498--4537 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4488 ACGTCTAGAG
4498 AATT-ACAATTATTTGT
1 AATTCACAATTATTTGT
4514 AA-TCACAA-TATATTGT
1 AATTCACAATTAT-TTGT
4530 AATTCACA
1 AATTCACA
4538 TAAATGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (17 bp):
AATTCACAATTATTTGT
Found at i:4755 original size:21 final size:20
Alignment explanation
Indices: 4731--4771 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4721 TTAAACTACT
*
4731 AAATGTTCTAAAAATTATAAA
1 AAATGTTATAAAAATT-TAAA
4752 AAATGTTATAAAAATTTAAA
1 AAATGTTATAAAAATTTAAA
4772 TATGTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATGTTATAAAAATTTAAA
Found at i:13441 original size:3 final size:3
Alignment explanation
Indices: 13433--13463 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13423 GTTAATAGCT
13433 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
13464 CTTTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16279 original size:6 final size:6
Alignment explanation
Indices: 16268--16313 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
16258 AGGTGGCTAC
16268 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
16314 CATTCCTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:27749 original size:40 final size:40
Alignment explanation
Indices: 27688--27793 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 40
27678 CATTTTTACA
* * **
27688 AAAACGCCGCAAAAGGT-AGAGCAATAACGGCGCTTAT-G
1 AAAACGCCGCTAAAGGTCAGAGCAATAACGACAATTATGG
* *
27726 AAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACAATTTTGGG
1 AAAA-CGCCGCTAAAGGTCAGAGCAATAACGACAATTAT-GG
*
27768 CAAACGCCGCTAAAGGTCAGAGCAAT
1 AAAACGCCGCTAAAGGTCAGAGCAAT
27794 TCAGAGCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 4 0.07
39 12 0.21
40 15 0.26
41 22 0.39
42 4 0.07
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (40 bp):
AAAACGCCGCTAAAGGTCAGAGCAATAACGACAATTATGG
Found at i:27753 original size:80 final size:79
Alignment explanation
Indices: 27647--27793 Score: 188
Period size: 80 Copynumber: 1.8 Consensus size: 79
27637 CGTTTGAGCA
* *
27647 GAAAACGCCGCAAAAGGTAAAGCAATAGCGGCATTTTTACAAAAACGCCGCAAAAGGT-AGAGCA
1 GAAAACGCCGCAAAAGGTAAAGCAATAGCGACAATTTTACAAAAACGCCGCAAAAGGTCAGAGCA
27711 ATAACGGCGCTTAT
66 ATAACGGCGCTTAT
* * **** *
27725 GAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACAATTTTGGGCAAACGCCGCTAAAGGTCAGAG
1 GAAAA-CGCCGCAAAAGGT-AAAGCAATAGCGACAATTTTACAAAAACGCCGCAAAAGGTCAGAG
27790 CAAT
64 CAAT
27794 TCAGAGCAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 5 0.09
79 12 0.21
80 32 0.56
81 8 0.14
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (79 bp):
GAAAACGCCGCAAAAGGTAAAGCAATAGCGACAATTTTACAAAAACGCCGCAAAAGGTCAGAGCA
ATAACGGCGCTTAT
Found at i:29524 original size:43 final size:43
Alignment explanation
Indices: 29470--29610 Score: 219
Period size: 43 Copynumber: 3.3 Consensus size: 43
29460 TTTGTTAATG
* * * *
29470 TTAGTGGCGTTTGTAGGAAAAGTGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
29513 TTAGAGGCGTTTGTGGGAAAGGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
29556 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAACGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
29599 TTAGCGGCGTTT
1 TTAGCGGCGTTT
29611 TTCCAAATAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:31073 original size:6 final size:6
Alignment explanation
Indices: 31062--31095 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
31052 TTTAAGAAAA
*
31062 GCTGCG GCTGCG GCTGCG GCTGCG GCTGCT GCTG
1 GCTGCG GCTGCG GCTGCG GCTGCG GCTGCG GCTG
31096 GGGACCAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.32, G:0.47, T:0.21
Consensus pattern (6 bp):
GCTGCG
Found at i:31414 original size:21 final size:20
Alignment explanation
Indices: 31388--31427 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
31378 TTGTTGAAAA
31388 CATAGA-GAGATTGAGGATTGT
1 CATAGATGAGA-TGA-GATTGT
31409 CATAGATGAGATGAGATTG
1 CATAGATGAGATGAGATTG
31428 GGTTTTGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (20 bp):
CATAGATGAGATGAGATTGT
Found at i:37526 original size:29 final size:31
Alignment explanation
Indices: 37480--37543 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
37470 GTTAATAATT
37480 TATAAGAATTAAATC-AAATCAAAATTTCATA
1 TATAAGAATTAAATCAAAATC-AAATTTCATA
* *
37511 TATAA-AATTACA-CAAAATCAAATTTTATA
1 TATAAGAATTAAATCAAAATCAAATTTCATA
37540 TATA
1 TATA
37544 CAAGTAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.47
30 11 0.37
31 5 0.17
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (31 bp):
TATAAGAATTAAATCAAAATCAAATTTCATA
Found at i:37556 original size:30 final size:30
Alignment explanation
Indices: 37495--37558 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
37485 GAATTAAATC
*
37495 AAATCAAAATTTCATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATAACACA
* * *
37525 AAATC-AAATTTTATATATACAAGTAATACA
1 AAATCAAAATTTCATATATA-AAATAACACA
37555 AAAT
1 AAAT
37559 TTTGAGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATAACACA
Found at i:44530 original size:37 final size:37
Alignment explanation
Indices: 44477--44550 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
44467 TATGTGCGAG
* *
44477 TATCGACTGAATGCAAAGATTGGCCTCAATGAATGGA
1 TATCGACTGAAAGCAAAGATTGGCCACAATGAATGGA
44514 TATCGACTGAAAGCAAAGATTGGCCACAATGAATGGA
1 TATCGACTGAAAGCAAAGATTGGCCACAATGAATGGA
44551 CTTGCTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (37 bp):
TATCGACTGAAAGCAAAGATTGGCCACAATGAATGGA
Found at i:45185 original size:22 final size:22
Alignment explanation
Indices: 45160--45205 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
45150 AAATGGTAAC
*
45160 AAAATAGTAAGAAAACAACAAG
1 AAAATAGCAAGAAAACAACAAG
* *
45182 AAAATAGCAGGAAAACAGCAAG
1 AAAATAGCAAGAAAACAACAAG
45204 AA
1 AA
45206 TACGGAGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.11, G:0.17, T:0.07
Consensus pattern (22 bp):
AAAATAGCAAGAAAACAACAAG
Done.