Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013645.1 Kokia drynarioides strain JFW-HI SEQ_128673, 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: 58310
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--50 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT AT -T AT A
1 AT AT AT AT A
51 AAATAAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2313 original size:19 final size:18
Alignment explanation
Indices: 2285--2323 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
2275 TTATGCACAT
2285 TAATTTTATTATTTTTAA
1 TAATTTTATTATTTTTAA
2303 TAATATTTATTATTTTTAA
1 TAAT-TTTATTATTTTTAA
2322 TA
1 TA
2324 TTTAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTTTATTATTTTTAA
Found at i:6489 original size:17 final size:17
Alignment explanation
Indices: 6463--6511 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
6453 TTTTATGAAT
6463 TTCT-CAATTTCAATTG
1 TTCTACAATTTCAATTG
6479 TTCTACAATTTCAATTG
1 TTCTACAATTTCAATTG
*
6496 TTCTACAATTCCAATT
1 TTCTACAATTTCAATT
6512 TTGTGAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 4 0.13
17 27 0.87
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (17 bp):
TTCTACAATTTCAATTG
Found at i:15235 original size:26 final size:25
Alignment explanation
Indices: 15192--15241 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
15182 AGATGCCTAG
*
15192 TTCAGGGACTAATATGGACAAAAAAA
1 TTCAGGGACAAATATGGA-AAAAAAA
15218 TTCAGGGACCAAAT-TGGAAAAAAA
1 TTCAGGGA-CAAATATGGAAAAAAA
15242 GTTGCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 12 0.55
27 4 0.18
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
TTCAGGGACAAATATGGAAAAAAAA
Found at i:15943 original size:30 final size:29
Alignment explanation
Indices: 15899--15965 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
15889 AAATTTTAAA
*
15899 TTAATAAAGAT-AAAATTATATTTTAACCTT
1 TTAA-AAAGATAAAAATT-TAATTTAACCTT
*
15929 TTAAAAATGATAAAAATTTAATTTAATCTT
1 TTAAAAA-GATAAAAATTTAATTTAACCTT
15959 TTAAAAA
1 TTAAAAA
15966 CTATAAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 3 0.09
30 24 0.73
31 6 0.18
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (29 bp):
TTAAAAAGATAAAAATTTAATTTAACCTT
Found at i:19502 original size:15 final size:15
Alignment explanation
Indices: 19484--19524 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
19474 GGAGCAGGTT
*
19484 TTGGAGAAGCACCTC
1 TTGGAGAAGCAACTC
19499 TTGGAGAAGCAACTC
1 TTGGAGAAGCAACTC
19514 TTGGAGAAGCA
1 TTGGAGAAGCA
19525 GCTCGAGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (15 bp):
TTGGAGAAGCAACTC
Found at i:19549 original size:6 final size:6
Alignment explanation
Indices: 19540--19564 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19530 AGGGGGAGGG
19540 GGTGGA GGTGGA GGTGGA GGTGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA G
19565 AAGCAACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:19617 original size:15 final size:15
Alignment explanation
Indices: 19597--19643 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19587 TCGTGGAGGG
* *
19597 GAAGCAGCCCTTGGA
1 GAAGCAACCCTAGGA
19612 GAAGCAACCCTAGGA
1 GAAGCAACCCTAGGA
* *
19627 GAGGCAACCCTCGGA
1 GAAGCAACCCTAGGA
19642 GA
1 GA
19644 TGGACCCCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.32, T:0.09
Consensus pattern (15 bp):
GAAGCAACCCTAGGA
Found at i:25569 original size:29 final size:29
Alignment explanation
Indices: 25538--25642 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 29
25528 ATTTTTTAAA
25538 TTTTAAAAATTTTAAAAATATAGAAATTAT
1 TTTTAAAAATTTTAAAAATATA-AAATTAT
25568 TTTTAAAAA--TTAAAAATCAATAAAATTA-
1 TTTTAAAAATTTTAAAAAT--ATAAAATTAT
* *
25596 --TTAAAAATGTATAAAAAGTATAAAAATAT
1 TTTTAAAAAT-TTTAAAAA-TATAAAATTAT
*
25625 TTTTTAAAATTTTAAAAA
1 TTTTAAAAATTTTAAAAA
25643 GTAATTAAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
26 7 0.11
28 16 0.26
29 12 0.19
30 20 0.32
31 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTTAAAAATTTTAAAAATATAAAATTAT
Found at i:31100 original size:27 final size:30
Alignment explanation
Indices: 31068--31123 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
31058 TAAAATAAAA
*
31068 TTAAAA-TTAAAAA-AGCAT-TTTATTAAT
1 TTAAAACTTAAAAATAACATATTTATTAAT
31095 TTAAAACTTAAAAATAACATATTTATTAA
1 TTAAAACTTAAAAATAACATATTTATTAA
31124 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 7 0.28
29 4 0.16
30 8 0.32
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAAACTTAAAAATAACATATTTATTAAT
Found at i:38531 original size:21 final size:21
Alignment explanation
Indices: 38489--38531 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38479 GTAGTCATCC
* * *
38489 TTAATTTTTTCAATCTCCTTT
1 TTAATATTTTCAACCTCATTT
*
38510 TTAATATTTTCGACCTCATTT
1 TTAATATTTTCAACCTCATTT
38531 T
1 T
38532 GCCAGGTTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAATATTTTCAACCTCATTT
Found at i:39859 original size:22 final size:22
Alignment explanation
Indices: 39832--39881 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
39822 GATTTTAATT
39832 TTTAAAAATTAT-AAAATGATTA
1 TTTAAAAATT-TGAAAATGATTA
* **
39854 TTTAAATATTTGAAAATTTTTA
1 TTTAAAAATTTGAAAATGATTA
39876 TTTAAA
1 TTTAAA
39882 TTATTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTAAAAATTTGAAAATGATTA
Found at i:49245 original size:25 final size:25
Alignment explanation
Indices: 49184--49299 Score: 148
Period size: 25 Copynumber: 4.8 Consensus size: 25
49174 TTCTGTTCAG
* *
49184 CACTTTGTGTGCTTCTGTT---CAG
1 CACTATGTGTGCTTCTGTTACCCAA
* *
49206 CACTATGTGTGCTTCTGTTATCCAG
1 CACTATGTGTGCTTCTGTTACCCAA
* *
49231 TACTGTGTGTGCTTCTGTTACCCAA
1 CACTATGTGTGCTTCTGTTACCCAA
*
49256 CACTGTGTGTGCTTCTGTTACCCAA
1 CACTATGTGTGCTTCTGTTACCCAA
49281 CACTATGTGTGCTTCTGTT
1 CACTATGTGTGCTTCTGTT
49300 TCCCTAGCAC
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
22 18 0.21
25 66 0.79
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (25 bp):
CACTATGTGTGCTTCTGTTACCCAA
Found at i:49323 original size:75 final size:72
Alignment explanation
Indices: 49184--49325 Score: 171
Period size: 75 Copynumber: 1.9 Consensus size: 72
49174 TTCTGTTCAG
* * * * * *
49184 CACTTTGTGTGCTTCTGTTCAGCACTATGTGTGCTTCTGTTATCCAGTACTGTGTGTGCTTCTGT
1 CACTGTGTGTGCTTCTGTTCAACACTATGTGTGCTTCTGTTATCCAGCACTGTATGTACCTCTGT
49249 TACCCAA
66 TACCCAA
49256 CACTGTGTGTGCTTCTGTTACCCAACACTATGTGTGCTTCTGTT-TCCCTAGCACT-TATGTACC
1 CACTGTGTGTGCTTCTGTT---CAACACTATGTGTGCTTCTGTTAT-CC-AGCACTGTATGTACC
49319 TCTGTTA
61 TCTGTTA
49326 AGTACTTCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
72 18 0.31
74 1 0.02
75 35 0.59
76 5 0.08
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (72 bp):
CACTGTGTGTGCTTCTGTTCAACACTATGTGTGCTTCTGTTATCCAGCACTGTATGTACCTCTGT
TACCCAA
Found at i:57711 original size:26 final size:25
Alignment explanation
Indices: 57681--57744 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
57671 AGGAGACATA
* *
57681 AAATTAAAAATAATTAGTATAAATTT
1 AAATTAAAAATAATGAGTA-AAAGTT
*
57707 AAATTTAAAATAATGAGTAAAAGTT
1 AAATTAAAAATAATGAGTAAAAGTT
* *
57732 ATATTGAAAATAA
1 AAATTAAAAATAA
57745 AACCTCTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (25 bp):
AAATTAAAAATAATGAGTAAAAGTT
Found at i:57934 original size:24 final size:24
Alignment explanation
Indices: 57894--57940 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
57884 TTCAATCTCT
*
57894 TTTTTATATTAAAATTTGAAAATG
1 TTTTTATATTAAAATTTAAAAATG
* *
57918 TTTTTATATTCATATTTAAAAAT
1 TTTTTATATTAAAATTTAAAAAT
57941 TTATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTTATATTAAAATTTAAAAATG
Done.