Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013697.1 Kokia drynarioides strain JFW-HI SEQ_128725, 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: 35114
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:8724 original size:26 final size:25
Alignment explanation
Indices: 8695--8754 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
8685 ATTTATCTCA
* *
8695 TAATATTTTATTAATTTAATATTAA-T
1 TAATATTTTAAT-ATTAAAT-TTAATT
8721 TAATGATTTTAATATTAAATTTAATT
1 TAAT-ATTTTAATATTAAATTTAATT
8747 TAATATTT
1 TAATATTT
8755 ATCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 8 0.27
26 15 0.50
27 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATATTTTAATATTAAATTTAATT
Found at i:8745 original size:36 final size:32
Alignment explanation
Indices: 8651--8754 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 32
8641 AAATCATATC
8651 ATTTTAATAGTTTTAATATTAAATTTAATTTAAT
1 ATTTT-ATA-TTTTAATATTAAATTTAATTTAAT
* ** **
8685 A-TTTATCTCATAATATTTTA-TTAATTTAAT
1 ATTTTATATTTTAATATTAAATTTAATTTAAT
8715 ATTAATTAATGATTTTAATATTAAATTTAATTTAAT
1 ATT--TT-AT-ATTTTAATATTAAATTTAATTTAAT
8751 ATTT
1 ATTT
8755 ATCTTGAAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
30 11 0.20
31 10 0.19
32 2 0.04
33 5 0.09
34 4 0.07
35 9 0.17
36 13 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
ATTTTATATTTTAATATTAAATTTAATTTAAT
Found at i:11404 original size:93 final size:93
Alignment explanation
Indices: 11292--11477 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
11282 TTAGCGTCTA
11292 AATGAAAATTCAAGCACATCAAAGGAGTTTACTGACATTGTACAGATTTCTATTTTATTCCACAG
1 AATGAAAATTCAAGCACATCAAAGGAGTTTACTGACATTGTACAGATTTCTATTTTATTCCACAG
11357 TTTTAAAAACCGACCTGCTTATAATCAT
66 TTTTAAAAACCGACCTGCTTATAATCAT
11385 AATGAAAATTCAAGCACATCAAAGGAGTTTACTGACATTGTACAGATTTCTATTTTATTCCACAG
1 AATGAAAATTCAAGCACATCAAAGGAGTTTACTGACATTGTACAGATTTCTATTTTATTCCACAG
11450 TTTTAAAAACCGACCTGCTTATAATCAT
66 TTTTAAAAACCGACCTGCTTATAATCAT
11478 TCACAAAGTA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (93 bp):
AATGAAAATTCAAGCACATCAAAGGAGTTTACTGACATTGTACAGATTTCTATTTTATTCCACAG
TTTTAAAAACCGACCTGCTTATAATCAT
Found at i:14193 original size:28 final size:28
Alignment explanation
Indices: 14149--14203 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
14139 TTCCGCGATA
* *
14149 GATTAACAATTTTGCCAATTTACCTCAG
1 GATTAACAATTTGGCCAATATACCTCAG
14177 GATTAACAATTTGGCCAATATACCTCA
1 GATTAACAATTTGGCCAATATACCTCA
14204 TGATGTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (28 bp):
GATTAACAATTTGGCCAATATACCTCAG
Found at i:19635 original size:346 final size:346
Alignment explanation
Indices: 18997--20031 Score: 1450
Period size: 346 Copynumber: 3.0 Consensus size: 346
18987 TTAGAAAGAA
* * * *
18997 ATACATTGCTTAATTTTATTT-TAT-TTTTCAAGTGGTTAGATTCTAGTTTCTATTTCGAATATT
1 ATACATTGCTCAATTTT-TTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGA-T
* * *
19060 TTTTTAGACCATTTGAAAAGTGAAGAAAAGCTTTCATCTTGTCTTTAATTTGTTAATATTGGTTC
64 TTTTTAGACAATTTGAAAAGTGAAGAAAAGCTTTCATCTTGTCTTTAATTTGTTAATGTTGGTCC
* * * * *
19125 GCTTGTAAGATAAAATATTGTGATTTTTTAAAAATAATAACAATAATTAAATATGTTAAATTAAA
129 ACTTGTAAGATAAGATATTGTGACTTTTTAAAAATAATAATAATAATTAAACATGTTAAATTAAA
* * **
19190 ATTTTATTACAGTAAAATTAATTTTATGTTAGAGTACACGTATCTTAACAAAATATTGGTTTTTG
194 ATTTTATTACAGTAAAATTAATTTTATGTTAGAGTACACATATATTAACAAAATATTAATTTTTG
* * * *
19255 AAAATTTTTAACTCAAAAAAATATGTTAAAATCTTTTAGGTACAACGTAAATAATATGAAAGCAA
259 AAAATTCTTAACTCAAAAAAGTATGTTGAAATCTTTTAGGTACAACGCAAATAATATGAAAGCAA
19320 AAGAAAGAAATATTAGTCTTTGC
324 AAGAAAGAAATATTAGTCTTTGC
19343 ATACATTGCTCAATTTTTTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGATTT
1 ATACATTGCTCAATTTTTTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGATTT
* *
19408 TTTAGACAATTTGAAAAGTGAAGAAAAGTTTTAATCTTGTCTTTAATTTGTTAATGTTGGTCCAC
66 TTTAGACAATTTGAAAAGTGAAGAAAAGCTTTCATCTTGTCTTTAATTTGTTAATGTTGGTCCAC
* *
19473 TTGTACGATAAGATATTGTGACTTTTTAAAAATAATAATAATAATTAAACATATTAAATTAAAAT
131 TTGTAAGATAAGATATTGTGACTTTTTAAAAATAATAATAATAATTAAACATGTTAAATTAAAAT
* * * *
19538 TTTATTACAGTAAAATTAATTTTATATTAGAATAAACATATATCAACAAAATATTAATTTTTGAA
196 TTTATTACAGTAAAATTAATTTTATGTTAGAGTACACATATATTAACAAAATATTAATTTTTGAA
*
19603 AATTCGTAACTCAAAAAAGTATGTTGAAATCTTTTAGGTACAACGCAAATAATATGAAAGTAAAG
261 AATTCTTAACTCAAAAAAGTATGTTGAAATCTTTTAGGTACAACGCAAATAATAT----G-AAA-
* *
19668 GAAAATCAGGACAATTAGAAAGAAATGTTATTCTTTGC
320 G-----C---A-AA--AGAAAGAAATATTAGTCTTTGC
* *
19706 ATACATTACTCAAATTTTTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGATTT
1 ATACATTGCTCAATTTTTTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGATTT
* * * ** *
19771 TTTAGATAATTTGAAATGTGAAGAAAAGCTTCCCCCTTGACTTTAATTTGTTAATGTTGGTCCAC
66 TTTAGACAATTTGAAAAGTGAAGAAAAGCTTTCATCTTGTCTTTAATTTGTTAATGTTGGTCCAC
* * * *
19836 TTATAAGATAAGATATTGTGACTTTTTAAAAATAATAATGATAATTAAACATGTTAGATTAAACT
131 TTGTAAGATAAGATATTGTGACTTTTTAAAAATAATAATAATAATTAAACATGTTAAATTAAAAT
* *
19901 TTTATTACA-T--AATTAATTTTATGTTGGAGTACATATATATTAACAAAATATTAATTTTTGAA
196 TTTATTACAGTAAAATTAATTTTATGTTAGAGTACACATATATTAACAAAATATTAATTTTTGAA
*
19963 AATTCTTAACTCAAAAAAGCATGTTGAAATCTTTTAGGTACAACGCAAATAATATGAAAGCAAAA
261 AATTCTTAACTCAAAAAAGTATGTTGAAATCTTTTAGGTACAACGCAAATAATATGAAAGCAAAA
20028 GAAA
326 GAAA
20032 ATCATGGCAA
Statistics
Matches: 615, Mismatches: 55, Indels: 41
0.86 0.08 0.06
Matches are distributed among these distances:
343 5 0.01
345 5 0.01
346 247 0.40
347 35 0.06
349 1 0.00
350 1 0.00
351 3 0.00
352 1 0.00
354 1 0.00
355 3 0.00
356 1 0.00
357 1 0.00
360 100 0.16
361 2 0.00
362 1 0.00
363 208 0.34
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (346 bp):
ATACATTGCTCAATTTTTTTATTTCTTTTCAAGTGGTTAGATTTTAGTTTCTATTTCGAAGATTT
TTTAGACAATTTGAAAAGTGAAGAAAAGCTTTCATCTTGTCTTTAATTTGTTAATGTTGGTCCAC
TTGTAAGATAAGATATTGTGACTTTTTAAAAATAATAATAATAATTAAACATGTTAAATTAAAAT
TTTATTACAGTAAAATTAATTTTATGTTAGAGTACACATATATTAACAAAATATTAATTTTTGAA
AATTCTTAACTCAAAAAAGTATGTTGAAATCTTTTAGGTACAACGCAAATAATATGAAAGCAAAA
GAAAGAAATATTAGTCTTTGC
Found at i:22064 original size:19 final size:20
Alignment explanation
Indices: 22036--22135 Score: 78
Period size: 20 Copynumber: 4.9 Consensus size: 20
22026 GAATTTTTTT
*
22036 AAATATTTTTTTTATTTTCA
1 AAATATTTTTTATATTTTCA
22056 AAATA-TTTTTATATTTTC-
1 AAATATTTTTTATATTTTCA
* * *
22074 TATTTTTTTAAAATTATATTTTCA
1 AAATATTTT----TTATATTTTCA
* * *
22098 AAATACTTTTTATATATTCG
1 AAATATTTTTTATATTTTCA
*
22118 AAATATTTTTTAGATTTT
1 AAATATTTTTTATATTTT
22136 TTAATTTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.03
19 15 0.25
20 29 0.48
23 10 0.16
24 5 0.08
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
AAATATTTTTTATATTTTCA
Found at i:22081 original size:17 final size:18
Alignment explanation
Indices: 22038--22083 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
22028 ATTTTTTTAA
22038 ATATTTTTTT-TATTTTC
1 ATATTTTTTTATATTTTC
* *
22055 AAAATATTTTTATATTTTC
1 -ATATTTTTTTATATTTTC
22074 -TATTTTTTTA
1 ATATTTTTTTA
22084 AAATTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
ATATTTTTTTATATTTTC
Found at i:22307 original size:21 final size:21
Alignment explanation
Indices: 22253--22309 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
22243 AATTAAAAAT
22253 ATTATATTTTTTACATTTTCGA
1 ATTAT-TTTTTTACATTTTCGA
* * *
22275 AATATTTGTTTACATTTTTGA
1 ATTATTTTTTTACATTTTCGA
22296 ATTATTTTTTTACA
1 ATTATTTTTTTACA
22310 AATGAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTATTTTTTTACATTTTCGA
Found at i:23292 original size:29 final size:30
Alignment explanation
Indices: 23259--23319 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
23249 TTTTGATTTT
*
23259 TTTCGTTTAT-TTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
*
23288 TTTCGTTTATATTTTAAATTTACTTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
23318 TT
1 TT
23320 ACTATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:31420 original size:2 final size:2
Alignment explanation
Indices: 31413--31438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31403 GAAGTGATTC
31413 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
31439 TTAGATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.