Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013010.1 Kokia drynarioides strain JFW-HI SEQ_128028, 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: 507880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 307 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:422502 original size:2 final size:2
Alignment explanation
Indices: 422495--422519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
422485 CAAATGGTGC
422495 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
422520 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:422925 original size:8 final size:8
Alignment explanation
Indices: 422908--422937 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
422898 TACTTTTTAA
*
422908 AAAAAATT
1 AAAAATTT
422916 AAAAATTT
1 AAAAATTT
422924 AAAAATTT
1 AAAAATTT
422932 AAAAAT
1 AAAAAT
422938 ATCTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAAATTT
Found at i:422965 original size:20 final size:19
Alignment explanation
Indices: 422934--422994 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
422924 AAAAATTTAA
422934 AAATATCTTTTTATAATTTTT
1 AAATA-CTTTTT-TAATTTTT
422955 AAATAC-TTTTT-ATTTTT
1 AAATACTTTTTTAATTTTT
422972 AATATA-TTTTTTGAATTTTT
1 AA-ATACTTTTTT-AATTTTT
422992 AAA
1 AAA
422995 ATTTTAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 8 0.22
18 9 0.25
19 5 0.14
20 9 0.25
21 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (19 bp):
AAATACTTTTTTAATTTTT
Found at i:435058 original size:17 final size:17
Alignment explanation
Indices: 435036--435070 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
435026 GTTGGAAGAG
435036 AAGAGAATAAAGGAAAC
1 AAGAGAATAAAGGAAAC
435053 AAGAGAATAAAGGAAAC
1 AAGAGAATAAAGGAAAC
435070 A
1 A
435071 TTCTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.23, T:0.06
Consensus pattern (17 bp):
AAGAGAATAAAGGAAAC
Found at i:440987 original size:31 final size:31
Alignment explanation
Indices: 440949--441011 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
440939 ATACTCAAAA
440949 AAGTGAGACAAAATGCATACCATAATAGTGT
1 AAGTGAGACAAAATGCATACCATAATAGTGT
*
440980 AAGTGAGACAAAATGCTTACCATAATAGTGT
1 AAGTGAGACAAAATGCATACCATAATAGTGT
441011 A
1 A
441012 CTACAAGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (31 bp):
AAGTGAGACAAAATGCATACCATAATAGTGT
Found at i:443036 original size:17 final size:19
Alignment explanation
Indices: 442998--443049 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
442988 AAAATTTAAA
442998 AATATATCTTGTTATAATTTTT
1 AATATATCTT-TT-T-ATTTTT
443020 AA-ATA-CTTTTTATTTTT
1 AATATATCTTTTTATTTTT
443037 AATATATCTTTTT
1 AATATATCTTTTT
443050 TGAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
19 8 0.29
20 3 0.11
21 3 0.11
22 2 0.07
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
AATATATCTTTTTATTTTT
Found at i:443049 original size:20 final size:20
Alignment explanation
Indices: 442998--443060 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 20
442988 AAAATTTAAA
*
442998 AATATATCTTGTTATAATTTTT
1 AATATATCTT-TT-TTATTTTT
443020 AA-ATA-C-TTTTTATTTTT
1 AATATATCTTTTTTATTTTT
443037 AATATATCTTTTTTGAATTTTT
1 AATATATCTTTTTT--ATTTTT
443059 AA
1 AA
443061 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 9 0.26
18 5 0.14
19 2 0.06
20 6 0.17
21 3 0.09
22 10 0.29
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
AATATATCTTTTTTATTTTT
Found at i:446344 original size:21 final size:21
Alignment explanation
Indices: 446320--446367 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
446310 ATAATAGCAT
* *
446320 AATCCAAATATAAATTTTAGA
1 AATCCAAACATAAAGTTTAGA
*
446341 AATCCAAACATAAAGTTTATA
1 AATCCAAACATAAAGTTTAGA
446362 AATCCA
1 AATCCA
446368 GATTACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (21 bp):
AATCCAAACATAAAGTTTAGA
Found at i:451716 original size:3 final size:3
Alignment explanation
Indices: 451710--451740 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
451700 TTAAAAAAGG
451710 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
451741 TTATTGTTAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:453557 original size:15 final size:16
Alignment explanation
Indices: 453539--453571 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
453529 AAAATTCAAT
453539 AAAAAAAAAGGT-TCA
1 AAAAAAAAAGGTCTCA
*
453554 AAAACAAAAGGTCTCA
1 AAAAAAAAAGGTCTCA
453570 AA
1 AA
453572 CGATATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAAAAAAGGTCTCA
Found at i:454923 original size:15 final size:16
Alignment explanation
Indices: 454903--454936 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
454893 AAGTTAAATT
*
454903 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
454918 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
454934 AAT
1 AAT
454937 AAGATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:457514 original size:101 final size:103
Alignment explanation
Indices: 457332--457567 Score: 363
Period size: 101 Copynumber: 2.3 Consensus size: 103
457322 ATTTCATTTA
* * *
457332 ATACTCACGATGACACATAGTCATTGGACCTCT-TAATCCGTAAAGGAATCATATACTCACGATG
1 ATACTCACGATGACACACAGTCATCGAACCT-TATAATCCGTAAAGGAATCATATACTCACGATG
*
457396 ACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
65 ACACATAGTCATCGGACCTCATAATCCGT-AAGGATTCAT
* *
457436 ATACTCACTAT-A-ACACAGTCATCGAACCTTATAATCCGT-AAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACACAGTCATCGAACCTTATAATCCGTAAAGGAATCATATACTCACGATGA
457498 CACATAGTCATCGGACCTCATAATCCGTAAGGATTCAT
66 CACATAGTCATCGGACCTCATAATCCGTAAGGATTCAT
*
457536 ATACTCACGATGACACATAGTCATCGAACCTT
1 ATACTCACGATGACACACAGTCATCGAACCTT
457568 TTTCATTTAC
Statistics
Matches: 121, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
100 20 0.17
101 51 0.42
102 39 0.32
103 1 0.01
104 10 0.08
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (103 bp):
ATACTCACGATGACACACAGTCATCGAACCTTATAATCCGTAAAGGAATCATATACTCACGATGA
CACATAGTCATCGGACCTCATAATCCGTAAGGATTCAT
Found at i:457528 original size:51 final size:52
Alignment explanation
Indices: 457332--457566 Score: 361
Period size: 51 Copynumber: 4.6 Consensus size: 52
457322 ATTTCATTTA
* * *
457332 ATACTCACGATGACACATAGTCATTGGACCTCTTAATCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
457384 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
457436 ATACTCACTAT-A-ACACAGTCATCGAACCTTATAATCCGT-AAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
457485 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
457536 ATACTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
457567 TTTTCATTTA
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
49 20 0.12
50 24 0.14
51 65 0.38
52 60 0.36
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:460929 original size:43 final size:43
Alignment explanation
Indices: 460882--460969 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
460872 ATATTACCAA
*
460882 AAATATGTGGACAAGCAA-TCAGCATTTGCAGTCAAGCTGCCAG
1 AAATATGTGGACAAGCAACT-AGCAATTGCAGTCAAGCTGCCAG
* *
460925 AAATATGTGGACAAGCCACTAGTAATTGCAGTCAAGCTGCCAG
1 AAATATGTGGACAAGCAACTAGCAATTGCAGTCAAGCTGCCAG
460968 AA
1 AA
460970 TTTTGTGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (43 bp):
AAATATGTGGACAAGCAACTAGCAATTGCAGTCAAGCTGCCAG
Found at i:468359 original size:28 final size:28
Alignment explanation
Indices: 468315--468377 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
468305 ACGTGCACAG
468315 TTTCATACAATCCCTTCTCATATTTATA
1 TTTCATACAATCCCTTCTCATATTTATA
*
468343 TTTCATACAATCTCTTCTCATATTTATA
1 TTTCATACAATCCCTTCTCATATTTATA
468371 TTT-ATAC
1 TTTCATAC
468378 TAACTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.12
28 30 0.88
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTCATACAATCCCTTCTCATATTTATA
Found at i:471717 original size:12 final size:12
Alignment explanation
Indices: 471700--471734 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
471690 TTTTATAATT
471700 TTTTTCTTCTTG
1 TTTTTCTTCTTG
471712 TTTTTCTTCTTG
1 TTTTTCTTCTTG
471724 TTTTTCTTCTT
1 TTTTTCTTCTT
471735 AAAGTCGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (12 bp):
TTTTTCTTCTTG
Found at i:473778 original size:122 final size:122
Alignment explanation
Indices: 473561--473806 Score: 343
Period size: 122 Copynumber: 2.0 Consensus size: 122
473551 TGGTTCACAT
* * *
473561 GGGCTGGGACACGACCGTGTGACCCTATTTCGATTTGACACACGATCTAGCCCACGATTTGACAC
1 GGGCTAGGACACGACCGCGTGACCCTATTTCGAGTTGACACACGATCTAGCCCACGATTTGACAC
*
473626 ACAGGCATGTGGGGTATTTTCACATGTTCACATAGCTAGTGACATGGTTTGTGACAC
66 ACAGGCATGTGGGGTATTTTCACATGTTCACATAGCTAGTCACATGGTTTGTGACAC
** * * * *
473683 GGGCTAGGACACGATTGCGTGACCCTTTTTTGAGTTGACACAC-AGTCTAGCCCAGGGTTTGACA
1 GGGCTAGGACACGACCGCGTGACCCTATTTCGAGTTGACACACGA-TCTAGCCCACGATTTGACA
** *
473747 CAC-GAGCATGTGGGGTATTTTCGTATGTTCACATGGCTAGTCACATGGTTTGTGACAC
65 CACAG-GCATGTGGGGTATTTTCACATGTTCACATAGCTAGTCACATGGTTTGTGACAC
473805 GG
1 GG
473807 TTGTGTATGG
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
121 2 0.02
122 107 0.98
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (122 bp):
GGGCTAGGACACGACCGCGTGACCCTATTTCGAGTTGACACACGATCTAGCCCACGATTTGACAC
ACAGGCATGTGGGGTATTTTCACATGTTCACATAGCTAGTCACATGGTTTGTGACAC
Found at i:477452 original size:92 final size:91
Alignment explanation
Indices: 477295--477496 Score: 244
Period size: 92 Copynumber: 2.2 Consensus size: 91
477285 TCAATGACAA
* * *
477295 ATGCACATAGTGTAAAGCCCGTAAGCTAAATATTCTCCCCTGTTAACTTACCAGATTGCTCATAA
1 ATGCACATAGTGCAAAGCCCGTAAGCTAAATATTCACCCCAGTTAAC-TACCAGATTGCTCATAA
*
477360 GAGTTATTCCAACCGATAACACACCAG
65 GAGCTATTCCAACCGATAACACACCAG
* * * *
477387 ATGCATATAGTGCAAAGCCCGTAGGCTAAATATTCACCCTCAGTTCAA-TGCCATATTGCTCATA
1 ATGCACATAGTGCAAAGCCCGTAAGCTAAATATTCACCC-CAGTT-AACTACCAGATTGCTCATA
* * * **
477451 AGAGCTATTTCGACCGTTAACATGCCAG
64 AGAGCTATTCCAACCGATAACACACCAG
*
477479 ATACACATAGTGCAAAGC
1 ATGCACATAGTGCAAAGC
477497 TCGATTTTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 87 0.94
93 4 0.04
94 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (91 bp):
ATGCACATAGTGCAAAGCCCGTAAGCTAAATATTCACCCCAGTTAACTACCAGATTGCTCATAAG
AGCTATTCCAACCGATAACACACCAG
Found at i:488341 original size:18 final size:18
Alignment explanation
Indices: 488318--488354 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
488308 ACATGCATTT
488318 TATTTAGTTGTCATTGCA
1 TATTTAGTTGTCATTGCA
*
488336 TATTTATTTGTCATTGCA
1 TATTTAGTTGTCATTGCA
488354 T
1 T
488355 TTCATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTTAGTTGTCATTGCA
Found at i:488363 original size:17 final size:18
Alignment explanation
Indices: 488325--488363 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
488315 TTTTATTTAG
*
488325 TTGTCATTGCATATTTAT
1 TTGTCATTGCATATTCAT
488343 TTGTCATTGCAT-TTCAT
1 TTGTCATTGCATATTCAT
488360 TTGT
1 TTGT
488364 TAGTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (18 bp):
TTGTCATTGCATATTCAT
Found at i:488971 original size:10 final size:10
Alignment explanation
Indices: 488958--488991 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
488948 AAAAATTCAC
488958 AAAAAGAAAG
1 AAAAAGAAAG
488968 AAAAAGAAAG
1 AAAAAGAAAG
*
488978 AAGAAGAAAAG
1 AAAAAG-AAAG
488989 AAA
1 AAA
488992 TATATTGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:496134 original size:38 final size:38
Alignment explanation
Indices: 496081--496179 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
496071 CAAAGTAACA
* *
496081 TCCAAATTTGAGCCCAAAACTGTC-TCCACATGAGTACT
1 TCCAAATTTGCGCCCAAAACTGTCGT-CACATGAGCACT
* * *
496119 TCCAAATTTGCGCCCACAACTATCGTCGCATGAGCACT
1 TCCAAATTTGCGCCCAAAACTGTCGTCACATGAGCACT
*
496157 TCCAAA-TTGCACCCAAAACTGTC
1 TCCAAATTTGCGCCCAAAACTGTC
496180 ACCGCAGGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
37 14 0.27
38 37 0.71
39 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.24
Consensus pattern (38 bp):
TCCAAATTTGCGCCCAAAACTGTCGTCACATGAGCACT
Found at i:504693 original size:18 final size:18
Alignment explanation
Indices: 504654--504707 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
504644 GTGGAAATAT
*
504654 CTCAAACGATCCAGTGATG
1 CTCAAACGAGCCAGT-ATG
** *
504673 CTCTTACGAGCTAGTATG
1 CTCAAACGAGCCAGTATG
504691 CTCAAACGAGCCAGTAT
1 CTCAAACGAGCCAGTAT
504708 ACTATTCCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (18 bp):
CTCAAACGAGCCAGTATG
Found at i:506937 original size:37 final size:39
Alignment explanation
Indices: 506879--506990 Score: 104
Period size: 38 Copynumber: 2.8 Consensus size: 39
506869 CTGATAGTTT
506879 GAAGCAATAA-AGTGACACCCAGTGTCTCATCGACCTAGCC
1 GAAGCAA-AATAG-GACACCCAGTGTCTCATCGACCTAGCC
* * ** * *
506919 GAAGCAAAGT-GG-TACCCAGTACCTCATCGAATCTATCC
1 GAAGCAAAATAGGACACCCAGTGTCTCATCG-ACCTAGCC
*
506957 GAAGTAAAATAAGGACACCCAGTGTCTCATCGAC
1 GAAGCAAAAT-AGGACACCCAGTGTCTCATCGAC
506991 TCAAGGTCGA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
37 14 0.25
38 15 0.27
39 2 0.04
40 10 0.18
41 14 0.25
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (39 bp):
GAAGCAAAATAGGACACCCAGTGTCTCATCGACCTAGCC
Done.