Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011286.1 Kokia drynarioides strain JFW-HI SEQ_126265, 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: 83988
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:13730 original size:18 final size:18
Alignment explanation
Indices: 13708--13772 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
13698 AAAAATTAAG
*
13708 AAAAACATAAATTAAAATT
1 AAAAA-ATAAATAAAAATT
*
13727 AAAAAATATATAAAAATT
1 AAAAAATAAATAAAAATT
** * *
13745 CGAAAATGATTAAAAATT
1 AAAAAATAAATAAAAATT
13763 ATAAAAATAA
1 A-AAAAATAA
13773 TAATAATATA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
18 24 0.69
19 11 0.31
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAAATAAATAAAAATT
Found at i:16097 original size:14 final size:15
Alignment explanation
Indices: 16075--16104 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16065 ATTTTTTCTC
16075 TTCTCCTTCTTCTTT
1 TTCTCCTTCTTCTTT
16090 TTCT-CTTCTTCTTT
1 TTCTCCTTCTTCTTT
16104 T
1 T
16105 ACTGCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTCCTTCTTCTTT
Found at i:18354 original size:61 final size:62
Alignment explanation
Indices: 18279--18400 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
18269 TTTCAGGAAT
*
18279 ATAATTTAACTCCTTTTTTT-TTATTACTGTTAACGAGGAAATTAAAACTTCCTGATTGTAG
1 ATAATTTAACTCCTTTTTTTATTATTACTGTTAACGAGGAAATTAAAACTTCCTAATTGTAG
*
18340 ATAATTTAACTCCTTTTTTTATTATTATTGTTAACGAGGAAATTAAAACTTCCTAATTGTA
1 ATAATTTAACTCCTTTTTTTATTATTACTGTTAACGAGGAAATTAAAACTTCCTAATTGTA
18401 ATCAATATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 20 0.34
62 38 0.66
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (62 bp):
ATAATTTAACTCCTTTTTTTATTATTACTGTTAACGAGGAAATTAAAACTTCCTAATTGTAG
Found at i:23415 original size:21 final size:21
Alignment explanation
Indices: 23390--23458 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
23380 GAGTCGACAT
23390 ACAGAATAAAGATTCAAGTAG
1 ACAGAATAAAGATTCAAGTAG
* * * * * *
23411 ACAGATTAGGTAGAGTCGA-CAT
1 ACAGAATA--AAGATTCAAGTAG
23433 ACAGAATAAAGATTCAAGTAG
1 ACAGAATAAAGATTCAAGTAG
23454 ACAGA
1 ACAGA
23459 TTAGGTAGAG
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
20 6 0.18
21 13 0.39
22 8 0.24
23 6 0.18
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.19
Consensus pattern (21 bp):
ACAGAATAAAGATTCAAGTAG
Found at i:23429 original size:43 final size:43
Alignment explanation
Indices: 23368--23540 Score: 328
Period size: 43 Copynumber: 4.0 Consensus size: 43
23358 TTCATTGCAA
*
23368 ACAGATTAGGGAGAGTCGACATACAGAATAAAGATTCAAGTAG
1 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
23411 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
1 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
*
23454 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAC
1 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
23497 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
1 ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
23540 A
1 A
23541 TATAGATTTG
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 127 1.00
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (43 bp):
ACAGATTAGGTAGAGTCGACATACAGAATAAAGATTCAAGTAG
Found at i:25000 original size:9 final size:9
Alignment explanation
Indices: 24982--25016 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
24972 TGACCAAAAA
24982 TAAATATTT
1 TAAATATTT
*
24991 TAAATTTTT
1 TAAATATTT
25000 TATAATATTT
1 TA-AATATTT
25010 TAAATAT
1 TAAATAT
25017 GATTAGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAAATATTT
Found at i:25077 original size:18 final size:18
Alignment explanation
Indices: 25051--25129 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
25041 TCAAATATAT
* *
25051 TAATTTTTACTATTTTTA
1 TAATATTTAATATTTTTA
*
25069 TAATATTTAATA-TTTAA
1 TAATATTTAATATTTTTA
*
25086 T-ATTTTTAATAATTTTTA
1 TAATATTTAAT-ATTTTTA
*
25104 TAGAT-TTTATTATTTTTA
1 TA-ATATTTAATATTTTTA
*
25122 TAAGATTT
1 TAATATTT
25130 TAAAAAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 8 0.16
17 7 0.14
18 27 0.55
19 5 0.10
20 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATATTTAATATTTTTA
Found at i:25101 original size:35 final size:34
Alignment explanation
Indices: 25053--25118 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
25043 AAATATATTA
*
25053 ATTTTTACTATTTTTATA-ATATTTAATATTTAAT
1 ATTTTTAATATTTTTATAGAT-TTTAATATTTAAT
*
25087 ATTTTTAATAATTTTTATAGATTTTATTATTT
1 ATTTTTAAT-ATTTTTATAGATTTTAATATTT
25119 TTATAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 18 0.64
36 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (34 bp):
ATTTTTAATATTTTTATAGATTTTAATATTTAAT
Found at i:32449 original size:25 final size:25
Alignment explanation
Indices: 32415--32486 Score: 110
Period size: 25 Copynumber: 2.8 Consensus size: 25
32405 CGAAATACTA
32415 AACAGAGAACACATAAGTGCTGGGC
1 AACAGAGAACACATAAGTGCTGGGC
*
32440 AACAGAGAACACATAAGTGATGGGC
1 AACAGAGAACACATAAGTGCTGGGC
32465 AACAGAGAGCACACA-AAGTGCT
1 AACAGAGA--ACACATAAGTGCT
32487 AAACAGAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 32 0.74
26 6 0.14
27 5 0.12
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.11
Consensus pattern (25 bp):
AACAGAGAACACATAAGTGCTGGGC
Found at i:32495 original size:23 final size:23
Alignment explanation
Indices: 32467--32605 Score: 148
Period size: 23 Copynumber: 6.3 Consensus size: 23
32457 TGATGGGCAA
*
32467 CAGAGAGCACACAAAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
*
32490 CAGAGAGTACACAAA--G-T-AT
1 CAGAGAGCACACAAAGTGCTAAT
*
32509 ---TGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
32529 TAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* * *
32552 TAGATAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
32575 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
32598 CAGAGAGC
1 CAGAGAGC
32606 GCGCTAGTGT
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.10
18 1 0.01
19 2 0.02
20 3 0.03
21 1 0.01
23 81 0.83
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:32525 original size:39 final size:39
Alignment explanation
Indices: 32471--32587 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 39
32461 GGGCAACAGA
*
32471 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTATT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTATT
** *
32510 GAGCACACAAAGTGCTAATTAGAGAGCACACGAAGTGCTAATT
1 GAGCACACAAAGTGCTAAACAGAGAGCACAC-AA-AG-T-ATT
* *
32553 AGATAGCACACACAGTGCTAATCAGAGAGCACACA
1 -G--AGCACACAAAGTGCTAAACAGAGAGCACACA
32588 CAGTGCTAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
39 28 0.43
40 2 0.03
41 1 0.02
42 1 0.02
43 3 0.05
44 1 0.02
45 1 0.02
46 28 0.43
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTATT
Found at i:36458 original size:87 final size:84
Alignment explanation
Indices: 36302--36462 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 84
36292 TACATGCATA
* *
36302 AGGTTGAGTTGTTACTCTTAATGAGTTCATATTCCAAGTTGGGTGGTCCTATTGAGACGAACTTA
1 AGGTTGAGTTATTACTCTTAATGAATTCATATTCCAAGTTGGGTGGTCCTATTGAGACGAACTTA
36367 ATGAATTCACCGACATGAG
66 ATGAATTCACCGACATGAG
* * * *
36386 AGGTTGAGTTTATTACTTTTAATGAATTCATA-TCCTAAAATTTGGGTGGTCCTATTGCGACGGA
1 AGGTTGAG-TTATTACTCTTAATGAATTCATATTCC---AAGTTGGGTGGTCCTATTGAGACGAA
*
36450 CTTGATGAATTCA
62 CTTAATGAATTCA
36463 TCGAACTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
84 11 0.17
85 20 0.30
87 35 0.53
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
AGGTTGAGTTATTACTCTTAATGAATTCATATTCCAAGTTGGGTGGTCCTATTGAGACGAACTTA
ATGAATTCACCGACATGAG
Found at i:43917 original size:10 final size:9
Alignment explanation
Indices: 43876--43913 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
43866 TATATTTATT
43876 TATTTAAAA
1 TATTTAAAA
43885 T-TTTAAAAA
1 TATTT-AAAA
*
43894 TATTAAAAA
1 TATTTAAAA
43903 TATTTAAAA
1 TATTTAAAA
43912 TA
1 TA
43914 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.12
9 20 0.80
10 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATTTAAAA
Found at i:44178 original size:56 final size:56
Alignment explanation
Indices: 44065--44179 Score: 169
Period size: 56 Copynumber: 2.1 Consensus size: 56
44055 TTTAGAAAAA
* *
44065 TTAAATTTGAAATAAATGGACGATTCATTCTGGTAAAAAAAATTAAACAAATGTTT
1 TTAAATTTGAAATAAATGGACGATTCATTCTAGTAAAAAAAATTAAAAAAATGTTT
* * *
44121 TTAAATTTGAAGTAAATGGACGATTCATTGTAGTAAAAAAATTTAAATAAAAT-TTT
1 TTAAATTTGAAATAAATGGACGATTCATTCTAGTAAAAAAAATTAAA-AAAATGTTT
44177 TTA
1 TTA
44180 TTTTTAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
56 49 0.92
57 4 0.08
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (56 bp):
TTAAATTTGAAATAAATGGACGATTCATTCTAGTAAAAAAAATTAAAAAAATGTTT
Found at i:46434 original size:30 final size:32
Alignment explanation
Indices: 46400--46460 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
46390 TAATTGAATT
*
46400 TAAATTTTAAA-ATT-TGAAAATTATAGGGAC
1 TAAATTTTAAATATTCTGAAAAGTATAGGGAC
*
46430 TAAATTTTAAATTTTCTGAAAAGTATAGGGA
1 TAAATTTTAAATATTCTGAAAAGTATAGGGA
46461 GTTATGGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
31 2 0.07
32 14 0.52
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (32 bp):
TAAATTTTAAATATTCTGAAAAGTATAGGGAC
Found at i:47368 original size:18 final size:18
Alignment explanation
Indices: 47312--47368 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
47302 ATTTATTATT
*
47312 AATTTTA-TATAAGATAGA
1 AATTTTATTATAAAATA-A
*
47330 AA--TTATTATAAAATAT
1 AATTTTATTATAAAATAA
*
47346 TATTTTATTATAAAATAA
1 AATTTTATTATAAAATAA
47364 AATTT
1 AATTT
47369 GGTTGTCGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 4 0.13
17 8 0.26
18 19 0.61
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
AATTTTATTATAAAATAA
Found at i:50260 original size:2 final size:2
Alignment explanation
Indices: 50253--50285 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50243 AATGGTAGTG
50253 TA TA TA TA 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 TA TA TA TA T
50286 TTGTTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71446 original size:52 final size:52
Alignment explanation
Indices: 71368--71508 Score: 237
Period size: 52 Copynumber: 2.7 Consensus size: 52
71358 TAAATGAAAA
* * *
71368 AGGTCCGATGATTATGTGTCATCGTGAGTATATGAATTCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
71420 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
71472 AGGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
71509 GAAATGAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 84 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:72743 original size:18 final size:17
Alignment explanation
Indices: 72711--72777 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
72701 ATTTTTATAT
72711 AATAT-ATATTTTATAAA
1 AATATCATA-TTTATAAA
72728 AATATCATAGTTTATAAAGA
1 AATATCATA-TTTAT-AA-A
*
72748 TAATATTCATATTTACAGAA
1 -AATA-TCATATTTATA-AA
72768 AATATCATAT
1 AATATCATAT
72778 AATCTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.12
18 14 0.33
19 6 0.14
20 3 0.07
21 9 0.21
22 5 0.12
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (17 bp):
AATATCATATTTATAAA
Done.