Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012352.1 Kokia drynarioides strain JFW-HI SEQ_127354, 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: 53745
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:521 original size:60 final size:60
Alignment explanation
Indices: 445--866 Score: 808
Period size: 60 Copynumber: 7.0 Consensus size: 60
435 GATTAATTGT
445 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
505 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
565 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
* *
625 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACTTATGAAAAAAAATAATGAAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
*
685 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACTTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
745 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
*
805 TTTTATGGAAGAGGGTGATAGAAAAGAGTAATGTACACGTATGAAAAAAAATAATGGAAG
1 TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
865 TT
1 TT
867 AGAGGCGAAA
Statistics
Matches: 357, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 357 1.00
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (60 bp):
TTTTATGGAAGAGGGTGATAGAAAAGAGTAACGTACACGTATGAAAAAAAATAATGGAAG
Found at i:4885 original size:30 final size:30
Alignment explanation
Indices: 4849--4915 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
4839 GGAAGCGAAG
4849 AGAGATGGGTGAGTGTGAATTTGTAGGCGA
1 AGAGATGGGTGAGTGTGAATTTGTAGGCGA
4879 AGAGATGGGTGAGTGTGAATTTGTAGGCGA
1 AGAGATGGGTGAGTGTGAATTTGTAGGCGA
4909 AGAGATG
1 AGAGATG
4916 TGGAGGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.03, G:0.43, T:0.25
Consensus pattern (30 bp):
AGAGATGGGTGAGTGTGAATTTGTAGGCGA
Found at i:6674 original size:21 final size:21
Alignment explanation
Indices: 6650--6689 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6640 CAATAACTTG
* *
6650 TATAATATATTTTAAAAAAAT
1 TATAAAATATATTAAAAAAAT
*
6671 TATAAAATATATTACAAAA
1 TATAAAATATATTAAAAAA
6690 GTACAAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAAAATATATTAAAAAAAT
Found at i:16439 original size:125 final size:125
Alignment explanation
Indices: 16217--16597 Score: 694
Period size: 125 Copynumber: 3.0 Consensus size: 125
16207 GAGAGATAAT
* *
16217 AGGAGAACAATCC-AGGTAATGGTTTAGTCATTTATCAGAATATCCGAAATCA-CTTCTCTCTAG
1 AGGAGAACAATCCGA-GAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGC-TCTCTCTAG
16280 TAATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
64 TAATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
16342 AGGAGAACAATCCGAGAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGCTCTCTCTAGTA
1 AGGAGAACAATCCGAGAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGCTCTCTCTAGTA
16407 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
66 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
*
16467 AGGAGAACAATCCGAGAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGTTCTCTCTAGTA
1 AGGAGAACAATCCGAGAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGCTCTCTCTAGTA
*
16532 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCTGCA
66 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
16592 AGGAGA
1 AGGAGA
16598 TGCAGTTAAG
Statistics
Matches: 250, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
125 248 0.99
126 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (125 bp):
AGGAGAACAATCCGAGAAATGGTTTAGTCATTTATCAGAATATCTGAAATCAGCTCTCTCTAGTA
ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
Found at i:20935 original size:20 final size:19
Alignment explanation
Indices: 20912--20955 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
20902 CAATCAATAA
**
20912 TTTTTAATTATTTCGAAGAG
1 TTTTTAATT-TTTAAAAGAG
20932 TTTTT-ATTTTTAAAAGAG
1 TTTTTAATTTTTAAAAGAG
20950 TTTTTA
1 TTTTTA
20956 TGCATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTTAATTTTTAAAAGAG
Found at i:20992 original size:23 final size:23
Alignment explanation
Indices: 20966--21009 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20956 TGCATATTTT
20966 TAATT-TTATATTTAATTTTATGC
1 TAATTATT-TATTTAATTTTATGC
*
20989 TAATTATTTTTTTAATTTTAT
1 TAATTATTTATTTAATTTTAT
21010 ATCTACCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TAATTATTTATTTAATTTTATGC
Found at i:21950 original size:38 final size:38
Alignment explanation
Indices: 21898--21976 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
21888 TTTTTCTTCT
21898 CCATTGTATCGAAGACCTCCATTGCACTCAAAGGGTCA
1 CCATTGTATCGAAGACCTCCATTGCACTCAAAGGGTCA
* *
21936 CCATTGTATTGAAGACCTCCGTTGCACTCAAAGGGTCA
1 CCATTGTATCGAAGACCTCCATTGCACTCAAAGGGTCA
21974 CCA
1 CCA
21977 CATCTGATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (38 bp):
CCATTGTATCGAAGACCTCCATTGCACTCAAAGGGTCA
Found at i:29594 original size:22 final size:23
Alignment explanation
Indices: 29535--29595 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
29525 AAAAAAAATT
*
29535 AAATTAAATT-AAATTTTTACGA
1 AAATTAAATTAAAATTTTTACAA
* * * *
29557 TAATAAAAATATAATTTTTA-AA
1 AAATTAAATTAAAATTTTTACAA
29579 AAATTAAATTAAAATTT
1 AAATTAAATTAAAATTT
29596 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATTAAATTAAAATTTTTACAA
Found at i:29657 original size:17 final size:17
Alignment explanation
Indices: 29635--29667 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29625 TACCTACATT
*
29635 AATTTAAAATTTTAAAA
1 AATTTAAAAATTTAAAA
29652 AATTTAAAAATTTAAA
1 AATTTAAAAATTTAAA
29668 TAAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAAAAATTTAAAA
Found at i:31106 original size:15 final size:14
Alignment explanation
Indices: 31081--31113 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
31071 GTGCTGGAAC
31081 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
31095 TTTTCTTTTTTTCTT
1 TTTTC-TTTTTTCTT
31110 TTTT
1 TTTT
31114 TAATTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:31114 original size:8 final size:7
Alignment explanation
Indices: 31081--31113 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
31071 GTGCTGGAAC
31081 TTTTCTT
1 TTTTCTT
31088 TTTTCTT
1 TTTTCTT
31095 TTTTCTTT
1 TTTTC-TT
31103 TTTTCTT
1 TTTTCTT
31110 TTTT
1 TTTT
31114 TAATTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:31274 original size:21 final size:22
Alignment explanation
Indices: 31250--31296 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
31240 ATATATTTAT
**
31250 AAATTTTA-AATAATTAAATTA
1 AAATTTTATAATAAAAAAATTA
*
31271 AAATTTTATCATAAAAAAATTA
1 AAATTTTATAATAAAAAAATTA
31293 AAAT
1 AAAT
31297 AATTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTTTATAATAAAAAAATTA
Found at i:34436 original size:17 final size:16
Alignment explanation
Indices: 34414--34447 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34404 TTTAAAAAAA
*
34414 AATATTTATATTATTTT
1 AATATTTA-ATAATTTT
34431 AATATTTAATAATTTT
1 AATATTTAATAATTTT
34447 A
1 A
34448 TATGCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTAATAATTTT
Found at i:36261 original size:5 final size:5
Alignment explanation
Indices: 36251--36278 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
36241 AAAAAAATTT
36251 AATGG AATGG AATGG AATGG AATGG AAT
1 AATGG AATGG AATGG AATGG AATGG AAT
36279 AGAAAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (5 bp):
AATGG
Found at i:37157 original size:2 final size:2
Alignment explanation
Indices: 37150--37177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37140 TTATCACATA
37150 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
37178 CATTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45265 original size:24 final size:25
Alignment explanation
Indices: 45237--45284 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
45227 AAACTTTAAT
*
45237 AAGTTTAAATAATAT-TAACAAATA
1 AAGTTAAAATAATATATAACAAATA
*
45261 AAGTTAAAATATTATATAACAAAT
1 AAGTTAAAATAATATATAACAAAT
45285 TCTATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
AAGTTAAAATAATATATAACAAATA
Done.