Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009956.1 Kokia drynarioides strain JFW-HI SEQ_124702, 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: 35215
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:633 original size:31 final size:31
Alignment explanation
Indices: 600--660 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
590 TAGAATAGTC
*
600 TTTATCACCGCTATTCT-AATAATATTTGATCT
1 TTTATC-CCACTATTCTAAAT-ATATTTGATCT
*
632 TTTGTCCCACTATTCTAAATATATTTGAT
1 TTTATCCCACTATTCTAAATATATTTGAT
661 ACACTTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.48
Consensus pattern (31 bp):
TTTATCCCACTATTCTAAATATATTTGATCT
Found at i:936 original size:32 final size:32
Alignment explanation
Indices: 900--996 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
890 TGACGTCGGC
*
900 TCATGCTTACCAACCATGCCTTTCCTCGTTTA
1 TCATGCTTACCAACCATGCCTTTCCTCATTTA
*
932 TCATGCTTACCAACCATGTCTTTCCTCATTTA
1 TCATGCTTACCAACCATGCCTTTCCTCATTTA
* *
964 TTATGCTTACCAACCTTGCCTTTCCTCATTTA
1 TCATGCTTACCAACCATGCCTTTCCTCATTTA
996 T
1 T
997 TTCTTTTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.20, C:0.32, G:0.07, T:0.41
Consensus pattern (32 bp):
TCATGCTTACCAACCATGCCTTTCCTCATTTA
Found at i:5489 original size:2 final size:2
Alignment explanation
Indices: 5482--5510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5472 GATACACTAA
5482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5511 ACCATTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19971 original size:96 final size:97
Alignment explanation
Indices: 19782--19974 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 97
19772 TCTTTGCGAA
* **
19782 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
* * * *
19847 GAATCGAAGATAAGGAAACATTGTCTCGATTT
66 AAACCGAAGATAAAGAAACATTGCCTCGATTT
* *
19879 AAGG-TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGC-ATATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTC
*
19942 GAAACCCGAA-ATGAAAG-AATATTGCCTCGATTT
65 GAAA-CCGAAGAT-AAAGAAACATTGCCTCGATTT
19975 TAAAGTTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
95 3 0.04
96 69 0.83
97 11 0.13
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAGAAACATTGCCTCGATTT
Found at i:20233 original size:29 final size:30
Alignment explanation
Indices: 20186--20242 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
20176 ATCGGAGTTC
*
20186 AAAATGAGACTTTTCGGATTCTCGGGGGCA
1 AAAATGAGAATTTTCGGATTCTCGGGGGCA
*
20216 AAAATGATAATTTT-GGATTCTCGGGGG
1 AAAATGAGAATTTTCGGATTCTCGGGGG
20243 TGAAACGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (30 bp):
AAAATGAGAATTTTCGGATTCTCGGGGGCA
Found at i:20255 original size:28 final size:29
Alignment explanation
Indices: 20196--20259 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
20186 AAAATGAGAC
*
20196 TTTTCGGATTCTCGGGGGCAAAAATGATAA
1 TTTT-GGATTCTCGGGGGCAAAAACGATAA
** *
20226 TTTTGGATTCTCGGGGG-TGAAACGGTAA
1 TTTTGGATTCTCGGGGGCAAAAACGATAA
20254 TTTTGG
1 TTTTGG
20260 GAAAATTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 13 0.43
30 4 0.13
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (29 bp):
TTTTGGATTCTCGGGGGCAAAAACGATAA
Found at i:20315 original size:59 final size:58
Alignment explanation
Indices: 20265--20478 Score: 218
Period size: 58 Copynumber: 3.6 Consensus size: 58
20255 TTTGGGAAAA
20265 TTCGGGGTAAAAAAATGAGATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGT-AAAAAATGAGATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
* * * * **
20324 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGTT
1 TTCGGGGTAAAAAATGAGATTTTTGAAAGTT-TAGGGTAAAAATAGAATTTTTGAAAG-T
* * * ** * *
20384 TTGCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGTGAAAATATAATTTTTGAAAG-
1 TT-CGGGGTAAAAAATGAGATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
*
20442 TTCGGGGGT-AAAAAT-AGAATTTTTGAACAATTTAGGG
1 TTC-GGGGTAAAAAATGAG-ATTTTTGAA-AGTTTAGGG
20479 ACCTACGGGA
Statistics
Matches: 134, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.01
57 15 0.11
58 33 0.25
59 31 0.23
60 26 0.19
61 28 0.21
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
TTCGGGGTAAAAAATGAGATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
Found at i:20317 original size:29 final size:28
Alignment explanation
Indices: 20268--20468 Score: 195
Period size: 29 Copynumber: 6.8 Consensus size: 28
20258 GGGAAAATTC
*
20268 GGGGTAAAAAAATGAGATTTTTGAAAGTTT
1 GGGGTAAAAATA-GA-ATTTTTGAAAGTTT
*
20298 AGGGTAAAAATAGAATTTTTGAAAGTTTT
1 GGGGTAAAAATAGAATTTTTGAAAG-TTT
* * * *
20327 GGGGTTAAAAATGGGATTTTTGGAAGTTCG
1 GGGG-TAAAAATAGAATTTTTGAAAGTT-T
20357 GGGGTAAAAATAGAATTTTTGAAAGTTTT
1 GGGGTAAAAATAGAATTTTTGAAAG-TTT
* * * *
20386 GCGGGGTTAAAAATGGGATTTTTGGAAGTTC
1 --GGGG-TAAAAATAGAATTTTTGAAAGTTT
* * *
20417 GGGGTGAAAATATAATTTTTGAAAGTTCG
1 GGGGTAAAAATAGAATTTTTGAAAGTT-T
20446 GGGGTAAAAATAGAATTTTTGAA
1 GGGGTAAAAATAGAATTTTTGAA
20469 CAATTTAGGG
Statistics
Matches: 140, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
28 29 0.21
29 53 0.38
30 34 0.24
31 6 0.04
32 18 0.13
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
GGGGTAAAAATAGAATTTTTGAAAGTTT
Found at i:20427 original size:89 final size:87
Alignment explanation
Indices: 20260--20478 Score: 237
Period size: 89 Copynumber: 2.5 Consensus size: 87
20250 GTAATTTTGG
* *
20260 GAAAATTC-GGGGTAAAAAAATGAGATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
1 GAAAGTTCGGGGGTAAAAATA-GA-ATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGT
* * *
20324 TTTGGGGTTAAAAATGGGATTTTT
64 TTCGGGGTTAAAAATAGAATTTTT
* * * * *
20348 GGAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGTTTTGCGGGGTTAAAAATGGGATTTTTGGAA
1 GAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAG-TTT--AGGG-TAAAAATAGAATTTTTGAAA
* *
20413 G-TTCGGGG-TGAAAATATAATTTTT
62 GTTTCGGGGTTAAAAATAGAATTTTT
*
20437 GAAAGTTCGGGGGTAAAAATAGAATTTTTGAACAATTTAGGG
1 GAAAGTTCGGGGGTAAAAATAGAATTTTTGAA-AGTTTAGGG
20479 ACCTACGGGA
Statistics
Matches: 110, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
87 14 0.13
88 11 0.10
89 57 0.52
90 10 0.09
91 18 0.16
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (87 bp):
GAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGTTTAGGGTAAAAATAGAATTTTTGAAAGTTT
CGGGGTTAAAAATAGAATTTTT
Found at i:22294 original size:17 final size:16
Alignment explanation
Indices: 22284--22338 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
22274 AAATAAACTT
22284 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
* *
22301 TAAACTTAAATTTCAA
1 TAAATTTAAATTTAAA
22317 TCAAATTTAAATTTAAAA
1 T-AAATTTAAATTT-AAA
22335 TAAA
1 TAAA
22339 AACAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.09
17 26 0.81
18 3 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:32453 original size:9 final size:9
Alignment explanation
Indices: 32441--32468 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
32431 AAAAAGAGAG
32441 GCTGATGCT
1 GCTGATGCT
32450 GCTGATGCT
1 GCTGATGCT
32459 GCTGATGCT
1 GCTGATGCT
32468 G
1 G
32469 ATGAGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (9 bp):
GCTGATGCT
Done.