Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009352.1 Kokia drynarioides strain JFW-HI SEQ_124059, 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: 19517
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:2852 original size:16 final size:17
Alignment explanation
Indices: 2818--2859 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2808 TAATCCTTTA
2818 AAAATTATAAAAAAAAT
1 AAAATTATAAAAAAAAT
* **
2835 -AAATTATTAAAATGAT
1 AAAATTATAAAAAAAAT
2851 AAAATTATA
1 AAAATTATA
2860 TTTTTACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATTATAAAAAAAAT
Found at i:3512 original size:45 final size:45
Alignment explanation
Indices: 3238--3520 Score: 211
Period size: 45 Copynumber: 6.3 Consensus size: 45
3228 CTATCTATGA
* * * * * *
3238 ACCTCCAAAGAAGGAAAAACTTGAGCCTAAGCCACCAGTTTATAC
1 ACCTCCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTATAC
* * * *
3283 ACCACCAAA-ACAAGAGAAGCCTGAACCCAAGCCACCAGTGTATGA-
1 ACCTCCAAAGA-AAGAAAAGCCTGAACCCAAACCACCAGTTTAT-AC
* * * *
3328 GCCACCAAAGAAGGAAAAGCCTG-AGCCAAAGCCACCAGTTTATAC
1 ACCTCCAAAGAAAGAAAAGCCTGAACCCAAA-CCACCAGTTTATAC
* * * * * *
3373 ACCTCCAAAAAAAGAGAAGCTTGAATCCAAACCACCGGTATATGA-
1 ACCTCCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTAT-AC
* * * * *
3418 ACCACCAAAGAAGGAAAGGCCTGAGCCTAAACCACCAG-TTAGTAC
1 ACCTCCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTA-TAC
*
3463 ACCTCCAAAGAAAGAAAAGCCAGAACCCAAACCACTC-GTTTAT-C
1 ACCTCCAAAGAAAGAAAAGCCTGAACCCAAACCAC-CAGTTTATAC
*
3507 AACCTCTAAAGAAA
1 -ACCTCCAAAGAAA
3521 CCACCAATTT
Statistics
Matches: 185, Mismatches: 41, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
44 11 0.06
45 161 0.87
46 13 0.07
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.13
Consensus pattern (45 bp):
ACCTCCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTATAC
Found at i:3519 original size:90 final size:89
Alignment explanation
Indices: 3233--3497 Score: 345
Period size: 90 Copynumber: 2.9 Consensus size: 89
3223 GCCACCTATC
* * * * *
3233 TATGAACCTCCAAAGAAGGAAAAACTTGAGCCTAAGCCACCAGTTTATACACCACCAAAACAAGA
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTTATACACCTCCAAAA-AAGA
* *
3298 GAAGCCTGAACCCAAGCCACCAGTG
65 GAAGCCTGAACCCAAACCACCAGTA
*
3323 TATGAGCCACCAAAGAAGGAAAAGCCTGAGCC-AAAGCCACCAGTTTATACACCTCCAAAAAAAG
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAA-CCACCAGTTTATACACCTCC-AAAAAAG
* * *
3387 AGAAGCTTGAATCCAAACCACCGGTA
64 AGAAGCCTGAACCCAAACCACCAGTA
*
3413 TATGAACCACCAAAGAAGGAAAGGCCTGAGCCTAAACCACCAG-TTAGTACACCTCCAAAGAAAG
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTTA-TACACCTCCAAA-AAAG
* *
3477 AAAAGCCAGAACCCAAACCAC
64 AGAAGCCTGAACCCAAACCAC
3498 TCGTTTATCA
Statistics
Matches: 153, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
89 8 0.05
90 138 0.90
91 7 0.05
ACGTcount: A:0.43, C:0.28, G:0.17, T:0.12
Consensus pattern (89 bp):
TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTTATACACCTCCAAAAAAGAG
AAGCCTGAACCCAAACCACCAGTA
Found at i:3531 original size:27 final size:27
Alignment explanation
Indices: 3501--3552 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3491 AAACCACTCG
* *
3501 TTTATCAACCTCTAAAGAAACCACCAA
1 TTTATCAACATCCAAAGAAACCACCAA
*
3528 TTTATGAACATCCAAAGAAACCACC
1 TTTATCAACATCCAAAGAAACCACC
3553 GTATGGTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.21
Consensus pattern (27 bp):
TTTATCAACATCCAAAGAAACCACCAA
Found at i:10065 original size:17 final size:17
Alignment explanation
Indices: 10040--10082 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
10030 CCCAACAAAT
*
10040 TTAAATTTATTTTAAAA
1 TTAAATTTATTCTAAAA
* *
10057 TTAAGTTTATTCTAAAT
1 TTAAATTTATTCTAAAA
10074 TTAAATTTA
1 TTAAATTTA
10083 AAATTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTCTAAAA
Found at i:11813 original size:59 final size:59
Alignment explanation
Indices: 11750--12170 Score: 363
Period size: 59 Copynumber: 7.1 Consensus size: 59
11740 CAAAAATTTT
* * * * * *
11750 ATTTTTAACCCCAAAACATCCAAAAATTTCATTTTTAAACTCGAACTTCCCAAAATCCC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCGAACTTCCAAAAATACC
* *
11809 ATTTTTAACCCTAAAACTTCCAAAAATTCAATTTTT-ACCCTCGAACTTCCAAAAATACC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAACCC-CGAACTTCCAAAAATACC
* *
11868 ATTTTTAACCCTAAAACTTCTAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAAT-CTC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCG-AACTTCCAAAAATAC-C
* * * * * *
11927 ATTTTT-ACCTCGAAACTCCCAAAAATTTCATTTTT-ACACTCGAACTCCCAAAAATACC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAAC-CCCGAACTTCCAAAAATACC
* ** * * * *
11985 ATTTTTTACCCTTAAACTTCTAAAAATTCCATTTTTAACCCCCAAAAGCTTCTAAAAATTCC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAA-CCCC-GAA-CTTCCAAAAATACC
* ** * * *
12047 ATTTTT-TCCCCTGAACATCCAAAAATTCCATTTTT-ACCCCTGAACATCCAAAAATTCC
1 ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAACCCC-GAACTTCCAAAAATACC
** * * * * *
12105 ATTTTTAACCCCAAATTTTCCCAAAACTACCA-TTTTGACCCCAAAACTTCCAAAAATTACT
1 ATTTTTAACCCCAAAACTT-CCAAAAATTCCATTTTTAACCCC-GAACTTCCAAAAA-TACC
12166 ATTTT
1 ATTTT
12171 GCCCTCGGGT
Statistics
Matches: 297, Mismatches: 51, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
58 67 0.23
59 149 0.50
60 30 0.10
61 34 0.11
62 17 0.06
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (59 bp):
ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCGAACTTCCAAAAATACC
Found at i:12171 original size:30 final size:29
Alignment explanation
Indices: 11732--12162 Score: 348
Period size: 29 Copynumber: 14.5 Consensus size: 29
11722 GAAGGTCCCT
**
11732 AAACTATCCAAAAATTTTATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCA
* * * *
11763 AAACATCCAAAAATTTCATTTTTAAACTC-
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * * *
11792 GAACTTCCCAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
11822 AAACTTCCAAAAATTCAATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CA
* * *
11851 GAACTTCCAAAAATACCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
11881 AAACTTCTAAAAATTCCATTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
11910 AAACTTCCAAAAA-TCTCATTTTTACCTCG
1 AAACTTCCAAAAATTC-CATTTTTACCCCA
* * *
11939 AAACTCCCAAAAATTTCATTTTTACACTC-
1 AAACTTCCAAAAATTCCATTTTTAC-CCCA
* * * **
11968 GAACTCCCAAAAATACCATTTTTTACCCTT
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
*
11998 AAACTTCTAAAAATTCCATTTTTAACCCCCA
1 AAACTTCCAAAAATTCCATTTTT-A-CCCCA
* * *
12029 AAAGCTTCTAAAAATTCCATTTTTTCCCCT
1 AAA-CTTCCAAAAATTCCATTTTTACCCCA
* * *
12059 GAACATCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
12088 GAACATCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
** * * *
12118 AATTTTCCCAAAACTACCATTTTGACCCCA
1 AAACTT-CCAAAAATTCCATTTTTACCCCA
12148 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
12163 ACTATTTTGC
Statistics
Matches: 327, Mismatches: 59, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.01
29 168 0.51
30 113 0.35
31 24 0.07
32 20 0.06
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:16965 original size:29 final size:30
Alignment explanation
Indices: 16911--17174 Score: 187
Period size: 29 Copynumber: 9.0 Consensus size: 30
16901 TTTGGGGAAG
*
16911 TTCGAGGTTAAAAGATGGAATTTTTAGATA-
1 TTCGAGGGTAAAA-ATGGAATTTTTAGATAT
16941 TTCGAGGGTAAAAATGGAATTTTTAGATA-
1 TTCGAGGGTAAAAATGGAATTTTTAGATAT
16970 TTCGAGGGTAAAAATGGAATTTTTAGA-AT
1 TTCGAGGGTAAAAATGGAATTTTTAGATAT
* * * * *
16999 TTCGA-GGTCGAAAATAGAGTTTTTGGACAT
1 TTCGAGGGT-AAAAATGGAATTTTTAGATAT
** *
17029 TT-G-GGGGCAAAATGGTAATTTTT-GAAAGT
1 TTCGAGGGTAAAAATGG-AATTTTTAGATA-T
* *
17058 TTC-AAGGTCAAAAATGGAATTTTTAGAAGAT
1 TTCGAGGGT-AAAAATGGAATTTTTAG-ATAT
*
17089 TT--AGGGTAAAAATGGAA-TTTTGGA-AGT
1 TTCGAGGGTAAAAATGGAATTTTTAGATA-T
* * * *
17116 TT-TAGGGGTAAAAATAGTATTTTT-GAAAAT
1 TTCGA-GGGTAAAAATGGAATTTTTAG-ATAT
* *
17146 TTCGAGGGTAAAAATGAAATTTTTGGATA
1 TTCGAGGGTAAAAATGGAATTTTTAGATA
17175 GTTTAGGGAC
Statistics
Matches: 192, Mismatches: 23, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 19 0.10
29 97 0.51
30 55 0.29
31 14 0.07
32 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGGAATTTTTAGATAT
Found at i:17101 original size:88 final size:88
Alignment explanation
Indices: 16970--17182 Score: 206
Period size: 88 Copynumber: 2.4 Consensus size: 88
16960 TTTTTAGATA
* * * *
16970 TTCGAGGGTAAAAATGGAATTTTTAG-A-ATTTCGAGGTCGAAAATAGAGTTTTTGGACA-TTT-
1 TTCGAAGGTAAAAATGGAATTTTTAGAAGATTTAG-GGTCAAAAATAGA-ATTTTGGA-AGTTTA
* * *
17031 GGGGGCAAAATGGTAATTTTTGAAAGT
63 GGGGGAAAAATAGT-ATTTTTGAAAAT
*
17058 TTC-AAGGTCAAAAATGGAATTTTTAGAAGATTTAGGGT-AAAAATGGAATTTTGGAAGTTTTAG
1 TTCGAAGGT-AAAAATGGAATTTTTAGAAGATTTAGGGTCAAAAATAGAATTTTGGAAG-TTTAG
*
17121 GGGTAAAAATAGTATTTTTGAAAAT
64 GGGGAAAAATAGTATTTTTGAAAAT
* * *
17146 TTCGAGGGTAAAAATGAAATTTTTGGATAG-TTTAGGG
1 TTCGAAGGTAAAAATGGAATTTTTAGA-AGATTTAGGG
17183 ACCTCCAGGG
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
86 1 0.01
87 11 0.10
88 67 0.64
89 21 0.20
90 5 0.05
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (88 bp):
TTCGAAGGTAAAAATGGAATTTTTAGAAGATTTAGGGTCAAAAATAGAATTTTGGAAGTTTAGGG
GGAAAAATAGTATTTTTGAAAAT
Found at i:17108 original size:59 final size:58
Alignment explanation
Indices: 16974--17170 Score: 177
Period size: 59 Copynumber: 3.4 Consensus size: 58
16964 TAGATATTCG
* * * * *
16974 AGGGTAAAAATGGAATTTTT-AGAA-TTTCGAGGTCGAAAATAGAGTTTTTGGACATTT
1 AGGGTAAAAATGGAATTTTTGA-AAGTTTCAAGGTCAAAAATAGAATTTTTGAAAATTT
* ** * *
17031 GGGGGCAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTTAGAAGATTT
1 AGGGTAAAAATGG-AATTTTTGAAAGTTTCAAGGTCAAAAATAGAATTTTT-GAAAATTT
* * * *
17091 AGGGTAAAAATGGAA-TTTTGGAAGTTTTAGGGGT-AAAAATAGTATTTTTGAAAATTT
1 AGGGTAAAAATGGAATTTTTGAAAGTTTCA-AGGTCAAAAATAGAATTTTTGAAAATTT
*
17148 CGAGGGTAAAAATGAAATTTTTG
1 --AGGGTAAAAATGGAATTTTTG
17171 GATAGTTTAG
Statistics
Matches: 113, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
57 17 0.15
58 34 0.30
59 41 0.36
60 21 0.19
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
AGGGTAAAAATGGAATTTTTGAAAGTTTCAAGGTCAAAAATAGAATTTTTGAAAATTT
Found at i:18343 original size:43 final size:43
Alignment explanation
Indices: 18295--18386 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
18285 GGGTCATTTG
*
18295 GGCCCATTGGAATTGGGCTCAGGTTTTGGGTCAGTTAGGATCA
1 GGCCCATTGGAATTGGGCTCAAGTTTTGGGTCAGTTAGGATCA
18338 GGCCCATTGGAATTGGGCTCAAGTTTTGGGTCAGTTAGGATCA
1 GGCCCATTGGAATTGGGCTCAAGTTTTGGGTCAGTTAGGATCA
18381 GGCCCA
1 GGCCCA
18387 GTTTGGGCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (43 bp):
GGCCCATTGGAATTGGGCTCAAGTTTTGGGTCAGTTAGGATCA
Done.