Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011391.1 Kokia drynarioides strain JFW-HI SEQ_126373, 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: 13274
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:53 original size:17 final size:16
Alignment explanation
Indices: 1--52 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
1 ATTTAAATTAAGTTTAAA
1 ATTT-AATTAA-TTTAAA
19 A-TTAATTTGAATTTAAA
1 ATTTAA-TT-AATTTAAA
36 ATTTAATTAATTTAAA
1 ATTTAATTAATTTAAA
52 A
1 A
53 AAGTCCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 11 0.35
17 13 0.42
18 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTTAATTAATTTAAA
Found at i:864 original size:21 final size:22
Alignment explanation
Indices: 816--870 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
806 ATAAATATTG
816 GCATTAATAGATATTAATAAAAT
1 GCATTAATA-ATATTAATAAAAT
* *
839 -TATTATTAATATTAAT-AAAT
1 GCATTAATAATATTAATAAAAT
859 GCATTAATAATA
1 GCATTAATAATA
871 AATGTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (22 bp):
GCATTAATAATATTAATAAAAT
Found at i:896 original size:15 final size:16
Alignment explanation
Indices: 826--910 Score: 66
Period size: 15 Copynumber: 5.2 Consensus size: 16
816 GCATTAATAG
826 ATATTAATAA-AATTA
1 ATATTAATAATAATTA
* * *
841 TTATTAATATTAATAA
1 ATATTAATAATAATTA
*
857 ATGCATTAATAATAAATGTT
1 AT--ATTAATAAT-AAT-TA
*
877 TTATTAATAATAA-TA
1 ATATTAATAATAATTA
*
892 ATATTATTAATAATTA
1 ATATTAATAATAATTA
908 ATA
1 ATA
911 AAAAAAAGGG
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
15 20 0.38
16 10 0.19
17 2 0.04
18 17 0.32
19 3 0.06
20 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATTAATAATAATTA
Found at i:1944 original size:29 final size:29
Alignment explanation
Indices: 1890--2236 Score: 244
Period size: 29 Copynumber: 11.9 Consensus size: 29
1880 CCTTGTAGGT
* *
1890 CCCTAAACTATCCAAGAATTCTATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
1920 CCCTAAACTTCCAAAAATACCA-TTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
1947 CCCTAAAACTTCTATAAATTCCATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
*
1977 CCCTAAACTTTCAAAAA-TCCAATTTTTGAC
1 CCCTAAACTTCCAAAAATTCC-ATTTTT-AC
* **
2007 CCCAAAACTTTTAAAAATT--ATATTTTAC
1 CCCTAAACTTCCAAAAATTCCAT-TTTTAC
*
2035 CCC-AAACTTTCAAAAA-TCTCATTTTTGAC
1 CCCTAAACTTCCAAAAATTC-CATTTTT-AC
* * * *
2064 CTCGAAACTTCTAAAAATTCCATTTTT-T
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
2092 CCCTCGAACTTCCAAAAATTCTATTTTTAT
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* * *** * **
2122 CCTTGAACTTTTGAAAATCCCATTTTGCC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
2151 CCCAAAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** *
2180 CCCCGAACTTCCAAAAAAATCCAGTTTTTA-
1 CCCTAAACTTCC-AAAAATTCCA-TTTTTAC
* *
2210 CCCTCGAACTTCCAAAAATTCAATTTT
1 CCCT-AAACTTCCAAAAATTCCATTTT
2237 GGCCTCGAAC
Statistics
Matches: 254, Mismatches: 45, Indels: 37
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.00
27 16 0.06
28 36 0.14
29 113 0.44
30 71 0.28
31 17 0.07
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:1978 original size:57 final size:57
Alignment explanation
Indices: 1906--2228 Score: 255
Period size: 57 Copynumber: 5.6 Consensus size: 57
1896 ACTATCCAAG
* *
1906 AATTCTATTTTTACCCCTAAACTTCCAAAAATACCA-TTTTACCCTAAAACTTCTATA
1 AATTCCATTTTTACCCCTAAACTTCCAAAAAT-CCATTTTTACCCTAAAACTTCTAAA
* * *
1963 AATTCCATTTTTACCCCTAAACTTTCAAAAATCCAATTTTTGACCCCAAAACTTTTAAA
1 AATTCCATTTTTACCCCTAAACTTCCAAAAATCC-ATTTTT-ACCCTAAAACTTCTAAA
* *
2022 AATT--ATATTTTACCCC-AAACTTTCAAAAATCTCATTTTTGA-CCTCGAAACTTCTAAA
1 AATTCCAT-TTTTACCCCTAAACTTCCAAAAATC-CATTTTT-ACCCT-AAAACTTCTAAA
* * * * ** * *
2079 AATTCCATTTTT-TCCCTCGAACTTCCAAAAATTCTATTTTTATCCTTGAACTTTTGAA
1 AATTCCATTTTTACCCCT-AAACTTCCAAAAA-TCCATTTTTACCCTAAAACTTCTAAA
* ** * *** *
2137 AATCCCATTTTGCCCCCAAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAA
1 AATTCCATTTTTACCCCTAAACTTCCAAAAAT-CCATTTTTACCCTAAAACTT-CTAAA
* *
2196 AAATCCAGTTTTTA-CCCTCGAACTTCCAAAAAT
1 AATTCCA-TTTTTACCCCT-AAACTTCCAAAAAT
2229 TCAATTTTGG
Statistics
Matches: 215, Mismatches: 34, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
56 4 0.02
57 74 0.34
58 65 0.30
59 53 0.25
60 19 0.09
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (57 bp):
AATTCCATTTTTACCCCTAAACTTCCAAAAATCCATTTTTACCCTAAAACTTCTAAA
Found at i:2201 original size:31 final size:31
Alignment explanation
Indices: 2135--2227 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
2125 TGAACTTTTG
* *
2135 AAAATCCCA-TTTTGCCCCCAAAACTTCC--A
1 AAAATCCCATTTTTACCCCC-GAACTTCCAAA
2164 AAAATCCCATTTTTACCCCCGAACTTCCAAA
1 AAAATCCCATTTTTACCCCCGAACTTCCAAA
*
2195 AAAAT-CCAGTTTTTACCCTCGAACTTCCAAA
1 AAAATCCCA-TTTTTACCCCCGAACTTCCAAA
2226 AA
1 AA
2228 TTCAATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
29 16 0.28
30 12 0.21
31 29 0.51
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (31 bp):
AAAATCCCATTTTTACCCCCGAACTTCCAAA
Found at i:2264 original size:28 final size:27
Alignment explanation
Indices: 2205--2283 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
2195 AAAATCCAGT
*
2205 TTTTACCCTCGAACTTCCAAAAATTCAA
1 TTTTAACCTCGAAC-TCCAAAAATTCAA
** *
2233 TTTTGGCCTCGAACTGCCAAAAATT-ATG
1 TTTTAACCTCGAACT-CCAAAAATTCA-A
2261 TTTTAACCTCGAAACTCCAAAAA
1 TTTTAACCTCG-AACTCCAAAAA
2284 ATTACCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.05
28 37 0.86
29 4 0.09
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTTAACCTCGAACTCCAAAAATTCAA
Found at i:2381 original size:29 final size:30
Alignment explanation
Indices: 2280--2419 Score: 85
Period size: 29 Copynumber: 4.8 Consensus size: 30
2270 CGAAACTCCA
* *
2280 AAAAATTACCATTTTACCCCCGGATGTCT-
1 AAAAATTACCATTTTACCCCCGAATGTTTC
* ** ** *
2309 AAAAACT-CCATTTT-CGACTTCGAAACTCTC
1 AAAAATTACCATTTTAC--CCCCGAATGTTTC
*
2339 -AAAATTACCCTTTTACCCCCGAATGTTT-
1 AAAAATTACCATTTTACCCCCGAATGTTTC
* * *
2367 AAAAATT-CCATTTTTAACCCTGAATTTTTC
1 AAAAATTACCA-TTTTACCCCCGAATGTTTC
* *
2397 CAAAATTACCATTTCACCCCCGA
1 AAAAATTACCATTTTACCCCCGA
2420 GAATCTAAAA
Statistics
Matches: 81, Mismatches: 21, Indels: 17
0.68 0.18 0.14
Matches are distributed among these distances:
27 1 0.01
28 9 0.11
29 46 0.57
30 21 0.26
31 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATTACCATTTTACCCCCGAATGTTTC
Done.