Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012081.1 Kokia drynarioides strain JFW-HI SEQ_127080, 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, 837
Length: 1395
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:900 original size:29 final size:29
Alignment explanation
Indices: 843--1135 Score: 297
Period size: 29 Copynumber: 10.0 Consensus size: 29
833 GAAGGTCCCT
*
843 AAACTATCTAAAAATTCCATTTTTTACCCCA
1 AAACT-TCCAAAAATTCCA-TTTTTACCCCA
* *
874 AAACTTCCAAAAATCCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
**
903 AAACTTCCAAAAATTCCATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
932 AAACTTTCAAAAA-TCTCATTTTGACCCTA
1 AAACTTCCAAAAATTC-CATTTTTACCCCA
* *
961 AAACTT-CAAAGAATTCTATTTTTACCCCC
1 AAACTTCCAAA-AATTCCATTTTTACCCCA
* * * *
990 GAACTTCCTAAAATCCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
1019 AAAGTTCCAAAAATTACATTTTTACCCC-
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
1047 GAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
1077 AAACTTCTAAAAATTCCATTTTTAGGCCC-
1 AAACTTCCAAAAATTCCATTTTTA-CCCCA
* *
1106 GAACTTCCAAAAATTCCATTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
1135 A
1 A
1136 TTTTTCCCAA
Statistics
Matches: 213, Mismatches: 41, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
28 28 0.13
29 142 0.67
30 38 0.18
31 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:1044 original size:116 final size:116
Alignment explanation
Indices: 839--1135 Score: 411
Period size: 116 Copynumber: 2.6 Consensus size: 116
829 CCCTGAAGGT
**
839 CCCT-AAACTATCTAAAAATTCCATTTTTTACCCCAAAACTTCCAAAAATCCCATTTTGACCCCA
1 CCCTAAAACT-TCTAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCA
* * * *
903 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTTCAAAAATCTCA-TTTTGA
64 AAACTTCCAAAAATTACATTTTTACCC-CAAACTTCCAAAAATCCCATTTTTGA
* *
956 CCCTAAAACTTC-AAAGAATTCTATTTTTACCCCCGAACTTCCTAAAATCCCATTTTGACCCCAA
1 CCCTAAAACTTCTAAA-AATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCAA
* *
1020 AAGTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
65 AACTTCCAAAAATTACATTTTTACCCCAAACTTCCAAAAATCCCATTTTTGA
** * *
1072 CCCTAAAACTTCTAAAAATTCCATTTTTAGGCCCGAACTTCCAAAAATTCCATTTTAACCCCAA
1 CCCTAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCAA
1136 TTTTTCCCAA
Statistics
Matches: 160, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
115 15 0.09
116 125 0.78
117 15 0.09
118 5 0.03
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32
Consensus pattern (116 bp):
CCCTAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCAAA
ACTTCCAAAAATTACATTTTTACCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:1148 original size:58 final size:57
Alignment explanation
Indices: 843--1135 Score: 363
Period size: 58 Copynumber: 5.0 Consensus size: 57
833 GAAGGTCCCT
* *
843 AAACTATCTAAAAATTCCATTTTTTACCCCAAAACTTCCAAAAATCCCATTTTGACCCCA
1 AAACT-TCCAAAAATTCCA-TTTTTACCCC-GAACTTCCAAAAATCCCATTTTGACCCCA
** * * *
903 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTTCAAAAATCTCATTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTGACCCCA
* *
961 AAACTT-CAAAGAATTCTATTTTTACCCCCGAACTTCCTAAAATCCCATTTTGACCCCA
1 AAACTTCCAAA-AATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTGACCCCA
* * *
1019 AAAGTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCA-TTTTGACCCCA
* * * *
1077 AAACTTCTAAAAATTCCATTTTTAGGCCCGAACTTCCAAAAATTCCATTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTGACCCCA
1135 A
1 A
1136 TTTTTCCCAA
Statistics
Matches: 203, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
57 25 0.12
58 134 0.66
59 39 0.19
60 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTGACCCCA
Found at i:1176 original size:116 final size:116
Alignment explanation
Indices: 839--1185 Score: 344
Period size: 116 Copynumber: 3.0 Consensus size: 116
829 CCCTGAAGGT
** *
839 CCCT-AAACTATCTAAA-AATTCCATTTTTTACCCCAAAACTTCCAAAAATCCCATTTTGACCCC
1 CCCTAAAACT-TC-AAAGAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCCC
* * * * ** * * *
902 AAAACTTCCAAAAATTCCATTTTTACCCTTAAACTTTCAAAAATCTCA-TTTTGA
63 AAAAGTTCCAAAAATTACAGTTTCACCC-CGAACATCCAAAAATCCCATTTTTGA
* * *
956 CCCTAAAACTTCAAAGAATTCTATTTTTACCCCCGAACTTCCTAAAATCCCATTTTGACCCCAAA
1 CCCTAAAACTTCAAAGAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCCCAAA
* * *
1021 AGTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
66 AGTTCCAAAAATTACAGTTTCACCCCGAACATCCAAAAATCCCATTTTTGA
** *
1072 CCCTAAAACTTCTAAA-AATTCCATTTTTAGGCCCGAACTTCCAAAAATTCCATTTTAACCCCAA
1 CCCTAAAACTTC-AAAGAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCCCAA
*** * * * *
1136 TTTTTCCCAAAATTACCGTTTCACCCTCGAGA-ATCCAAAATTACCATTTT
65 AAGTTCCAAAAATTACAGTTTCACCC-CGA-ACATCCAAAAATCCCATTTT
1186 GCCCCTGGGT
Statistics
Matches: 198, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
115 15 0.08
116 144 0.73
117 33 0.17
118 6 0.03
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (116 bp):
CCCTAAAACTTCAAAGAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAACCCCAAA
AGTTCCAAAAATTACAGTTTCACCCCGAACATCCAAAAATCCCATTTTTGA
Done.