Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011940.1 Kokia drynarioides strain JFW-HI SEQ_126938, 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: 7499
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:845 original size:17 final size:17
Alignment explanation
Indices: 817--886 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
807 GACCCAACAG
*
817 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTGA
* *
834 AAATTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
851 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
868 AATTTAAATTTATTT-A
1 AATTTAAATTTATTTGA
884 AAT
1 AAT
887 AATGTCCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 4 0.08
17 44 0.92
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:2708 original size:30 final size:29
Alignment explanation
Indices: 2614--2988 Score: 218
Period size: 29 Copynumber: 12.8 Consensus size: 29
2604 TAGATTGTTC
* * * *
2614 AAAAATTACATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTGACCCCGAAACTTCT
* *
2643 AAAAATTTCATTTTCACCCTCG-AACTTC-
1 AAAAATTCCATTTTGACCC-CGAAACTTCT
*
2671 CAAAATTCCATTTTCGACCCCGAAACTTCT
1 AAAAATTCCATTTT-GACCCCGAAACTTCT
* * *
2701 AAAAATTCCATTTTCACCCCCG-AACCTCC
1 AAAAATTCCATTTTGA-CCCCGAAACTTCT
**
2730 AAAAA-TCTCATTTTCGACCCTAAAACTT-T
1 AAAAATTC-CATTTT-GACCCCGAAACTTCT
* *
2759 CAAAATTTCCATTTTTGACCCCAAAACTTCT
1 -AAAAATTCCA-TTTTGACCCCGAAACTTCT
* * *
2790 AAAAATTCCATTTTTACCCCCAAACCTCT
1 AAAAATTCCATTTTGACCCCGAAACTTCT
*
2819 AAAATTTCCATTTTGACCCCGAAACTT-T
1 AAAAATTCCATTTTGACCCCGAAACTTCT
* *
2847 CGAAAATTACCATTTTG-CCCTCG-AA-TGTCC
1 -AAAAATT-CCATTTTGACCC-CGAAACT-TCT
* *
2877 AAAAACTCCATTTTTGACCACGAAAC-TCT
1 AAAAATTCCA-TTTTGACCCCGAAACTTCT
** * *
2906 CGAAATTACCCTTTT-ACCCCCAAA-TGTCT
1 AAAAATT-CCATTTTGACCCCGAAACT-TCT
* * * * *
2935 CAAAATTCCCTTTTAACCCC-AAATTTTCC
1 AAAAATTCCATTTTGACCCCGAAA-CTTCT
* *
2964 CAAAATTACCATTTTGCCCCCGAAA
1 AAAAATT-CCATTTTGACCCCGAAA
2989 ATCCAAAATT
Statistics
Matches: 274, Mismatches: 43, Indels: 56
0.73 0.12 0.15
Matches are distributed among these distances:
28 38 0.14
29 148 0.54
30 78 0.28
31 10 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATTCCATTTTGACCCCGAAACTTCT
Found at i:2940 original size:29 final size:29
Alignment explanation
Indices: 2903--3001 Score: 96
Period size: 28 Copynumber: 3.4 Consensus size: 29
2893 ACCACGAAAC
* *
2903 TCTCGAAATTACCCTTTTACCCCCAAATG
1 TCTCAAAATTACCCTTTTACCCCCAAATA
* *
2932 TCTCAAAATT-CCCTTTTAACCCCAAATTT
1 TCTCAAAATTACCCTTTTACCCCCAAA-TA
* * *
2961 TCCCAAAATTACCATTTTGCCCCCGAAA-A
1 TCTCAAAATTACCCTTTTACCCCC-AAATA
2990 TC-CAAAATTACC
1 TCTCAAAATTACC
3002 ATTTCGCCCC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 25 0.42
29 21 0.36
30 10 0.17
31 3 0.05
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.30
Consensus pattern (29 bp):
TCTCAAAATTACCCTTTTACCCCCAAATA
Found at i:2970 original size:116 final size:117
Alignment explanation
Indices: 2766--2996 Score: 281
Period size: 116 Copynumber: 2.0 Consensus size: 117
2756 TTTCAAAATT
* *
2766 TCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACCTCTAAAATTTCCATT
1 TCCATTTTTGACCACAAAACTTCTAAAAATTCCACTTTTACCCCCAAACCTCTAAAATTTCCATT
* * * **
2831 TTGACCCCGAAACTTTCGAAAATTACCATTTTGCCCTCGAATGTCCAAAAAC
66 TTAACCCCGAAACTTTCCAAAATTACCATTTTGCCCCCGAAAATCCAAAAAC
* ** ** *
2883 TCCATTTTTGACCACGAAAC-TCTCGAAATTACC-CTTTTACCCCCAAATGTCTCAAAA-TTCCC
1 TCCATTTTTGACCACAAAACTTCTAAAAATT-CCACTTTTACCCCCAAACCTCT-AAAATTTCCA
*
2945 TTTTAACCCC-AAATTTTCCCAAAATTACCATTTTGCCCCCGAAAATCCAAAA
64 TTTTAACCCCGAAACTTT-CCAAAATTACCATTTTGCCCCCGAAAATCCAAAA
2997 TTACCATTTC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
115 6 0.06
116 67 0.69
117 24 0.25
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (117 bp):
TCCATTTTTGACCACAAAACTTCTAAAAATTCCACTTTTACCCCCAAACCTCTAAAATTTCCATT
TTAACCCCGAAACTTTCCAAAATTACCATTTTGCCCCCGAAAATCCAAAAAC
Found at i:3346 original size:96 final size:96
Alignment explanation
Indices: 3240--3421 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 96
3230 AAAACTTTAA
* *
3240 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCGAAAATTTACGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-GAAAATTTACGCCTTAACTTACTAGATGCA
*
3302 AATTTTCTTCAAATCGAA-ATAATCGAATACCCTT
63 AACTTTCTTCAAATC-AAGATAATCGAATACCCTT
* * *
3336 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGATGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTACGCCTTAACTTACTAGATGCAAAC
3401 TTTCTTCAAATCAAGATAATC
66 TTTCTTCAAATCAAGATAATC
3422 AAACATCCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
95 2 0.03
96 65 0.86
97 9 0.12
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTACGCCTTAACTTACTAGATGCAAAC
TTTCTTCAAATCAAGATAATCGAATACCCTT
Found at i:4270 original size:32 final size:31
Alignment explanation
Indices: 4203--4278 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
4193 TCAACAAGTT
*
4203 TAATTAATTAATATGAGTTATTAAATTAAAC
1 TAATTAATTTATATGAGTTATTAAATTAAAC
*
4234 TAATTAATTTATCATGAGTTATTAAATT-CAC
1 TAATTAATTTAT-ATGAGTTATTAAATTAAAC
*
4265 GTAATTGATTTATA
1 -TAATTAATTTATA
4279 AGTTAATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
TAATTAATTTATATGAGTTATTAAATTAAAC
Done.