Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012499.1 Kokia drynarioides strain JFW-HI SEQ_127503, 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: 5460
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1539 original size:17 final size:18
Alignment explanation
Indices: 1507--1541 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1497 ATCACATTAA
*
1507 AAATTTTTAATGAATATC
1 AAATTTTTAATAAATATC
1525 AAATTTTTAA-AAATATC
1 AAATTTTTAATAAATATC
1542 TTGTTAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
AAATTTTTAATAAATATC
Found at i:2801 original size:20 final size:21
Alignment explanation
Indices: 2776--2822 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2766 TTTATATTGT
*
2776 TGTTTT-GATGCTTTTTTTAC
1 TGTTTTGGATGATTTTTTTAC
* *
2796 TGTTTTGGTTGATTTTTTTGC
1 TGTTTTGGATGATTTTTTTAC
2817 TGTTTT
1 TGTTTT
2823 TGAGTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.68
Consensus pattern (21 bp):
TGTTTTGGATGATTTTTTTAC
Found at i:2823 original size:22 final size:21
Alignment explanation
Indices: 2787--2843 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
2777 GTTTTGATGC
2787 TTTTTTTACTGTTTTG-GTTGA
1 TTTTTTTACTGTTTTGAGTT-A
*
2808 TTTTTTTGCTGTTTTTGAGTTA
1 TTTTTTTACTG-TTTTGAGTTA
*
2830 -TTTTTTATTGTTTT
1 TTTTTTTACTGTTTT
2844 AATTGTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 6 0.19
23 3 0.10
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTTTACTGTTTTGAGTTA
Found at i:2843 original size:20 final size:20
Alignment explanation
Indices: 2775--2843 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
2765 ATTTATATTG
*
2775 TTGTTTTGATGCT-TTTTTTA
1 TTGTTTTGA-GTTATTTTTTA
*
2795 CTGTTTTG-GTTGATTTTTT-
1 TTGTTTTGAGTT-ATTTTTTA
2814 TGCTGTTTTTGAGTTATTTTTTA
1 T--TG-TTTTGAGTTATTTTTTA
2837 TTGTTTT
1 TTGTTTT
2844 AATTGTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
18 2 0.05
20 17 0.44
21 4 0.10
22 12 0.31
23 4 0.10
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (20 bp):
TTGTTTTGAGTTATTTTTTA
Found at i:2867 original size:12 final size:12
Alignment explanation
Indices: 2847--2880 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2837 TTGTTTTAAT
*
2847 TGTTATTTTCG-
1 TGTTATTTTTGC
2858 TGTTATTTTTGC
1 TGTTATTTTTGC
2870 TGTTATTTTTG
1 TGTTATTTTTG
2881 TTGCTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:2890 original size:12 final size:12
Alignment explanation
Indices: 2861--2907 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
2851 ATTTTCGTGT
* *
2861 TATTTTTGCTGT
1 TATTTTTGTTGC
2873 TATTTTTGTTGC
1 TATTTTTGTTGC
* *
2885 TGTTTTTATTGC
1 TATTTTTGTTGC
2897 TATTTTTGTTG
1 TATTTTTGTTG
2908 TTTTTAATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.68
Consensus pattern (12 bp):
TATTTTTGTTGC
Found at i:2903 original size:68 final size:67
Alignment explanation
Indices: 2807--2937 Score: 162
Period size: 68 Copynumber: 1.9 Consensus size: 67
2797 GTTTTGGTTG
*
2807 ATTTTTTTGCTGTTTTTGAGTTATTTTTTATTG-TTTTAATTGTTATTTT-CGTGTTATTTTTGC
1 ATTTTTTTGCTGTTTTTGAGCTATTTTTTATTGTTTTTAA-TGTTATTTTAC-TGTTATTTTTGC
2870 TGTT
64 TGTT
* *
2874 ATTTTTGTTGCTGTTTTT-ATTGCTA-TTTTTGTTGTTTTTAATGTTGTTTTACTGTTATTTTTG
1 ATTTTT-TTGCTGTTTTTGA--GCTATTTTTTATTGTTTTTAATGTTATTTTACTGTTATTTTTG
2937 C
63 C
2938 AGCTGTTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
67 7 0.12
68 39 0.70
69 10 0.18
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.68
Consensus pattern (67 bp):
ATTTTTTTGCTGTTTTTGAGCTATTTTTTATTGTTTTTAATGTTATTTTACTGTTATTTTTGCTG
TT
Found at i:2906 original size:56 final size:55
Alignment explanation
Indices: 2846--2982 Score: 132
Period size: 56 Copynumber: 2.4 Consensus size: 55
2836 ATTGTTTTAA
* * ** *
2846 TTGTTATTTTCGTGTTATTTTTGCTGTTATTTTTGTTGCTGTTTTTATTGCTATTT
1 TTGTT-TTTTAGTGTTATTTTTACTGTTATTTTTGCAGCTGTTTTGATTGCTATTT
* * *
2902 TTGTTGTTTTTAATGTT-GTTTTACTGTTATTTTTGCAGCTGTTTTGGTTGCTATTT
1 TTG-T-TTTTTAGTGTTATTTTTACTGTTATTTTTGCAGCTGTTTTGATTGCTATTT
* * *
2958 CTGTTGTTTGGATGTTATTTTTACT
1 TTGTTTTTTAG-TGTTATTTTTACT
2983 ATTGTTTCAC
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
54 4 0.06
55 5 0.08
56 45 0.70
57 9 0.14
58 1 0.02
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.64
Consensus pattern (55 bp):
TTGTTTTTTAGTGTTATTTTTACTGTTATTTTTGCAGCTGTTTTGATTGCTATTT
Found at i:3105 original size:27 final size:26
Alignment explanation
Indices: 3075--3159 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 26
3065 CTTAATATAA
3075 TTTTTAATGTATTTTAAATTTATTTAT
1 TTTTTAATGT-TTTTAAATTTATTTAT
* *
3102 TTTTTAATGTTTTTAAGTGTATTTGAT
1 TTTTTAATGTTTTTAAATTTATTT-AT
*
3129 ATATTATATAT-TTTTTAAATTTATTGTAT
1 -T-TTTTA-ATGTTTTTAAATTTATT-TAT
3158 TT
1 TT
3160 AATAAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 12 0.25
27 13 0.27
28 2 0.04
29 18 0.38
30 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (26 bp):
TTTTTAATGTTTTTAAATTTATTTAT
Found at i:5086 original size:822 final size:771
Alignment explanation
Indices: 3504--5096 Score: 2272
Period size: 822 Copynumber: 2.0 Consensus size: 771
3494 TGATTAATGC
3504 TTGGTTTTAGAAACTTTTAAAGTTTTTGTTGTTCAAAAAAATCATTTTCTAAATGAAAGTTTCCA
1 TTGGTTTTAGAAACTTTTAAAGTTTTTGTTGTTCAAAAAAATCATTTTCTAAATGAAAGTTTCCA
*
3569 ATACAATCAAAAAAAATTTCTAATTTCTAAATTGAACAAGTCACCGATAATTACCTGGTCTTTAC
66 ACACAATCAAAAAAAATTTCTAATTTCTAAATTGAACAAGTCACCGATAATTACCTGGTCTTTAC
3634 AATCCTCAACCAAACCTAGTTATTTTCTAATCTGATCCCAAGCTTCTTCAACAAAACTTGCACAA
131 AATCCTCAACCAAACCTAGTTATTTTCTAATCTGATCCCAAGCTTCTTCAACAAAACTTGCACAA
3699 TGTATTTCTTCTCCAATGTCCGAATATGTTAAGGACTCAGTAACCAAATTATTCGATAATGACAT
196 TGTATTTCTTCTCCAATGTCCGAATATGTTAAGGACTCAGTAACCAAATTATTCGATAATGACAT
3764 GGCACCATTTTATGTTTACCTATTACATATACAAAAAAAAAAGTTGAACCCCAAAATGGAGAATA
261 GGCACCATTTTATGTTTACCTATTACATATACAAAAAAAAAAGTTGAACCCCAAAATGGAGAATA
* * *
3829 AGTGAGAATTTTGTGGAACTGTAAAAAGATTAGTAGGAAGGAACGATATTTACATTGAGATTATA
326 AGTGAAAATTTTGTGGAACTATAAAAAGATTAGTAGGAAGGAACGATATTTACATCGAGATTATA
*
3894 TGTAATGTTTGGGTATTTTGCGATTATAACATAAAGATCACGAAATTTGTCGATGCGATTTTGAG
391 TGTAATGTTTGGGTATTTTGCGATTATAAAATAAAGATCACGAAATTTGTCGATGCGATTTTGAG
*
3959 TTTTTGATTTTAGATTCTCAGAGGTTAGTCTCTTTTCCTTTGTGTGTTTGGCTCGAAACTGTTTT
456 TTTTTGATTTTAGATTCTCAGAGGTTAGTCACTTTTCCTTTGTGTGTTTGGCTCGAAACTGTTTT
4024 ATTCATGGTTTCTTTTCTGATTCGGGGTTCATGTTGGAAAAATATTTAGAAAACTAGCTAGGGTA
521 ATTCATGGTTTCTTTTCTGATTCGGGGTTCATGTTGGAAAAATATTTAGAAAACTAGCTAGGGTA
* * *
4089 GGCACAATAGAGTTTTAATTTCTTTTCTAAAATAGGCCTTTACCGTGATATTTAAAGTAATAAAT
586 GGCACAATACAATTTTAATTTCTTTTCTAAAATAGGCCTTTACCGTGATACTTAAAGTAATAAAT
4154 TTGATAAATTAAATAGTTGTGTTCCAAGGCCCAAGAAATGTTCAAATCGCAAGGAAGGTTTGGGA
651 TTGATAAATTAAATAGTTGTGTTCCAAGGCCCAAGAAATGTTCAAATCGCAAGGAAGGTTTGGGA
4219 TATGACTGCATTGTTTTAATCGGTTTGAATTATAGTCCAATGTCTTAAACCTTTCT
716 TATGACTGCATTGTTTTAATCGGTTTGAATTATAGTCCAATGTCTTAAACCTTTCT
************************ *
4275 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGTT-TT-AGAAA
1 --------------------------TTGGTTTTAGAAACTTTTAAAGTTTTTGTTGTTCA-AAA
**
4338 CTTTTAAAGTTTTTGTTGTTCTAAAAAATCATTTTCTAAATGAAAGTTTCCAACACAATCAAAAA
39 -----AAA-----TCAT-TT-T-------------CTAAATGAAAGTTTCCAACACAATCAAAAA
* * *
4403 AAATTTCTAATTTTTAAATTGAACAGGTCACCGATAATTACCTGGTCTTTACAATCCTCGACCAA
79 AAATTTCTAATTTCTAAATTGAACAAGTCACCGATAATTACCTGGTCTTTACAATCCTCAACCAA
*
4468 ACCTAGTTATTTTCTAATCTGATCCCAAGCTTCTTCAACAAAACTTGCACAGTGTATTTCTTCTC
144 ACCTAGTTATTTTCTAATCTGATCCCAAGCTTCTTCAACAAAACTTGCACAATGTATTTCTTCTC
* * *
4533 CAATGTCTGAATCTGTTAAGGACTCAGTAACCAAATTATTCGATAATGACGTGGCACCATTTTAT
209 CAATGTCCGAATATGTTAAGGACTCAGTAACCAAATTATTCGATAATGACATGGCACCATTTTAT
* *
4598 GTTTACCTATTACATATACAAAAAAAAAAAGTTGAACCCCAAAATTGAGAATGAGTGAAAATTTT
274 GTTTACCTATTACATATAC-AAAAAAAAAAGTTGAACCCCAAAATGGAGAATAAGTGAAAATTTT
4663 GTGGAACTATAAAAAGATTAGTAGGAAGGAACGATATTTACATCGAGATTATATGTAATGTTTGG
338 GTGGAACTATAAAAAGATTAGTAGGAAGGAACGATATTTACATCGAGATTATATGTAATGTTTGG
4728 GTATTTTGCGATTATAAAATAAAGATCACGAAATTTGTCGATGCGATTTTGAGTTTTTGATTTTA
403 GTATTTTGCGATTATAAAATAAAGATCACGAAATTTGTCGATGCGATTTTGAGTTTTTGATTTTA
4793 GATTCTCAGAGGTTAGTCACTTTTCCTTTGTGTGTTTGGCTCGAAACTGTTTTATTCATGGTTTC
468 GATTCTCAGAGGTTAGTCACTTTTCCTTTGTGTGTTTGGCTCGAAACTGTTTTATTCATGGTTTC
4858 TTTTCTGATTCGGGGTTCATGTTGGAAAAATATTTAGAAAACTAGCTAGGGTAGGCACAATACAA
533 TTTTCTGATTCGGGGTTCATGTTGGAAAAATATTTAGAAAACTAGCTAGGGTAGGCACAATACAA
4923 TTTTAATTTCTTTTCTAAAATAGGCCTTTACCGTGATACTTAAAGTAATAAATTTGATAAATTAA
598 TTTTAATTTCTTTTCTAAAATAGGCCTTTACCGTGATACTTAAAGTAATAAATTTGATAAATTAA
* *
4988 ATAGTTGTGTTCCAAGGCCCAGGATATGTTCAAATCGCAAGGAAGGTTTGGGATATGACTGCATT
663 ATAGTTGTGTTCCAAGGCCCAAGAAATGTTCAAATCGCAAGGAAGGTTTGGGATATGACTGCATT
5053 GTTTTAATCGGTTTGAATTATAGTCCAATGTCTTAAACCTTTCT
728 GTTTTAATCGGTTTGAATTATAGTCCAATGTCTTAAACCTTTCT
5097 ACTAAACGAT
Statistics
Matches: 722, Mismatches: 47, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
795 1 0.00
796 5 0.01
797 5 0.01
801 3 0.00
806 2 0.00
807 2 0.00
808 1 0.00
821 236 0.33
822 467 0.65
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.35
Consensus pattern (771 bp):
TTGGTTTTAGAAACTTTTAAAGTTTTTGTTGTTCAAAAAAATCATTTTCTAAATGAAAGTTTCCA
ACACAATCAAAAAAAATTTCTAATTTCTAAATTGAACAAGTCACCGATAATTACCTGGTCTTTAC
AATCCTCAACCAAACCTAGTTATTTTCTAATCTGATCCCAAGCTTCTTCAACAAAACTTGCACAA
TGTATTTCTTCTCCAATGTCCGAATATGTTAAGGACTCAGTAACCAAATTATTCGATAATGACAT
GGCACCATTTTATGTTTACCTATTACATATACAAAAAAAAAAGTTGAACCCCAAAATGGAGAATA
AGTGAAAATTTTGTGGAACTATAAAAAGATTAGTAGGAAGGAACGATATTTACATCGAGATTATA
TGTAATGTTTGGGTATTTTGCGATTATAAAATAAAGATCACGAAATTTGTCGATGCGATTTTGAG
TTTTTGATTTTAGATTCTCAGAGGTTAGTCACTTTTCCTTTGTGTGTTTGGCTCGAAACTGTTTT
ATTCATGGTTTCTTTTCTGATTCGGGGTTCATGTTGGAAAAATATTTAGAAAACTAGCTAGGGTA
GGCACAATACAATTTTAATTTCTTTTCTAAAATAGGCCTTTACCGTGATACTTAAAGTAATAAAT
TTGATAAATTAAATAGTTGTGTTCCAAGGCCCAAGAAATGTTCAAATCGCAAGGAAGGTTTGGGA
TATGACTGCATTGTTTTAATCGGTTTGAATTATAGTCCAATGTCTTAAACCTTTCT
Done.