Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009056.1 Kokia drynarioides strain JFW-HI SEQ_123755, 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: 3916
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:906 original size:29 final size:29
Alignment explanation
Indices: 854--1111 Score: 258
Period size: 29 Copynumber: 8.8 Consensus size: 29
844 TTGGAGGTCG
* * *
854 AAAATGGAGTTTTTAGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
*
884 AAAATGAAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* *
913 AAAATGGAATTTTGGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
943 AAATTTGAATTTTTGGAAG-TTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
972 AAAGCAT--AATTTTTGGAAGTTTTGGGGTTA
1 AAA--ATGGAATTTTTGGAAGTTTCGGGG-TA
*
1002 AAAATGGAATTTTTGGAAGTTTTGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* * *
1031 AAAATGTAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
1061 AAAATGGAA-TTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
1089 AAAATGGAATTTTCGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
1112 AGGGACCTCC
Statistics
Matches: 194, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.08
29 94 0.48
30 82 0.42
31 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:1111 original size:59 final size:59
Alignment explanation
Indices: 854--1111 Score: 319
Period size: 59 Copynumber: 4.4 Consensus size: 59
844 TTGGAGGTCG
* * * * *
854 AAAATGGAGTTTTTAGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
913 AAAATGGAATTTTGGGAAGTTTTGGGGTCAAAATTTGAATTTTTGGAAGTTC-AGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTA
* *
972 AAAGCAT--AATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTTG-GGGTA
1 AAA--ATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGTA
* *
1031 AAAATGTAATTTTTAGAAGTTTTGGGGTCAAAAATGGAA-TTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
*
1089 AAAATGGAATTTTCGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
1112 AGGGACCTCC
Statistics
Matches: 171, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
57 5 0.03
58 29 0.17
59 133 0.78
60 2 0.01
61 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:2036 original size:3 final size:3
Alignment explanation
Indices: 2028--2073 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
2018 TTAATTAATG
*
2028 TTA TTA TTA ATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2074 ATGTCATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2787 original size:13 final size:13
Alignment explanation
Indices: 2769--2794 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2759 TTGGGCTTGA
2769 TTTGTAATTGGAC
1 TTTGTAATTGGAC
2782 TTTGTAATTGGAC
1 TTTGTAATTGGAC
2795 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:2831 original size:17 final size:16
Alignment explanation
Indices: 2811--2873 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
2801 TAAATAAATT
*
2811 TAAATTTTAATTTATAA
1 TAAATTTAAATTTA-AA
2828 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
* *
2845 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
2862 TAAATTTAAATT
1 TAAATTTAAATT
2874 CTGTTGGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 38 0.97
18 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:2833 original size:23 final size:22
Alignment explanation
Indices: 2798--2840 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
2788 ATTGGACATT
2798 ATTTAAATAAATTTAAATTTTA
1 ATTTAAATAAATTTAAATTTTA
2820 ATTTATAATAAATTTAAATTT
1 ATTTA-AATAAATTTAAATTT
2841 CAAATAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTTA
Found at i:3387 original size:31 final size:32
Alignment explanation
Indices: 3325--3388 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3315 CTTAACAACC
*
3325 CAATAACTTAAATAAAAACTTTTTGAATAGTT
1 CAATAACTTAAATAAAAACTTTTCGAATAGTT
3357 CAATAACTTAAATAAAAAC-TTTCGAATAGTT
1 CAATAACTTAAATAAAAACTTTTCGAATAGTT
3388 C
1 C
3389 GATGATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (32 bp):
CAATAACTTAAATAAAAACTTTTCGAATAGTT
Done.