Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000746.1 Kokia drynarioides strain JFW-HI SEQ_111783, 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: 7064
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6398 original size:79 final size:78
Alignment explanation
Indices: 6246--6406 Score: 227
Period size: 79 Copynumber: 2.1 Consensus size: 78
6236 TGGAATAGGG
* * *
6246 TATTCGATTATCTCGATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
1 TATTAGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCAAAACC
*
6311 AGAGATAAAGAAAA
66 AGAAATAAA-AAAA
*
6325 TATTAGATTAT-TCAGATTTGAAGAAAAATTGCGCCTAGTAAGTTAAGACACAAATTTTCAAAAC
1 TATTAGATTATCTC-GATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCAAAAC
*
6389 TC-GAAATAAAAGAA
65 -CAGAAATAAAAAAA
6403 TATT
1 TATT
6407 TCCTCGATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
78 9 0.12
79 64 0.86
80 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (78 bp):
TATTAGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCAAAACC
AGAAATAAAAAAA
Found at i:6672 original size:29 final size:29
Alignment explanation
Indices: 6639--6800 Score: 157
Period size: 30 Copynumber: 5.5 Consensus size: 29
6629 CAAAAATATG
**
6639 ATTTTTGGATGCTCAGGGGTAAAATGGTA
1 ATTTTTGGACACTCAGGGGTAAAATGGTA
* * **
6668 ATTTTTGGACAATCGGGGGCGCAAATGGTA
1 ATTTTTGGACACTCAGGGG-TAAAATGGTA
6698 ATTTTTGGACACTCGAGGGGTAAAATGGTA
1 ATTTTTGGACACTC-AGGGGTAAAATGGTA
* * * *
6728 ATTTTCGGATATTC-GGGAGTAAAACGGTA
1 ATTTTTGGACACTCAGGG-GTAAAATGGTA
* * *
6757 A-TTTTGGACACTTCAAGAGCAAAATGGTA
1 ATTTTTGGACAC-TCAGGGGTAAAATGGTA
6786 ATTTTTGGACACTCA
1 ATTTTTGGACACTCA
6801 AGAACAAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
28 10 0.09
29 41 0.39
30 51 0.48
31 4 0.04
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (29 bp):
ATTTTTGGACACTCAGGGGTAAAATGGTA
Found at i:6801 original size:29 final size:29
Alignment explanation
Indices: 6639--6809 Score: 137
Period size: 29 Copynumber: 5.8 Consensus size: 29
6629 CAAAAATATG
** * *
6639 ATTTTTGGATGCTCAGGGGTAAAATGGTA
1 ATTTTTGGACACTCAGGAGCAAAATGGTA
* * * *
6668 ATTTTTGGACAATCGGGGGCGCAAATGGTA
1 ATTTTTGGACACTCAGGAGC-AAAATGGTA
* *
6698 ATTTTTGGACACTCGAGGGGTAAAATGGTA
1 ATTTTTGGACACTC-AGGAGCAAAATGGTA
* * * * * *
6728 ATTTTCGGATATTCGGGAGTAAAACGGTA
1 ATTTTTGGACACTCAGGAGCAAAATGGTA
*
6757 A-TTTTGGACACTTCAAGAGCAAAATGGTA
1 ATTTTTGGACAC-TCAGGAGCAAAATGGTA
* *
6786 ATTTTTGGACACTCAAGAACAAAA
1 ATTTTTGGACACTCAGGAGCAAAA
6810 ATGCAATTTT
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
28 7 0.06
29 53 0.46
30 50 0.44
31 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (29 bp):
ATTTTTGGACACTCAGGAGCAAAATGGTA
Found at i:6811 original size:30 final size:30
Alignment explanation
Indices: 6658--6820 Score: 100
Period size: 30 Copynumber: 5.5 Consensus size: 30
6648 TGCTCAGGGG
* ** **
6658 TAAAATGGTAATTTTTGGACAATCGGGGGC
1 TAAAATGGTAATTTTTGGACACTCAAGAAC
** * ***
6688 GCAAATGGTAATTTTTGGACACTCGAGGGG
1 TAAAATGGTAATTTTTGGACACTCAAGAAC
* * * * * *
6718 TAAAATGGTAATTTTCGGATATTC-GGGAG
1 TAAAATGGTAATTTTTGGACACTCAAGAAC
* *
6747 TAAAACGGTAA-TTTTGGACACTTCAAGAGC
1 TAAAATGGTAATTTTTGGACAC-TCAAGAAC
6777 -AAAATGGTAATTTTTGGACACTCAAGAAC
1 TAAAATGGTAATTTTTGGACACTCAAGAAC
* *
6806 AAAAAT-GCAATTTTT
1 TAAAATGGTAATTTTT
6821 AGAAGTTTAG
Statistics
Matches: 106, Mismatches: 23, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
28 7 0.07
29 39 0.37
30 60 0.57
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGACACTCAAGAAC
Found at i:6817 original size:29 final size:30
Alignment explanation
Indices: 6758--6820 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
6748 AAAACGGTAA
* *
6758 TTTTGGACACTTCAAGAGCAAAATGGTAAT
1 TTTTGGACACTTCAAGAACAAAATGGCAAT
6788 TTTTGGACAC-TCAAGAACAAAAAT-GCAAT
1 TTTTGGACACTTCAAGAAC-AAAATGGCAAT
6817 TTTT
1 TTTT
6821 AGAAGTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (30 bp):
TTTTGGACACTTCAAGAACAAAATGGCAAT
Found at i:6838 original size:29 final size:29
Alignment explanation
Indices: 6806--7022 Score: 175
Period size: 30 Copynumber: 7.5 Consensus size: 29
6796 ACTCAAGAAC
* *
6806 AAAAATGCAATTTTTAGAAGTTTAGGGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
* *
6835 -AAAA--CAATTTTCGGAAAGTTT-GGGGT
1 AAAAATGTAATTTTTGG-AAGTTTAGGGGT
* *
6861 CAAAAAT-AATATTTTTGGAAGTTCAGGGGT
1 -AAAAATGTA-ATTTTTGGAAGTTTAGGGGT
*
6891 -AAAATGGTAA-TTTTGGAAGTTTAGAGGT
1 AAAAAT-GTAATTTTTGGAAGTTTAGGGGT
* *
6919 AAAATTGTAATTTTTTGGAAG-TTCGAGGGT
1 AAAAATGTAA-TTTTTGGAAGTTTAG-GGGT
* *
6949 -AAAATGGTAATTTTTAGAAGTTTAGGAGT
1 AAAAAT-GTAATTTTTGGAAGTTTAGGGGT
*
6978 AAAAATGTAATTTTTGTGAAGTTT-GGGTGC
1 AAAAATGTAATTTTTG-GAAGTTTAGGG-GT
7008 AAAAATGTAATTTTT
1 AAAAATGTAATTTTT
7023 TAAAGTTCGA
Statistics
Matches: 153, Mismatches: 18, Indels: 33
0.75 0.09 0.16
Matches are distributed among these distances:
26 13 0.08
27 6 0.04
28 33 0.22
29 41 0.27
30 60 0.39
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:6999 original size:59 final size:58
Alignment explanation
Indices: 6871--7000 Score: 178
Period size: 59 Copynumber: 2.2 Consensus size: 58
6861 CAAAAATAAT
* *
6871 ATTTTTG-GAAGTTCAGGGGTAAAATGGTAATTTTGGAAGTTTAGAGGTAAAATTGTA
1 ATTTTTGTGAAGTTCAGGGGTAAAATGGTAATTTTAGAAGTTTAGAGGTAAAAATGTA
6928 ATTTTT-TGGAAGTTC-GAGGGTAAAATGGTAATTTTTAGAAGTTTAG-GAGTAAAAATGTA
1 ATTTTTGT-GAAGTTCAG-GGGTAAAATGGTAA-TTTTAGAAGTTTAGAG-GTAAAAATGTA
6987 ATTTTTGTGAAGTT
1 ATTTTTGTGAAGTT
7001 TGGGTGCAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
57 7 0.11
58 22 0.34
59 35 0.54
60 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (58 bp):
ATTTTTGTGAAGTTCAGGGGTAAAATGGTAATTTTAGAAGTTTAGAGGTAAAAATGTA
Found at i:7029 original size:59 final size:59
Alignment explanation
Indices: 6867--7022 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 59
6857 GGGTCAAAAA
* * *
6867 TAATATTTTTGGAAGTTC-AGGGGTAAAATGGTAA-TTTTGGAAGTTTAGAGGTAAAATTG
1 TAAT-TTTTTGGAAGTTCGA-GGGAAAAATGGTAATTTTTAGAAGTTTAGAGGTAAAAATG
*
6926 TAATTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTAG-GAGTAAAAATG
1 TAATTTTTTGGAAGTTCGAGGGAAAAATGGTAATTTTTAGAAGTTTAGAG-GTAAAAATG
*
6985 TAA-TTTTTGTGAAGTTTG-GGTGCAAAAAT-GTAATTTTT
1 TAATTTTTTG-GAAGTTCGAGG-G-AAAAATGGTAATTTTT
7023 TAAAGTTCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
58 36 0.41
59 46 0.53
60 5 0.06
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (59 bp):
TAATTTTTTGGAAGTTCGAGGGAAAAATGGTAATTTTTAGAAGTTTAGAGGTAAAAATG
Found at i:7041 original size:29 final size:28
Alignment explanation
Indices: 6915--7050 Score: 82
Period size: 30 Copynumber: 4.6 Consensus size: 28
6905 GGAAGTTTAG
*
6915 AGGTAAAATTGTAATTTTTTGGAAGTTCGA
1 AGGTAAAA-TGTAATTTTTT-AAAGTTCGA
* *
6945 GGGTAAAATGGTAA-TTTTTAGAAGTT-TA
1 AGGTAAAAT-GTAATTTTTTA-AAGTTCGA
* * *
6973 GGAGTAAAAATGTAATTTTTGTGAAGTTTG-
1 AG-GT-AAAATGTAATTTTT-TAAAGTTCGA
7003 -GGTGCAAAAATGTAATTTTTTAAAGTTCGA
1 AGGT---AAAATGTAATTTTTTAAAGTTCGA
*
7033 AGGTCAAAATATAATTTT
1 AGGT-AAAATGTAATTTT
7051 GGAAAGTTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
28 5 0.06
29 37 0.43
30 40 0.47
31 4 0.05
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (28 bp):
AGGTAAAATGTAATTTTTTAAAGTTCGA
Found at i:7041 original size:30 final size:29
Alignment explanation
Indices: 6915--7050 Score: 93
Period size: 29 Copynumber: 4.6 Consensus size: 29
6905 GGAAGTTTAG
* *
6915 AGGTAAAATTGTAATTTTTTGGAAGTTCGA
1 AGGTAAAAATGTAATTTTTT-AAAGTTCGA
* *
6945 GGGT-AAAATGGTAA-TTTTTAGAAGTT-TA
1 AGGTAAAAAT-GTAATTTTTTA-AAGTTCGA
* * *
6973 GGAGTAAAAATGTAATTTTTGTGAAGTTTG-
1 AG-GTAAAAATGTAATTTTT-TAAAGTTCGA
7003 -GGTGCAAAAATGTAATTTTTTAAAGTTCGA
1 AGGT--AAAAATGTAATTTTTTAAAGTTCGA
* *
7033 AGGTCAAAATATAATTTT
1 AGGTAAAAATGTAATTTT
7051 GGAAAGTTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
28 5 0.06
29 40 0.47
30 36 0.42
31 4 0.05
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (29 bp):
AGGTAAAAATGTAATTTTTTAAAGTTCGA
Done.