Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013179.1 Kokia drynarioides strain JFW-HI SEQ_128198, 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: 2697
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:359 original size:98 final size:98
Alignment explanation
Indices: 187--479 Score: 437
Period size: 98 Copynumber: 3.0 Consensus size: 98
177 AATCTTGAAA
* * * *
187 AAGGGTATTCGATTATCCCGGTTTGAAG-AAAAGTCGCGCCTAGTAAGTTAAGGCACAACTTTTC
1 AAGGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
* * *
251 AAGACTCGAAATAATGGAATATTGCCTCGGTTT
66 AAGACCCGAAATAAAGGAATATTGCCTCGATTT
* * *
284 AAGGGTACTCGATTATTCCGATTTGAAGAAAAAATCGCACCTAGTGAGTTAAGGCACAAATTTTC
1 AAGGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
349 AAGACCCGAAATAAAGGAATATTGCCTCGATTT
66 AAGACCCGAAATAAAGGAATATTGCCTCGATTT
* * * *
382 AAGGGTACTCGATTATTTCGGTTTGAAGAAAAAATAGTGCCTAGTAAGTTAAGACACAAATTTTC
1 AAGGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
447 ATA-ACCCGAAATAAAGGAATATTGCCTCGATTT
66 A-AGACCCGAAATAAAGGAATATTGCCTCGATTT
480 TAAATATTTT
Statistics
Matches: 177, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
97 25 0.14
98 151 0.85
99 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (98 bp):
AAGGGTACTCGATTATTCCGGTTTGAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
AAGACCCGAAATAAAGGAATATTGCCTCGATTT
Found at i:925 original size:57 final size:56
Alignment explanation
Indices: 801--975 Score: 162
Period size: 57 Copynumber: 3.1 Consensus size: 56
791 TCGCGAGCAG
* * * * * *
801 AAATGTAATTTTT-GAAAGTTCAGGGTTAAAAT-TGGAATTTTTGGAAGTTCGAGGGAA
1 AAATGGAATTTTTGGAAA-TTTAGGGCTAAAATGT-G-ATTTTTGAAAGTTTGGGGGAA
858 AAATTGGAATTTTTGGAAATTTGAGGG-TAAAATGTGATTTTTGAAAGTTTGGGGGTAA
1 AAA-TGGAATTTTTGGAAATTT-AGGGCTAAAATGTGATTTTTGAAAGTTTGGGGG-AA
* * *
916 AAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGT-AATTTTGAGAA-TTTGGGGGAA
1 AAATGGAATTTTTGGAAATTTA-GGGCTAAAATGTGATTTTTGA-AAGTTTGGGGGAA
972 AAAT
1 AAAT
976 TCTAATTTGA
Statistics
Matches: 102, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
56 7 0.07
57 54 0.53
58 32 0.31
59 9 0.09
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (56 bp):
AAATGGAATTTTTGGAAATTTAGGGCTAAAATGTGATTTTTGAAAGTTTGGGGGAA
Found at i:955 original size:86 final size:87
Alignment explanation
Indices: 742--956 Score: 226
Period size: 86 Copynumber: 2.5 Consensus size: 87
732 GTTTGGGACT
* * *
742 AAAATGCAA-TTTTGGAAAGTTTTA-GGGCAAAAACGTGAA-TTTTGGAAATTCGCGAGCAGAAA
1 AAAATGGAATTTTTGG-AAG-TTTAGGGGCAAAAATGT-AATTTTTGGAAATTCGAGAGCAGAAA
*
804 TGTAATTTTTGAAAGTTCAGGGTTA
63 TGTAATTTTTGAAAGTTCAGGGGTA
* * * * * *
829 AAATTGGAATTTTTGGAAG-TTCGAGGG-AAAAATTGGAATTTTTGGAAATTTGAGGGTA-AAAT
1 AAAATGGAATTTTTGGAAGTTTAG-GGGCAAAAA-TGTAATTTTTGGAAATTCGAGAGCAGAAAT
* **
891 GTGATTTTTGAAAGTTTGGGGGTA
64 GTAATTTTTGAAAGTTCAGGGGTA
915 AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTT
957 GAGAATTTGG
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
85 2 0.02
86 60 0.57
87 37 0.35
88 6 0.06
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAATTCGAGAGCAGAAATGT
AATTTTTGAAAGTTCAGGGGTA
Found at i:995 original size:26 final size:27
Alignment explanation
Indices: 954--1009 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
944 AAAATGTAAT
954 TTTGAGAATTTGGGGGAAAAATTCTAA
1 TTTGAGAATTTGGGGGAAAAATTCTAA
* * *
981 TTTGATAATTTGGGGG-GAAATTGTAA
1 TTTGAGAATTTGGGGGAAAAATTCTAA
1007 TTT
1 TTT
1010 TTGAGAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (27 bp):
TTTGAGAATTTGGGGGAAAAATTCTAA
Found at i:1020 original size:29 final size:29
Alignment explanation
Indices: 801--1046 Score: 143
Period size: 29 Copynumber: 8.6 Consensus size: 29
791 TCGCGAGCAG
* * **
801 AAATGTAATTTTTGA-AAGTTCAGGGTTAA
1 AAATGTAATTTTTGAGAAATT-TGGGGGAA
* * * * *
830 AATTGGAATTTTTG-GAAGTTCGAGGGAA
1 AAATGTAATTTTTGAGAAATTTGGGGGAA
* * *
858 AAATTGGAATTTTTG-GAAATTTGAGGGTA
1 AAA-TGTAATTTTTGAGAAATTTGGGGGAA
* *
887 AAATGTGATTTTTGA-AAGTTTGGGGGTAA
1 AAATGTAATTTTTGAGAAATTTGGGGG-AA
* * *
916 AAATGGAATTTTTG-GAAGTTTAGGGGCAA
1 AAATGTAATTTTTGAGAAATTT-GGGGGAA
945 AAATGTAA-TTTTGAG-AATTTGGGGGAA
1 AAATGTAATTTTTGAGAAATTTGGGGGAA
* * *
972 AAATTCTAA--TTTGA-TAATTTGGGGGGA
1 AAA-TGTAATTTTTGAGAAATTTGGGGGAA
* * *
999 AATTGTAATTTTTGAGAAATTTAGAGGTAA
1 AAATGTAATTTTTGAGAAATTT-GGGGGAA
**
1029 ACGTGTAATTTTTGAGAA
1 AAATGTAATTTTTGAGAA
1047 GTTCGAGGGT
Statistics
Matches: 173, Mismatches: 31, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
26 4 0.02
27 27 0.16
28 42 0.24
29 76 0.44
30 24 0.14
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTTTGAGAAATTTGGGGGAA
Done.