Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005737.1 Kokia drynarioides strain JFW-HI SEQ_119975, 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: 7604
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Found at i:3811 original size:36 final size:36
Alignment explanation
Indices: 3741--3841 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
3731 GGTAACAGGC
* * * *
3741 ATGACCTTTGGGTCAATAGAGTGAAAAATAAGCATA
1 ATGACCTTTGGGTCAATAGGGAGTAAAACAAGCATA
* *
3777 ATGACCTTTGGGTCAATAGGGAGTAAAACGAGCATC
1 ATGACCTTTGGGTCAATAGGGAGTAAAACAAGCATA
* * *
3813 ATGATCTTTGTGGTTAACAGGGAGTAAAA
1 ATGACCTTTG-GGTCAATAGGGAGTAAAA
3842 TGAATAACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
36 39 0.71
37 16 0.29
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (36 bp):
ATGACCTTTGGGTCAATAGGGAGTAAAACAAGCATA
Found at i:4479 original size:47 final size:48
Alignment explanation
Indices: 4337--4498 Score: 120
Period size: 47 Copynumber: 3.4 Consensus size: 48
4327 AACTCATGCT
* * *
4337 TGTAATGGTAGAAGTATACGGTAGGAGAGAGGTTGTTCTCTGACTTAAG
1 TGTATTGGTAGTAGTATA-GGTAGGAGAGAGGTTGTTCTCTGACTTGAG
* * * ** * *
4386 TTGTTTTGGTAGTTGTATA-ATAGGTATCGA--TAGTTCTGTAGA-TTGAG
1 -TGTATTGGTAGTAGTATAGGTAGG-AGAGAGGTTGTTCTCT-GACTTGAG
*
4433 -GTATTGGTAGTAGTACAGGTAGGAGAGAGGTTGTTCTCTGACTTGAG
1 TGTATTGGTAGTAGTATAGGTAGGAGAGAGGTTGTTCTCTGACTTGAG
*
4480 TTGT-TTCGGTAGTTGTATA
1 -TGTATT-GGTAGTAGTATA
4499 ACAGGTATCG
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
45 17 0.20
46 6 0.07
47 23 0.28
48 8 0.10
49 15 0.18
50 14 0.17
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (48 bp):
TGTATTGGTAGTAGTATAGGTAGGAGAGAGGTTGTTCTCTGACTTGAG
Found at i:4482 original size:94 final size:95
Alignment explanation
Indices: 4342--4530 Score: 308
Period size: 94 Copynumber: 2.0 Consensus size: 95
4332 ATGCTTGTAA
* * *
4342 TGGTAGAAGTATACGGTAGGAGAGAGGTTGTTCTCTGACTTAAGTTGTTTTGGTAGTTGTATAAT
1 TGGTAGAAGTACACGGTAGGAGAGAGGTTGTTCTCTGACTTAAGTTGTTTCGGTAGTTGTATAAC
*
4407 AGGTATCGATAGTTCTGTAGATTGAGGTAT
66 AGGTATCGATAGTTCTGTACATTGAGGTAT
* *
4437 TGGTAGTAGTACA-GGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGGTAGTTGTATAAC
1 TGGTAGAAGTACACGGTAGGAGAGAGGTTGTTCTCTGACTTAAGTTGTTTCGGTAGTTGTATAAC
*
4501 AGGTATCGATAGTTCTTTACATTGAGGTAT
66 AGGTATCGATAGTTCTGTACATTGAGGTAT
4531 CGATAGCTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 76 0.87
95 11 0.13
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (95 bp):
TGGTAGAAGTACACGGTAGGAGAGAGGTTGTTCTCTGACTTAAGTTGTTTCGGTAGTTGTATAAC
AGGTATCGATAGTTCTGTACATTGAGGTAT
Found at i:4516 original size:47 final size:46
Alignment explanation
Indices: 4371--4516 Score: 120
Period size: 47 Copynumber: 3.1 Consensus size: 46
4361 GAGAGAGGTT
*
4371 GTTCTCTGACTTAAGTTGTTTTGGTAGTTGTATAATAGGTATCGATA
1 GTTCTCTGACTTGAGTTG-TTTGGTAGTTGTATAATAGGTATCGATA
* * * * ** *
4418 GTTCTGTAGA-TTGAG--GTATTGGTAGTAGTACAGGTAGG-AGAGAGGTT
1 GTTCTCT-GACTTGAGTTGT-TTGGTAGTTGTATA-ATAGGTATCGA--TA
*
4465 GTTCTCTGACTTGAGTTGTTTCGGTAGTTGTATAACAGGTATCGATA
1 GTTCTCTGACTTGAGTTGTTT-GGTAGTTGTATAATAGGTATCGATA
4512 GTTCT
1 GTTCT
4517 TTACATTGAG
Statistics
Matches: 73, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
44 1 0.01
45 16 0.22
46 6 0.08
47 28 0.38
48 7 0.10
49 15 0.21
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (46 bp):
GTTCTCTGACTTGAGTTGTTTGGTAGTTGTATAATAGGTATCGATA
Found at i:6130 original size:26 final size:27
Alignment explanation
Indices: 6088--6198 Score: 111
Period size: 27 Copynumber: 4.1 Consensus size: 27
6078 AAATTTGTAA
6088 AGGGAAAAACTGTAAAATCTAAAAAAT
1 AGGGAAAAACTGTAAAATCTAAAAAAT
* *
6115 AGGG-AAAACTGGAAAATCTGAAAAAT
1 AGGGAAAAACTGTAAAATCTAAAAAAT
* * *
6141 AGGTG-AAAATTATAAAATTTAAAAAAT
1 AGG-GAAAAACTGTAAAATCTAAAAAAT
* **
6168 AAGGGCAAATTTGTAAAATCT-AAAAAT
1 -AGGGAAAAACTGTAAAATCTAAAAAAT
6195 AGGG
1 AGGG
6199 GACACACGAC
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 27 0.38
27 29 0.41
28 15 0.21
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (27 bp):
AGGGAAAAACTGTAAAATCTAAAAAAT
Found at i:6533 original size:147 final size:147
Alignment explanation
Indices: 6292--6583 Score: 494
Period size: 147 Copynumber: 2.0 Consensus size: 147
6282 GACTAAGACC
6292 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCGTGTGATGGTCTGTGTGGTCCAC
1 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCGTGTGATGGTCTGTGTGGTCCAC
** * ** * *
6357 GAGTGGCCCTAGGCACAATTTTCGTTGATTTGATTGTAAAAGAACACATGCATGTTACCAGAATC
66 GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAAAACACATGCATGTTACCAGAATC
*
6422 TCGAGCGATGTCCCTTA
131 TCAAGCGATGTCCCTTA
* *
6439 ATGTGGAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCGTGTGATGGTTTGTGTGGTCCAC
1 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCGTGTGATGGTCTGTGTGGTCCAC
6504 GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAAAACACATGCATGTTACCAGAATC
66 GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAAAACACATGCATGTTACCAGAATC
6569 TCAAGCGATGTCCCT
131 TCAAGCGATGTCCCT
6584 CATGTTCAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 135 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (147 bp):
ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCGTGTGATGGTCTGTGTGGTCCAC
GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAAAACACATGCATGTTACCAGAATC
TCAAGCGATGTCCCTTA
Done.