Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013699.1 Kokia drynarioides strain JFW-HI SEQ_128727, 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: 7839
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:5630 original size:218 final size:218
Alignment explanation
Indices: 5249--6038 Score: 1285
Period size: 218 Copynumber: 3.6 Consensus size: 218
5239 CAAAGCGATG
* * * *
5249 CGGTCATCTTCCCAATGAGATACTGAGAAGAAGATCAAACCAAACTCACGCTTGATATGAGCAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
* *
5314 GCTTCGAATCCCAGCTTCCTGATGAGGTACGGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTT
66 GCTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
*
5379 CCTGACCATCTTCATGATGAGGTACGAAGAAGTGGACCAAAATCGTCTTCCTGATAAGATACAGA
131 CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAAATCGTCTTCCTGATAAGATACAGA
* *
5444 GAAGCAAATTGAAACCAACAGCA
196 GAAACGAATTGAAACCAACAGCA
5467 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
*
5532 GCTTCGAATCCCCGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
66 GCTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
*
5597 CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAAATCGTCTTCCTAATAAGATACAGA
131 CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAAATCGTCTTCCTGATAAGATACAGA
*
5662 GAAACGAACTGAAACCAACAGCA
196 GAAACGAATTGAAACCAACAGCA
5685 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
*
5750 GCTTCGAATCCCAGCTTCCTAATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
66 GCTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
* *
5815 CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCCTTCCTGATGAGATACAG
131 CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAAATCGT-CTTCCTGATAAGATACAG
5880 AGAAACGAATTGAAACCAAC-GACA
195 AGAAACGAATTGAAACCAACAG-CA
** * * *
5904 TAGTCATCTTCCCGATGAGATACTAAGAAGAAGACCAAATCAAACTCACGCCCGATGTGAGCAAA
1 CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
* * * ** * * * * *
5969 TCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTC
66 GCTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
6034 CCTGA
131 CCTGA
6039 TGAGATATAG
Statistics
Matches: 536, Mismatches: 34, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
218 380 0.71
219 156 0.29
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (218 bp):
CGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAA
GCTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAATGGTTGGCTT
CCTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAAATCGTCTTCCTGATAAGATACAGA
GAAACGAATTGAAACCAACAGCA
Found at i:6518 original size:6 final size:6
Alignment explanation
Indices: 6497--6587 Score: 59
Period size: 6 Copynumber: 15.8 Consensus size: 6
6487 TGTTTAAAAA
* * * *
6497 TTAAAT TT-ATT TTAAAT TTAAAT TT-ATT TTGAAT TTAAAT TT-GAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
6542 TTAAGT TTAAAT TT-ATT TTCAAAT TTAAAA TT--AT TATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT T-TAAAT TTAAA
6588 ATAAGTAAAG
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 17 0.27
6 38 0.59
7 7 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:6545 original size:52 final size:51
Alignment explanation
Indices: 6461--6587 Score: 157
Period size: 52 Copynumber: 2.5 Consensus size: 51
6451 CCAAACTCCC
* *
6461 TTTAAGTTTATTTTAAAAATTAAATTTGTTTAAAAATTAAATTTATTTT-AAA
1 TTTAAATTTATTTT-AAATTTAAATTTGTTT-AAAATTAAATTTATTTTCAAA
* **
6513 TTTAAATTTATTTTGAATTTAAATTTGATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTG-TTTAAAATTAAATTTATTTTCAAA
* *
6565 TTTAAAATTATTATAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
6588 ATAAGTAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
51 26 0.40
52 39 0.60
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (51 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTAAAATTAAATTTATTTTCAAA
Found at i:6589 original size:17 final size:17
Alignment explanation
Indices: 6461--6587 Score: 139
Period size: 17 Copynumber: 7.4 Consensus size: 17
6451 CCAAACTCCC
*
6461 TTTAAGTTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
6479 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
*
6496 ATTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
6513 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
6530 TTTAAATTTGA-TTTAAG
1 TTTAAATTT-ATTTTAAA
6547 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
6565 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
6582 TTTAAA
1 TTTAAA
6588 ATAAGTAAAG
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.01
17 67 0.72
18 25 0.27
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:7371 original size:3 final size:3
Alignment explanation
Indices: 7363--7391 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7353 TTAATGATAT
7363 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
7392 GTATTAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.