Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013895.1 Kokia drynarioides strain JFW-HI SEQ_128924, 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: 12483
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:1130 original size:137 final size:137
Alignment explanation
Indices: 884--1159 Score: 498
Period size: 137 Copynumber: 2.0 Consensus size: 137
874 CAAAAGTATG
*
884 ATGTGATCCTCCAACACCCAAAGACCAATCATGATGAACATCTAAATGATCAATAAAGGATTGAC
1 ATGTGATCCTCCAACACCCAAAGACCAATCATGATGAACATCTAAATGATCAACAAAGGATTGAC
949 TCAAAATGAAAAGAATCCACGAATCAATTTCAAGACAAAACACTTTTCTTCATGTATGAACAAAA
66 TCAAAATGAAAAGAATCCACGAATCAATTTCAAGACAAAACACTTTTCTTCATGTATGAACAAAA
*
1014 GGAGGGA
131 GGAAGGA
* * *
1021 ATGTGATCCTCCAACACCCAAAGACCAATCATTATGAGCATCTAAATGATCAACAGAGGATTGAC
1 ATGTGATCCTCCAACACCCAAAGACCAATCATGATGAACATCTAAATGATCAACAAAGGATTGAC
*
1086 TCAAAATGAAAAGAATCCACGAATCAATTTCAAGACAAAACACTTTTCTTCATGTATGAACAGAA
66 TCAAAATGAAAAGAATCCACGAATCAATTTCAAGACAAAACACTTTTCTTCATGTATGAACAAAA
1151 GGAAGGA
131 GGAAGGA
1158 AT
1 AT
1160 TAAACTGAAA
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (137 bp):
ATGTGATCCTCCAACACCCAAAGACCAATCATGATGAACATCTAAATGATCAACAAAGGATTGAC
TCAAAATGAAAAGAATCCACGAATCAATTTCAAGACAAAACACTTTTCTTCATGTATGAACAAAA
GGAAGGA
Found at i:3154 original size:30 final size:30
Alignment explanation
Indices: 3120--3354 Score: 253
Period size: 30 Copynumber: 7.9 Consensus size: 30
3110 AGAGGTCCCT
* *
3120 AACTTTTCCAAAATTATATTTTGACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTTA
* *
3150 AACTTTTCTAAAATTACATTTTAATCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTTA
*
3180 AACTTTTTCAAAATTACATTTTAACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTTA
* * *
3210 AACTTTTCCAAAATCATATTTTAATCCC-AA
1 AACTTTTCCAAAATTACATTTTAA-CCCTTA
* *
3240 AACTTTTCCAAAATTACATTTTGACCCTCCA
1 AACTTTTCCAAAATTACATTTTAACCCT-TA
* * * *
3271 AAATTTTCCAAAATCATATTTTGACCC--A
1 AACTTTTCCAAAATTACATTTTAACCCTTA
* * *
3299 AACTTTTCTAAAATCACATTTTAACCCATA
1 AACTTTTCCAAAATTACATTTTAACCCTTA
* *
3329 AA-ATTTCCAAAATCACATTTTAACCC
1 AACTTTTCCAAAATTACATTTTAACCC
3355 CCGAGCTTCT
Statistics
Matches: 176, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
28 24 0.14
29 25 0.14
30 99 0.56
31 28 0.16
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTAACCCTTA
Found at i:3192 original size:60 final size:60
Alignment explanation
Indices: 3120--3351 Score: 281
Period size: 60 Copynumber: 3.9 Consensus size: 60
3110 AGAGGTCCCT
* * * **
3120 AACTTTTCCAAAATTATATTTTGACCCTTAAACTTTTCTAAAATTACATTTTAATCCTTA
1 AACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCACATTTTAATCCCAA
* * *
3180 AACTTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTAATCCCAA
1 AACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCACATTTTAATCCCAA
* * * *
3240 AACTTTTCCAAAATTACATTTTGACCCTCCAAAATTTTCCAAAATCATATTTTGA-CCC-A
1 AACTTTTCCAAAATTACATTTTGACCCT-TAAACTTTTCCAAAATCACATTTTAATCCCAA
* * * * *
3299 AACTTTTCTAAAATCACATTTTAACCCATAAA-ATTTCCAAAATCACATTTTAA
1 AACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCACATTTTAA
3352 CCCCCGAGCT
Statistics
Matches: 150, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
57 18 0.12
58 3 0.02
59 25 0.17
60 81 0.54
61 23 0.15
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (60 bp):
AACTTTTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCACATTTTAATCCCAA
Found at i:7625 original size:62 final size:60
Alignment explanation
Indices: 7558--7686 Score: 163
Period size: 62 Copynumber: 2.1 Consensus size: 60
7548 GGGAGATATA
* *
7558 AAAAAAAAGAAGTAATG-AAAG-AAAGAAAAAGGCAAGGTGAAAACCCGCAAAGGGTATCTTT
1 AAAAAAAAGAA-TAA-GAAAAGAAAAGAAAAAGGCAAGATGAAAACCCGCAAAGGGCATC-TT
* * *
7619 ATAAAAAAGAATAAGAAAAGAAAAAGGAAAAGTCAAGATGAAAACCCGCAAAGGGCATCTT
1 AAAAAAAAGAATAAGAAAAG-AAAAGAAAAAGGCAAGATGAAAACCCGCAAAGGGCATCTT
7680 AAAAAAA
1 AAAAAAA
7687 TCTCCTTCAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 1 0.02
60 7 0.12
61 18 0.31
62 33 0.56
ACGTcount: A:0.58, C:0.10, G:0.20, T:0.12
Consensus pattern (60 bp):
AAAAAAAAGAATAAGAAAAGAAAAGAAAAAGGCAAGATGAAAACCCGCAAAGGGCATCTT
Found at i:9569 original size:49 final size:50
Alignment explanation
Indices: 9459--9951 Score: 292
Period size: 49 Copynumber: 10.1 Consensus size: 50
9449 GAAGATATGG
* * * *
9459 AGGGAAAGGTTTAAGTCGCAACGACGAACCTTA-TACCT-C-AGAAGCATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAACC-TAGTACCTACGAGGA-CATGA
* * *
9508 A-GGAAAGATTTAAGCCGCAACGGCGAATCC-AATA-CTGCGAGGACATGG
1 AGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTACGAGGACATGA
* * * * **
9556 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCT-C-AAAAGCATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTACGAGGA-CATGA
* * ** * * *
9605 AAGGAAATATTTAAGCCGCAAATGCGAATCTAGTACC-ATGAGGACATGC
1 AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTACGAGGACATGA
* * * * *
9654 AGGGAATGATTTAAGTCGCAACAGCGAACCTTGTACCTTA-GAAG-CATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACC-TACGAGGACATGA
* * * * *
9703 AGGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACC-ACAATGATATAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTACGAGGACATGA
* * * ** * * **
9752 AGGGAAGGGTTTAAGTCGCAACAACGAACCTTGTACCT-CAAAAACATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTACGAGGACATGA
* * *
9801 AGGGAAAGATTTAAGCTGTAACGGCGAATCC-AGTACC-ACGAGGACATGG
1 AGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTACGAGGACATGA
* * *
9850 AGGGAAA-AGTTTAAGTCGCAACGACGAACCTTA-TACCTTA-GAAG-CATGA
1 AGGGAAAGA-TTTAAGCCGCAACGGCGAACC-TAGTACC-TACGAGGACATGA
* * *
9899 AGGGAAAGATTTAAACCGTAACGGTGAATCC-AGTACC-ACGAGGACATGGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCTACGAGGACAT-GA
9949 AGG
1 AGG
9952 AATGGTTCTC
Statistics
Matches: 335, Mismatches: 79, Indels: 59
0.71 0.17 0.12
Matches are distributed among these distances:
47 5 0.01
48 46 0.14
49 259 0.77
50 23 0.07
51 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.18
Consensus pattern (50 bp):
AGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCTACGAGGACATGA
Found at i:9669 original size:98 final size:98
Alignment explanation
Indices: 9443--9958 Score: 658
Period size: 98 Copynumber: 5.3 Consensus size: 98
9433 CAGGTTTCAT
* * *
9443 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCTCAGAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
*
9508 A-GGAAAGATTTAAGCCGCAACGGCGAATCCAA
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
** * * *
9540 TACTGCGAGGACATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * ** *
9605 AAGGAAATATTTAAGCCGCAAATGCGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * *
9638 TACCATGAGGACATGCAGGGAATGATTTAAGTCGCAAC-AGCGAACCTTGTACCTTAGAAGCATG
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGA-CGAACCTTGTACCTCAGAAGCATG
*
9702 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAA
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * ** * * * *
9736 TACCACAATGATATAAAGGGAAGGGTTTAAGTCGCAACAACGAACCTTGTACCTCAAAAACATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* *
9801 AGGGAAAGATTTAAGCTGTAACGGCGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * *
9834 TACCACGAGGACATGGAGGGAAAAGTTTAAGTCGCAACGACGAACCTTATACCTTAGAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * *
9899 AGGGAAAGATTTAAACCGTAACGGTGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* *
9932 TACCACGAGGACATGGAAGGAATGGTT
1 TACCACGAGGACATGGAGGGAAAGGTT
9959 CTCGCTTAGG
Statistics
Matches: 355, Mismatches: 61, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
97 58 0.16
98 296 0.83
99 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (98 bp):
TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
Done.