Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010312.1 Kokia drynarioides strain JFW-HI SEQ_125174, 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: 17380
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:52 original size:11 final size:12
Alignment explanation
Indices: 28--57 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
18 CAATCCAAAT
28 TTTATTATTTTA
1 TTTATTATTTTA
40 TTTATTA-TTTA
1 TTTATTATTTTA
51 TTTATTA
1 TTTATTA
58 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:6674 original size:40 final size:41
Alignment explanation
Indices: 6612--6688 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
6602 CTTCGACTAA
* *
6612 AAAAAAAGGAGGTTGAGTTGAAAAC-C-CAAAGGGCGGCTT
1 AAAAAAAGGAGGTCGAGATGAAAACTCACAAAGGGCGGCTT
*
6651 AAAAAAAGTGGGGTCGAGATGAAAACTCACAAAGGGCG
1 AAAAAAAG-GAGGTCGAGATGAAAACTCACAAAGGGCG
6689 TCTCAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.25
40 14 0.44
41 1 0.03
42 9 0.28
ACGTcount: A:0.43, C:0.13, G:0.31, T:0.13
Consensus pattern (41 bp):
AAAAAAAGGAGGTCGAGATGAAAACTCACAAAGGGCGGCTT
Found at i:7694 original size:50 final size:50
Alignment explanation
Indices: 7567--7694 Score: 184
Period size: 50 Copynumber: 2.6 Consensus size: 50
7557 ATTTTTTACC
* * * **
7567 CCTAAAGCTATGGAGGTGCAGATTGAAATCGCAACGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAACGACAAATCTCATTCA
* * *
7617 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAACGACAAATCTCATTCA
7667 CCTAAAGCTGTAGAGGGGCAGATTGAAG
1 CCTAAAGCTGTAGAGGGGCAGATTGAAG
7695 TCACAAGGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAACGACAAATCTCATTCA
Found at i:7960 original size:39 final size:40
Alignment explanation
Indices: 7748--8079 Score: 304
Period size: 40 Copynumber: 8.4 Consensus size: 40
7738 AGTTACAACC
* * *
7748 TCCAATCTCTTACCCTAACCAGAGGGCATATTGAAGACCA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * * * *
7788 TCCGATCTCTTA-CCTCGATCATG-GGGCAGATTGAAAACTA
1 TCCAATCTTTTACCCT-AACCA-GAGGGCAGATTGAAGACAA
* * ** * *
7828 TCCAACCTTTTACCTTAATTAGAGGGCAGATTAAAGACGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
*
7868 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * *
7908 TCCAATCTCTTACCCCAACCATG-GGGCAAATTGAA-ACAA
1 TCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* *
7947 TCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAG-CAA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
*
7986 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* ** * *
8026 T-TAGATCTCCTA-CCTCGACCATG-GGGCAGATTCAA-ACAA
1 TCCA-ATCTTTTACCCT-AACCA-GAGGGCAGATTGAAGACAA
8065 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
8080 CTAAAGTTAT
Statistics
Matches: 238, Mismatches: 41, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
39 88 0.37
40 145 0.61
41 5 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
Found at i:8020 original size:118 final size:119
Alignment explanation
Indices: 7748--8079 Score: 461
Period size: 118 Copynumber: 2.8 Consensus size: 119
7738 AGTTACAACC
* * * *
7748 TCCAATCTCTTACCCTAACCAGAGGGCATATTGAAGACCATCCGATCTCTTACCTCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
* * * ** * *
7813 GCAGATTGAAAACTATCCAACCTTTTACCTTAATTAGAGGGCAGATTAAAGACGA
66 GCAGATTG-AAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACAA
* * * *
7868 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCCAACCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
*
7933 GCAAATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAG-CAA
66 GCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACAA
* *
7986 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT-TAGATCTCCTACCTCGACCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCA-ATCTCTTACCTCGACCATGG
*
8050 GGCAGATTCAAACAATCCAATCTTTTACCC
65 GGCAGATTGAAACAATCCAATCTTTTACCC
8080 CTAAAGTTAT
Statistics
Matches: 187, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
117 1 0.01
118 86 0.46
119 36 0.19
120 64 0.34
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (119 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
GCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACAA
Found at i:8666 original size:16 final size:17
Alignment explanation
Indices: 8624--8673 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
8614 TAATTTATTT
*
8624 ATTAAATAAATAAACAA
1 ATTAAAGAAATAAACAA
8641 A-TAAAGAAATAAA-AGA
1 ATTAAAGAAATAAACA-A
*
8657 ATTAAA-AAATATACAA
1 ATTAAAGAAATAAACAA
8673 A
1 A
8674 CCCAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 6 0.21
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (17 bp):
ATTAAAGAAATAAACAA
Found at i:10560 original size:60 final size:60
Alignment explanation
Indices: 10491--10639 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
10481 ACATTAAAAC
* * *
10491 GGGTCAGATTTGAATTTTTTAAAACTTT-AGGGGTTAAATTTAAATTTTTAG-AGAATTTAA
1 GGGTCAGATTTGAATTTTTGAAAACTTTGA-GGGTGAAATTTAAATTTTTAGAAG-ATTCAA
* * **
10551 GGGTCAGATTTGAATTTTTGGAAAA-TTTGAGGGTGAAATTTGAATTTTTGGAAGATTCGG
1 GGGTCAGATTTGAATTTTT-GAAAACTTTGAGGGTGAAATTTAAATTTTTAGAAGATTCAA
*
10611 GGGTCAAATTTGAATTTTTGAAAACTTTG
1 GGGTCAGATTTGAATTTTTGAAAACTTTG
10640 GGTGTCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
59 5 0.06
60 65 0.84
61 7 0.09
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.41
Consensus pattern (60 bp):
GGGTCAGATTTGAATTTTTGAAAACTTTGAGGGTGAAATTTAAATTTTTAGAAGATTCAA
Found at i:10647 original size:30 final size:29
Alignment explanation
Indices: 10491--10648 Score: 140
Period size: 30 Copynumber: 5.3 Consensus size: 29
10481 ACATTAAAAC
* *
10491 GGGTCAGATTTGAATTTTT-TAAAACTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAA-TTT-G
* * * * *
10521 GGGTTAAATTTAAATTTTTAGAGAATTTAA
1 GGGTCAAATTTGAATTTTTGGAAAATTT-G
*
10551 GGGTCAGATTTGAATTTTTGGAAAATTTG
1 GGGTCAAATTTGAATTTTTGGAAAATTTG
* * *
10580 AGGGTGAAATTTGAATTTTTGGAAGATTCGG
1 -GGGTCAAATTTGAATTTTTGGAAAATT-TG
10611 GGGTCAAATTTGAATTTTT-GAAAACTTTG
1 GGGTCAAATTTGAATTTTTGGAAAA-TTTG
10640 GGTGTCAAA
1 GG-GTCAAA
10649 AAATGATTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.07
30 93 0.89
31 4 0.04
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTG
Found at i:11935 original size:17 final size:17
Alignment explanation
Indices: 11913--11963 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
11903 GAAATTGGGT
11913 TTGTATATATTT-TTTAA
1 TTGTAT-TATTTATTTAA
* *
11930 TTGTATTATTTCTTTAT
1 TTGTATTATTTATTTAA
11947 TTGT-TTATTTATTTAA
1 TTGTATTATTTATTTAA
11963 T
1 T
11964 AAATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (17 bp):
TTGTATTATTTATTTAA
Found at i:12614 original size:50 final size:50
Alignment explanation
Indices: 12560--12671 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
12550 CAGGAGTATA
* * *
12560 AGATTCGTCC-TTGTGACTTCAATT-TTCCCCTCTACAGCTTTAGGTGAATG
1 AGATT-GTCCATTGCGACTTC-ATTCTACCCCTCTACAACTTTAGGTGAATG
* * *
12610 AGATTTTCCATTGCGGCTTCATTCTACCCCTCTACAACTTTAGGTGTATG
1 AGATTGTCCATTGCGACTTCATTCTACCCCTCTACAACTTTAGGTGAATG
* *
12660 AGTTTTTCCATT
1 AGATTGTCCATT
12672 ACGGTTTCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 6 0.11
50 47 0.89
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (50 bp):
AGATTGTCCATTGCGACTTCATTCTACCCCTCTACAACTTTAGGTGAATG
Found at i:12703 original size:50 final size:50
Alignment explanation
Indices: 12576--12684 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
12566 GTCCTTGTGA
* * *
12576 CTTCAATTTTCCCCTCTACAGCTTTAGGTGAATGAGATTTTCCATTGCGG
1 CTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTTCCATTACGG
* * * *
12626 CTTCATTCTACCCCTCTACAACTTTAGGTGTATGAGTTTTTCCATTACGG
1 CTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTTCCATTACGG
*
12676 TTTCAATCT
1 CTTCAATCT
12685 GCACCCCCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (50 bp):
CTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTTCCATTACGG
Done.