Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013848.1 Kokia drynarioides strain JFW-HI SEQ_128876, 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: 11384
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--27 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
28 TTATAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2523 original size:49 final size:49
Alignment explanation
Indices: 2413--2931 Score: 315
Period size: 49 Copynumber: 10.6 Consensus size: 49
2403 AAGATTTACT
* * * * *
2413 GTTGCGGCTTCAATCTTT-CCTGTCATACTTCTAAGGTACTGGGTTCCCC
1 GTTGCGACTTAAATCTTTCCCT-TCATATTTCTAAGGTACTAGGTTCGCC
* * *
2462 GTAGCAGA-TTAAATTTTTCCTTTCATATTTCTAAGGTA-TAAGGTTCGCC
1 GTTGC-GACTTAAATCTTTCCCTTCATATTTCTAAGGTACT-AGGTTCGCC
* *
2511 GTTGCGACTTAAACCTTTCCCTCCATATCTTCGT--GGTACT-GGATTCGCC
1 GTTGCGACTTAAATCTTTCCCTTCATAT-TTC-TAAGGTACTAGG-TTCGCC
* *
2560 GTTGC-AGCTTAAATCTTTCCCTTCAT-GTTCTTAAGGTA-TAAGGTTCGTC
1 GTTGCGA-CTTAAATCTTTCCCTTCATATTTC-TAAGGTACT-AGGTTCGCC
* * * * *
2609 ATTGCGACTTAAATTTTTCCCTCCATATCTTC-ATGGTACT-GGATTCTCC
1 GTTGCGACTTAAATCTTTCCCTTCATAT-TTCTAAGGTACTAGG-TTCGCC
* * * * * *
2658 ATTACGACTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTC
1 GTTGCGACTTAAATCTTTCCCTTCATATTTCTAAGGTACTAGGTTCGCC
* * * **
2707 GTTGTGACTTAAA-CATTTCCCTCCATATCTTCGT--GGTACTAGATTCGTT
1 GTTGCGACTTAAATC-TTTCCCTTCATAT-TTC-TAAGGTACTAGGTTCGCC
* * * *
2756 GTTGCTG-CTTAAATCTTTACCTTCATGTTTTTTAGGTA-TAAGGTTCGCC
1 GTTGC-GACTTAAATCTTTCCCTTCATATTTCTAAGGTACT-AGGTTCGCC
* * * * * *
2805 GTTGCAAC-TAAA-CATTTCCCTCCATATCTTC-ATGATACTAGATTCGCA
1 GTTGCGACTTAAATC-TTTCCCTTCATAT-TTCTAAGGTACTAGGTTCGCC
* * **
2853 GTTGCGGCTTAAATCTTTCCCTTCATGTTTCTAAGGTA-TAAGGTTCAAC
1 GTTGCGACTTAAATCTTTCCCTTCATATTTCTAAGGTACT-AGGTTCGCC
* *
2902 ATTGCGAC-TAAAACATTTCCCTTCATATTT
1 GTTGCGACTTAAATC-TTTCCCTTCATATTT
2932 TCGTGGTACT
Statistics
Matches: 359, Mismatches: 74, Indels: 74
0.71 0.15 0.15
Matches are distributed among these distances:
47 6 0.02
48 55 0.15
49 274 0.76
50 19 0.05
51 5 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (49 bp):
GTTGCGACTTAAATCTTTCCCTTCATATTTCTAAGGTACTAGGTTCGCC
Found at i:2970 original size:98 final size:98
Alignment explanation
Indices: 2470--2970 Score: 619
Period size: 98 Copynumber: 5.1 Consensus size: 98
2460 CCGTAGCAGA
* * * *
2470 TTAAATTTTTCCTTTCATATTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCC
1 TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTCC
* *
2535 ATATCTTCGTGGTACTGGATTCGCCGTTGCAGC
66 ATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
* * **
2568 TTAAATCTTTCCCTTCATG-TTCTTAAGGTATAAGGTTCGTCATTGCGACTTAAATTTTTCCCTC
1 TTAAATCTTTCCCTTCATGTTTC-TAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTC
* * * * * *
2632 CATATCTTCATGGTACTGGATTCTCCATTACGAC
65 CATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
* * * *
2666 TTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTCGTTGTGACTTAAACATTTCCCTCC
1 TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTCC
** *
2731 ATATCTTCGTGGTACTAGATTCGTTGTTGCTGC
66 ATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
* * * *
2764 TTAAATCTTTACCTTCATGTTTTTTAGGTATAAGGTTCGCCGTTGCAAC-TAAACATTTCCCTCC
1 TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTCC
* * *
2828 ATATCTTCATGATACTAGATTCGCAGTTGCGGC
66 ATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
** * * *
2861 TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCAACATTGCGACTAAAACATTTCCCTTC
1 TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTCC
* * *
2926 ATATTTTCGTGGTACTAGATTTGCCGTTACGGC
66 ATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
* *
2959 TTTAATTTTTCC
1 TTAAATCTTTCC
2971 TAACTCATCT
Statistics
Matches: 343, Mismatches: 57, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
97 88 0.26
98 252 0.73
99 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (98 bp):
TTAAATCTTTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCGTTGCGACTTAAACATTTCCCTCC
ATATCTTCGTGGTACTAGATTCGCCGTTGCGGC
Found at i:5009 original size:23 final size:25
Alignment explanation
Indices: 4983--5028 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4973 CCAATTAGGG
4983 AATTAT-TTTTTAG-ATTTAATTCT
1 AATTATCTTTTTAGAATTTAATTCT
5006 AATTATCTTTTTAGAATTTAATT
1 AATTATCTTTTTAGAATTTAATT
5029 TGGATCCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
AATTATCTTTTTAGAATTTAATTCT
Found at i:6107 original size:13 final size:14
Alignment explanation
Indices: 6091--6120 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6081 TTAGTCATTT
6091 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
6104 TTTTTATTTTATTA
1 TTTTTATTTTATTA
6118 TTT
1 TTT
6121 GCATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:6145 original size:14 final size:13
Alignment explanation
Indices: 6124--6155 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
6114 ATTATTTGCA
6124 TTTTTAATTTAAT
1 TTTTTAATTTAAT
6137 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
6151 TTTTT
1 TTTTT
6156 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:9053 original size:6 final size:5
Alignment explanation
Indices: 9028--9087 Score: 57
Period size: 6 Copynumber: 10.6 Consensus size: 5
9018 ATTAGTATAA
9028 TTATT TTCATAT TTATTT TTAGTT TTAGTT TTATT TTATT TTATTT TTAGTT
1 TTATT TT-AT-T TTA-TT TTA-TT TTA-TT TTATT TTATT TTA-TT TTA-TT
9080 TTATT TTA
1 TTATT TTA
9088 ATTATGCAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 17 0.35
6 28 0.57
7 4 0.08
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:9062 original size:22 final size:22
Alignment explanation
Indices: 9039--9087 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
9029 TATTTTCATA
9039 TTTATTTTTAGTTTTAGTTTTAT
1 TTTA-TTTTAGTTTTAGTTTTAT
*
9062 TTTATTTTATTTTTAGTTTTAT
1 TTTATTTTAGTTTTAGTTTTAT
9084 TTTA
1 TTTA
9088 ATTATGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTATTTTAGTTTTAGTTTTAT
Found at i:10048 original size:11 final size:11
Alignment explanation
Indices: 10034--10058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10024 AGAAAAATTG
10034 AGAAAAAAAAA
1 AGAAAAAAAAA
10045 AGAAAAAAAAA
1 AGAAAAAAAAA
10056 AGA
1 AGA
10059 CAAATGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Done.