Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009995.1 Kokia drynarioides strain JFW-HI SEQ_124750, 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: 1887
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.36
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:131 original size:49 final size:49
Alignment explanation
Indices: 1--204 Score: 188
Period size: 49 Copynumber: 4.2 Consensus size: 49
* * *
1 TCCCTTCATG-CTTCTGAGGTACAAGG-TTCACCGTTGCGACTTAAACCTT
1 TCCCTTCATGTCTTC-GAGGTAC-TGGATTCGCCGTTACGACTTAAACCTT
* ** *
50 TCCC-T-ATGTCTTCGTGGTACTGGATTCGCCGTTACGGTTTAAATCTT
1 TCCCTTCATGTCTTCGAGGTACTGGATTCGCCGTTACGACTTAAACCTT
*
97 TCCCTTCATG-CTTCTGAGGTACATGG-GTCGCCGTTACGACTTAAACCTT
1 TCCCTTCATGTCTTC-GAGGTAC-TGGATTCGCCGTTACGACTTAAACCTT
* * ** * *
146 TCCC-TCTATGTCTTCGTGGTACTGGATTCGTCGTTGTGGCTTAAATCTT
1 TCCCTTC-ATGTCTTCGAGGTACTGGATTCGCCGTTACGACTTAAACCTT
195 TCCCTTCATG
1 TCCCTTCATG
205 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
46 2 0.02
47 31 0.25
48 15 0.12
49 69 0.55
50 9 0.07
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.37
Consensus pattern (49 bp):
TCCCTTCATGTCTTCGAGGTACTGGATTCGCCGTTACGACTTAAACCTT
Found at i:466 original size:98 final size:98
Alignment explanation
Indices: 297--1292 Score: 1455
Period size: 98 Copynumber: 10.2 Consensus size: 98
287 NNNNNNNGCT
* *
297 ACTTAAACCTTTCCC-CTTGTGTCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCC
1 ACTTAAACCTTTCCCTC-TATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
* *
361 TTCATGCTTCTGAGGTATAAGGTTCACCGTTGCG
65 TTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
* * * * * *
395 ACTTAAACCTTTCCCCCTATGTCTTCGTGGTACCGGATTCACTGTTGCAGCCTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
460 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
66 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
493 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
*
558 TCATGCTTCTGAGGTACAAGGTTCGCCATTGCG
66 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
* *
591 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGTCATTGCGGCTTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * *
656 TCATGCTTCTGAGGTACAAGCTGT-GCCATTGTG
66 TCATGCTTCTGAGGTACAAGGT-TCGCCGTTGCG
* ** * * *
689 ACTTAAACCTTTCCCTCTATATCTTCGTGGTACTGGATTCGTTGTTACGGTTTAAATCTTTCCCG
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* *
754 TCATGCTTCTGAGGTACAAGGTTCACCGTTGTG
66 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
* *
787 ACTTAAACCTTTGCCTCTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
*
852 TCATG-TCTCTAAGGTACAAGGTTCGCCGTTGCTG
66 TCATGCT-TCTGAGGTACAAGGTTCGCCGTTGC-G
* * *
886 -CTTAAACCTTTCCC-CTTGTGTCTTCGTGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCC
1 ACTTAAACCTTTCCCTC-TATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
*
949 TTCATGCTTCTGAGGTACAAGGTTCACCGTTGCG
65 TTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
* * * * *
983 ACTTAAACCTTTCCCCCTATGTCTTCGTGGTACTGGATTCACTGTTGCAGCCTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* *
1048 TCATGCTTCTGAGGTACAAGGTTCACCGTTGNG
66 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
1081 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
** **
1146 TCATG-TCTCTGATATACAAGGTTCGCTATTGCG
66 TCATGCT-TCTGAGGTACAAGGTTCGCCGTTGCG
* * * * *
1179 ACTTAAATCTTTCCCTCTATATCTTCGTGGTTCTGCATTCACCGTTGCGGCTTAAATCTTTCCCT
1 ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* *
1244 TCATGCTTTTGAGGTACAAGGTTTGCCGTTGCG
66 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
1277 ACTTAAACCTTTCCCT
1 ACTTAAACCTTTCCCT
1293 TCAAATCGTC
Statistics
Matches: 813, Mismatches: 74, Indels: 22
0.89 0.08 0.02
Matches are distributed among these distances:
97 5 0.01
98 802 0.99
99 6 0.01
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (98 bp):
ACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCG
Done.