Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014626.1 Kokia drynarioides strain JFW-HI SEQ_129665, 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: 33460
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:7238 original size:10 final size:10
Alignment explanation
Indices: 7223--7278 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
7213 ATTATATATA
7223 TTTTAATAAT
1 TTTTAATAAT
7233 TTTTAAT--T
1 TTTTAATAAT
*
7241 TTTTAAAAAT
1 TTTTAATAAT
*
7251 AGTTTTTATAAT
1 --TTTTAATAAT
*
7263 TTTTAAAAAT
1 TTTTAATAAT
7273 TTTTAA
1 TTTTAA
7279 ATTTTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
8 7 0.19
10 22 0.59
12 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:7265 original size:22 final size:21
Alignment explanation
Indices: 7227--7294 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
7217 TATATATTTT
*
7227 AATAATTTTTAATTTTTTAAA
1 AATAATTTTTAAATTTTTAAA
*
7248 AATAGTTTTTATAATTTTT--A
1 AATAATTTTTA-AATTTTTAAA
7268 AA-AATTTTTAAA-TTTTAAA
1 AATAATTTTTAAATTTTTAAA
7287 AATTAATT
1 AA-TAATT
7295 AAATGCTGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.10
18 2 0.05
19 10 0.26
20 3 0.08
21 14 0.36
22 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
AATAATTTTTAAATTTTTAAA
Found at i:8542 original size:21 final size:21
Alignment explanation
Indices: 8511--8558 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
8501 CCTCAACCCG
*
8511 AACTT-GAACTTAAAACCCTA
1 AACTTGGAACTTAAAACCCCA
*
8531 AACTTGGAACTTACAACCCCA
1 AACTTGGAACTTAAAACCCCA
8552 AATCTTG
1 AA-CTTG
8559 AATCGAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 15 0.62
22 4 0.17
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (21 bp):
AACTTGGAACTTAAAACCCCA
Found at i:13951 original size:21 final size:20
Alignment explanation
Indices: 13921--13961 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
13911 CCTTCTTCAA
* *
13921 CTTCACCTCCACTTCCCTCC
1 CTTCACCTCCAATACCCTCC
13941 CTTCAACCTCCAATACCCTCC
1 CTTC-ACCTCCAATACCCTCC
13962 ACAATCACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.56, G:0.00, T:0.27
Consensus pattern (20 bp):
CTTCACCTCCAATACCCTCC
Found at i:17095 original size:31 final size:31
Alignment explanation
Indices: 17060--17124 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
17050 CTTAAAGCTC
*
17060 AGTGACTTAAATAAAAACTT-TCGAATAGTTT
1 AGTGACTTAAATAAAAACTTGT-GAATAATTT
*
17091 AGTGACTTAAATGAAAACTTGTGAATAATTT
1 AGTGACTTAAATAAAAACTTGTGAATAATTT
17122 AGT
1 AGT
17125 AACCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTGTGAATAATTT
Found at i:21536 original size:15 final size:16
Alignment explanation
Indices: 21503--21543 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
21493 CAAACTACCT
21503 AAACTTGAAAAGATCC
1 AAACTTGAAAAGATCC
*
21519 AAACTTGAAATG-TCC
1 AAACTTGAAAAGATCC
*
21534 AAACTAGAAA
1 AAACTTGAAA
21544 CAACCTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (16 bp):
AAACTTGAAAAGATCC
Found at i:22802 original size:8 final size:8
Alignment explanation
Indices: 22789--22823 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
22779 CAAATTATTC
*
22789 AAAAAGGA
1 AAAAAGAA
22797 AAAAAGAAA
1 AAAAAG-AA
22806 AAAAAGAA
1 AAAAAGAA
22814 AAAAAGAA
1 AAAAAGAA
22822 AA
1 AA
22824 CATAGATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:22811 original size:17 final size:17
Alignment explanation
Indices: 22789--22823 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
22779 CAAATTATTC
*
22789 AAAAAGGAAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
22806 AAAAAGAAAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
22823 A
1 A
22824 CATAGATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAA
Found at i:25538 original size:2 final size:2
Alignment explanation
Indices: 25533--25566 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25523 GTGTGTGTGT
25533 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
25567 AATGGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25917 original size:16 final size:17
Alignment explanation
Indices: 25896--25929 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
25886 CACTGAAGCG
25896 TATTATTTTC-TTTATT
1 TATTATTTTCTTTTATT
25912 TATTATTTTCTTTTATT
1 TATTATTTTCTTTTATT
25929 T
1 T
25930 CCCTTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTATTTTCTTTTATT
Done.