Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012955.1 Kokia drynarioides strain JFW-HI SEQ_127973, 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: 2106
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.37
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:629 original size:15 final size:15
Alignment explanation
Indices: 587--642 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
577 TTTTGGGTAG
* *
587 TTTGTAATTGAGTCA
1 TTTGTAATTGGGCCA
602 TTTGT-ATTCGGGCCA
1 TTTGTAATT-GGGCCA
* *
617 TCTGTAATTGGGCGA
1 TTTGTAATTGGGCCA
632 TTTGTAATTGG
1 TTTGTAATTGG
643 ACTTTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.09
15 28 0.82
16 3 0.09
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.43
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:667 original size:13 final size:14
Alignment explanation
Indices: 632--672 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
622 AATTGGGCGA
632 TTTG-TAATTGGAC
1 TTTGTTAATTGGAC
645 TTTGTT--TTGGAC
1 TTTGTTAATTGGAC
657 TTT-TTAATTGGAC
1 TTTGTTAATTGGAC
670 TTT
1 TTT
673 CTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 13 0.52
14 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (14 bp):
TTTGTTAATTGGAC
Found at i:696 original size:17 final size:17
Alignment explanation
Indices: 674--742 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
664 TTGGACTTTC
674 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
691 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
*
708 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
724 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
740 TAA
1 TAA
743 GTCCAGACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
15 7 0.15
16 12 0.26
17 28 0.60
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:708 original size:7 final size:6
Alignment explanation
Indices: 674--724 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
664 TTGGACTTTC
* *
674 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAAATT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
720 TAAAT
1 TAAAT
725 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 27 0.71
7 3 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:1533 original size:139 final size:139
Alignment explanation
Indices: 1282--1558 Score: 491
Period size: 139 Copynumber: 2.0 Consensus size: 139
1272 NNNNNNNNNN
1282 CATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGA
1 CATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGA
* *
1347 TGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTC
66 TGATCCCATCACTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTC
1412 TCAGTATCC
131 TCAGTATCC
*
1421 CATCTGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGA
1 CATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGA
* * * *
1486 TGATCCCATCACTGTTTCAGTCTATTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTC
66 TGATCCCATCACTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTC
1551 TCAGTATC
131 TCAGTATC
1559 TTATCAGGAA
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 131 1.00
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (139 bp):
CATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGA
TGATCCCATCACTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTC
TCAGTATCC
Done.