Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012288.1 Kokia drynarioides strain JFW-HI SEQ_127289, 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: 2398
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:653 original size:17 final size:17
Alignment explanation
Indices: 633--742 Score: 130
Period size: 17 Copynumber: 6.4 Consensus size: 17
623 CTTTATTTAT
* *
633 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
650 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
668 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
685 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
702 TTTAAATTTNTAAACAAA
1 TTTAAATTT-AAAATAAA
*
720 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
737 TCTAAA
1 TTTAAA
743 GGGAGTTTGG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
17 50 0.64
18 28 0.36
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:678 original size:6 final size:6
Alignment explanation
Indices: 633--710 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
623 CTTTATTTAT
* * *
633 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
680 -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
711 NTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:689 original size:11 final size:11
Alignment explanation
Indices: 651--709 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
641 TATAATAATT
651 TTAAATTTGAAA
1 TTAAATTT-AAA
*
663 ATAAATTTAAA
1 TTAAATTTAAA
674 CTTAAA-TTAAA
1 -TTAAATTTAAA
685 TTTAAATTTAAA
1 -TTAAATTTAAA
*
697 ATAAATTTAAA
1 TTAAATTTAAA
708 TT
1 TT
710 TNTAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:689 original size:35 final size:33
Alignment explanation
Indices: 633--742 Score: 130
Period size: 35 Copynumber: 3.2 Consensus size: 33
623 CTTTATTTAT
*
633 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTA-AATAAATTTAAATTT-AAAATAAA
*
668 TTTAAACTTAAATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAA-TAAATTTAAATTTAAAATAAA
* *
702 TTTAAATTTNTAAACAAATTTAATTTTAAAATAAA
1 TTTAAA-TT-TAAATAAATTTAAATTTAAAATAAA
*
737 TCTAAA
1 TTTAAA
743 GGGAGTTTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 16 0.24
35 46 0.70
36 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (33 bp):
TTTAAATTTAAATAAATTTAAATTTAAAATAAA
Found at i:700 original size:52 final size:52
Alignment explanation
Indices: 633--742 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
623 CTTTATTTAT
* * * *
633 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
** **
685 TTTAAATTTAAAATAAATTTAAATTTNTAAACAAATTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
*
737 TCTAAA
1 TTTAAA
743 GGGAGTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:1405 original size:201 final size:200
Alignment explanation
Indices: 981--1949 Score: 1141
Period size: 201 Copynumber: 4.8 Consensus size: 200
971 ACTTGGCTTT
* * * **
981 CTTCTCAATATCTCATCTGGGAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAACGTCTCATC
1 CTTCTCAGTATCTCATCAGGGAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
** * * *
1046 AGGAAGCT-GGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTAAGTGCCTT
65 AGGAAGCTAGGG-TTCGAAGATTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTC
* *
1110 ATCAGGAAGATGATTACATCGCT-GTTTGTTTCAATTTGCTCCTCTGTATCTCATCC-GGAAGAC
129 ATCAGGAAG--G-TGAC--CGCTCGTTTGTTTCAATTCGCTCCTCTGTATCTCATCCAGGAAGAC
1173 GAATTTGGTTCA
189 GAATTTGGTTCA
* *
1185 CTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGGAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
* *
1250 GGAAGATAGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
66 GGAAGCTAGGGTTCGAAGA-TTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
* * *
1315 TCAGGAAGGTGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTTA-CCAGGAAGGCGAATT
130 TCAGGAAGGTGACCGC-TCGTTTGTTTCAATTCGCTCCTCTGTATCTCATCCAGGAAGACGAATT
1379 TGGTTCA
194 TGGTTCA
* * * * **
1386 CTTCTTAGTATCTCATCAGGGAGCTGA-CTGTGTTATTACTTCGACCTACTTCTCAACGTCTCAT
1 CTTCTCAGTATCTCATCAGGGAGCTAACCT-T-TTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
* ** *
1450 CAGGAAG-TTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCT
64 CAGGAAGCTAGGG-TTCGAAGATTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCT
* *
1514 CATCAGGAAGATGATTACATCGCT-GTTTGTTTCAATTCGCTCCTCCGTATCTCATCCA--AAGA
128 CATCAGGAAG--G-TGAC--CGCTCGTTTGTTTCAATTCGCTCCTCTGTATCTCATCCAGGAAGA
*
1576 TGAATTTGGTTCA
188 CGAATTTGGTTCA
* *
1589 CTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGGAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
*
1654 GGAAGTTAGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
66 GGAAGCTAGGGTTCGAAGA-TTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
* *
1719 TC-GAGAAGGTGACCGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCAT-CAGGAAGGCGAAT
130 TCAG-GAAGGTGACCGC-TCGTTTGTTTCAATTCGCTCCTCTGTATCTCATCCAGGAAGACGAAT
1782 TTGGTTCA
193 TTGGTTCA
* * * * * *
1790 CTTCTCAGTATCTCATCAGGGAGCTATCCACTTTATGGCTTCGTCCTGCTTCTCTGTGTCTCTTC
1 CTTCTCAGTATCTCATCAGGGAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
* * * * * * * *
1855 AGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCATGAGTTTGATTTGGTCTGCTTCTCAGTA
65 AGGAAGCTAGGGTTCGAAGATTTGCTCACTTTGAGCCT-CGTTTG----GGTCTTCTTCTCAGTG
* *
1920 TCTTATCAGGAAGATGACCGCATCGTTTGT
125 TCTCATCAGGAAGGTGACCGC-TCGTTTGT
1950 GGATAATCGC
Statistics
Matches: 662, Mismatches: 74, Indels: 56
0.84 0.09 0.07
Matches are distributed among these distances:
198 3 0.00
199 6 0.01
200 37 0.06
201 182 0.27
202 140 0.21
203 138 0.21
204 108 0.16
205 4 0.01
206 43 0.06
207 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (200 bp):
CTTCTCAGTATCTCATCAGGGAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
GGAAGCTAGGGTTCGAAGATTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCAT
CAGGAAGGTGACCGCTCGTTTGTTTCAATTCGCTCCTCTGTATCTCATCCAGGAAGACGAATTTG
GTTCA
Found at i:1744 original size:404 final size:405
Alignment explanation
Indices: 981--1880 Score: 1491
Period size: 404 Copynumber: 2.2 Consensus size: 405
971 ACTTGGCTTT
* * * *
981 CTTCTCAATATCTCATCTGGGAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAACGTCTCATC
1 CTTCTCAGTATCTCATCAGGGAGCTAACCGTGTTATTACTTCGACCTACTTCTCAACGTCTCATC
*
1046 AGGAAGCTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTAAGTGCCTTA
66 AGGAAGCTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTAAGTGCCTCA
* * *
1111 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTTGCTCCTCTGTATCTCATCCGGAAGACGAA
131 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCTCATCCGAAAGACGAA
1176 TTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
196 TTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
1241 GTCTCATCAGGAAGATAGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
261 GTCTCATCAGGAAGATAGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
* *
1306 AGTGTCTCATCAGGAAGGTGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTTACCAGGAA
326 AGTGTCTCATCAGGAAGGTGACCGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAA
1371 GGCGAATTTGGTTCA
391 GGCGAATTTGGTTCA
* * *
1386 CTTCTTAGTATCTCATCAGGGAGCTGACTGTGTTATTACTTCGACCTACTTCTCAACGTCTCATC
1 CTTCTCAGTATCTCATCAGGGAGCTAACCGTGTTATTACTTCGACCTACTTCTCAACGTCTCATC
* *
1451 AGGAAGTTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCA
66 AGGAAGCTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTAAGTGCCTCA
*
1516 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCTCATCC-AAAGATGAA
131 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCTCATCCGAAAGACGAA
1580 TTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
196 TTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* *
1645 GTCTCATCAGGAAGTTAGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
261 GTCTCATCAGGAAGATAGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
*
1710 AGTGTCTCATC-GAGAAGGTGACCGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGA
326 AGTGTCTCATCAG-GAAGGTGACCGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGA
1774 AGGCGAATTTGGTTCA
390 AGGCGAATTTGGTTCA
* * ** * * *** *
1790 CTTCTCAGTATCTCATCAGGGAGCTATCCACT-TTATGGCTTCGTCCTGCTTCTCTGTGTCTCTT
1 CTTCTCAGTATCTCATCAGGGAGCTAACC-GTGTTATTACTTCGACCTACTTCTCAACGTCTCAT
*
1854 CAGGAAGCTGGGGTTCGAAGATTTGCT
65 CAGGAAGCTGGGATTCGAAGATTTGCT
1881 TACATCGAGC
Statistics
Matches: 459, Mismatches: 34, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
403 1 0.00
404 284 0.62
405 174 0.38
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (405 bp):
CTTCTCAGTATCTCATCAGGGAGCTAACCGTGTTATTACTTCGACCTACTTCTCAACGTCTCATC
AGGAAGCTGGGATTCGAAGATTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTAAGTGCCTCA
TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCTCATCCGAAAGACGAA
TTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
GTCTCATCAGGAAGATAGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGGTGACCGCATCGTTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAA
GGCGAATTTGGTTCA
Done.