Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006620.1 Kokia drynarioides strain JFW-HI SEQ_121210, 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: 14142
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:763 original size:17 final size:17
Alignment explanation
Indices: 718--780 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
708 TTATTTATTT
*
718 TAAATTTTAAATCTGAAAA
1 TAAA-TTTAAA-CTTAAAA
* *
737 TAATTTTAAACTTAAAT
1 TAAATTTAAACTTAAAA
*
754 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
771 TAAATTTAAA
1 TAAATTTAAA
781 GGGAGTATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 29 0.76
18 6 0.16
19 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:1522 original size:205 final size:205
Alignment explanation
Indices: 1122--2391 Score: 1775
Period size: 205 Copynumber: 6.2 Consensus size: 205
1112 CTCGACCTTT
** * ** ** ** * *
1122 TTCTCAGTATCTCATCAGGAAGATGGTCGCATCACTTGTTTTGATCCATTTCTCTGTGTTTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
* *
1187 AGGAAGAC-AGATTTGG-CTCACTTCTTTGTATCTCATCAAGG-AGCTAACCACTTTATTGCTTC
66 AGGAAGACGA-ATTTGGTCT-ACTTCTTTGTATCTCATC-AGGAAGCTAACC-GTTTATTGCTCC
* * * * * * *
1249 AACCTGCTTCTCAGTGT-CTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGAG
127 GATCTGCTTCTCGGTGTGCT-ATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAG
1313 TTTGATTTGGTCTTC
191 TTTGATTTGGTCTTC
* * * * *
1328 TTCTCAGTATCTTATCAGGAAGATGACTGTGTCGCTTGTTTCAATTCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
* * *
1393 AGGGAGGCGAATTTGGTCTACTT-TTTCGTATCTCAACAGGAAGCTAACCGTTTATTGCTCCGAT
66 AGGAAGACGAATTTGGTCTACTTCTTT-GTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGAT
* * * *
1457 TTGCTTCTCGGTGTGCTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGAGTTTG
130 CTGCTTCTCGGTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTG
**
1522 ATTTAATCTTC
195 ATTTGGTCTTC
* *
1533 TTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATT
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
* * * *
1598 AGGAAGACGAATTTGGTCTACTTCGTTGTATCTCATTAGGAATCTAACCGTTTATTGCTTCGATC
66 AGGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATC
* * * *
1663 TGCTTCTCGGTGTGTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGAGTTTGA
131 TGCTTCTCGGTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTGA
*
1728 TTTAGTCTTC
196 TTTGGTCTTC
*
1738 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
*
1803 AGGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAATCTAACCGTTTATTGCTCCGATC
66 AGGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATC
* * *
1868 TGCTTCTCGGTGTGTTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGGGTTTGG
131 TGCTTCTCGGTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTGA
1933 TTTGGTCTTC
196 TTTGGTCTTC
*
1943 TTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
**
2008 AGGGAA-ACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGAT
66 A-GGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGAT
*
2072 CTGCTTCTCGGTGTGTTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTG
130 CTGCTTCTCGGTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTG
*
2137 GTTTGGTCTTC
195 ATTTGGTCTTC
*
2148 TTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
* ** * *
2213 AGGAAAACGAATTTTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACTGTTTATTGCTCTGA
66 AGGAAGACGAA--TTTGGTCTACTTCTTTGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGA
*
2278 TCTGCTTCTCGACGTGT-C-ATCAGGAAGCTGGGATTCGAAGACTTGCTCATATCGAGCGTG-GT
129 TCTGCTTCTCG--GTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAG-
*
2340 TTTGGTTTGGTCTTC
191 TTTGATTTGGTCTTC
* * *
2355 TTCTCAATGTCTCATCAGGAAGATGATCGCGTCGTTT
1 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTT
2392 TGTGGATAAT
Statistics
Matches: 982, Mismatches: 69, Indels: 25
0.91 0.06 0.02
Matches are distributed among these distances:
204 4 0.00
205 728 0.74
206 93 0.09
207 153 0.16
209 4 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (205 bp):
TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATC
AGGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATC
TGCTTCTCGGTGTGCTATCAGGAAGCTGGGATTCGAAGACTTGCTCACATCGAGCGTGAGTTTGA
TTTGGTCTTC
Done.