Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006465.1 Kokia drynarioides strain JFW-HI SEQ_121048, 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: 4384
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Found at i:384 original size:216 final size:216
Alignment explanation
Indices: 4--4373 Score: 4452
Period size: 216 Copynumber: 20.4 Consensus size: 216
1 AAC
** * * *
4 TTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGTTTACTTAAAGTATTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * *
69 TCCAATCCTTCAAGCAATTTTTCTAACATTCCGTTCTCGAGAAGTCGCATCATTTGGTCTAAA-A
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * * *
133 GGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACATGAGAATTGTGT
131 -GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
*
198 CTCTATTGGTTCTTGGACGAAT
195 CTCTCTTGGTTCTTGGACGAAT
** * * *
220 TTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGGTTACTTAAAGTATTCAACACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * * *
285 TCAAATCCTTCGAGCAATTTTTCTAATATTCCGTGCTCGGGAAGTCGCATCATTTGGTCTATAA-
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTA-AAT
* * * *
349 GGTTTGTCATTTTGTAAACAAGTTTTGGGCTTTGAA-TAAAAATCTTATTTACGTGAGAATTATT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATTTACGTGAGAATTGTT
* *
413 TCTCTCTTGGTTGTTGGACAAAT
194 TCTCTCTTGGTTCTTGGACGAAT
* * * * * * *
436 TTCCGAACTTGCCAAACCTTTACGAGTTCTTTTTTAACTTCGATTCCTTAAAGTATTCAAGATGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * **
501 TCCATTCCTTCGAGTAATTTTT-TGAACA-TCCAACGCTCGAGATATCAG-ATCATTTCATCTAA
66 TCCATTCCTTCGAGCAATTTTTCT-AACATTCC-ATGCTCGAGAAATC-GCATCATTTGGTCTAA
*
563 ATAGTTTTTCATTTTGTAAA-ATAGTTTTGGTCTTTG-------AA-TTGTTTACGTGAGAATTG
128 ATAGTTTTTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* * *
619 TTTCTCTCTTCGTTCTTTGACGAAC
192 TTTCTCTCTTGGTTCTTGGACGAAT
* * * * * * * *
644 TTCCGAAATTGAT-AAACATTTATGAGTACTTCTATAACTTCGGTTCATTATAGTGTTCAAGACG
1 TTCTGAAATTG-TCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACG
* * * * *
708 ATCCATTGCTTCTAGCAATTTTTTTAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAAT
65 ATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAT
** *
773 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTTAGAATTGTTT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * *
838 CTCTTTTGGTTTTTGGATGATCT
195 CTCTCTTGGTTCTTGGACGA-AT
* ** * * *
861 TTC-GAACTTGTCAAACTTTGCCAAGTTCTTTTATAACTTCGATTCCTTCAAGTATTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * * *
925 TCCATTCCTTC-ATGTAATTTTT-TGAACATTACACGCTTTG-GAAATCGAATCATTGGGTCTAA
66 TCCATTCCTTCGA-GCAATTTTTCT-AACATTCCATGC-TCGAGAAATCGCATCATTTGGTCTAA
* * * * *
987 ATAGTTTCTCATTTTGTAAACAAATTTTGTTCTTTCAATTAAAAACTTATTTACGTGAGAATTAT
128 ATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
*
1052 TTCTCTCTTGGTTGTTGGACGAACT
193 TTCTCTCTTGGTTCTTGGACGAA-T
* * * * * *
1077 TT-TGAACTTGTCAAACTTTTAAGAGTT-TTTTTTAAACTTCAGTTCCTTAAAGTGTTCAAGATG
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTAT-AACTTCGGTTCCTTAAAGTATTCAAGACG
* * * * *
1140 ATACATTCCTTCGA-CTAATTTTT-TGAACATTCAACGCTCGAGAAATCTCATCA-ATGGTCTAA
65 ATCCATTCCTTCGAGC-AATTTTTCT-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAA
* * * *
1202 ATAGTTTTTCATTTTGTAAA-ATAGATTTGGTCTTTAAATTAAAAACTTGTTTATGTGAGAATTG
128 ATAGTTTTTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* * * *
1266 TTTCTCTCTTAGTTCTTTGACAAAC
192 TTTCTCTCTTGGTTCTTGGACGAAT
* * * * * * * *
1291 TTCCGAAATTGACAAACATTTATGGGATCTTTTATAACTTCGGTTCATTAAAGTGTTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * *
1356 TCCATTCCTTCTAGCAGTTTTTCGAACATTTCATTCTCGAGAAATCGCATCATTTGGTCTAAATA
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * * ** *
1421 GTTTGTCATTTTGTAAATAAGTTTTGGTCTTTGAATTAAAAACATATTTATTTGAGAATTATTTC
131 GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
*
1486 TCTCTTGGTTTTTGGACGAAT
196 TCTCTTGGTTCTTGGACGAAT
* * ** * * * * *
1507 TTC-CAAACTTGACAAACTTTGCCAAGTTCTTTTATAACTTTGATTCCTTAAATTATTCAAGACA
1 TTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACG
* * * * * * *
1571 ATTCATTCCTTTGAGCAATTTTTCGAACATTCCACGCTCTGA-AAATCGCATCACTCGGTCAAAA
65 ATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTC-GAGAAATCGCATCATTTGGTCTAAA
* *
1635 TAGTTTCTT-ATTTTGTTAACAAGTTTTGGTCTTTCAATTAAAAACTTATTTACGTGAGAATTGT
129 TAGTTT-TTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
1699 TTCTCTCTTGGTTCTTGGACGAACT
193 TTCTCTCTTGGTTCTTGGACGAA-T
* * * *** * *
1724 TT-TAAAATTGACAAACTTTTACAAGTTCTTTTATAACTTCGGTGGATCAAAGTATCCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * * * * *
1788 TCAATTCCTTCTAGTAGTTTTTCAAACATTCCATTCTTGGGAAATCGCATCATTTGGTCTAAATA
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * * *
1853 GTTTTTCATTTTGTAAAAAAGTTTTGATCTTTGAATTAAAAACTTATTTAAGTGAGAATTGTGTC
131 GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
1918 TCTCTTGGTTCTTGGACGAACT
196 TCTCTTGGTTCTTGGACGAA-T
* * * * *
1940 TT-TAAAATTGTCGAACTTTTATGAGTTATTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * *
2004 TCCAATCCTTCGAGCAATTTTTCAAACATTCCATGCTCGAGAAGTCGCATCATTTGGTCTAAAAA
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * * *
2069 GTTTGTCATTTTGTAAACAAGTTGTGGCCTTTGAATTAAAAACTTATTTACGTGAGAATCGTTTC
131 GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* *
2134 TCTCTTGGTTGTTGGACGAAC
196 TCTCTTGGTTCTTGGACGAAT
* * * * *
2155 TTCTGAACTTGTCAAACTTTTAAGAGTTCTTTTTTAACTT-GTATTCCTTAAAGTGTTCAAGACG
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCG-GTTCCTTAAAGTATTCAAGACG
* * * * * *
2219 ATCCATTCCTTCTG-GTAATTTTTCGAACATTCAACGCTCGAGAAATCACATCATTTGGTCTAAG
65 ATCCATTCCTTC-GAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAA
* * *
2283 TAGTTTTTCATTTTGTTAAA-TAGTTTTGTTCTTTGAATTAAAAACTTGTTTACGTGAGAATTGT
129 TAGTTTTTCATTTTG-TAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * *
2347 TTCCCTCTAGGTTCTTTGACGAAC
193 TTCTCTCTTGGTTCTTGGACGAAT
* * * * * * *
2371 TTCCGAAATTGACAAACATTTT-TGAGTTCTTTTATAATTTCGGTTCATAAAAGTGTTCAAGACG
1 TTCTGAAATTGTCAAAC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACG
* * * * * *
2435 ATCCATTCTTTCTAGCAGTTTTTCGAACATTCCATTCTC-AGGAAAACGCATCATTTGGTCTAAA
65 ATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGA-GAAATCGCATCATTTGGTCTAAA
* * * ** * *
2499 TAGTTTGTCATATTTGTAAACAAGTTTTGGTCTTCGAATTAAAAATTTATTTATTTGGGAATTCT
129 TAGTTTTTCAT-TTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * * *
2564 CTGTCTCTTGGTTTTTGGACAAAC
193 TTCTCTCTTGGTTCTTGGACGAAT
* * * * * * * *
2588 TTCGGAACTTGACAAACTTTTTCAAGTTCTTTTATAACTTTGATTCCTTAAAGTATTCAAGATGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * *
2653 TCCATTCCTTCGAGCAATTTTTCGAACATTCCACGCTTTG-GAAATCGCATTATTTGGTCTAAAA
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGC-TCGAGAAATCGCATCATTTGGTCTAAAT
* * * *
2717 AGTTTCTCATTTTGTAAACAAGTTTTGGTCTTTCAATTAAAAACTTATTTATGTGAGAATTGTTC
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * *
2782 CACTATTGGTTCATGGACGAAC
195 CTCTCTTGGTTCTTGGACGAAT
* * * * * * * * * *
2804 TTC-CAATCTTGT-AGACATTTTATGAGCTGTTTTATAACTTCAGTTGCTTAGAGTATTCAAGAT
1 TTCTGAA-ATTGTCAAAC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGAC
* * * * * ***
2867 GATCCACTCTTTCGAGTAGTTTTT-TGAACATTCCATGCTCGGGAAATCGCATCATTCAATCTAA
64 GATCCATTCCTTCGAGCAATTTTTCT-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAA
** *
2931 ATAGTTTTTCATTTTGTAATGAAGTTTTGG---TTGAATTAAAAA--AATTT---TGAGAATTGT
128 ATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
*
2988 TTCTCTCTTGGTTTTTGGACGAACT
193 TTCTCTCTTGGTTCTTGGACGAA-T
* ** * * *
3013 TTC-GAACTTGTCAAACTTTGCCAAGTTCTTTTATAACTTCGATTCCTTAAAGTGTTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * * * *
3077 TCCATT-CTTCGAGCAA-TTTTCTAAACATTCAACGCTCTAAAAATTGAATCATTCGGTCTAAAT
66 TCCATTCCTTCGAGCAATTTTTCT-AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAT
** * * *
3140 AGTTTCCCATTTTATAAACAAGTTTTGGTCTTTCAATT-AAAACTTATGTACGTGAGAATTGTTT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
**
3204 CTCTCTTGGTTCTTGGACGAGC
195 CTCTCTTGGTTCTTGGACGAAT
* * *
3226 TTCTGAAATTGACAAACTCTTACGAGTTCTTTTATAAATTCGGTTCAC-TAAAGTATTCAAGACG
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTC-CTTAAAGTATTCAAGACG
* * * * * * * * *
3290 AACCTTTCCTTCTAGCAGTTTTTCGAACATTCCATTCTCGATAAATTGCATCATTTGATCTAAAT
65 ATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAT
* * * *
3355 AGTTTTTCATTTTGTAAACAAATTTTGATCTTTGAATTAAAAACTTATTTACGTGGGAATTGTGT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* *
3420 CTCTCTTGGTTCTTGGACAAAC
195 CTCTCTTGGTTCTTGGACGAAT
** * * *
3442 TTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGTTTACTTAAAGTATTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * *
3507 TCCAATCCTTCAAGCAATTTTTCTAACATTCCGTTCTCGAGAAGTCGCATCATTTGGTCTAAA-A
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
* * * *
3571 GGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACATGAGAATTGTGT
131 -GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
*
3636 CTCTATTGGTTCTTGGACGAAT
195 CTCTCTTGGTTCTTGGACGAAT
** * * *
3658 TTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGGTTACTTAAAGTATTCAACACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * * * * *
3723 TCAAATCCTTCGAGCAATTTTTCTAATATTCCGTGCTCGGGAAGTCGCATCATTTGGTCTATAA-
66 TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTA-AAT
* * * *
3787 GGTTTGTCATTTTGTAAACAAGTTTTGGGCTTTGAA-TAAAAATCTTATTTACGTGAGAATTATT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATTTACGTGAGAATTGTT
* * *
3851 TCTCTCTTGGTTGTTGAACAAAT
194 TCTCTCTTGGTTCTTGGACGAAT
* * * * * *
3874 TTCCGAACTTGCCAAACCTTTACGAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAGATGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * **
3939 TCCATTCCTTCGAGTAATTTTT-TGAACA-TCCAATGCTCGAGATATCAG-ATCATTTCATCTAA
66 TCCATTCCTTCGAGCAATTTTTCT-AACATTCC-ATGCTCGAGAAATC-GCATCATTTGGTCTAA
* * *
4001 ATAGTTTTTCATTTTGTAAA-ATAGTTTTGGTCTTCG-------AA-TTGTTTACGTGAGAATGG
128 ATAGTTTTTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* * * *
4057 TTTCTCTCTTCGTTCTTTGATGAAC
192 TTTCTCTCTTGGTTCTTGGACGAAT
* * * * * * * *
4082 TTCAGAAATTGAT-AAACATTTATGAGTACTTCTATAACTTCGGTTCATTATAGTGTTCAAGACG
1 TTCTGAAATTG-TCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACG
* * * * *
4146 ATCCATTGCTTCTAGCAATTTTTCAAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAAT
65 ATCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAAT
** *
4211 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTTAGAATTGTTT
130 AGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * *
4276 CTCTTTTGGTTTTTGGATGATCT
195 CTCTCTTGGTTCTTGGACGA-AT
* ** * * *
4299 TTC-GAACTTGTCAAACTTTGCCAAGTTCTTTTATAACTTCGATTCCTTCAAGTATTCAAGACGA
1 TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
4363 TCCATTCCTTC
66 TCCATTCCTTC
4374 ATGTAATTTT
Statistics
Matches: 3444, Mismatches: 608, Indels: 204
0.81 0.14 0.05
Matches are distributed among these distances:
206 4 0.00
207 64 0.02
208 405 0.12
209 21 0.01
210 10 0.00
211 7 0.00
213 14 0.00
214 88 0.03
215 299 0.09
216 2330 0.68
217 201 0.06
218 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (216 bp):
TTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
TCCATTCCTTCGAGCAATTTTTCTAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
GTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
TCTCTTGGTTCTTGGACGAAT
Found at i:2308 original size:20 final size:21
Alignment explanation
Indices: 2269--2309 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2259 AGAAATCACA
*
2269 TCATTTGGTCTAAGTAGTTTT
1 TCATTTGGTCTAAATAGTTTT
*
2290 TCATTTTGT-TAAATAGTTTT
1 TCATTTGGTCTAAATAGTTTT
2310 GTTCTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (21 bp):
TCATTTGGTCTAAATAGTTTT
Done.