Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014412.1 Kokia drynarioides strain JFW-HI SEQ_129450, 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: 3764
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:376 original size:190 final size:189
Alignment explanation
Indices: 68--441 Score: 445
Period size: 190 Copynumber: 2.0 Consensus size: 189
58 TGTAAACAAA
*
68 TTTTGGTCTTTGAATTAAAAACTTATTTACGTAAGAATTATTCTCTATTGGTTCTAAGATGAACT
1 TTTTGGCCTTTGAATTAAAAACTTATTTACGTAAGAATTATTCTCTATTGGTTCTAAGATGAACT
* * * * * * *
133 TCTGAACTTATTAAACTTTTATGAGTTCTTTTATAACTTCTGTTCCTTAAAGTATTGAAGAAAAT
66 TCTAAACATATAAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCATAAAGTATTAAAGAAAAT
* * *
198 CTATTCCCTT-GAGTAATTTTC-CGGGTAAT-CAAGTCATTTGGTCTAAATAGTTTTTTATC
131 CCATT-CCTTCGAGCAATTTTCTCGGGAAATAC-A-TCATTTGGTCTAAATAGTTTTTTATC
* * * * **
257 TTTTGGCCTTTGAATTTAAAA-TTGATTTACTTAAGAATTGTTTCTCTCTTGGTTCTTGGATGAA
1 TTTTGGCCTTTGAATTAAAAACTT-ATTTACGTAAGAATT-ATTCTCTATTGGTTCTAAGATGAA
*
321 CTT-TCAAACATGTAAAACTTTTACGAGTTCTTTTATAACTGT-GGTTCCATAAAGTATTAAAGA
64 CTTCT-AAACATATAAAACTTTTACGAGTTCTTTTATAACT-TCGGTTCCATAAAGTATTAAAGA
** *
384 CGATCCATTCCTTCGAGCAATTTTCTTGGGAAATATCATCATTTGGTCTAAATAGTTT
127 AAATCCATTCCTTCGAGCAATTTTCTCGGGAAATA-CATCATTTGGTCTAAATAGTTT
442 GTCATTTTCT
Statistics
Matches: 156, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
188 2 0.01
189 38 0.24
190 87 0.56
191 27 0.17
192 1 0.01
193 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (189 bp):
TTTTGGCCTTTGAATTAAAAACTTATTTACGTAAGAATTATTCTCTATTGGTTCTAAGATGAACT
TCTAAACATATAAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCATAAAGTATTAAAGAAAAT
CCATTCCTTCGAGCAATTTTCTCGGGAAATACATCATTTGGTCTAAATAGTTTTTTATC
Found at i:1384 original size:50 final size:52
Alignment explanation
Indices: 1298--1395 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 52
1288 TGCATAACTT
*
1298 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGATAG
1 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGATAG
* * * *
1350 GATTT-ATGATGCATA-TTTAACTAACGTGTAAGTTACTTAATGCATG
1 GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATG
1396 TCATTGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 27 0.66
51 9 0.22
52 5 0.12
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (52 bp):
GATTTAATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGATAG
Found at i:1420 original size:50 final size:50
Alignment explanation
Indices: 1298--1428 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
1288 TGCATAACTT
*
1298 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGATAG
1 GATTT-ATGATGCAAAC-TTAACTAACATGGAAGTTACATAATGCATGATAG
* * * * * *
1350 GATTTATGATGCATATTTAACTAACGTGTAAGTTACTTAATGCATG-TCATT
1 GATTTATGATGCAAACTTAACTAACATGGAAGTTACATAATGCATGAT-A-G
*
1401 G-TTTATGATGCAGACTTAACTAATCATG
1 GATTTATGATGCAAACTTAACTAA-CATG
1429 AGAGTTAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 47 0.71
51 13 0.20
52 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAACTTAACTAACATGGAAGTTACATAATGCATGATAG
Found at i:1661 original size:17 final size:17
Alignment explanation
Indices: 1630--1662 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1620 CAAACACTTA
1630 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
1647 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
1663 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:3216 original size:201 final size:201
Alignment explanation
Indices: 3009--3382 Score: 464
Period size: 201 Copynumber: 1.9 Consensus size: 201
2999 TACTTCTGTT
* * * * * * **
3009 CCTTAAAAGTATTCAAGACGATCCATTCCTTC-AAAAATTTTCGGCACGTTCCATGCTCGGGAAA
1 CCTT-AAACTATTCAACACGATCCATTCCATCGAAAAATTTTCGGAACATTCCACGCTCGAAAAA
* * * *
3073 TTGAATCATTTTGTCTAAATAGTTTGTCAGTTTGTAAACATGTTT-TGGCCTTTAAATTAAAAAC
65 TCGAATCATTTGGTCTAAATAGTTTGTCAGTTTGTAAAAAGGTTTGT-GCCTTTAAATTAAAAAC
3137 TCATTTACGTGAGAATTATTTCTCTCTTGGTCCTGGGACAAACTTTCGAACTTGCCAAACTTTTA
129 TCATTTACGTGAGAATTATTTCTCTCTTGGTCCTGGGACAAACTTTCGAACTTGCCAAACTTTTA
3202 CTTTAGAA
194 CTTTAGAA
* ** ** *
3210 CCTTAAACTATTCAACACGATCCATTTCATCGAGCAATTTTTTGAACATTTCACGCTCGAAAAAT
1 CCTTAAACTATTCAACACGATCCATTCCATCGAAAAATTTTCGGAACATTCCACGCTCGAAAAAT
* * * * *
3275 CGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGGTTTGTGTCTTTGAATTAAAAACTT
66 CGAATCATTTGGTCTAAATAGTTTGTCAGTTTGTAAAAAGGTTTGTGCCTTTAAATTAAAAACTC
* * * * *
3340 ATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
131 ATTTACGTGAGAATTATTTCTCTCTTGGTCCTGGGACAAACTT
3383 CAGAACTCGT
Statistics
Matches: 143, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
200 23 0.16
201 119 0.83
202 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (201 bp):
CCTTAAACTATTCAACACGATCCATTCCATCGAAAAATTTTCGGAACATTCCACGCTCGAAAAAT
CGAATCATTTGGTCTAAATAGTTTGTCAGTTTGTAAAAAGGTTTGTGCCTTTAAATTAAAAACTC
ATTTACGTGAGAATTATTTCTCTCTTGGTCCTGGGACAAACTTTCGAACTTGCCAAACTTTTACT
TTAGAA
Found at i:3436 original size:416 final size:415
Alignment explanation
Indices: 2524--3537 Score: 1173
Period size: 417 Copynumber: 2.4 Consensus size: 415
2514 CTGCGAAATG
* * *
2524 TTTCTCTTGGTTCTTTGACGAACTTAATAACTTC-TCAAACTTTAATGAGATCCTTTATTACTTC
1 TTTCTCTTGGTTCTTGGACGAACTTAAGAAC-TCGTCAAACTTTTATGAGATCCTTTATTACTTC
2588 GGTT-CTTCAAAAGTATTCAAGACAATCCATTCCTTCGAAAAATTTATCGAACATTCCTTGCTCG
65 GGTTCCTT-AAAAGTATTCAAGACAATCCATTCCTTC-AAAAATTT-TCGAACATTCCTTGCTCG
* * *
2652 GGAAATTGAATCATTTCGTCTAAATAGTTTGCCATTTTGTAAAGATGTTTTGGTCTTAGAATTAA
127 GGAAATTGAATCATTTCGTCTAAATAGTTTGACATTTTGTAAACATGTTTTGGCCTTAGAATTAA
* * **
2717 AAACTCATTTACGTGAGAATTGTTTCTCTCTTGATTCTGGGAAGAACTTCTGAACTTGTTAAACT
192 AAACTCATTTACGTGAGAATTATTTCTCTCTTGATCCTGGGAAGAACTTCTGAACTTGCCAAACT
** * *
2782 TTTACGAGTTTCTTTATAACTTCGGTTCATAAAAGTATTTAAGACGATGCATTCCTTCAAGCAAT
257 TTTACGAGTAACCTTATAACTTC-ATTCATAAAAGTATTTAAGACGATGCATTCCTTCAAGCAAT
* * *
2847 TTTCTCAAGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTCTAAACAAGTTTTGGTCTTT
321 TTGCTCAAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGGTTTGGTCTTT
* *
2912 TAATTGAAAACTTATTTACGTGAGAATTGT
386 GAATTAAAAACTTATTTACGTGAGAATTGT
* * * * *
2942 TTT-TCTTTGTTCTCGGACGAACTTAAGAACTTGTCAAACTTTTTTGAGATCCTTTATTACTTCT
1 TTTCTCTTGGTTCTTGGACGAACTTAAGAACTCGTCAAACTTTTATGAGATCCTTTATTACTTCG
* * * *
3006 GTTCCTTAAAAGTATTCAAGACGATCCATTCCTTCAAAAATTTTCGGCACGTTCCATGCTCGGGA
66 GTTCCTTAAAAGTATTCAAGACAATCCATTCCTTCAAAAATTTTC-GAACATTCCTTGCTCGGGA
* * *
3071 AATTGAATCATTTTGTCTAAATAGTTTGTCAGTTTGTAAACATGTTTTGGCCTTTA-AATTAAAA
130 AATTGAATCATTTCGTCTAAATAGTTTGACATTTTGTAAACATGTTTTGGCC-TTAGAATTAAAA
*
3135 ACTCATTTACGTGAGAATTATTTCTCTCTTGGTCCTGGGACA-AACTT-TCGAACTTGCCAAACT
194 ACTCATTTACGTGAGAATTATTTCTCTCTTGATCCTGGGA-AGAACTTCT-GAACTTGCCAAACT
* * * * * ** *
3198 TTTACTTTAG-AACCTTA-AAC-T-ATTCA-ACACGATCCATTTCA-TCGA-GCAATTTTTTGAA
257 TTTAC--GAGTAACCTTATAACTTCATTCATAAAAG-T--ATTTAAGACGATGC-ATTCCTTCAA
*
3256 -C-ATTTCACGCTCGAA-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGGT
316 GCAATTT---GCTC-AAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGGT
*
3317 TTGTGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGT
377 TTG-GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * * * *
3357 TTCTCTCTTGGTTCTTGGACGAACTTCAGAACTCGTAAAACTTTTACGAGTTCCGTTATAACTTC
1 TT-TCTCTTGGTTCTTGGACGAACTTAAGAACTCGTCAAACTTTTATGAGATCCTTTATTACTTC
* * * * *
3422 GGTTCCTT-AAAGTATTTAAGACAATCCATTCATTTGAGCAAATTTTTGAACATTCCTTGCTCGG
65 GGTTCCTTAAAAGTATTCAAGACAATCCATTC-CTTCA-AAAATTTTCGAACATTCCTTGCTCGG
* * * * *
3486 GTAATCGAATCATTTGGTCTAAATAGTTTGACATTTTGTAAATAGGTTTTGG
128 GAAATTGAATCATTTCGTCTAAATAGTTTGACATTTTGTAAACATGTTTTGG
3538 GATGAACTTC
Statistics
Matches: 507, Mismatches: 68, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
412 7 0.01
413 8 0.02
414 17 0.03
415 86 0.17
416 166 0.33
417 208 0.41
418 15 0.03
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (415 bp):
TTTCTCTTGGTTCTTGGACGAACTTAAGAACTCGTCAAACTTTTATGAGATCCTTTATTACTTCG
GTTCCTTAAAAGTATTCAAGACAATCCATTCCTTCAAAAATTTTCGAACATTCCTTGCTCGGGAA
ATTGAATCATTTCGTCTAAATAGTTTGACATTTTGTAAACATGTTTTGGCCTTAGAATTAAAAAC
TCATTTACGTGAGAATTATTTCTCTCTTGATCCTGGGAAGAACTTCTGAACTTGCCAAACTTTTA
CGAGTAACCTTATAACTTCATTCATAAAAGTATTTAAGACGATGCATTCCTTCAAGCAATTTGCT
CAAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTCTAAACAAGGTTTGGTCTTTGAATT
AAAAACTTATTTACGTGAGAATTGT
Done.