Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009626.1 Kokia drynarioides strain JFW-HI SEQ_124342, 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, 877
Length: 1463
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Found at i:375 original size:216 final size:216
Alignment explanation
Indices: 1--1193 Score: 1480
Period size: 216 Copynumber: 5.5 Consensus size: 216
* * * *
1 TAGTAGTCGAGATGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCAT
1 TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* * * *
66 CATTTAGTCTAAAA-CGTTTTTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAATCTTTTTT
66 CATTTGGTC-AAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTTT
* * *
130 ACGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAAGTTCCGAACTTGTCAAACATTTACTATAT
130 ACGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTATAT
*
195 CTTTTATAACTTCAGTTCCTGA
195 CTTTTATAACTTCGGTTCCTGA
* * * *
217 TAGTAGTCAAGACGATCCATTTCTTTGACCAA-TTTTCTGAAGATTCCATTATTGGGAAATCGCA
1 TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTC-GAACATTCCATGATCGGGAAATCGCA
* * * *
281 TCATTTGGTCAAAATAATTTGTCATTTTGTAAATAGCTTTTGGTATTGGAATTAAAAACTTTTTT
65 TCATTTGGTCAAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTTT
* * * *
346 ACGTTAGAATTCTTTCTCTCATGGTTCTTGGACGTACTTTCGAACTTGTCAAACATTTACTAGT-
130 ACGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTA-TA
410 TCTTTTTATAACTTCGGTTCCTGA
194 TC-TTTTATAACTTCGGTTCCTGA
* * * * * *
434 TAGTAGTCAAGATGATCAATTCCCTCGACCAATTTTTCAAACATTCCATGATCGGGAAATCACAT
1 TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* * *
499 CATTTGGTTTAAAA-AGTTTGTCATTTTGTAAAGAA-CTTTTGGCCTTTGAAATAAAAACTTTTT
66 CATTTGG-TCAAAATAGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTTTT
* * * * * * *
562 T-CGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAACCTCTGTACTGGT-AAACATTTACAAGT
129 TACGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTA-T
* *
625 -TCTTTTATAACTTCGATTCTTGA
193 ATCTTTTATAACTTCGGTTCCTGA
* * * * * *
648 GAGTATTCCAGACGATCCATTCCTTTGACCAATTTTTCGATCATTCCATGATCAGGAAATCGTAT
1 TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* *
713 CATTTGG-AATAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAATCTTTTTT
66 CATTTGGTCA-AAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTTT
* * *
777 ACGTGAGAATTCTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTTAAACATTTACTA-AT
130 ACGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTATA-
*
841 TCTTTTATAACTTTGGTTCCTGA
194 TCTTTTATAACTTCGGTTCCTGA
* *
864 TAGTAGTCAAGACGATCCATTTCTTTGACCAATTTTTCGAACATTCCATGATCGGGATATCGCAT
1 TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* *
929 CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTATGAATTAAAAACTTTTTT
66 CATTTGGTCAAAATAGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTTTTT
* * * * * * * * *
993 ATGAGAGAATTGTTTCTCTATTAGTTCTTGGACGAACTTTCGAACTTGTTAAACCTTTACGA-AT
130 ACGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTATA-
* *
1057 TCTTTTATAACATCGGTTCCTAA
194 TCTTTTATAACTTCGGTTCCTGA
* * ** * *
1080 GAGTATTCAAGATC-ATCCATTCCTTTGACTTATTTTCCGAATATTCCATGATCGGGAAATCGCA
1 TAGTAGTCAAGA-CGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCA
*
1144 TCATTT-GTCAAAATAGTTTGTCATTTTGTAAATTA-CTTTTGGTCTTTGAA
65 TCATTTGGTCAAAATAGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAA
1194 CACAACACAT
Statistics
Matches: 841, Mismatches: 119, Indels: 35
0.85 0.12 0.04
Matches are distributed among these distances:
212 1 0.00
213 5 0.01
214 123 0.15
215 103 0.12
216 476 0.57
217 122 0.15
218 11 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
TAGTAGTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
CATTTGGTCAAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAAACTTTTTTA
CGTGAGAATTCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTATATC
TTTTATAACTTCGGTTCCTGA
Found at i:806 original size:431 final size:426
Alignment explanation
Indices: 1--1193 Score: 1568
Period size: 431 Copynumber: 2.8 Consensus size: 426
* * *
1 TAGTAGTCGAGATGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCAT
1 TAGTAGTCAAGATGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* * * *
66 CATTTAGTCTAAAACGTTTTTCATTTTGTAAAAAGCTTTTGGTCTTTGAATTAAAATCTTTTTTA
66 CATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTA
* * * * * *
131 CGTGAGAATTGTTTCTCTCTTGGTTCTTGGAAGAAGTTCCGAACTTGTCAAACATTTACTATATC
130 CGAGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA-CTCTGAACTGGT-AAACATTTACAAT-TC
* * * *
196 TTTTATAACTTC-AGTTCCTGATAGTAGTCAAGACGATCCATTTCTTTGACCAA-TTTTCTGAAG
192 TTTTATAACTTCGA-TTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-G-AT
* * *
259 ATTCCATTATTGGGAAATCGCATCATTTGGTCAAAATAATTTGTCATTTTGTAAATAGCTTTTGG
254 ATTCCATGATCGGGAAATCGCATCATTTGG-CAAAATAGTTTGTCATTTTGTAAATAGCTTTTGG
* * * * *
324 TATTGGAATTAAAAACTTTTTTACGTTAGAATTCTTTCTCTCATGGTTCTTGGACGTACTTTCGA
318 TCTTTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCATGGTTCTTGGACGAACTTCCGA
*
389 ACTTGTCAAACATTTACTAGTTCTTTTTATAACTTCGGTTCCTGA
383 ACTTGTCAAACATTTACTAATTC-TTTTATAACTTCGGTTCCTGA
* * * * *
434 TAGTAGTCAAGATGATCAATTCCCTCGACCAATTTTTCAAACATTCCATGATCGGGAAATCACAT
1 TAGTAGTCAAGATGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* * *
499 CATTTGGTTTAAAAAGTTTGTCATTTTGTAAAGAACTTTTGGCCTTTGAAATAAAAACTTTTTT-
66 CATTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AACTTTTGGTCTTTGAATTAAAAACTTTTTTA
* *
563 CGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAACCTCTGTACTGGTAAACATTTACAAGTTCT
130 CGAGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA-CTCTGAACTGGTAAACATTTACAA-TTCT
* *
628 TTTATAACTTCGATTCTTGAGAGTATTCCAGACGATCCATTCCTTTGACCAATTTTTCGATCATT
193 TTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAT-ATT
* * * *
693 CCATGATCAGGAAATCGTATCATTTGGAATAAATAGTTTGTCATTTTGTAAAAAGCTTTTGGTCT
257 CCATGATCGGGAAATCGCATCATTTGGCA-AAATAGTTTGTCATTTTGTAAATAGCTTTTGGTCT
* * * *
758 TTGAATTAAAATCTTTTTTACGTGAGAATTCTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACT
321 TTGAATTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCATGGTTCTTGGACGAACTTCCGAACT
* *
823 TGTTAAACATTTACTAATTCTTTTATAACTTTGGTTCCTGA
386 TGTCAAACATTTACTAATTCTTTTATAACTTCGGTTCCTGA
* * *
864 TAGTAGTCAAGACGATCCATTTCTTTGACCAATTTTTCGAACATTCCATGATCGGGATATCGCAT
1 TAGTAGTCAAGATGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
* *
929 CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTATGAATTAAAAACTTTTTTA
66 CATTTGGTCTAAAAAGTTTGTCATTTTGTAAA-AACTTTTGGTCTTTGAATTAAAAACTTTTTTA
* * * * * *
994 TGAGAGAATTGTTTCTCTATTAGTTCTTGGACGAACTTTCGAACTTGTTAAACCTTTACGAATTC
130 CGAGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTCT-GAAC-TGGTAAACATTTAC-AATTC
* * * ** *
1059 TTTTATAACATCGGTTCCTAAGAGTATTCAAGATC-ATCCATTCCTTTGACTTATTTTCCGAATA
192 TTTTATAACTTCGATTCCTGAGAGTATTCAAGA-CGATCCATTCCTTTGACCAATTTTTCG-ATA
*
1123 TTCCATGATCGGGAAATCGCATCATTTGTCAAAATAGTTTGTCATTTTGTAAATTA-CTTTTGGT
255 TTCCATGATCGGGAAATCGCATCATTTGGCAAAATAGTTTGTCATTTTGTAAA-TAGCTTTTGGT
1187 CTTTGAA
319 CTTTGAA
1194 CACAACACAT
Statistics
Matches: 663, Mismatches: 84, Indels: 28
0.86 0.11 0.04
Matches are distributed among these distances:
430 140 0.21
431 264 0.40
432 141 0.21
433 116 0.17
434 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (426 bp):
TAGTAGTCAAGATGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCAT
CATTTGGTCTAAAAAGTTTGTCATTTTGTAAAAACTTTTGGTCTTTGAATTAAAAACTTTTTTAC
GAGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTCTGAACTGGTAAACATTTACAATTCTTTT
ATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGATATTCCAT
GATCGGGAAATCGCATCATTTGGCAAAATAGTTTGTCATTTTGTAAATAGCTTTTGGTCTTTGAA
TTAAAAACTTTTTTACGTGAGAATTCTTTCTCTCATGGTTCTTGGACGAACTTCCGAACTTGTCA
AACATTTACTAATTCTTTTATAACTTCGGTTCCTGA
Done.