Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006039.1 Kokia drynarioides strain JFW-HI SEQ_120502, 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, 868
Length: 1447
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:354 original size:72 final size:72
Alignment explanation
Indices: 229--368 Score: 244
Period size: 72 Copynumber: 1.9 Consensus size: 72
219 CGAACTTCCG
*
229 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTACAGCATTCAAGACGATACAT
1 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGCATTCAAGACGATACAT
294 TCCTCTA
66 TCCTCTA
* * *
301 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
1 AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGCATTCAAGACGATACAT
366 TCC
66 TCC
369 ATCAAGCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (72 bp):
AACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGCATTCAAGACGATACAT
TCCTCTA
Found at i:690 original size:216 final size:213
Alignment explanation
Indices: 301--1447 Score: 1202
Period size: 216 Copynumber: 5.3 Consensus size: 213
291 CATTCCTCTA
301 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
1 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
* * * *
366 TCCATCAAGCAATTTTCTGAACATTCCATGCTCGTGAAATTGCATCATTTGGTCTAAATAGTTTG
66 TCCTTCGAGCAATTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * **
431 TCATTGTGTAAAAAACTTTTGGTCACTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTTT
130 TCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAA-ACTTATTTACGTGAGAATTGTTTCTC-TT
*
496 TGGTTCTTGGATGAACTTCTG
193 TGGTTCTTGGACGAACTTCTG
* * * * * * * *
517 AACTTATCAAATTTTTACGAGTTCTTTTATAATTTCAGTTTCATAAAGCATTCAAGACGATTCAT
1 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
* * * *
582 TCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTAAATATTTTT
66 TCCTTCGAGCAA-TTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * * *
647 TCATTTTGTTAAAAGGTTTCGTTGTTTGAATTAAAAGCTTATTTACGTGAGAATTGTTTCTCTCT
130 TCATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAA-CTTATTTACGTGAGAATTGTTTCTCT-T
*
712 TGGTTCGTGGACGAACTT-TCG
193 TGGTTCTTGGACGAACTTCT-G
** * *
733 AACTAGTCAAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
1 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
* * * * * *
798 TCCTTCGAGCAATTTTCTGAACATTCAATTCTTGAGAAATGGCAGCATTTGGTCTAAAGAGTTTG
66 TCCTTCGAGCAATTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTG
* * * *
863 TCATTTT-AAAAACAAGTTTTGGTCTTTGCATCAAAAACTTATTTACGTGAGAATTGTTTCGC-T
130 TCATTTTGTAAAA-AAGTTTTGGTCTTTGAAT-TAAAACTTATTTACGTGAGAATTGTTTCTCTT
* * *
926 TGGTTCTTGGACAAACTTTTT
193 TGGTTCTTGGACGAACTTCTG
** * * * *
947 AACTTGTT-AAACTTTTACGAGTTCTTTTATAACTTCAATTCCTTATAGTAATCAAGATGATACA
1 AACTT-TTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
* * * * * * * * *
1011 TTCCTTCGAGCAACTTTCTTAACATTCTAAGCTCGAAAAATCCCATCATTT-TTCTAAATTGTAT
65 TTCCTTCGAGCAATTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* * * *
1075 GTCATTTTGTAAACAAGTTTT-GTCTTTAAATTAAAAACTTATTTACGTAAGAATTATTTCTCTC
129 GTCATTTTGTAAAAAAGTTTTGGTCTTTGAATT-AAAACTTATTTACGTGAGAATT-GTT-TCTC
* **
1139 TCTTTGTTCTTGGACGAACTTCCA
191 T-TTGGTTCTTGGACGAACTTCTG
* * *
1163 AACTTTTCAAACCTTTACGAGTTCTTTTATAACTCCGGTTCCTTAAAGTATTCAACAAC-ATCCA
1 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA-GACGATCCA
* * * * *
1227 TTCCTTTC-AGCAATTTT-GAACATTCCATTCTTGGGTAATCGCATCATTTAGTCTAAATAGTTT
65 TTCC-TTCGAGCAATTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTT
* * * * * ** *
1290 TTCGTTTTGTAAACAAGTTTTTGGTGTTTAAAGCGAAAACTTATTAACGTGAGAATTGTTTCTC-
129 GTCATTTTGTAAAAAAG-TTTTGGTCTTTGAA-TTAAAACTTATTTACGTGAGAATTGTTTCTCT
** * * *
1354 TTGACTGTTAGATGAACTTCTG
192 TTGGTTCTTGGACGAACTTCTG
* * * *
1376 AACTTTTTAAACTTTTACCAGTTCTTTTATAACTT-GGTTCCCTACAA-TATTCAAGATGATCCA
1 AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTA-AAGTATTCAAGACGATCCA
1439 TTCCTTCGA
65 TTCCTTCGA
Statistics
Matches: 765, Mismatches: 141, Indels: 54
0.80 0.15 0.06
Matches are distributed among these distances:
211 4 0.01
212 54 0.07
213 73 0.10
214 139 0.18
215 44 0.06
216 410 0.54
217 41 0.05
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (213 bp):
AACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
TCCTTCGAGCAATTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGT
CATTTTGTAAAAAAGTTTTGGTCTTTGAATTAAAACTTATTTACGTGAGAATTGTTTCTCTTTGG
TTCTTGGACGAACTTCTG
Found at i:1214 original size:430 final size:427
Alignment explanation
Indices: 300--1447 Score: 1337
Period size: 430 Copynumber: 2.7 Consensus size: 427
290 ACATTCCTCT
300 AAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
1 AAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
* * * * *
365 TTCCATCAAGCAATTTTCTGAACATTCCATGCTCGTGAAATTGCATCATTTGGTCTAAATAGTTT
66 TTCCTTC-AGCAATTTTCTGAACATTCCATTCTTGAGAAATCGCATCATTTGGTCTAAATAGTTT
* ** * *
430 GTCATTGTGTAAAA-AACTTTTGGTCACTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCT
130 GTCATT-T-TAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTC-
* * * *
494 TTTGGTTCTTGGATGAACTTCTGAACTTATCAAATTTTTACGAGTTCTTTTATAATTTCAGTTTC
192 -TTGGTTCTTGGATGAACTTCTGAACTTATTAAACTTTTACGAGTTCTTTTATAACTTCAGTTCC
* * * * ** *
559 ATAAAGCATTCAAGACGATTCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCG
256 ATAAAGTATTCAAGATGATACATTCCTTCGAGCAATTTTTC-AACATTCCAAGCTCGAAAAATCC
* * * * * *
624 CATCATTCGGTCTAAATATTTTTTCATTTTGTTAAAAGGTTTCGTTGTTTGAATTAAAAGCTTAT
320 CATCATTCGGTCTAAATATTATGTCATTTTGTTAAAAAGTTTCGTTCTTTAAATTAAAAACTTAT
* *
689 TTACGTGAGAATTGTTTCTCTCTTGGTTCGTGGACGAACTTTC
385 TTACGTAAGAATTGTTTCTCTCTTGGTTCGTGGACGAACTTCC
* ** * *
732 GAACTAGTCAAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGACGATCCA
1 AAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
* * * *
797 TTCCTTCGAGCAATTTTCTGAACATTCAATTCTTGAGAAATGGCAGCATTTGGTCTAAAGAGTTT
66 TTCCTTC-AGCAATTTTCTGAACATTCCATTCTTGAGAAATCGCATCATTTGGTCTAAATAGTTT
* *
862 GTCATTTTAAAAACAAGTTTTGGTCTTTGCATCAAAAACTTATTTACGTGAGAATTGTTTCGCTT
130 GTCATTTT-AAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTT
** * * * * *
927 GGTTCTTGGACAAACTTTTTAACTTGTTAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTTA
194 GGTTCTTGGATGAACTTCTGAACTTATTAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATA
* * *
992 TAGTAATCAAGATGATACATTCCTTCGAGCAACTTTCTT-AACATTCTAAGCTCGAAAAATCCCA
259 AAGTATTCAAGATGATACATTCCTTCGAGCAA-TTT-TTCAACATTCCAAGCTCGAAAAATCCCA
** *
1056 TCATT-TTTCTAAAT-TGTATGTCATTTTG-TAAACAAGTTTTG-TCTTTAAATTAAAAACTTAT
322 TCATTCGGTCTAAATAT-TATGTCATTTTGTTAAA-AAGTTTCGTTCTTTAAATTAAAAACTTAT
* * *
1117 TTACGTAAGAATTATTTCTCTCTCTTTGTTCTTGGACGAACTTCC
385 TTACGTAAGAATT-GTT-TCTCTCTTGGTTCGTGGACGAACTTCC
* * *
1162 AAACTTTTCAAACCTTTACGAGTTCTTTTATAACTCCGGTTCCTTAAAGTATTCAACAAC-ATCC
1 AAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA-GACGATCC
* * *
1226 ATTCCTTTCAGCAA-TTT-TGAACATTCCATTCTTGGGTAATCGCATCATTTAGTCTAAATAGTT
65 ATTCC-TTCAGCAATTTTCTGAACATTCCATTCTTGAGAAATCGCATCATTTGGTCTAAATAGTT
* * * * * * * *
1289 TTTCGTTTTGTAAACAAGTTTTTGGTGTTTAAAGCGAAAACTTATTAACGTGAGAATTGTTTCTC
129 TGTCATTTT-AAAACAAG-TTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTC
** * * * * * *
1354 TTGACTGTTAGATGAACTTCTGAACTTTTTAAACTTTTACCAGTTCTTTTATAACTT-GGTTCCC
192 TTGGTTCTTGGATGAACTTCTGAACTTATTAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCA
*
1418 TACAA-TATTCAAGATGATCCATTCCTTCGA
257 TA-AAGTATTCAAGATGATACATTCCTTCGA
Statistics
Matches: 606, Mismatches: 98, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
428 116 0.19
429 115 0.19
430 196 0.32
431 13 0.02
432 166 0.27
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (427 bp):
AAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
TTCCTTCAGCAATTTTCTGAACATTCCATTCTTGAGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTAAAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGG
TTCTTGGATGAACTTCTGAACTTATTAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATAAA
GTATTCAAGATGATACATTCCTTCGAGCAATTTTTCAACATTCCAAGCTCGAAAAATCCCATCAT
TCGGTCTAAATATTATGTCATTTTGTTAAAAAGTTTCGTTCTTTAAATTAAAAACTTATTTACGT
AAGAATTGTTTCTCTCTTGGTTCGTGGACGAACTTCC
Done.