Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012631.1 Kokia drynarioides strain JFW-HI SEQ_127640, 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: 1700
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.39
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:555 original size:216 final size:214
Alignment explanation
Indices: 1--1092 Score: 1440
Period size: 216 Copynumber: 5.1 Consensus size: 214
* *
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAGTTTCGAACCTGTCAAACTTTTACTAG
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
* * * * * *
66 TTCTTTTATAACTTTGGATACTTCAATTATTCATGACGATCTATTTTTTCGAGCAA-TTTTCTAA
66 TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCTTTC-AGCAATTTTTC-AA
* * * * *
130 ACATTCCATGGTCGAGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAACTTTT
129 ATATTCCAT-CTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTT
*
195 GGTCTTTAAATTAAAAACTTA-
193 GGTCTTTGAATTAAAAACTTAT
* *
216 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCGAACTTTTACGAG
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
* * ** * * * * * *
281 TTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATT-TTTTAGTGCAATTTTTCGA
66 TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCTTTCA--GCAATTTTTCAA
* * * * * *
345 ACATTCCATCATTGGGAAATCGCGTCACTTGGTCTAAATAATTTGTCATTTTGTAAACAAGTTTT
129 ATATTCCATC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTT
*
410 GGTCTTTAAATTAAAAACTTAT
193 GGTCTTTGAATTAAAAACTTAT
* * * * *
432 TTACGTGACAATTGTTTCTCTCTTTGTTCTTGGATGAACTTTCGAACCTGACAACCTTTTACTAG
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
* *
497 TTCTTTTATAACTTTGGAACCTTAAAGTATTCAAGACGATCCATTCATTTCAGCAATTTTCCAAA
66 TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTC-TTTCAGCAATTTTTCAAA
* * * * * *
562 TTTTCCAAGCTCAGTAAATCGTATCATTTGGTCTAAATAGTTTGTCGTTTTGCAAACAAGTTTTG
130 TATTCC-ATCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTG
*
627 GTCGTTGAATTAAAAACTTAT
194 GTCTTTGAATTAAAAACTTAT
648 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
* *
713 TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCATTTCAGTAATTTTTCGAA
66 TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTC-TTTCAGCAATTTTTCAAA
* * * *
778 TTTTCCATGCTCGGCAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTAGCAAACAACTTTTG
130 TATTCCAT-CTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTG
*
843 CTCTTTGAATTAAAAACTTAT
194 GTCTTTGAATTAAAAACTTAT
* * *
864 TTAGGTGAGAATTGTTTCTTTCTTTG-TCTTTGTACGAACTTTCGAACTTGTCAAACTTTTACT-
1 TTACGTGAGAATTGTTTCTCTCTTTGTTC-TTGGACGAACTTTCGAACTTGTCAAACTTTTACTA
* *
927 GTTCTTTTATAACTTTGGATCCTTAAATTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAA
65 GTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCTTTC-AGCAATTTTTCAA
* * * *
992 GTATACCATTCTCGGCG-AATCGCATCATTTAGCCTAAATAGTTTGTCATTTTGCAAACAAGTTT
129 ATATTCCA-TCTCGG-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTT
1056 TGGTCTTTGAATTAAAAACTTAT
192 TGGTCTTTGAATTAAAAACTTAT
*
1079 TTACATGAGAATTG
1 TTACGTGAGAATTG
1093 NNNNNNNNNN
Statistics
Matches: 769, Mismatches: 95, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
213 1 0.00
214 6 0.01
215 323 0.42
216 433 0.56
217 2 0.00
218 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (214 bp):
TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACTAG
TTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCTTTCAGCAATTTTTCAAAT
ATTCCATCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGT
CTTTGAATTAAAAACTTAT
Found at i:1568 original size:216 final size:216
Alignment explanation
Indices: 1192--1700 Score: 761
Period size: 216 Copynumber: 2.4 Consensus size: 216
1182 NNNNNNNNNN
* *
1192 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAAATTGTAAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAA
* *
1257 CTTTTA-TGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTCGAGC
66 CTTTTACT-AGTTATTTTATAACTTCAGATCCCTAAAGTATTCAACAAGATCCATTCCTTCGAGC
* * * *
1321 AATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTA
130 AATTTTCCGAACATTCCAAGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCA
1386 AACAAGTTTTGGTCTTTGAATT
195 AACAAGTTTTGGTCTTTGAATT
* * * * *
1408 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACAAAGTTCCGAACCTATCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAA
* ** * * * *
1473 CTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCCATTCATTTC-AGC
66 CTTTTACTAGTTATTTTATAACTTCAGATCCCTAAAGTATTCAACAAGATCCATTC-CTTCGAGC
** *
1537 AATTTTCCGAATTTTCCAAGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCGTTTTGCA
130 AATTTTCCGAACATTCCAAGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCA
1602 AACAAGTTTTGGTCTTTGAATT
195 AACAAGTTTTGGTCTTTGAATT
* *
1624 AAAAACTTATTTACGTGAGAATTGTTTCTCGCTTTGTTCTTGGATGAACTTTCGAACTTGTCAAA
1 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAA
1689 CTTTTACTAGTT
66 CTTTTACTAGTT
Statistics
Matches: 261, Mismatches: 30, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
216 257 0.98
217 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGTCAAA
CTTTTACTAGTTATTTTATAACTTCAGATCCCTAAAGTATTCAACAAGATCCATTCCTTCGAGCA
ATTTTCCGAACATTCCAAGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAA
ACAAGTTTTGGTCTTTGAATT
Done.