Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012440.1 Kokia drynarioides strain JFW-HI SEQ_127444, 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: 2462
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.37
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:791 original size:215 final size:215
Alignment explanation
Indices: 1--801 Score: 808
Period size: 216 Copynumber: 3.7 Consensus size: 215
* * * * * *
1 GGTCATTGAATTAAAAACTTATTTACGTGAGAATTTATTATCTCTTGGATCATGGACAAACTTTC
1 GGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTTTTTCTCTCTTGGTTCATAGACAAACTTTC
* * ** *
66 GAAC-TGTACAAACTTTTACCAGTTGTTCTATAACTTTGGTT-TATTAAAGTATTCATGACGATC
66 GAACTTG-ACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCA-TAAAGTATTCATGACGATC
* * * * *
129 CTTTCCTTCGAGTAATTTTACGAACATTCCAAGCACGGGGAACCGCATCATTCTGCCTAAATAGT
129 CATTCCTTCGAGCAATTTTACGAACATTCCATGCACGGGAAATCGCATCATT-TGCCTAAATAGT
*
194 TTTTCATTTTCTAAACAACTTTT
193 TTGTCATTTTCTAAACAACTTTT
* * * * * * * * ** *
217 GGTCTATAAATTAAAAAGTTATTTAAGTGAGTGTTGTTTCTCTCATT-GTTCTTGGATGAACTTC
1 GGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTTTTTCTCTC-TTGGTTCATAGACAAACTTT
* * * * * *
281 CGAACTTGACGAAGTTTTACGAGTTCTTCTAAAACTTCAGTTCCTTGAAGTATTCATGATGATCC
65 CGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCC
* * * * *
346 GTTCCTTCTAGCAATTTTCCGAACATTCCATGCACGGGAAATCGCATCATTTTGTCTAAATTGTT
130 ATTCCTTCGAGCAATTTTACGAACATTCCATGCACGGGAAATCGCATCA-TTTGCCTAAATAGTT
*
411 TGTCATTTTGTAAACAACTTTT
194 TGTCATTTTCTAAACAACTTTT
** * *** * * * **
433 TATCTTTGAATTAAAAACCTATTTATACGAGAGTTGTCTT-TCTCTTGCTTCTTAGATGAAC-TT
1 GGTCTTTGAATTAAAAACTTATTTACGTGAGAGTT-TTTTCTCTCTTGGTTCATAGACAAACTTT
* * ** * * *
496 CCAAGCTTGACAAACTTTTACGAGTTCTTCAATAACTTTGGTTTC-TCAAAGTATTCAGGACAAT
65 CGAA-CTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCAT-AAAGTATTCATGACGAT
* * **
560 CCATTCCTTAGAGCAATTTGT-TGAACATTCCATGCTTGGGAAATCGCATCATTTGGCCTAAATA
128 CCATTCCTTCGAGCAATTT-TACGAACATTCCATGCACGGGAAATCGCATCATTT-GCCTAAATA
* *
624 CTTTGTCATTTTCTAAACTACTTTT
191 GTTTGTCATTTTCTAAACAACTTTT
* * *
649 GGTCTTTGAA-TGAAAACTTATTCACGTGAGAGTTTTTTCTATCTTGGTTCATAGACAAACTTTC
1 GGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTTTTTCTCTCTTGGTTCATAGACAAACTTTC
* * * *
713 GAACATGGCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCATAAAGTATTCATGACCATCCA
66 GAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCA
*
778 TTCCTTCGAGCAATTTTCCGAACA
131 TTCCTTCGAGCAATTTTACGAACA
802 NNNNNNNNNN
Statistics
Matches: 470, Mismatches: 101, Indels: 29
0.78 0.17 0.05
Matches are distributed among these distances:
214 4 0.01
215 115 0.24
216 342 0.73
217 9 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (215 bp):
GGTCTTTGAATTAAAAACTTATTTACGTGAGAGTTTTTTCTCTCTTGGTTCATAGACAAACTTTC
GAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCA
TTCCTTCGAGCAATTTTACGAACATTCCATGCACGGGAAATCGCATCATTTGCCTAAATAGTTTG
TCATTTTCTAAACAACTTTT
Found at i:1287 original size:214 final size:214
Alignment explanation
Indices: 852--1513 Score: 662
Period size: 216 Copynumber: 3.1 Consensus size: 214
842 NNNNNNNNNN
** * * * * * *
852 AGTTGTTTCTCCCATTG-TTCTTGGACGAACTTCCGAATTTGACGAAGTTTTACGAGTTCTTCTA
1 AGTTGTTTCTATC-TTGCTTCTTAGACGAACTTCCCAACTTGACAAAATTTTACGAGTTCTTTTA
* * * *
916 A-AACTTTAGTTCCTTAAAGTATTCATGACGATCCGTTCCTTCA-AGTAATTTTCCGAACATTTC
65 ATAACTTTAGTTCC-TAAAGTATTCATGACAATCCATTCCTT-AGAGCAATTTT-TGAACATTTC
* ** * **
979 ATGCACT-GGAAATCGCATCATTTTGTCTAAATTGTTTGTCATTTTCTAAACAACTTTTTATCTT
127 ATGC-TTGGGAAATCGCATCA-TTTGTCTAAATACTTTGTCAATTTCTAAACAACTTTTGGTCTT
* * * *
1043 TGAATTAAAAACCTATTTATGCGAG
190 TGAATGAAAAACTTATTTACGTGAG
* *
1068 AGTTGTCTT-TCTCTTGCTTCTTAGATGAAC-TCCCAAGCTTGACAAAATTTTACGAGTT-TTTT
1 AGTTGT-TTCTATCTTGCTTCTTAGACGAACTTCCCAA-CTTGACAAAATTTTACGAGTTCTTTT
* * * *
1130 AATAACTTTGGTTTCTCAAAGTATTCAGGACAATCCATTCCTTAGAGCAATTTGTTGAACATTCC
64 AATAACTTTAGTTCCT-AAAGTATTCATGACAATCCATTCCTTAGAGCAATTT-TTGAACATTTC
* * * *
1195 ATGCTTGGGAAATCTCATC-TTGGTCTAAATACTCTGTCAATTTCTAAACTACTTTTGGTCTTTG
127 ATGCTTGGGAAATCGCATCATTTGTCTAAATACTTTGTCAATTTCTAAACAACTTTTGGTCTTTG
*
1259 AATGAAAAACTTATTCACGTGAG
192 AATGAAAAACTTATTTACGTGAG
* * * * *
1282 AGTTGTTTCTATCTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTTACGAGTTCTTTT-A
1 AGTTGTTTCTATCTTGCTTCTTAGACGAACTTCCCAACTTGACAAAATTTTACGAGTTCTTTTAA
* * * * *
1346 TAACTTCAGTTCCATAAAGTATTCATGACCATCCATTCCTTCGACCAATTTTTCGAACATTTCGT
66 TAACTTTAGTTCC-TAAAGTATTCATGACAATCCATTCCTTAGAGCAATTTTT-GAACATTTCAT
* * *
1411 GCTTGGGAAATCGCATCATTTTTTCTAAA-CCATTTGTC-ATTTGGTAAACAACTTTTGGTCTTT
129 GCTTGGGAAATCGCATCA-TTTGTCTAAATAC-TTTGTCAATTT-CTAAACAACTTTTGGTCTTT
*
1474 GAATGAAAAACTTATTTACATGAG
191 GAATGAAAAACTTATTTACGTGAG
* * *
1498 AATTGTTCCTCTCTTG
1 AGTTGTTTCTATCTTG
1514 GATATTGGAT
Statistics
Matches: 370, Mismatches: 59, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
213 4 0.01
214 166 0.45
215 30 0.08
216 167 0.45
217 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (214 bp):
AGTTGTTTCTATCTTGCTTCTTAGACGAACTTCCCAACTTGACAAAATTTTACGAGTTCTTTTAA
TAACTTTAGTTCCTAAAGTATTCATGACAATCCATTCCTTAGAGCAATTTTTGAACATTTCATGC
TTGGGAAATCGCATCATTTGTCTAAATACTTTGTCAATTTCTAAACAACTTTTGGTCTTTGAATG
AAAAACTTATTTACGTGAG
Found at i:1861 original size:215 final size:212
Alignment explanation
Indices: 1651--2368 Score: 705
Period size: 215 Copynumber: 3.3 Consensus size: 212
1641 ATCATTTTCT
** * *
1651 CTAAATAGTTTGTCATTTGGTATACAACTTTTGGTCATTGAATT-AAAACTTATTTACGTGAGAA
1 CTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTC-TTGAATTAAAAACTTATTTACGTGAGAG
* * * *
1715 TT-TATTATCTCTTGGATCATGGACAAACTTTCGAAATTTACAAACTTTTACCAATTGTTCTATA
65 TTGT-TT-TCTCTTGGATCTTGGACAAACTTTCGAACTTGACAAACTTTTACCAATTCTTCTATA
* *
1779 ACTTTGGTTCATTAAAGTATTCATGACGATCCTTTCCTTCGAACAATTTTTCGAACATTCCAAGC
128 ACTTTGGTTC-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGC
*
1844 ACAGGGAACCGCATCATTCTGC
192 AC-GGGAACCGCATCATTATGC
* * *
1866 CTAAATAGTTTTTCATTTTCTAAACAACTTTTGGTCTATAAATTAAAAAGTTATTTACGTGAGAG
1 CTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCT-TGAATTAAAAACTTATTTACGTGAGAG
* * * * * *
1931 TTGTTTCTCTCATT-GTTCTTGGACGAACTTCCGAACTTGACGAAGTTTTA-CAAGTTCTTCTAA
65 TTGTTT-TCTC-TTGGATCTTGGACAAACTTTCGAACTTGACAAACTTTTACCAA-TTCTTCTAT
** * * * * *
1994 AACTTCAGTTCGTTAAAGTATTCATGATGATCCATTCCTACGAGCAATTTTCCAAACAATCCAAG
127 AACTTTGGTTC-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAG
* * *
2059 CACGGGAATCGTATGATTATGC
191 CACGGGAACCGCATCATTATGC
* ** *
2081 CTAAATTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAACCTATTTACGCT-AGA
1 CTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTC-TTGAATTAAAAACTTATTTACG-TGAGA
* * * * * *
2145 GTTGTCTTTCTCTTGCATCTTAGATAAACTTTC-AAGCTTGACAAACTTTTACGAGTTCTTCAAT
64 GTTGT-TTTCTCTTGGATCTTGGACAAACTTTCGAA-CTTGACAAACTTTTACCAATTCTTCTAT
* * * *
2209 AACTTTGGTTTCTTAAAGTATTCAGGACAATCCATTCCTTAGAGCAATTTGTT-GAACATTCCAT
127 AACTTTGG-TTCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TTCGAACATTCCAA
** ** *
2273 GCTTGGGAAATTGCATCATT-TAGT
190 GCACGGG-AACCGCATCATTAT-GC
* ** * * * *
2297 CTAAATACTTTGTCATTTTCTAAATTACTTTTAGTCTTTGAATGAAAAACTTATTCACATGAGAG
1 CTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTC-TTGAATTAAAAACTTATTTACGTGAGAG
2362 TTGTTTT
65 TTGTTTT
2369 TATTTGAATA
Statistics
Matches: 409, Mismatches: 78, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
214 5 0.01
215 206 0.50
216 195 0.48
217 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (212 bp):
CTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTGAATTAAAAACTTATTTACGTGAGAGT
TGTTTTCTCTTGGATCTTGGACAAACTTTCGAACTTGACAAACTTTTACCAATTCTTCTATAACT
TTGGTTCTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCACGG
GAACCGCATCATTATGC
Found at i:2383 original size:38 final size:38
Alignment explanation
Indices: 2333--2409 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2323 ACTTTTAGTC
*
2333 TTTGAATGAAAAACTTATTCACATGAGAGTTGTTTTTA
1 TTTGAATAAAAAACTTATTCACATGAGAGTTGTTTTTA
*
2371 TTTGAATAAAAAACTTATTCACGTGAGAGTTGTTTTTA
1 TTTGAATAAAAAACTTATTCACATGAGAGTTGTTTTTA
2409 T
1 T
2410 CTTGGTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (38 bp):
TTTGAATAAAAAACTTATTCACATGAGAGTTGTTTTTA
Done.