Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006464.1 Kokia drynarioides strain JFW-HI SEQ_121047, 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: 4288
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Found at i:384 original size:216 final size:216
Alignment explanation
Indices: 1--4288 Score: 4403
Period size: 216 Copynumber: 19.9 Consensus size: 216
** * * *
1 AACTTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGTTTACTTAAAGTATTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * * *
66 CGATCCAATCCTTCAAGCAATTTTTCTAACATTCCGTTCTCGAGAAGTCGCATCATTTGGTCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* *
131 A-AGGTTTGTCATTTTGTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACATGAGAATTG
131 ATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* *
195 TGTCTCTATTGGTTCTTGGACG
195 TTTCTCTCTTGGTTCTTGGACG
* ** * * *
217 AATTTCTGAAATTGTTGAACTTTTACGAGTTCTTTTATAACTTTGGTTACTTAAAGTATTCAACA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * *
282 CGATCAAATCCTTCGAGCAATTTTTCTAATATTCCGTGCTCGGGAAGTCGCATCATTTGGTCTAT
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA-
* *
347 AA-GGTTTGTCATTTTGTAAACAAGTTTTGGGCTTTGAA-TAAAAATCTTATTTACGTGAGAATT
130 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATTTACGTGAGAATT
* * * *
410 ATTTCTCTCTTGGTTGTTGAACA
194 GTTTCTCTCTTGGTTCTTGGACG
* * * * * *
433 AATTTCCGAACTTGCCAAACCTTTACGAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * **
498 TGATCCATTCCTTCGAGTAATTTTTTGAACA-TCCAATGCTCGAGATATCAG-ATCATTTCATCT
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCC-ATGCTCGGGAAATC-GCATCATTTGGTCT
* * *
561 AAATAGTTTTTCATTTTGTAAA-ATAGTTTTGGTCTTCG-------AA-TTGTTTACGTGAGAAT
129 AAATAGTTTGTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * *
617 GGTTTCTCTCTTCGTTCTTTGATG
193 TGTTTCTCTCTTGGTTCTTGGACG
* * * * * * * *
641 AACTTCAGAAATTGAT-AAACATTTATGAGTACTTCTATAACTTCGGTTCATTATAGTGTTCAAG
1 AACTTCTGAAATTG-TCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG
* * * * *
705 ACGATCCATTGCTTCTAGCAATTTTTCAAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTA
65 ACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
* ** *
770 AATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTTAGAATTG
130 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* * *
835 TTTCTCTTTTGGTTTTTGGATG
195 TTTCTCTCTTGGTTCTTGGACG
* * ** * * *
857 ATCTT-TCGAACTTGTCAAACTTTGCCAAGTTCTTTTATAACTTCGATTCCTTCAAGTATTCAAG
1 AACTTCT-GAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG
* * ** * * *
921 ACGATCCATTCCTTC-ATGTAATTTTTCGAACATTACACGCTTTGTAAATCGAATCATTGGGTCT
65 ACGATCCATTCCTTCGA-GTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * *
985 AAATAGTTTCTCATTTTGTAAACAAATTTTGTTCTTTCAATTAAAAACTTATTTACGTGAGAATT
129 AAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* *
1050 ATTTCTCTCTTGGTTGTTGGACG
194 GTTTCTCTCTTGGTTCTTGGACG
* * * * * *
1073 AACTTTTGAACTTGTCAAAATTTTAAGAGTTCTTTT-TAAACTTCAGTTCCTTAAAGTGTTCAAG
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTAT-AACTTCGGTTCCTTAAAGTATTCAAG
* * * * * ** *
1137 ATGATCCATTCCTTCGACTAATTTTTTGAACATTCAACGCTCTAGAAATCTCATCA-TTGGTCTA
65 ACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
* * * *
1201 AATAGTTTCTCATTTTGTAAA-ATAGATTTGGTCTTTAAATTAAAAACTTGTTTACGTGAGAATT
130 AATAGTTTGTCATTTTGTAAACA-AGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* *
1265 GTTTCTCTCTTAGTTCTTTGACG
194 GTTTCTCTCTTGGTTCTTGGACG
** * * * * * * * *
1288 AACTTCCAAAATTGACAAACATTTATGGGATCTTTTATAATTTCGGTTCATTAAAGTGTTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * *
1353 CGATCCATTCCTTCTAGCAGTTTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * * ** *
1418 ATAGTTTGTCATTTTGTAAATAAGTTTTGGTATTTGAATTAAAAACATATTTATTTGAGAATTAT
131 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
*
1483 TTCTCTCTTGGTTTTTGGACG
196 TTCTCTCTTGGTTCTTGGACG
* * * * * *
1504 AATTTC-CAAACTTGACAAACTTTGCTA--AGTTCTTTTATAACTTTGATTCCTTAAATTATTCA
1 AACTTCTGAAA-TTGTCAAACTTT--TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCA
* * * * * * * * *
1566 AGACAATTCATTCATTTGAGCAATTTTTCGAACATTCCACGCTCTGGAAATCACATCATTCGGTC
63 AGACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
* * *
1631 TAAATAGTTTCTCATTTTGTAAACAAGTTTTGGACTTTCAATTAAAAA-TTATTTACGTGAGAAT
128 TAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* * * * *
1695 TGTTCCACTATTGGTTCATGGATG
193 TGTTTCTCTCTTGGTTCTTGGACG
** * * * *
1719 AACTT-TCGATCTTGT-AGACATTTTACGAGTTCTTTTATAACTTCAGTTCCTTAGAGTTTTCAA
1 AACTTCT-GAAATTGTCAAAC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA
* ** * * *
1782 GATGATCCATT-CTTACGAGTTGTTTTTAGAACATTCCATGCTCGGGAAATTGCATCTTTTGGTC
64 GACGATCCATTCCTT-CGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
* * * * *
1846 TAAA-ATTTTTTTCATTTT-TAAACAAGTTTTGGCCTTTGAATTAAAAACTTGTTTACATGAGAA
128 TAAATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAA
* * *
1909 TTGTTTCTCTCTTGGCTCTTAGACA
192 TTGTTTCTCTCTTGGTTCTTGGACG
* * * * *
1934 AAATTCT-AAACTT-TACAAACTTTTACGAGTTCTTTTATATCTTTGGCTCCTTGAAGTATAT-A
1 AACTTCTGAAA-TTGT-CAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTAT-TCA
* * ** * *
1996 AGACGATCCATTCCTTC-ACGTAGTTTTTCGTACATTCCATGCTCGAAAAATCGCATCATTCGAT
63 AGACGATCCATTCCTTCGA-GTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGT
* * * * *
2060 CTAAATAGCTTT-TCATTTTGTAATCAAGTTTTGGTGTTTGTATT-AAAACTTATTTATGTGATA
127 CTAAATAG-TTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
* * *
2123 ATTATTTCTCTCTTTGTTATTGGAC-
191 ATTGTTTCTCTCTTGGTTCTTGGACG
* * * * * * *
2148 AAATTGTCGAAGTTGTTAAAATTTTACAAGTTCTTTTTTAACTTCGGTTCCTTAAAGTATTCAAG
1 AACTTCT-GAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG
* ** * * *
2213 ACGGTCCATTCCTTTTAGTAGTGTTTCGAACATTCCATGCTCGGGAAATCGCATCATTCGGTCTA
65 ACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
** **
2278 AATTTTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTGAGAATTG
130 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* *
2343 TTTCTCTCTTGGTTTTTGGATG
195 TTTCTCTCTTGGTTCTTGGACG
* * * * * *
2365 AACTT-TCGAACTTGTCAAAC-TTTGCCATGTTCTTTTATAACTACGATTCCTTAAAGTGTTCAA
1 AACTTCT-GAAATTGTCAAACTTTTACGA-GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA
* * * * * ** *
2428 TACGATCCATTCCTTCGAGAAATTTTTCGAACATTCCACGCTCTGAAAATCGCATCATTCAGTTT
64 GACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * * *
2493 AAATAGTTTCTCATTTTGTAAACAAGTTTTGATCTTTCAATTAAATACTTATTTACGTGAAAATT
129 AAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
2558 GTTTCTCTCTTGGTTCTTGGACG
194 GTTTCTCTCTTGGTTCTTGGACG
* * * * *
2581 AGCTTCTGAAATTGACAAACTTTTAGGAGTTCTTTTATAACTTCGGTTCATTAAAGTACTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
** * * * * **
2646 CGATCCATTCCTTTTAGTAGTTTTTTGAACATTCTATTCTCGGGAAATCGCATCATTTCATCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * ** *
2711 ATAGTTTTTCGTTTTGTAAACAAGTTTTGAACTTTGAATTAAAAACTTATTTATGTGAGAATTG-
131 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
2775 -TCTCTCTTGGTTCTTGGACG
196 TTCTCTCTTGGTTCTTGGACG
* * *
2795 AACTTCTGAAATTGTCGAACTTTTACGAATTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * * *
2860 CAATCCAATCCTTCAAGCAATTTTTCAAACATTCCATGCTCGGGAAGTCTCATCATTTTGTCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * * *
2925 AAAGTTTGTCATTTTGTAAACAAATTTTGGCCTTTGAATTAAAAACTTATTTTCGTGAGAATTGT
131 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * *
2990 TTCTCTCTTGGTTGTTAGACA
196 TTCTCTCTTGGTTCTTGGACG
* * * * ** *
3011 AACTTCCGAACTTATCAAACTTTTACGAGTTCTTTTTTAACTTTTGTTCCTTAAAGTGTTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * ** *
3076 CGATCCATT-CTTGCGAGTAATTTTCCAAACATTCAACGCTCATGAAATCGCACCATTTGGTCTA
66 CGATCCATTCCTT-CGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTA
* * *
3140 AATAGTTTTTCATTTTGTAAA-ATAGTTTTGGTCTTTGACTTAAAAAACTTGTTTACGTGAGAAT
130 AATAGTTTGTCATTTTGTAAACA-AGTTTTGGTCTTTGAATT-AAAAACTTATTTACGTGAGAAT
* *
3204 TGTTTCTCTCTTGGTTCTTTGACA
193 TGTTTCTCTCTTGGTTCTTGGACG
* * * * *
3228 AACTTCCGAAATTGACAAACTTTTATGAGTTCTTTTATAACTTCGGTTCATTAAAGTGTTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * * * * *
3293 CAATCCATTCCTTCTAGCAGTTTTTCAAATATTCAATTCTCAGGAAATCACATCATTTGGTCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * * * * **
3358 ATAGTTTGTCATTTTGTACACAAGTTTTAGTCTCTGAATTAGAAACTTTTTTATTTGAGAATTGT
131 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
*
3423 TTCTCTCTTGGTT-TATGGATG
196 TTCTCTCTTGGTTCT-TGGACG
* * * ** * * * * * * *
3444 AACTTC-CAAACTTGACAAAATTTGCCAAATTCTTTTTTATA-TTCTGTTACTTAAAGTGTTAAA
1 AACTTCTGAAA-TTGTCAAACTTTTACGAGTTCTTTTATA-ACTTCGGTTCCTTAAAGTATTCAA
* * * * * * * *
3507 GATGATCCATTCCTTCGATTAAATTTTCGAACATTCAACGCTTGAGAAATTGCATCATTTGGTCT
64 GACGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT
* * * * * *
3572 AAATAGTTCT-TCATTTTGTAAATAAGTTTTGGTCATTCAATTAAAAGCTTGTTTATGTGAGAAT
129 AAATAGTT-TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
* *
3636 TTTTTCTCTCTTGGTTCTTGGATG
193 TGTTTCTCTCTTGGTTCTTGGACG
* * * * *
3660 AACTTTTGAAATTGACAAACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAATATTCAACA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * *
3725 AGATCCATTCCTTCTAGTAGTTTTTCGAACATTCCATTG-TCGAGATATCGCATCATTTGGTCTA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCA-TGCTCGGGAAATCGCATCATTTGGTCTA
* * * * * * * *
3789 AATATTTTTTCATTTTGAAAATAAGTTTTGATCTTGGAATTAAAAACCTT-TTTCCGTGAGAGTT
130 AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATTTACGTGAGAATT
3853 GTTTCTCTCTTGGTTCTTGGACG
194 GTTTCTCTCTTGGTTCTTGGACG
* * * * * *
3876 AACTTCTGAAATTGACAAACTTTTACGGGTTATTTTATATCTTCGGTTCATTAAAGTATTCAGGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * *
3941 CGATCCATTCCTTCTAGTAGTTTTTCGAACATTTCATTCTCGGGAAATCACATCATTTGGCCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
* * *
4006 ATTGTTTTTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTG-
131 ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
4070 -TCTCTCTTGGTTCTTGGACG
196 TTCTCTCTTGGTTCTTGGACG
*
4090 AACTTCTGAAATTGTCGAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
1 AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * *
4155 CAATCCAATCCTTCAAGCAATTTTTCAAACATTCCATGCTCGGGAAGTCGCATCATTTTGTCTAA
66 CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
** * *
4220 A-AGGTTTGTCATTTTGTAAACAAAATTTGGCCTTTGAATTAAAAACTTATTTTCGTGAGAATTG
131 ATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
4284 TTTCT
195 TTTCT
Statistics
Matches: 3374, Mismatches: 616, Indels: 164
0.81 0.15 0.04
Matches are distributed among these distances:
207 1 0.00
208 164 0.05
209 4 0.00
210 2 0.00
213 2 0.00
214 418 0.12
215 639 0.19
216 1931 0.57
217 207 0.06
218 6 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (216 bp):
AACTTCTGAAATTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAA
ATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
TTCTCTCTTGGTTCTTGGACG
Found at i:2080 original size:646 final size:646
Alignment explanation
Indices: 18--4288 Score: 4665
Period size: 646 Copynumber: 6.6 Consensus size: 646
8 GAAATTGTTG
* * * *
18 AACTTTTACGAGTTCTTTTATAACTT-TGTTTACTTAAAGTATTCAAGACGATCCAATCCTTCAA
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCA-TTAAAGTATTCAAGACGATCCATTCCTTCTA
* * * * * *
82 GCAATTTTTCTAACATTCCGTTCTCGAGAAGTCGCATCATTTGGTCTAAA-AGGTTTGTCATTTT
65 GCAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATA-GTTTTTCATTTT
* ** * *
146 GTAAACAAGTTTTGGCCTTTGAATTAAAAACTTATTTACATGAGAATTGTGTCTCTATTGGTTCT
129 GTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* ** * * *
211 TGGACGAATTTCTGAAATTGTTGAACTTT--TACGAGTTCTTTTATAACTTTGGTTACTTAAAGT
194 TGGACGAATTTC-CAAATTGTCAAACTTTGCTA--AGTTCTTTTATAACTTCGATTCCTTAAAGT
* * * * * * *
274 ATTCAACACGATCAAATCCTTCGAGCAATTTTTCTAATATTCCGTGCTCGGGAAGTCGCATCATT
256 ATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATT
* *
339 TGGTCTATAA-GGTTTGTCATTTTGTAAACAAGTTTTGGGCTTTGAA-TAAAAATCTTATTTACG
321 TGGTCTA-AATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAA-CTTATTTACG
* * ** * * *
402 TGAGAATTATTTCTCTCTTGGTTGTT-GAACAAATTTCCGAACTTGCCAA-ACCTTTACGAGTTC
384 TGAGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTT-CGAACTTGTCAACA-TTTTACGAGTTC
* * * *
465 TTTTTTAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGTAATTTTTTGAACA-
447 TTTTATAACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTAATTTTTAGAACAT
* * **
529 TCCAATGCTCGAGATATCAG-ATCATTTCATCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGG
512 TCC-ACGCTCGAGAAATC-GCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGG
* * * * *
593 TCTTCG-------AA-TTGTTTACGTGAGAATGGTTTCTCTCTTCGTTCTTTGATGAACTTCAGA
575 TCTTTGAATTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTC-TA
*
650 AATTGATA
639 AATTGACA
* * * * * * *
658 AACATTTATGAGTACTTCTATAACTTCGGTTCATTATAGTGTTCAAGACGATCCATTGCTTCTAG
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
* *
723 CAATTTTTCAAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
66 CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
* * * *
788 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTTAGAATTGTTTCTCTTTTGGTTTTTG
131 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * * * *
853 GATGATCTTTCGAACTTGTCAAACTTTGCCAAGTTCTTTTATAACTTCGATTCCTTCAAGTATTC
196 GACGA-ATTTCCAAATTGTCAAACTTTGCTAAGTTCTTTTATAACTTCGATTCCTTAAAGTATTC
* * * ** * * *
918 AAGACGATCCATTCCTTC-ATGTAATTTTTCGAACATTACACGCTTTGTAAATCGAATCATTGGG
260 AAGACGATCCATTCCTTCGA-GCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGG
* * * *
982 TCTAAATAGTTTCTCATTTTGTAAACAAATTTTGTTCTTTCAATTAAAAACTTATTTACGTGAGA
324 TCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
* * * * * *
1047 ATTATTTCTCTCTTGGTTGTTGGACGAACTTTTGAACTTGTCAAAATTTTAAGAGTTCTTTT-TA
389 ATTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAACATTTTACGAGTTCTTTTAT-
* * *
1111 AACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGACTAATTTTTTGAACATTCAACG
453 AACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTAATTTTTAGAACATTCCACG
* * * * *
1176 CTCTAGAAATCTCATCA-TTGGTCTAAATAGTTTCTCATTTTGTAAAATAGATTTGGTCTTTAAA
518 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGGTCTTTGAA
* *
1240 TTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTAGTTCTTTGACGAACTTCCAAAATTGACA
583 TTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTT-CTAAATTGACA
* * * * * *
1305 AACATTTATGGGATCTTTTATAATTTCGGTTCATTAAAGTGTTCAAGACGATCCATTCCTTCTAG
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
* *
1370 CAGTTTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
66 CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
* * * * * *
1435 AAATAAGTTTTGGTATTTGAATTAAAAACATATTTATTTGAGAATTATTTCTCTCTTGGTTTTTG
131 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * *
1500 GACGAATTTCCAAACTTGACAAACTTTGCTAAGTTCTTTTATAACTTTGATTCCTTAAATTATTC
196 GACGAATTTCCAAA-TTGTCAAACTTTGCTAAGTTCTTTTATAACTTCGATTCCTTAAAGTATTC
* * * * * * * *
1565 AAGACAATTCATTCATTTGAGCAATTTTTCGAACATTCCACGCTCTGGAAATCACATCATTCGGT
260 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGT
* * *
1630 CTAAATAGTTTCTCATTTTGTAAACAAGTTTTGGACTTTCAATTAAAAA-TTATTTACGTGAGAA
325 CTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAA
* * * * *
1694 TTGTTCCACTATTGGTTCATGGATGAACTTTCGATCTTGT-AGACATTTTACGAGTTCTTTTATA
390 TTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCA-ACATTTTACGAGTTCTTTTATA
* * ** *
1758 ACTTCAGTTCCTTAGAGTTTTCAAGATGATCCATT-CTTACGAGTTGTTTTTAGAACATTCCATG
454 ACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTT-CGAGTAATTTTTAGAACATTCCACG
* * * * *
1822 CTCGGGAAATTGCATCTTTTGGTCTAAA-ATTTTTTTCATTTT-TAAACA-AGTTTTGGCCTTTG
518 CTCGAGAAATCGCATCATTTGGTCTAAATA-GTTTTTCATTTTGTAAA-ATAGTTTTGGTCTTTG
* * * * * *
1884 AATTAAAAACTTGTTTACATGAGAATTGTTTCTCTCTTGGCTCTTAGACAAAATTCTAAACTTTA
581 AATTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTCTAAA-TTGA
1949 CA
645 CA
* * * * *
1951 AACTTTTACGAGTTCTTTTATATCTTTGGCTCCTTGAAGTATAT-AAGACGATCCATTCCTTC-A
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTAT-TCAAGACGATCCATTCCTTCTA
* * * ** * * *
2014 CGTAGTTTTTCGTACATTCCATGCTCGAAAAATCGCATCATTCGATCTAAATAGCTTTTCATTTT
65 -GCAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTT
* * * * * * *
2079 GTAATCAAGTTTTGGTGTTTGTATT-AAAACTTATTTATGTGATAATTATTTCTCTCTTTGTTAT
129 GTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* * * * * * * *
2143 TGGACAAATTGTCGAAGTTGTTAAAATTTTAC-AAGTTCTTTTTTAACTTCGGTTCCTTAAAGTA
194 TGGACGAATT-TCCAAATTG-TCAAACTTTGCTAAGTTCTTTTATAACTTCGATTCCTTAAAGTA
* ** * * * *
2207 TTCAAGACGGTCCATTCCTTTTAGTAGTGTTTCGAACATTCCATGCTCGGGAAATCGCATCATTC
257 TTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTT
** **
2272 GGTCTAAATTTTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATTTGA
322 GGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
* * * *
2337 GAATTGTTTCTCTCTTGGTTTTTGGATGAACTTTCGAACTTGTCAA-ACTTTGCCATGTTCTTTT
387 GAATTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAACATTTTACGA-GTTCTTTT
* * * * *
2401 ATAACTAC-GATTCCTTAAAGTGTTCAATACGATCCATTCCTTCGAGAAATTTTTCGAACATTCC
451 ATAACTTCAG-TTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTAATTTTTAGAACATTCC
** * * *
2465 ACGCTCTGA-AAATCGCATCATTCAGTTTAAATAGTTTCTCATTTTGTAAACA-AGTTTTGATCT
515 ACGCTC-GAGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAA-ATAGTTTTGGTCT
* * * * * *
2528 TTCAATTAAATACTTATTTACGTGAAAATTGTTTCTCTCTTGGTTCTTGGACGAGCTTCTGAAAT
578 TTGAATTAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTCT-AAAT
2593 TGACA
642 TGACA
* * *
2598 AACTTTTAGGAGTTCTTTTATAACTTCGGTTCATTAAAGTACTCAAGACGATCCATTCCTTTTAG
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
* * * ** *
2663 TAGTTTTTTGAACATTCTATTCTCGGGAAATCGCATCATTTCATCTAAATAGTTTTTCGTTTTGT
66 CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
**
2728 AAACAAGTTTTGAACTTTGAATTAAAAACTTATTTATGTGAGAATTG--TCTCTCTTGGTTCTTG
131 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * * *
2791 GACGAACTTCTGAAATTGTCGAACTTTTACGAA-TTCTTTTATAACTTCGATTCCTTAAAGTATT
196 GACGAATTTC-CAAATTGTCAAAC-TTTGCTAAGTTCTTTTATAACTTCGATTCCTTAAAGTATT
* * * * * * *
2855 CAAGACAATCCAATCCTTCAAGCAATTTTTCAAACATTCCATGCTCGGGAAGTCTCATCATTTTG
259 CAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGG
* * * *
2920 TCTAAAAAGTTTGTCATTTTGTAAACAAATTTTGGCCTTTGAATTAAAAACTTATTTTCGTGAGA
324 TCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
* * ** * * *
2985 ATTGTTTCTCTCTTGGTTGTTAGACAAACTTCCGAACTTATCAA-ACTTTTACGAGTTCTTTTTT
389 ATTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAACA-TTTTACGAGTTCTTTTAT
** * * *
3049 AACTTTTGTTCCTTAAAGTGTTCAAGACGATCCATT-CTTGCGAGTAATTTTCCA-AACATTCAA
453 AACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTT-CGAGTAATTTT-TAGAACATTCCA
*
3112 CGCTC-ATGAAATCGCACCATTTGGTCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGGTCTTT
516 CGCTCGA-GAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGGTCTTT
* * *
3176 GACTTAAAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACAAACTTCCGAAATT
580 GAATT-AAAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTT-CTAAATT
3241 GACA
643 GACA
* * *
3245 AACTTTTATGAGTTCTTTTATAACTTCGGTTCATTAAAGTGTTCAAGACAATCCATTCCTTCTAG
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
* * * * * *
3310 CAGTTTTTCAAATATTCAATTCTCAGGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGT
66 CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
* * * * * *
3375 ACACAAGTTTTAGTCTCTGAATTAGAAACTTTTTTATTTGAGAATTGTTTCTCTCTTGGTT-TAT
131 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT-T
* * * * * * * * *
3439 GGATGAACTTCCAAACTTGACAAAATTTGCCAAATTCTTTTTTATA-TTCTG-TTACTTAAAGTG
195 GGACGAATTTCCAAA-TTGTCAAACTTTGCTAAGTTCTTTTATA-ACTTC-GATTCCTTAAAGTA
* * ** * * * * * *
3502 TTAAAGATGATCCATTCCTTCGATTAAATTTTCGAACATTCAACGCTTGAGAAATTGCATCATTT
257 TTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTT
* * * * * *
3567 GGTCTAAATAGTTCT-TCATTTTGTAAATAAGTTTTGGTCATTCAATTAAAAGCTTGTTTATGTG
322 GGTCTAAATAGTT-TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTG
* * * *
3631 AGAATTTTTTCTCTCTTGGTTCTTGGATGAACTTTTGAAATTGACAA-ACTTTTACGAGTTCTTT
386 AGAATTGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAACA-TTTTACGAGTTCTTT
* * * * * * * * *
3695 TATAACTTCGGTTCATTAAAATATTCAACAAGATCCATTCCTTCTAGTAGTTTTTCGAACATTCC
450 TATAACTTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTAATTTTTAGAACATTCC
* * * *
3760 ATTG-TCGAGATATCGCATCATTTGGTCTAAATATTTTTTCATTTTG-AAAATAAGTTTTGATCT
515 A-CGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAAT-AGTTTTGGTCT
* * * *
3823 TGGAATTAAAAACCTT-TTTCCGTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAAA
578 TTGAATTAAAAA-CTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTCT-AAA
3887 TTGACA
641 TTGACA
* * * *
3893 AACTTTTACGGGTTATTTTATATCTTCGGTTCATTAAAGTATTCAGGACGATCCATTCCTTCTAG
1 AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
* * * * *
3958 TAGTTTTTCGAACATTTCATTCTCGGGAAATCACATCATTTGGCCTAAATTGTTTTTCATTTTGT
66 CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
* *
4023 AAACAAGTTTTGATCTTTGAATTAAAAACTTATTTACGTGAGAATTG--TCTCTCTTGGTTCTTG
131 AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * *
4086 GACGAACTTCTGAAATTGTCGAACTTT--TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTAT
196 GACGAATTTC-CAAATTGTCAAACTTTGCTA--AGTTCTTTTATAACTTCGATTCCTTAAAGTAT
* * * * * *
4149 TCAAGACAATCCAATCCTTCAAGCAATTTTTCAAACATTCCATGCTCGGGAAGTCGCATCATTTT
258 TCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTG
** * *
4214 GTCTAAA-AGGTTTGTCATTTTGTAAACAAAATTTGGCCTTTGAATTAAAAACTTATTTTCGTGA
323 GTCTAAATA-GTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
4278 GAATTGTTTCT
387 GAATTGTTTCT
Statistics
Matches: 3048, Mismatches: 501, Indels: 158
0.82 0.14 0.04
Matches are distributed among these distances:
639 43 0.01
640 423 0.14
641 25 0.01
642 1 0.00
644 2 0.00
645 204 0.07
646 966 0.32
647 820 0.27
648 248 0.08
649 308 0.10
650 8 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (646 bp):
AACTTTTACGAGTTCTTTTATAACTTCGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCTAG
CAGTTTTTCGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGT
AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
GACGAATTTCCAAATTGTCAAACTTTGCTAAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCA
AGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
TAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
TGTTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTTGTCAACATTTTACGAGTTCTTTTATAAC
TTCAGTTCCTTAAAGTGTTCAAGATGATCCATTCCTTCGAGTAATTTTTAGAACATTCCACGCTC
GAGAAATCGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAAATAGTTTTGGTCTTTGAATTA
AAAACTTGTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGACGAACTTCTAAATTGACA
Found at i:3153 original size:21 final size:20
Alignment explanation
Indices: 3129--3168 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3119 GAAATCGCAC
*
3129 CATTTGGTCTAAATAGTTTTT
1 CATTTGGT-AAAATAGTTTTT
*
3150 CATTTTGTAAAATAGTTTT
1 CATTTGGTAAAATAGTTTT
3169 GGTCTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (20 bp):
CATTTGGTAAAATAGTTTTT
Done.