Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002457.1 Kokia drynarioides strain JFW-HI SEQ_114577, 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: 2964
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Found at i:793 original size:216 final size:215
Alignment explanation
Indices: 1--2964 Score: 3217
Period size: 216 Copynumber: 13.8 Consensus size: 215
* * *
1 ACTTGGCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTACAGTATTCAACAAGATCCAAT
1 ACTT-GCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * * *
66 CCTTAAAGC-AATTTTCCAAGCATTCCATGCTCGAGAAATCGCATCATTTAGTCTAACTAGTTTG
65 CCTTAGAGCAAATTTTCGAA-CATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* * * * * *
130 TCACTTTG-TAAACAAGTTTTAGTCATTGAATTAAATACTTATTTACGAGAGAATTGTCTCTCTC
129 TCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * * * *
194 TTGGTTCATGGACGATCTATCCA
193 TTTGTTCTTGGACGAACTTTCGA
** ** * * * * *** * * * *
217 ACTTGTTTAACTTCGAGGAGATCTTTTATAACTTAACTTCCTTGAAGTATTCAAGATGATCCATT
1 ACTTG-CAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * ** * *
282 CCTTCGAGCAATTTTTCGAACATTCCAAGCTCGACAAATCGTATCATTTGGTCTAAATAGTTTGT
65 CCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTAT
* * *
347 CTTTTTGCAAACAAGTTTTGGTCTTT-AATTTAAAAACTTATTTACGTGAGAATTCTTTCTCTCT
130 CATTTTGCTAACAAGTTTTGGTCTTTGAA-TTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
*
411 TTGTTCTTGGATGAACTTTCGA
194 TTGTTCTTGGACGAACTTTCGA
* * * *
433 A-TTGCAAAACTTTTACGAGTTGTTTGTTAACTTCGGTTCCCA-AAAGTTTTCAACTAGATCCAT
1 ACTTGC-AAACTTTTACGAGTTATTTTTTAACTTCGGTT-CCATAAAGTATTCAACAAGATCCAT
* * * * *
496 TCCTTAGAGC-TATTTCCCGAACACTCCATGCTCAGGAAATCGCATTATTTGGTCTAAATAGTTT
64 TCCTTAGAGCAAATTT-TCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTT
* * * * *
560 GTCATTTTG-TAAACAAGTTTTGTTCTCTGAATTAAATACTTATTTACGTGAGAAATGTTTCTCT
128 ATCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
*
624 CTTTGTTCTTGGACGAACTTCCGA
192 CTTTGTTCTTGGACGAACTTTCGA
* * * * * * * * *
648 ACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATACATAAAGTATTCAAGACGATCAATT
1 ACTTG-CAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * * *
713 CTTTCGAACAAATTTTCGAACATTCCATGCTTGTGAAATCACATCATTTGGTCTAAATAGTTTAT
65 CCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTAT
*
778 CATTTTGCTAACAAGTTTTGGTCTTTGAATT-AAAACTTATTTACGTTAGAATTGTTTCTCTCTT
130 CATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT
* *
842 TGTTTTTGGACGAACTTCCGA
195 TGTTCTTGGACGAACTTTCGA
* * * * * * *
863 ACTTAGTAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTACAGTATTAAACAAGGTCCAAT
1 ACTT-GCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * *
928 CCTTAAAGC-AATTTTCCTAACATTCCATGCGT-GGCATATCGCATCATTTGGTCTAAATAGTTT
65 CCTTAGAGCAAATTTT-CGAACATTCCATGC-TCGGGAAATCGCATCATTTGGTCTAAATAGTTT
* * * *
991 ATCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCATGTGAGAATTGTTTCTCTC
128 ATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* *
1056 TTTGTTCTTGGACAAACTTCCGA
193 TTTGTTCTTGGACGAACTTTCGA
* * * * * * *
1079 ACTTGGCAAAATTTTACGAGTTATTTTTTAACTTCCGTTCCCTACAGTATTGAACAAGATCTAAT
1 ACTT-GCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * * * * * *
1144 CCTTAAAGCAACTTTCCGAGCATTCCATGCTCAGGAAATCGTATCATTTAGTCTAACTAGTTCGA
65 CCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT-TA
* ** * * *
1209 -CATTTTG-TAAACAAGTTTTAGTCAATGAATTAAATACTTATTTACGAGAGAATTGTCTCTCTC
129 TCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
* * * * *
1272 TTGGTTCATGGATGATCTATCGA
193 TTTGTTCTTGGACGAACTTTCGA
* * ** * * * * *** * * * * *
1295 ACTTTTCTAACTTCGAGGAGATCTTTTATAACTTAACTTTCTTAAAGTATTCAAGACGATACATT
1 AC-TTGCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * *
1360 CCTTCGA-CCAATTTTCCGAACATTCCATGCTTGAGAAATCGCATCATTTGGTCAAAATAGTTTA
65 CCTTAGAGCAAATTTT-CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* *
1424 TCATTTTGCAAACAAGTTTTGGTCTTTCAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
129 TCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
1489 TTGTTCTTGGACGAACTTTCGA
194 TTGTTCTTGGACGAACTTTCGA
* * * * * *
1511 A-TTGCAAAAGTTTTACGAGTTATTTGTTAACATCGGTTCCCTACAGTATTCAACAAGATCTATT
1 ACTTGC-AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * ** *
1575 CCTTAGAGCAAATTTCCGAACATTCCTTGATCGGGAAATCAAATCATTTGGTCTAAATAGTTTGT
65 CCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTAT
* * *
1640 CATTTCG-TGAACAAATTTTGGTCTTTGAATTAAAAACATATTTACGTGAGAATTGTTTCTCTCT
130 CATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
*
1704 TTGTTCTTGGACAAACTTTCGA
194 TTGTTCTTGGACGAACTTTCGA
* *
1726 A-TTGCAAAACTTTTACAAGTTATTTTTTTAACTTCGGTTTCC-TAAAGTTTTCAACAAGATCCA
1 ACTTGC-AAACTTTTACGAGTTA-TTTTTTAACTTCGG-TTCCATAAAGTATTCAACAAGATCCA
* *
1789 TTCCTTAGAGC-TATTTTCCGAACACTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT
63 TTCCTTAGAGCAAATTTT-CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT
* *
1853 TATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATGTACGTGAGAATTGTTTCTCT
127 TATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
1918 CTTTGTTCTTGGACGAACTTTCGA
192 CTTTGTTCTTGGACGAACTTTCGA
1942 A-TTGCAACACTTTTACGAGTTATTTTTTAACTTCGGTTCCCA-AAAGTATTCAACAAGATCCAT
1 ACTTGCAA-ACTTTTACGAGTTATTTTTTAACTTCGGTT-CCATAAAGTATTCAACAAGATCCAT
* * * * *
2005 TCGTTAGAGCAAATTTTCGAACATTCCATGCTCGAGAAATCGAATCTTTTGGTCTAAATAGTTTG
64 TCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* *
2070 TCATTTTG-TGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTC
129 TCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
*
2134 TTTCTTCTTGGACGAACTTTCGA
193 TTTGTTCTTGGACGAACTTTCGA
* * * * * * * * *
2157 ACTTGTCAAACTTTTGCTAGGTCTTTTATAACTTTGGATCCATAAAGTATTCAAGACGATCCATT
1 ACTTG-CAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * *
2222 CCTTAAAG-AAATTTTCCAAACATTCCATGCTCGGCAAATCGCATCATTTGGTATAAATAGTTTG
65 CCTTAGAGCAAATTTT-CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* * * *
2286 TCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCATGTGAGAATTG-TT-TCTCT
129 TCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
* *
2349 TTGTTCTTGGATGAAC-TTCATA
194 TTGTTCTTGGACGAACTTTC-GA
* * * ** * * * * * *
2371 ACTTGTCAAACTTTTACTAGGTCTTTCATAACTTCGGATCCAGAAAGTATTGAAGATGATCTATT
1 ACTTG-CAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * * * * *
2436 CTTTCGAAC-AATTTTCCAGACATTCTATGCTTGGGAAATCTCATCATTTGGTCTAAATAGTTTA
65 CCTTAGAGCAAATTTTCGA-ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* * *
2500 TCATTTTGC-AAC---TTTTCGTCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCACT
129 TCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
*
2561 TTGTTCTTTGACGAACTTTCGA
194 TTGTTCTTGGACGAACTTTCGA
2583 A-TTGCAAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCA-AAAGTATTCAACAAGATCCAT
1 ACTTGC-AAACTTTTACGAGTTATTTTTTAACTTCGGTT-CCATAAAGTATTCAACAAGATCCAT
* * * * * ** * *
2646 TCGTTAGAGCAAATTTCCGAA-ATTCCTTGATAGGGAAATCAAATCATTTGGTCGAAATAGTTTG
64 TCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTA
* * *
2710 TCATTTCG-TGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTG
129 TCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTC
2774 TTTGTTCTTGGACGAACTTTCGA
193 TTTGTTCTTGGACGAACTTTCGA
* * *
2797 A-TTGCAAAACTTTTACAAGTTATTTTTTAACTTCGGTTCCCTAAAGTTTTCAACAAGATCCATT
1 ACTTGC-AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATT
* * * *
2861 CCTTAGAGCTATTTTTCGAGCACTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTAT
65 CCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTAT
*
2926 CATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTT
130 CATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTT
Statistics
Matches: 2289, Mismatches: 399, Indels: 121
0.81 0.14 0.04
Matches are distributed among these distances:
210 79 0.03
211 59 0.03
212 30 0.01
213 13 0.01
214 288 0.13
215 793 0.35
216 999 0.44
217 28 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (215 bp):
ACTTGCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCATAAAGTATTCAACAAGATCCATTC
CTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTATC
ATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTT
GTTCTTGGACGAACTTTCGA
Found at i:876 original size:431 final size:429
Alignment explanation
Indices: 8--2964 Score: 3338
Period size: 431 Copynumber: 6.9 Consensus size: 429
1 ACTTGGC
* * *
8 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTACAGTATTCAACAAGATCCAATCCTTAAA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * *
73 GCAATTTTCC-AAGCATTCCATGCTCGAGAAATCGCATCATTTAGTCTAACTAGTTTGTCACTTT
66 GCAATTTTCCGAA-CATTCCATGCTCG-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* * * * * * * *
137 GTAAACAAGTTTTAGTCATTGAATTAAATACTTATTTACGAGAGAATTGTCTCTCTCTTGGTTCA
129 GCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCT
* ** ** * * * *** * *
202 TGGACGATCTATCC-AACTTGTTTAACTTCGAGGAGATCTTTTATAACTTAACTTCCTTGAAGTA
194 TGGACGAACT-TCCGAACTTG-CAAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTA
* * * * * ** **
266 TTCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTCGACAAATCGTATCATTT
257 TTCAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTT
* * *
331 GGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTT-AATTTAAAAACTTATTTACGTG
322 GGTCTAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAA-TTAAAAACTTATTTACGTG
* *
395 AGAATTCTTTCTCTCTTTGTTCTTGGATGAACTTTCGAATTGCA
386 AGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATTGCA
* * * * *
439 AAACTTTTACGAGTTGTTTGTTAACTTCGGTTCCCAAAAGTTTTCAACTAGATCCATTCCTTAGA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * * *
504 GCTATTTCCCGAACACTCCATGCTCAGGAAATCGCATTATTTGGTCTAAATAGTTTGTCATTTTG
66 GCAATTTTCCGAACATTCCATGCTC-GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
* * * * *
569 TAAACAAGTTTTGTTCTCTGAATTAAATACTTATTTACGTGAGAAATGTTTCTCTCTTTGTTCTT
130 CAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTT
* * * * *
634 GGACGAACTTCCGAACTTGTCAAACTTTTACTAGTTCTTTTATAACATCGGATACATAAAGTATT
195 GGACGAACTTCCGAACTTG-CAAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTATT
* * * * * * * *
699 CAAGACGATCAATTCTTTCGAACAAATTTTCGAACATTCCATGCTTGTGAAATCACATCATTTGG
259 CAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGG
*
764 TCTAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAATT-AAAACTTATTTACGTTAGA
324 TCTAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
* * *
828 ATTGTTTCTCTCTTTGTTTTTGGACGAACTTCCGAACTTAG-T
389 ATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAA-TT-GCA
* * * * * *
870 AAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTACAGTATTAAACAAGGTCCAATCCTTAAA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * * *
935 GCAATTTTCCTAACATTCCATGCGT-GGCATATCGCATCATTTGGTCTAAATAGTTTATCTTTTT
66 GCAATTTTCCGAACATTCCATGC-TCGG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
* *
999 GCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCATGTGAGAATTGTTTCTCTCTTTGTTCT
129 GCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCT
* * * * * *
1064 TGGACAAACTTCCGAACTTGGCAAAATTTTACGAGTTATTTTTTAACTTCCGTTCCCTACAGTAT
194 TGGACGAACTTCCGAACTT-GCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTAT
* * * * * * * * ** *
1129 TGAACAAGATCTAATCCTTAAAGCAACTTTCCGAGCATTCCATGCTCAGGAAATCGTATCATTTA
258 TCAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTTG
* * * ** * *
1194 GTCTAACTAGTTCGA-CATTTTG-TAAACAAGTTTTAGTCAATGAATTAAATACTTATTTACGAG
323 GTCTAAATAGTT-TATCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTG
* * * * * * *
1257 AGAATTGTCTCTCTCTTGGTTCATGGATGATCTATCGAACTTTTC-
386 AGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAA--TTGCA
* ** * * * * *** * * * * * *
1302 TAACTTCGAGGAGATCTTTTATAACTTAACTTTCTTAAAGTATTCAAGACGATACATTCCTTCGA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * * *
1367 CCAATTTTCCGAACATTCCATGCTTGAGAAATCGCATCATTTGGTCAAAATAGTTTATCATTTTG
66 GCAATTTTCCGAACATTCCATGCTCG-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
*
1432 CAAACAAGTTTTGGTCTTTCAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTT
130 CAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTT
* * * * *
1497 GGACGAACTTTCGAA-TTGCAAAAGTTTTACGAGTTATTTGT-TAACATCGGTTCCCTACAGTAT
195 GGACGAACTTCCGAACTTGC-AAACTTTTACGAGTTATTT-TATAACTTCGGTTCCATAAAGTAT
* * * * *
1560 TCAACAAGATCTATTCCTTAGAGCAAATTTCCGAACATTCCTTGATCGGGAAATCAAATCATTTG
258 TCAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTTG
* * * *
1625 GTCTAAATAGTTTGTCATTTCG-TGAACAAATTTTGGTCTTTGAATTAAAAACATATTTACGTGA
323 GTCTAAATAGTTTATCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
*
1689 GAATTGTTTCTCTCTTTGTTCTTGGACAAACTTTCGAATTGCA
387 GAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATTGCA
* * *
1732 AAACTTTTACAAGTTATTTTTTTAACTTCGGTTTCCTAAAGTTTTCAACAAGATCCATTCCTTAG
1 AAACTTTTACGAGTTA-TTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAG
* * *
1797 AGCTATTTTCCGAACACTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTATCATTTT
65 AGCAATTTTCCGAACATTCCATGCTC-GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT
*
1862 GCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATGTACGTGAGAATTGTTTCTCTCTTTGTTCT
129 GCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCT
* *
1927 TGGACGAACTTTCGAA-TTGCAACACTTTTACGAGTTATTTTTTAACTTCGGTTCCCA-AAAGTA
194 TGGACGAACTTCCGAACTTGCAA-ACTTTTACGAGTTATTTTATAACTTCGGTT-CCATAAAGTA
* * *
1990 TTCAACAAGATCCATTCGTTAGAGCAAATTTTCGAACATTCCATGCTCGAGAAATCGA-ATCTTT
257 TTCAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATC-ACATCATT
* *
2054 TGGTCTAAATAGTTTGTCATTTTG-TGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGT
321 TGGTCTAAATAGTTTATCATTTTGCT-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGT
* *
2118 GAGAATTATTTCTCTCTTTCTTCTTGGACGAACTTTCGAACTTGTC-
385 GAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAA-TTG-CA
* * * * * * * * * * *
2164 AAACTTTTGCTAGGTCTTTTATAACTTTGGATCCATAAAGTATTCAAGACGATCCATTCCTTAAA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * * *
2229 GAAATTTTCCAAACATTCCATGCTCGGCAAATCGCATCATTTGGTATAAATAGTTTGTCTTTTTG
66 GCAATTTTCCGAACATTCCATGCTCGG-AAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
* *
2294 CAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCATGTGAGAATTG-TT-TCTCTTTGTTCTT
130 CAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTT
* ** * * * * * *
2357 GGATGAACTTCATAACTTGTCAAACTTTTACTAGGTCTTTCATAACTTCGGATCCAGAAAGTATT
195 GGACGAACTTCCGAACTTG-CAAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTATT
* * * * * * * * * * *
2422 GAAGATGATCTATTCTTTCGAAC-AATTTTCCAGACATTCTATGCTTGGGAAATCTCATCATTTG
259 CAACAAGATCCATTCCTTAGAGCAAATTTTCGA-ACATTCCATGCTCGGGAAATCACATCATTTG
* *
2486 GTCTAAATAGTTTATCATTTTGC-AAC---TTTTCGTCTTTGAATTAAAAACTTATATACGTGAG
323 GTCTAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAG
* *
2547 AATTGTTTCTCACTTTGTTCTTTGACGAACTTTCGAATTGCA
388 AATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATTGCA
* *
2589 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCAAAAGTATTCAACAAGATCCATTCGTTAGA
1 AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
* * * * ** * *
2654 GCAAATTTCCGAA-ATTCCTTGATAGGGAAATCAAATCATTTGGTCGAAATAGTTTGTCATTTCG
66 GCAATTTTCCGAACATTCCATGCT-CGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
** * *
2718 TGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTGTTTGTTCTT
130 CAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTT
* * * * *
2783 GGACGAACTTTCGAA-TTGCAAAACTTTTACAAGTTATTTTTTAACTTCGGTTCCCTAAAGTTTT
195 GGACGAACTTCCGAACTTGC-AAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTATT
* * * * *
2847 CAACAAGATCCATTCCTTAGAGCTATTTTTCGAGCACTCCATGCTCGGGAAATCGCATCATTTGG
259 CAACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGG
*
2912 TCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTT
324 TCTAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTT
Statistics
Matches: 2130, Mismatches: 351, Indels: 92
0.83 0.14 0.04
Matches are distributed among these distances:
424 84 0.04
425 172 0.08
426 99 0.05
429 64 0.03
430 171 0.08
431 1289 0.61
432 247 0.12
433 4 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (429 bp):
AAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGA
GCAATTTTCCGAACATTCCATGCTCGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGC
AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTG
GACGAACTTCCGAACTTGCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCATAAAGTATTCA
ACAAGATCCATTCCTTAGAGCAAATTTTCGAACATTCCATGCTCGGGAAATCACATCATTTGGTC
TAAATAGTTTATCATTTTGCTAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAAT
TGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATTGCA
Found at i:1272 original size:647 final size:644
Alignment explanation
Indices: 6--2964 Score: 3341
Period size: 647 Copynumber: 4.6 Consensus size: 644
1 ACTTG
* * * *
6 GCAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCTACAGTATTCAACAAGATCCAA-TCCTT
1 GCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCAAAAGTATTCAACAAGAT-CAATTCGTT
* * * *
70 A-AAGC-AATTTTCCAAGCATTCCATGCTCGAGAAATCGCATCATTTAGTCTAACTAGTTTGTCA
65 AGAA-CAAATTTTCGAA-CATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCA
* * * * * * * *
133 CTTTGTAAACAAGTTTTAGTCATTGAATTAAATACTTATTTACGAGAGAATTGTCTCTCTCTTGG
128 TTTTGTGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
* * * * * * ** * * * *** * *
198 TTCATGGACGATCTATCCAACTTGTTTAACTTCGA-GGAGATCTTTTATAACTTAACTTCCTTGA
193 TTCTTGGACGAACTTTCGAACTTGCTAAACTTTTACGG-GTTATTTTTTAACTTCGGTTCCCTAA
* * * * * * *
262 AGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTCGACAAATCGTATC
257 AGTATTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGCAAATCGCATC
*
327 ATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTT-AATTTAAAAACTTATTTA
322 ATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAA-TTAAAAACTTATTCA
* ** * *
391 CGTGAGAATTCTTTCTCTCTTTGTTCTTGGATGAACTTTCGAATTGCAAAACTTTTACGAGTTGT
386 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAATTGCAAAACTTTTACGAGTTAT
* * * * * * *
456 TTGTTAACTTCGGTTCCCAAAAGTTTTCAACTAGATCCATTCCTTAGAGCTATTTCCCGAACACT
451 TTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAAAGCAATTTTCCGAACACT
*
521 CCATGCTCAGGAAATCGCATTATTTGGTCTAAATAGTTTG-TCATTTTGTAAACAAGTTTTGTTC
516 CCATGCTCAGGAAATCGCATCATTTGGTCTAAATAG-TTGATCATTTTGTAAACAAGTTTTG-TC
* * * *
585 TCTGAATTAAATACTTATTTACGTGAGAAATGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAAC
579 TTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAA-
650 TT
643 TT
* * * * * * * *
652 GTCAAACTTTTACTAGTTCTTTTATAACATCGGAT-ACATAAAGTATTCAAGACGATCAATTCTT
1 G-CAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCA-AAAGTATTCAACAAGATCAATTCGT
* * * *
716 TCGAACAAATTTTCGAACATTCCATGCTTGTGAAATCACATCATTTGGTCTAAATAGTTTATCAT
64 TAGAACAAATTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCAT
*
781 TTTGCT-AACAAGTTTTGGTCTTTGAATT-AAAACTTATTTACGTTAGAATTGTTTCTCTCTTTG
129 TTTG-TGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG
* * *
844 TTTTTGGACGAACTTCCGAACTTAG-TAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTAC
193 TTCTTGGACGAACTTTCGAACTT-GCTAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTAA
* * * * * *
908 AGTATTAAACAAGGTCCAATCCTTAAAGCAATTTTCCTAACATTCCATGCGT-GGCATATCGCAT
257 AGTATTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGC-TCGGCAAATCGCAT
*
972 CATTTGGTCTAAATAGTTTATCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCA
321 CATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCA
*
1037 TGTGAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAACTTGGCAAAA-TTTTACGAGTT
386 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAA-TT-GCAAAACTTTTACGAGTT
* * * * * * *
1101 ATTTTTTAACTTCCGTTCCCTACAGTATTGAACAAGATCTAATCCTTAAAGCAACTTTCCGAGCA
449 ATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAAAGCAATTTTCCGAACA
* * * *
1166 TTCCATGCTCAGGAAATCGTATCATTTAGTCTAACTAGTTCGA-CATTTTGTAAACAAGTTTTAG
514 CTCCATGCTCAGGAAATCGCATCATTTGGTCTAAATAGTT-GATCATTTTGTAAACAAGTTTT-G
** * * * * * * * *
1230 TCAATGAATTAAATACTTATTTACGAGAGAATTGTCTCTCTCTTGGTTCATGGATGATCTATCGA
577 TCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGA
1295 ACTTT
642 A--TT
* * ** * * * *** * ** * * *
1300 TCTAACTTCGAGGAGATCTTTTATAACTTAACTTTCTTAAAGTATTCAAGACGAT-ACATTCCTT
1 GCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCAAAAGTATTCAACAAGATCA-ATTCGTT
* * * * * *
1364 CG-ACCAATTTTCCGAACATTCCATGCTTGAGAAATCGCATCATTTGGTCAAAATAGTTTATCAT
65 AGAACAAATTTT-CGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCAT
** *
1428 TTTGCAAACAAGTTTTGGTCTTTCAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
129 TTTGTGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* * * * * *
1493 TCTTGGACGAACTTTCGAA-TTGCAAAAGTTTTACGAGTTATTTGTTAACATCGGTTCCCTACAG
194 TCTTGGACGAACTTTCGAACTTGCTAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTAAAG
* * * * * **
1557 TATTCAACAAGATCTATTCCTTAGAGCAAATTTCCGAACATTCCTTGATCGGGAAATCAAATCAT
259 TATTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGCAAATCGCATCAT
* * ** * * *
1622 TTGGTCTAAATAGTTTGTCATTTCGTGAACAAATTTTGGTCTTTGAATTAAAAACATATTTACGT
324 TTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCACGT
* *
1687 GAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTTCGAATTGCAAAACTTTTACAAGTTATTTT
389 GAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAATTGCAAAACTTTTACGAGTTA-TTT
* * * *
1752 TTTAACTTCGGTTTCCTAAAGTTTTCAACAAGATCCATTCCTTAGAGCTATTTTCCGAACACTCC
453 TTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAAAGCAATTTTCCGAACACTCC
* * *
1817 ATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTT
518 ATGCTCAGGAAATCGCATCATTTGGTCTAAATAGTTGATCATTTTGTAAACAAGTTTT-GTCTTT
*
1882 GAATTAAAAACTTATGTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATT
582 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATT
* *
1945 GCAACACTTTTACGAGTTATTTTTTAACTTCGGTTCCCAAAAGTATTCAACAAGATCCATTCGTT
1 GCAA-ACTTTTACGAGTTATTTTATAACTTCGGTTCCCAAAAGTATTCAACAAGATCAATTCGTT
* *
2010 AGAGCAAATTTTCGAACATTCCATGCTCGAGAAATCGA-ATCTTTTGGTCTAAATAGTTTGTCAT
65 AGAACAAATTTTCGAACATTCCATGCTCGAGAAATC-ACATCATTTGGTCTAAATAGTTTGTCAT
* * *
2074 TTTGTGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTTCT
129 TTTGTGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
* * * * * * *
2139 TCTTGGACGAACTTTCGAACTTG-TCAAACTTTTGCTAGG-TCTTTTATAACTTTGGATCCATAA
194 TCTTGGACGAACTTTCGAACTTGCT-AAACTTTTAC-GGGTTATTTTTTAACTTCGGTTCCCTAA
* * * * *
2202 AGTATTCAAGACGATCCATTCCTTAAAGAAATTTTCCAAACATTCCATGCTCGGCAAATCGCATC
257 AGTATTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGCAAATCGCATC
* *
2267 ATTTGGTATAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCAT
322 ATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCAC
** ** * * *
2332 GTGAGAATTG-TT-TCTCTTTGTTCTTGGATGAACTTCATAACTTGTC-AAACTTTTACTAGGTC
387 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAA-TTG-CAAAACTTTTACGAGTTA
** * ** * * * * * *
2394 TTTCATAACTTCGGATCCAGAAAGTATTGAAGATGATCTATTCTTTCGAA-CAATTTTCC-AGAC
450 TTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTT-AAAGCAATTTTCCGA-AC
* * ** * * *
2457 ATTCTATGCTTGGGAAATCTCATCATTTGGTCTAAATAGTTTATCATTTTG----CAACTTTTCG
513 ACTCCATGCTCAGGAAATCGCATCATTTGGTCTAAATAGTTGATCATTTTGTAAACAAGTTTT-G
* * *
2518 TCTTTGAATTAAAAACTTATATACGTGAGAATTGTTTCTCACTTTGTTCTTTGACGAACTTTCGA
577 TCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGA
2583 ATT
642 ATT
* *
2586 GCAAAACTTTTACGAGTTATTTTTTAACTTCGGTTCCCAAAAGTATTCAACAAGATCCATTCGTT
1 GC-AAACTTTTACGAGTTATTTTATAACTTCGGTTCCCAAAAGTATTCAACAAGATCAATTCGTT
* * * * * * * *
2651 AGAGCAAATTTCCGAA-ATTCCTTGATAGGGAAATCAAATCATTTGGTCGAAATAGTTTGTCATT
65 AGAACAAATTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCATT
* * *
2715 TCGTGAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTGTTTGTT
130 TTGTGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTT
* **
2780 CTTGGACGAACTTTCGAA-TTGCAAAACTTTTACAAGTTATTTTTTAACTTCGGTTCCCTAAAGT
195 CTTGGACGAACTTTCGAACTTGCTAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTAAAGT
* * * * * *
2844 TTTCAACAAGATCCATTCCTTAGAGCTATTTTTCGAGCACTCCATGCTCGGGAAATCGCATCATT
260 ATTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGCAAATCGCATCATT
* *
2909 TGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTT
325 TGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTT
Statistics
Matches: 1960, Mismatches: 312, Indels: 89
0.83 0.13 0.04
Matches are distributed among these distances:
638 2 0.00
639 142 0.07
640 119 0.06
641 150 0.08
642 2 0.00
644 1 0.00
645 124 0.06
646 437 0.22
647 909 0.46
648 74 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (644 bp):
GCAAACTTTTACGAGTTATTTTATAACTTCGGTTCCCAAAAGTATTCAACAAGATCAATTCGTTA
GAACAAATTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAATAGTTTGTCATTT
TGTGAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC
TTGGACGAACTTTCGAACTTGCTAAACTTTTACGGGTTATTTTTTAACTTCGGTTCCCTAAAGTA
TTCAACAAGATCCATTCCTTAGAGCAATTTTCCGAACATTCCATGCTCGGCAAATCGCATCATTT
GGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTCACGTGA
GAATTGTTTCTCTCTTTGTTCTTGGACAAACTTCCGAATTGCAAAACTTTTACGAGTTATTTTTT
AACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAAAGCAATTTTCCGAACACTCCATG
CTCAGGAAATCGCATCATTTGGTCTAAATAGTTGATCATTTTGTAAACAAGTTTTGTCTTTGAAT
TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAATT
Done.