Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015226.1 Kokia drynarioides strain JFW-HI SEQ_130270, 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: 713267
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:630115 original size:156 final size:152
Alignment explanation
Indices: 629602--630589 Score: 1435
Period size: 145 Copynumber: 6.4 Consensus size: 152
629592 GGCTGCTTTA
* * *
629602 CCTATTAGCTCGGCTGGTTAGAGCGTCGTGCAAATAACGCGAAGGTCGCAGGTCCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
* *
629667 TGGGCCATTTGTAATTTTGTTTTATATATCCATTTTAAAAACGGCAACGTTTTCCATTATTTATT
66 TGGGCCATTTGTAATTTTGTTTTAGATATCCA-TTT----A---TAACGTTTTCCATTATTTATT
629732 AAAACAGAATTTAAAATTAAACGTCAATGG
123 AAAACAGAATTTAAAATTAAACGTCAATGG
* * *
629762 CCTCTTAGCTCAGCTGGTTAGTGCGTCGTGTTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
629827 TGGGCCATTTGTAATTTTGTTTT--ATAT--A--T-CAACGTTTTCCATTATTTATTAAAACAGA
66 TGGGCCATTTGTAATTTTGTTTTAGATATCCATTTATAACGTTTTCCATTATTTATTAAAACAGA
629885 ATTTAAAATTAAACGTCAATGG
131 ATTTAAAATTAAACGTCAATGG
629907 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
629972 TGGGCCATTTGTAATTTTGTTTTAGATATCCTATTTATAACGTTTTCCATTATTTATTAAAAATA
66 TGGGCCATTTGTAATTTTGTTTTAGATATCC-ATTTATAACGTTTTCCATTATTTATT--AAA-A
* *
630037 CAAAATTTAAAATTAAACGTCAAGGG
127 CAGAATTTAAAATTAAACGTCAATGG
630063 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
630128 TGGGCCATTTGTAATTTTGTTTTAGATATCCA---CTAACGTTTTCCATTATTTATTAAAACAGA
66 TGGGCCATTTGTAATTTTGTTTTAGATATCCATTTATAACGTTTTCCATTATTTATTAAAACAGA
630190 ATTTAAAATTAAACGTCAATGG
131 ATTTAAAATTAAACGTCAATGG
* *
630212 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAAGTCGCAGGTTCGAGACCTGTA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
630277 TGGGCCATTTGATATAATTTTGTTTTATATATCCATTT-TAAACGTTTTCCATTATTTATTAAAA
66 TGGGCCATTTG---TAATTTTGTTTTAGATATCCATTTAT-AACGTTTTCCATTATTTATTAAAA
* *
630341 CAGAATTTAAAATTAAACGTTAAAGG
127 CAGAATTTAAAATTAAACGTCAATGG
630367 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
* * *
630432 TGGGCCATTTGTAATTTTGTTTTAAATATCCTTTTTATAAACGACAACGTTTCCATTATTTA-TA
66 TGGGCCATTTGTAATTTTGTTTTAGATATCC-ATTTAT-AACG-----TTTTCCATTATTTATTA
630496 GAAAC-GAAATTTAAAATTAAACGTCAATGG
124 -AAACAG-AATTTAAAATTAAACGTCAATGG
** ** *
630526 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACATGAAGGTTACAGGTTTGAGACCTGC
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
630590 GTTTTCTTAT
Statistics
Matches: 769, Mismatches: 32, Indels: 55
0.90 0.04 0.06
Matches are distributed among these distances:
145 136 0.18
147 4 0.01
149 99 0.13
150 4 0.01
152 61 0.08
153 24 0.03
154 7 0.01
155 126 0.16
156 122 0.16
158 7 0.01
159 97 0.13
160 82 0.11
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (152 bp):
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
TGGGCCATTTGTAATTTTGTTTTAGATATCCATTTATAACGTTTTCCATTATTTATTAAAACAGA
ATTTAAAATTAAACGTCAATGG
Found at i:630173 original size:305 final size:301
Alignment explanation
Indices: 629602--630589 Score: 1461
Period size: 305 Copynumber: 3.2 Consensus size: 301
629592 GGCTGCTTTA
* * *
629602 CCTATTAGCTCGGCTGGTTAGAGCGTCGTGCAAATAACGCGAAGGTCGCAGGTCCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
629667 TGGGCCATTTGTAATTTTGTTTTATATATCCATTTTAAAAACGGCAACGTTTTCCATTATTTATT
66 TGGGCCATTTGTAATTTTGTTTTATATATCCA-TTT----A---TAACGTTTTCCATTATTTATT
* * * *
629732 AAAACAGAATTTAAAATTAAACGTCAATGGCCTCTTAGCTCAGCTGGTTAGTGCGTCGTGTTAAT
123 AAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAAT
*
629797 AACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTATATAT---C-A
188 AACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATATCCACTA
629858 ACGTTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGG
253 ACGTTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGG
629907 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
629972 TGGGCCATTTGTAATTTTGTTTTAGATATCCTATTTATAACGTTTTCCATTATTTATTAAAAATA
66 TGGGCCATTTGTAATTTTGTTTTATATATCC-ATTTATAACGTTTTCCATTATTTATT--AAA-A
* *
630037 CAAAATTTAAAATTAAACGTCAAGGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACG
127 CAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACG
*
630102 CGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAGATATCCACTAACGT
192 CGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATATCCACTAACGT
630167 TTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGG
257 TTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGG
* *
630212 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAAGTCGCAGGTTCGAGACCTGTA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
630277 TGGGCCATTTGATATAATTTTGTTTTATATATCCATTT-TAAACGTTTTCCATTATTTATTAAAA
66 TGGGCCATTTG---TAATTTTGTTTTATATATCCATTTAT-AACGTTTTCCATTATTTATTAAAA
*
630341 CAGAATTTAAAATTAAACGTTAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACG
127 CAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACG
630406 CGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATATCCTTTTTA-T
192 CGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATATCC-----ACT
*
630470 AAACGACAACGTTTCCATTATTTA-TAGAAAC-GAAATTTAAAATTAAACGTCAATGG
252 -AACG-----TTTTCCATTATTTATTA-AAACAG-AATTTAAAATTAAACGTCAATGG
** ** *
630526 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACATGAAGGTTACAGGTTTGAGACCTGC
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
630590 GTTTTCTTAT
Statistics
Matches: 632, Mismatches: 26, Indels: 41
0.90 0.04 0.06
Matches are distributed among these distances:
298 20 0.03
300 3 0.00
301 116 0.18
304 120 0.19
305 222 0.35
306 2 0.00
307 24 0.04
308 20 0.03
309 5 0.01
313 3 0.00
314 97 0.15
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (301 bp):
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
TGGGCCATTTGTAATTTTGTTTTATATATCCATTTATAACGTTTTCCATTATTTATTAAAACAGA
ATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAA
GGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATATCCACTAACGTTTTC
CATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGG
Found at i:630463 original size:460 final size:451
Alignment explanation
Indices: 629602--630589 Score: 1507
Period size: 460 Copynumber: 2.1 Consensus size: 451
629592 GGCTGCTTTA
* * *
629602 CCTATTAGCTCGGCTGGTTAGAGCGTCGTGCAAATAACGCGAAGGTCGCAGGTCCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
629667 TGGGCCATTTGTAATTTTGTTTTATATATCCATTTTAAAAACGGCAACGTTTTCCATTATTTATT
66 TGGGCCATTTGTAATTTTGTTTTAGATATCC--------AAC-GCAACGTTTTCCATTATTTATT
* * *
629732 AAAACAGAATTTAAAATTAAACGTCAATGGCCTCTTAGCTCAGCTGGTTAGTGCGTCGTGTTAAT
122 AAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAAT
*
629797 AACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTATATATCAACGT
187 AACGCGAAAGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTATATATCAACGT
*
629862 TTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTA
252 TTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTA
629927 GAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGT
317 GAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGT
* *
629992 TTTAGATATCCTATTTAT-AACG-TTTTCCATTATTTATTAAAAATACAAAATTTAAAATTAAAC
382 TTTAAATATCCTATTTATAAACGAGTTTCCATTATTTA-T-AAAA-ACAAAATTTAAAATTAAAC
630055 GTCAAGGG
444 GTCAAGGG
630063 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
*
630128 TGGGCCATTTGTAATTTTGTTTTAGATATCC-AC-TAACGTTTTCCATTATTTATTAAAACAGAA
66 TGGGCCATTTGTAATTTTGTTTTAGATATCCAACGCAACGTTTTCCATTATTTATTAAAACAGAA
630191 TTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAA
131 TTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAA
*
630256 GTCGCAGGTTCGAGACCTGTATGGGCCATTTGATATAATTTTGTTTTATATATCCATTTTAAACG
196 GTCGCAGGTTCGAGACCTGCATGGGCCATTTG---TAATTTTGTTTTATATAT-C------AACG
*
630321 TTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTTAAAGGCCTATTAGCTCAGCTGGTT
251 TTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTT
630386 AGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTG
316 AGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTG
* * *
630451 TTTTAAATATCCTTTTTATAAACGACAACGTTTCCATTATTTATAGAAACGAAATTTAAAATTAA
381 TTTTAAATATCCTATTTATAAACG---A-GTTTCCATTATTTATAAAAACAAAATTTAAAATTAA
*
630516 ACGTCAATGG
442 ACGTCAAGGG
** ** *
630526 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACATGAAGGTTACAGGTTTGAGACCTGC
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
630590 GTTTTCTTAT
Statistics
Matches: 488, Mismatches: 23, Indels: 30
0.90 0.04 0.06
Matches are distributed among these distances:
450 121 0.25
452 2 0.00
453 18 0.04
454 1 0.00
460 149 0.31
461 96 0.20
463 84 0.17
464 3 0.01
465 1 0.00
466 13 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (451 bp):
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
TGGGCCATTTGTAATTTTGTTTTAGATATCCAACGCAACGTTTTCCATTATTTATTAAAACAGAA
TTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAA
GTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTATATATCAACGTTTTCCATTA
TTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTCGT
GCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAATAT
CCTATTTATAAACGAGTTTCCATTATTTATAAAAACAAAATTTAAAATTAAACGTCAAGGG
Found at i:630578 original size:159 final size:156
Alignment explanation
Indices: 629857--630589 Score: 1043
Period size: 155 Copynumber: 4.7 Consensus size: 156
629847 TTTATATATC
629857 AACGTTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCT
1 AACG-TTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCT
629922 GGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTG-TAA
65 GGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGATAA
*
629986 TTTTGTTTTAGATATCC-TATTTATAACG
130 TTTTGTTTTAAATATCCAT-TTTA-AACG
* * *
630014 ---TTTTCCATTATTTATTAAAAATACAAAATTTAAAATTAAACGTCAAGGGCCTATTAGCTCAG
1 AACGTTTCCATTATTTATT--AAA-ACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAG
630076 CTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTG-T
63 CTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGAT
* *
630140 AATTTTGTTTTAGATATCCA--CT-AACG
128 AATTTTGTTTTAAATATCCATTTTAAACG
*
630166 ---TTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTG
1 AACGTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTG
* *
630228 GTTAGAGCGTCGTGCTAATAACGCGAAAGTCGCAGGTTCGAGACCTGTATGGGCCATTTGATATA
66 GTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTG--ATA
*
630293 ATTTTGTTTTATATATCCATTTTAAACG
129 ATTTTGTTTTAAATATCCATTTTAAACG
* * *
630321 ---TTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTTAAAGGCCTATTAGCTCAGCTG
1 AACGTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTG
630383 GTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTG-TAAT
66 GTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGATAAT
*
630447 TTTGTTTTAAATATCCTTTTTATAAACG
131 TTTGTTTTAAATATCC-ATTT-TAAACG
630475 ACAACGTTTCCATTATTTA-TAGAAAC-GAAATTTAAAATTAAACGTCAATGGCCTATTAGCTCA
1 --AACGTTTCCATTATTTATTA-AAACAG-AATTTAAAATTAAACGTCAATGGCCTATTAGCTCA
** ** *
630538 GCTGGTTAGAGCGTCGTGCTAATAACATGAAGGTTACAGGTTTGAGACCTGC
62 GCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
630590 GTTTTCTTAT
Statistics
Matches: 533, Mismatches: 24, Indels: 36
0.90 0.04 0.06
Matches are distributed among these distances:
149 99 0.19
150 3 0.01
152 59 0.11
153 18 0.03
154 8 0.02
155 125 0.23
156 121 0.23
158 3 0.01
159 97 0.18
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (156 bp):
AACGTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCAGCTG
GTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGATAAT
TTTGTTTTAAATATCCATTTTAAACG
Found at i:630794 original size:460 final size:455
Alignment explanation
Indices: 629602--630871 Score: 1275
Period size: 460 Copynumber: 2.8 Consensus size: 455
629592 GGCTGCTTTA
* * * * *
629602 CCTATTAGCTCGGCTGGTTAGAGCGTCGTGCAAATAACGCGAAGGTCGCAGGTCCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACACGAAGGTCACAGGTTCGAGACCTGCA
* * ** * * * *
629667 TGGGCCATTTGTAATTTTGTTTTATATATCCATTTTAAAAACGGCAACGTTTTCCATTATTTATT
66 TGGGCCATTTATAATTTTG-----TAGA---A----AACCAC--TAACGTTTTACAGTATTTATC
** * * * * *
629732 AAAACAGAATTTAAAATTAAACGTCAATGGCCTCTTAGCTCAGCTGGTTAGTGCGTCGTGTTAAT
117 AAAACAGAATTTAAAATTAAACAACAATAGCCTATTAGCTCAGCTAGTTAGAGCGTCGTGCTAAT
* * *
629797 AACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTG-TAATTTTGTTTTATAT-----A-
182 AACGCGAAAGTCGCAGGTTCGAAACCTGCATCGGCCATTTGATAATTTTGTTTTATATAAAAAAG
** *
629855 -TCAACGTTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAATGGCCTATTAGCTCA
247 GGAAACGTTTTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCA
629919 GCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGT
312 GCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGT
* *
629984 AATTTTGTTTTAGATATCCTATTTATAACGTTTTCCATTATTTATTAAAAATACAAAATTTAAAA
377 AATTTTGTTTTAAATATCCTATTTATAACGGTTTCCATTATTTATTAAAAATACAAAATTTAAAA
630049 TTAAACGTCAAGGG
442 TTAAACGTCAAGGG
* *
630063 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACACGAAGGTCACAGGTTCGAGACCTGCA
* * * * * *
630128 TGGGCCATTTGTAATTTTGTTTTAGATATCCACTAACGTTTTCCATTATTTATTAAAACAGAATT
66 TGGGCCATTTATAATTTTG---TAGAAAACCACTAACGTTTTACAGTATTTATCAAAACAGAATT
** * *
630193 TAAAATTAAACGTCAATGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAAGT
128 TAAAATTAAACAACAATAGCCTATTAGCTCAGCTAGTTAGAGCGTCGTGCTAATAACGCGAAAGT
* * * *** ****
630258 CGCAGGTTCGAGACCTGTATGGGCCATTTGATATAATTTTGTTTTATATATCCATTTTAAACGTT
193 CGCAGGTTCGAAACCTGCATCGGCCATTTG--ATAATTTTGTTTTATATAAAAAAGGGAAACGTT
*
630323 TTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTTAAAGGCCTATTAGCTCAGCTGGTTAG
256 TTCCATTATTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAG
630388 AGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTT
321 AGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTT
* * *
630453 TTAAATATCCTTTTTATAAACGACAACGTTTCCATTATTTA-T-AGAA-ACGAAATTTAAAATTA
386 TTAAATATCCTATTTAT-AACG-----GTTTCCATTATTTATTAAAAATACAAAATTTAAAATTA
*
630515 AACGTCAATGG
445 AACGTCAAGGG
* * * *
630526 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACATGAAGGTTACAGGTTTGAGACCTGCG
1 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACACGAAGGTCACAGGTTCGAGACCTGCA
*** * ** * *
630591 T-TTTC-TTATATACCTTTTG-AGGAAAACGGC-AGCGTTTTAC-GTGTTTATCAAAACAGAATT
66 TGGGCCATT-TATA-ATTTTGTA-GAAAACCACTAACGTTTTACAGTATTTATCAAAACAGAATT
* * * * *
630651 TCAAGTTAAATAACAATAGCCTATTAGCTCAGCTAGTTCGAGCGTTGTGCTAATAACGC-AAAGA
128 TAAAATTAAACAACAATAGCCTATTAGCTCAGCTAGTTAGAGCGTCGTGCTAATAACGCGAAAG-
* * *
630715 TCGCAGGTTCGAAACTTGCATCGGCCA-TTG-TAATTTTGTTTTATTTGAGAAAAAGGGCAACGT
192 TCGCAGGTTCGAAACCTGCATCGGCCATTTGATAATTTTGTTTTATAT-A-AAAAAGGGAAACGT
** * * * * ** * * ** * **
630778 TTTATACTATTTATTTAAATATAATTTTTTGAGTTAAGCAACAATGGTTTATTA-CTTCAGCTGG
255 TTTCCATTATTTATTAAAACAGAA--TTTAAAATTAAACGTCAAAGGCCTATTAGC-TCAGCTGG
*
630842 TTAGAGTGTCGTGCTAATAACGCGAAGGTC
317 TTAGAGCGTCGTGCTAATAACGCGAAGGTC
630872 ATAGGTATGA
Statistics
Matches: 700, Mismatches: 84, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
450 121 0.17
452 3 0.00
453 16 0.02
454 15 0.02
455 1 0.00
456 24 0.03
457 8 0.01
458 145 0.21
459 14 0.02
460 155 0.22
461 87 0.12
462 4 0.01
463 90 0.13
464 3 0.00
465 1 0.00
466 13 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (455 bp):
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACACGAAGGTCACAGGTTCGAGACCTGCA
TGGGCCATTTATAATTTTGTAGAAAACCACTAACGTTTTACAGTATTTATCAAAACAGAATTTAA
AATTAAACAACAATAGCCTATTAGCTCAGCTAGTTAGAGCGTCGTGCTAATAACGCGAAAGTCGC
AGGTTCGAAACCTGCATCGGCCATTTGATAATTTTGTTTTATATAAAAAAGGGAAACGTTTTCCA
TTATTTATTAAAACAGAATTTAAAATTAAACGTCAAAGGCCTATTAGCTCAGCTGGTTAGAGCGT
CGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTTGTAATTTTGTTTTAAA
TATCCTATTTATAACGGTTTCCATTATTTATTAAAAATACAAAATTTAAAATTAAACGTCAAGGG
Found at i:630888 original size:23 final size:23
Alignment explanation
Indices: 630858--630904 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
630848 TGTCGTGCTA
630858 ATAACGCGAAGGTCATAGGTATG
1 ATAACGCGAAGGTCATAGGTATG
630881 ATAACGCGAAGGTCATAGGTATG
1 ATAACGCGAAGGTCATAGGTATG
630904 A
1 A
630905 GACCTGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (23 bp):
ATAACGCGAAGGTCATAGGTATG
Found at i:631706 original size:8 final size:8
Alignment explanation
Indices: 631693--631722 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
631683 ATCACCTCAC
631693 TTTTTTAT
1 TTTTTTAT
631701 TTTTTTAT
1 TTTTTTAT
631709 TTTTTTAT
1 TTTTTTAT
631717 TTTTTT
1 TTTTTT
631723 TGGGNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:640219 original size:83 final size:82
Alignment explanation
Indices: 640125--640279 Score: 206
Period size: 83 Copynumber: 1.9 Consensus size: 82
640115 GACACCTGGC
* * *
640125 TTGCTTTTATTTT-TATT-TTTTACTTTCTTAATAACAAATGGTTAATTTTCAATTTTGATCCCT
1 TTGCTTTTATTTTCTATTATTTTACATTCTTAAT-A-AAATGCTTAATTTTCAAATTTGATCCCT
*
640188 CTACTTTTTGATAATTGTT
64 CTAATTTTTGATAATTGTT
* * *
640207 TTGCTTTTTATTTTCTTTTATTTTACATTCTTAGTAAAATGCTTAATTTTCAAATTTGATCTCTC
1 TTGC-TTTTATTTTCTATTATTTTACATTCTTAATAAAATGCTTAATTTTCAAATTTGATCCCTC
640272 TAATTTTT
65 TAATTTTT
640280 AATTATATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
82 4 0.06
83 42 0.67
84 4 0.06
85 13 0.21
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (82 bp):
TTGCTTTTATTTTCTATTATTTTACATTCTTAATAAAATGCTTAATTTTCAAATTTGATCCCTCT
AATTTTTGATAATTGTT
Found at i:641189 original size:38 final size:39
Alignment explanation
Indices: 641147--641250 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 39
641137 ACATATATTT
* *
641147 TAATTT-TTAAATATAAAATAATTAAATACAAGTATTAA
1 TAATTTATTAAATATAAAATAATTAAATACAAGCAATAA
**
641185 TAATTATATTATAA-ATAAAATAA--GCATACAAGCAATAA
1 TAATT-TATTA-AATATAAAATAATTAAATACAAGCAATAA
* *
641223 CAATTTATT-AATATATAATAATTAAATA
1 TAATTTATTAAATATAAAATAATTAAATA
641251 ATAAATAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
35 2 0.04
36 8 0.15
37 4 0.08
38 23 0.44
39 1 0.02
40 12 0.23
41 2 0.04
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (39 bp):
TAATTTATTAAATATAAAATAATTAAATACAAGCAATAA
Found at i:643581 original size:6 final size:6
Alignment explanation
Indices: 643570--643626 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
643560 TTTCTTTGAT
* ** * *
643570 TTTTTC TTTTTC TTTTTC TTTTAC -TTTGA TTTTTC TTTTCC ATTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
643617 TTTCTTC TTT
1 TTT-TTC TTT
643627 AATTGCTACT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
5 3 0.08
6 31 0.77
7 6 0.15
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:643615 original size:29 final size:30
Alignment explanation
Indices: 643563--643619 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
643553 TATATACTTT
* *
643563 CTTTGATTTTTTCTTTTTCTTTTTCTTTTA
1 CTTTGATTTTTTCTTTTCCATTTTCTTTTA
643593 CTTTGA-TTTTTCTTTTCCATTTTCTTT
1 CTTTGATTTTTTCTTTTCCATTTTCTTT
643620 CTTCTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.74
Consensus pattern (30 bp):
CTTTGATTTTTTCTTTTCCATTTTCTTTTA
Found at i:643619 original size:23 final size:23
Alignment explanation
Indices: 643576--643619 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
643566 TGATTTTTTC
*
643576 TTTTTCTTTTTCTTTTACTTTGA
1 TTTTTCTTTTCCTTTTACTTTGA
643599 TTTTTCTTTTCCATTTT-CTTT
1 TTTTTCTTTTCC-TTTTACTTT
643620 CTTCTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTCTTTTCCTTTTACTTTGA
Found at i:650465 original size:40 final size:42
Alignment explanation
Indices: 650417--650494 Score: 142
Period size: 40 Copynumber: 1.9 Consensus size: 42
650407 TGATTTGATT
650417 AAATTTTAAATATGATTTG-A-ATGTGTTATTTACATTAATA
1 AAATTTTAAATATGATTTGAATATGTGTTATTTACATTAATA
650457 AAATTTTAAATATGATTTGAATATGTGTTATTTACATT
1 AAATTTTAAATATGATTTGAATATGTGTTATTTACATT
650495 TATTGTCCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 19 0.53
41 1 0.03
42 16 0.44
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (42 bp):
AAATTTTAAATATGATTTGAATATGTGTTATTTACATTAATA
Found at i:651629 original size:5 final size:5
Alignment explanation
Indices: 651621--651659 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
651611 GATGAACACT
651621 ATCAC ATCAC ATCAC ATCAC ATCAC ATCAC ATCAC ATCA
1 ATCAC ATCAC ATCAC ATCAC ATCAC ATCAC ATCAC ATCA
651660 ATACTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCAC
Found at i:656177 original size:112 final size:113
Alignment explanation
Indices: 656044--656246 Score: 264
Period size: 112 Copynumber: 1.8 Consensus size: 113
656034 TACTCGGGTA
* * *
656044 ATTTTTCTTAAATTTTTCAAAACATCAAACCTTAAAACAATATTGATACCAAG-TAGAGTATCAA
1 ATTTTTCTTAAATTTTCCAAAACATCAAACCTCAAAACAATATTGATACCAAGCAAGAGTATCAA
*
656108 TAAATTTTGAAATGTATCGATACTTTGTTAAGGGTATCGATCCTTTTG
66 TAAATTTTGAAAGGTATCGATACTTTGTTAAGGGTATCGATCCTTTTG
* * ** *** * *
656156 ATTTTTGTTCAATTTTCCAAAACATCAAATGTCAAATTGATATTGATATCAAGCAAGGGTATCAA
1 ATTTTTCTTAAATTTTCCAAAACATCAAACCTCAAAACAATATTGATACCAAGCAAGAGTATCAA
**
656221 TAAATTTTTTAAGGTATCGATACTTT
66 TAAATTTTGAAAGGTATCGATACTTT
656247 TCATTTTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
112 43 0.57
113 32 0.43
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (113 bp):
ATTTTTCTTAAATTTTCCAAAACATCAAACCTCAAAACAATATTGATACCAAGCAAGAGTATCAA
TAAATTTTGAAAGGTATCGATACTTTGTTAAGGGTATCGATCCTTTTG
Found at i:660317 original size:26 final size:27
Alignment explanation
Indices: 660280--660333 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
660270 ATGAATTTAA
*
660280 AATTAATTATTTCAATATTTGTA-TTT
1 AATTAATAATTTCAATATTTGTACTTT
**
660306 AATTAATAATTTTTATATTTGTACTTT
1 AATTAATAATTTCAATATTTGTACTTT
660333 A
1 A
660334 GTTTAGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (27 bp):
AATTAATAATTTCAATATTTGTACTTT
Found at i:660927 original size:45 final size:45
Alignment explanation
Indices: 660833--661013 Score: 301
Period size: 45 Copynumber: 4.0 Consensus size: 45
660823 CGGAGGAGTA
*
660833 GAGTATTGCGATGACTCATCAAACTGAGCC-GATATCCTTGGCTT
1 GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGGCTT
*
660877 GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGTCTT
1 GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGGCTT
* *
660922 GAGTATTGCGTTGGCTCGTCAAACTGAGCCTGATATCCTTGGCTT
1 GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGGCTT
* *
660967 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGGCTT
661012 GA
1 GA
661014 TGAGCTAGGG
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 29 0.23
45 99 0.77
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGATGACTCGTCAAACTGAGCCTGATATCCTTGGCTT
Found at i:662978 original size:16 final size:16
Alignment explanation
Indices: 662957--663006 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
662947 TGATGGAGAT
662957 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
662973 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
662988 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
663003 ATTA
1 ATTA
663007 GCTAGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:663683 original size:20 final size:21
Alignment explanation
Indices: 663658--663700 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
663648 TACTTACTAC
663658 TATTAAC-AAAAAAATAAAAT
1 TATTAACTAAAAAAATAAAAT
* *
663678 TATTAACTAACAAAATTAAAT
1 TATTAACTAAAAAAATAAAAT
663699 TA
1 TA
663701 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TATTAACTAAAAAAATAAAAT
Found at i:663801 original size:23 final size:22
Alignment explanation
Indices: 663775--663852 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
663765 TTATAACAAC
663775 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
663798 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
663821 CTTAAAATAATCAAATTAACTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
663847 ATTAAA
1 ATTAAA
663853 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:663893 original size:18 final size:18
Alignment explanation
Indices: 663872--663906 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
663862 AATTAAATTT
663872 AAAATTAACCAAACTTAA
1 AAAATTAACCAAACTTAA
*
663890 AAAATTAATCAAACTTA
1 AAAATTAACCAAACTTA
663907 CATTTCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:664087 original size:7 final size:7
Alignment explanation
Indices: 664071--664100 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
664061 CCTTCCCCTT
664071 CTTC-TC
1 CTTCTTC
664077 CTTCTTC
1 CTTCTTC
664084 CTTCTTC
1 CTTCTTC
664091 CTTCTTC
1 CTTCTTC
664098 CTT
1 CTT
664101 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTCTTC
Found at i:665889 original size:18 final size:18
Alignment explanation
Indices: 665863--665901 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
665853 GTTTGGATAA
**
665863 AAATATAAATTCAAAAAT
1 AAATATAAATAAAAAAAT
*
665881 AAATTTAAATAAAAAAAT
1 AAATATAAATAAAAAAAT
665899 AAA
1 AAA
665902 GCTCGTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATATAAATAAAAAAAT
Found at i:670754 original size:9 final size:9
Alignment explanation
Indices: 670742--670771 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
670732 CCCAAAAACT
*
670742 TTCATCACC
1 TTCATCATC
670751 TTCATCATC
1 TTCATCATC
670760 TTCATCATC
1 TTCATCATC
670769 TTC
1 TTC
670772 TCAAACGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (9 bp):
TTCATCATC
Found at i:674169 original size:23 final size:25
Alignment explanation
Indices: 674141--674189 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
674131 ATTAAAATGT
*
674141 AATTTTTTTTAA-AATTGATA-TAG
1 AATTTTTTGTAATAATTGATAGTAG
*
674164 AATTTTTTGTAATTATTGATAGTAG
1 AATTTTTTGTAATAATTGATAGTAG
674189 A
1 A
674190 GGCCTGTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 7 0.32
25 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (25 bp):
AATTTTTTGTAATAATTGATAGTAG
Found at i:678390 original size:2 final size:2
Alignment explanation
Indices: 678383--678408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
678373 TTATGTCATC
678383 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
678409 GAATAGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:679679 original size:30 final size:30
Alignment explanation
Indices: 679645--679732 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
679635 GAAGCGCGAA
*
679645 GAGAAGCGACAGGAAAAGCATGAC-AGACAT
1 GAGAAGCGACACGAAAAGCATGACAAG-CAT
* * *
679675 GAGAAGCGGCATGACAAA-CATGAGAAGCAT
1 GAGAAGCGACACGA-AAAGCATGACAAGCAT
* * *
679705 GAAAAGCGACACGAAAAGAATGAGAAGC
1 GAGAAGCGACACGAAAAGCATGACAAGC
679733 GGCATGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 3 0.06
30 40 0.83
31 5 0.10
ACGTcount: A:0.48, C:0.16, G:0.30, T:0.07
Consensus pattern (30 bp):
GAGAAGCGACACGAAAAGCATGACAAGCAT
Found at i:679688 original size:21 final size:21
Alignment explanation
Indices: 679662--679702 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
679652 GACAGGAAAA
*
679662 GCATGACAGACATGAGAAGCG
1 GCATGACAAACATGAGAAGCG
679683 GCATGACAAACATGAGAAGC
1 GCATGACAAACATGAGAAGC
679703 ATGAAAAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.29, T:0.10
Consensus pattern (21 bp):
GCATGACAAACATGAGAAGCG
Found at i:679727 original size:21 final size:21
Alignment explanation
Indices: 679703--679743 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
679693 CATGAGAAGC
679703 ATGAAAAGCGACACGAAAAGA
1 ATGAAAAGCGACACGAAAAGA
* * *
679724 ATGAGAAGCGGCATGAAAAG
1 ATGAAAAGCGACACGAAAAG
679744 TACGGGAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.12, G:0.29, T:0.07
Consensus pattern (21 bp):
ATGAAAAGCGACACGAAAAGA
Found at i:693326 original size:20 final size:21
Alignment explanation
Indices: 693287--693327 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
693277 CGTTTTAAGT
* *
693287 TAAAATTGATATGATGTGATA
1 TAAAATGGATATGATATGATA
693308 TAAAATGGA-ATGATATGATA
1 TAAAATGGATATGATATGATA
693328 AGGAGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (21 bp):
TAAAATGGATATGATATGATA
Found at i:695452 original size:22 final size:22
Alignment explanation
Indices: 695427--695468 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
695417 TATCAGATTC
695427 TCTTCATTTTGATTTGATATAA
1 TCTTCATTTTGATTTGATATAA
695449 TCTTCATTTTGATTTGATAT
1 TCTTCATTTTGATTTGATAT
695469 TTATAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (22 bp):
TCTTCATTTTGATTTGATATAA
Found at i:699454 original size:7 final size:7
Alignment explanation
Indices: 699442--699477 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
699432 ACAAAAAACT
699442 ATATAAA
1 ATATAAA
699449 ATATAAA
1 ATATAAA
699456 ATATAAA
1 ATATAAA
699463 ATATAAA
1 ATATAAA
699470 ATATAAA
1 ATATAAA
699477 A
1 A
699478 AAAAATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATATAAA
Found at i:699930 original size:29 final size:31
Alignment explanation
Indices: 699885--699964 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
699875 AAATTGAATC
*
699885 AAATCAAAATTCCATGTATAAAATT--ACACA-
1 AAATCAAAGTT-CATGTATAAAATTGAACA-AT
*
699915 AAATCAAAGTTCATGTATATAATTGAACAAT
1 AAATCAAAGTTCATGTATAAAATTGAACAAT
* *
699946 AAATCATAGTTCATATATA
1 AAATCAAAGTTCATGTATA
699965 GTTTTGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 12 0.28
30 11 0.26
31 20 0.47
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (31 bp):
AAATCAAAGTTCATGTATAAAATTGAACAAT
Found at i:700356 original size:17 final size:17
Alignment explanation
Indices: 700334--700369 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
700324 TCTATTAATT
*
700334 ATATTTTATTAAAAAAA
1 ATATTTTAATAAAAAAA
*
700351 ATATTTTAATAAATAAA
1 ATATTTTAATAAAAAAA
700368 AT
1 AT
700370 TACTTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTTAATAAAAAAA
Found at i:701040 original size:31 final size:32
Alignment explanation
Indices: 701003--701073 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
700993 ATTTAACAGC
* *
701003 TCAGTGACTTAAATA-AAAGATTTT-TAATAGT
1 TCAGTGACTTAAA-AGAAAAATTTTCGAATAGT
* *
701034 TTAGTGATTTAAAAGAAAAATTTTCGAATAGT
1 TCAGTGACTTAAAAGAAAAATTTTCGAATAGT
701066 TCAGTGAC
1 TCAGTGAC
701074 CAAATTGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 1 0.03
31 19 0.59
32 12 0.38
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (32 bp):
TCAGTGACTTAAAAGAAAAATTTTCGAATAGT
Found at i:701072 original size:32 final size:31
Alignment explanation
Indices: 700983--701073 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
700973 GGAACTTTGT
* *
700983 TTAAA-AAAAAA-TTT-AACAGCTCAGTGAC
1 TTAAATAAAAAATTTTGAATAGTTCAGTGAC
* * * *
701011 TTAAATAAAAGATTTTTAATAGTTTAGTGAT
1 TTAAATAAAAAATTTTGAATAGTTCAGTGAC
701042 TTAAA-AGAAAAATTTTCGAATAGTTCAGTGAC
1 TTAAATA-AAAAATTTT-GAATAGTTCAGTGAC
701074 CAAATTGTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 5 0.10
29 5 0.10
30 4 0.08
31 23 0.47
32 12 0.24
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAAATTTTGAATAGTTCAGTGAC
Found at i:708552 original size:26 final size:26
Alignment explanation
Indices: 708520--708570 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
708510 TAACAGCAAA
* * *
708520 TTTTGAAGAAGGAAAGGAAGCAAAAT
1 TTTTGAAGAAGAAAAAGAAACAAAAT
708546 TTTTGAAGAAGAAAAAGAAACAAAA
1 TTTTGAAGAAGAAAAAGAAACAAAA
708571 GGTTAGCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.18
Consensus pattern (26 bp):
TTTTGAAGAAGAAAAAGAAACAAAAT
Found at i:711428 original size:26 final size:26
Alignment explanation
Indices: 711379--711428 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
711369 TCTGTTTAAA
**
711379 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
711405 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
711429 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:712497 original size:23 final size:23
Alignment explanation
Indices: 712421--712570 Score: 160
Period size: 23 Copynumber: 6.5 Consensus size: 23
712411 TAAACGGAAC
* * *
712421 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
712443 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* **
712465 GGGCAACAGAGAGCACACGCAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
712491 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
712514 AAACAGAGAGCACATACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
712537 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
712560 AAACAGAGAGC
1 AAACAGAGAGC
712571 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.17
23 69 0.65
25 13 0.12
26 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:712525 original size:46 final size:46
Alignment explanation
Indices: 712421--712570 Score: 187
Period size: 46 Copynumber: 3.2 Consensus size: 46
712411 TAAACGGAAC
* * * * *
712421 AAACAGAGAGTAC-CGAAGTACTAAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACGCAGTGCTAATCAGAGAGCACACAAAGTGCT
*
712465 GGGCAACAGAGAGCACACGCAGTGCTAATCAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACGCAGTGCTAATCAGAGAGCACACAAAGTGCT
**
712514 AAACAGAGAGCACATACAGTGCTAATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACGCAGTGCTAATCAGAGAGCACACAAAGTGCT
712560 AAACAGAGAGC
1 AAACAGAGAGC
712571 GCGCTAGTGT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
46 54 0.59
47 11 0.12
48 20 0.22
49 7 0.08
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (46 bp):
AAACAGAGAGCACACGCAGTGCTAATCAGAGAGCACACAAAGTGCT
Found at i:712559 original size:69 final size:68
Alignment explanation
Indices: 712421--712570 Score: 187
Period size: 69 Copynumber: 2.2 Consensus size: 68
712411 TAAACGGAAC
* * **
712421 AAACAGAGAGTAC-CGAAGTACTAAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACGC
1 AAACAGAGAGCACACAAAGTACTAAACAGAGAGCACATAAGTGCT--G-AACAGAGAGCACACAA
712485 AGTGCT
63 AGTGCT
* *
712491 AATCAGAGAGCACACAAAGTGCTAAACAGAGAGCACATACAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGCACACAAAGTACTAAACAGAGAGCACATA-AGTGCTGAA-CAGAGAGCACACAAA
712555 GTGCT
64 GTGCT
712560 AAACAGAGAGC
1 AAACAGAGAGC
712571 GCGCTAGTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
68 2 0.03
69 28 0.40
70 11 0.16
71 23 0.33
72 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (68 bp):
AAACAGAGAGCACACAAAGTACTAAACAGAGAGCACATAAGTGCTGAACAGAGAGCACACAAAGT
GCT
Found at i:712671 original size:24 final size:26
Alignment explanation
Indices: 712633--712680 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
712623 TCTACATGGG
712633 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
712659 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
712681 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.