Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009406.1 Hibiscus syriacus cultivar Beakdansim tig00113338_pilon, 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: 689325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:538622 original size:19 final size:20
Alignment explanation
Indices: 538579--538624 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
538569 AATTAAAAAA
*
538579 TATTTTAATATGTTTCAATT
1 TATTTTTATATGTTTCAATT
538599 T-TTTTTATAT-TTT-AATGT
1 TATTTTTATATGTTTCAAT-T
538617 TATTTTTA
1 TATTTTTA
538625 GTTTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 5 0.22
19 14 0.61
20 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTTTATATGTTTCAATT
Found at i:540245 original size:39 final size:39
Alignment explanation
Indices: 540202--540315 Score: 176
Period size: 39 Copynumber: 2.9 Consensus size: 39
540192 AGTTAAATAT
*
540202 GAAGACTCC-ACGACTGCATGGTGTCTTCAGGCAAATGAA
1 GAAGAC-CCAACGATTGCATGGTGTCTTCAGGCAAATGAA
540241 GAAGACCCAACGATTGCATGGTGTCTTCAGGCAAATGAA
1 GAAGACCCAACGATTGCATGGTGTCTTCAGGCAAATGAA
** *
540280 GAAGACCCAACGATTGCATGACGTCTTCAGACAAAT
1 GAAGACCCAACGATTGCATGGTGTCTTCAGGCAAAT
540316 AAAAAATATC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 2 0.03
39 68 0.97
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (39 bp):
GAAGACCCAACGATTGCATGGTGTCTTCAGGCAAATGAA
Found at i:541398 original size:28 final size:27
Alignment explanation
Indices: 541366--541420 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
541356 ATAAATGAAC
541366 TTGAAATCCTAAATTTACACAAATCAAT
1 TTGAAATCCTAAATTTACAC-AATCAAT
*
541394 TTGAAATCCTGAATTTACACAATCAAT
1 TTGAAATCCTAAATTTACACAATCAAT
541421 AGAACCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (27 bp):
TTGAAATCCTAAATTTACACAATCAAT
Found at i:545023 original size:10 final size:10
Alignment explanation
Indices: 545008--545032 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
544998 CAGCCTTCCT
545008 CCGCGTAACA
1 CCGCGTAACA
545018 CCGCGTAACA
1 CCGCGTAACA
545028 CCGCG
1 CCGCG
545033 GTGACAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.08
Consensus pattern (10 bp):
CCGCGTAACA
Found at i:549542 original size:15 final size:16
Alignment explanation
Indices: 549524--549559 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
549514 TAATAATCTA
*
549524 TTATTTTATTAA-ATT
1 TTATTTTACTAATATT
549539 TTATTTTACTAATATT
1 TTATTTTACTAATATT
549555 TTATT
1 TTATT
549560 ACTTTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTACTAATATT
Found at i:550700 original size:21 final size:21
Alignment explanation
Indices: 550674--550716 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
550664 TTCTGGGTTG
550674 TGTGCATCGATGCA-TCTTCAA
1 TGTGCATCGATGCACTC-TCAA
550695 TGTGCATCGATGCACTCTCAA
1 TGTGCATCGATGCACTCTCAA
550716 T
1 T
550717 TAAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTCTCAA
Found at i:564574 original size:145 final size:142
Alignment explanation
Indices: 564314--564603 Score: 537
Period size: 145 Copynumber: 2.0 Consensus size: 142
564304 TGGATCATCT
564314 GCTTAGTGCATTCCACCATGTATCCGGAATAACTGTTGAAATCATCAAAGTACATTAGGGAAAAA
1 GCTTAGTGCATTCCACCATGTATCCGGAATAACTGTTGAAATCATCAAAGTACATTAGGGAAAAA
564379 AACAGGAAAAACTTGGATTGGATTAGAATAGAGTACCTTAAGCTTATCCCCCATGAACGCCGGAG
66 AACAGGAAAAACTTGGATTGGATTAGAATAGAGTACCTTAAGCTTATCCCCCATGAACGCCGGAG
564444 CAGCGATACGGC
131 CAGCGATACGGC
564456 GCTTAGTGCATTCCACCATGTATCCGGAATAACTCTGTTGAAATCATCAAAGTACATTAGGGAGA
1 GCTTAGTGCATTCCACCATGTATCCGGAATAA--CTGTTGAAATCATCAAAGTACATTA-GG-GA
564521 AAAAAACAGG-AAAACTTGGATTGGATTAGAATAGAGTACCTTAAGCTTATCCCCCATGAACGCC
62 AAAAAACAGGAAAAACTTGGATTGGATTAGAATAGAGTACCTTAAGCTTATCCCCCATGAACGCC
564585 GGAGCAGCGATACGGC
127 GGAGCAGCGATACGGC
564601 GCT
1 GCT
564604 GGTGGTACCA
Statistics
Matches: 144, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
142 32 0.22
144 25 0.17
145 75 0.52
146 12 0.08
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (142 bp):
GCTTAGTGCATTCCACCATGTATCCGGAATAACTGTTGAAATCATCAAAGTACATTAGGGAAAAA
AACAGGAAAAACTTGGATTGGATTAGAATAGAGTACCTTAAGCTTATCCCCCATGAACGCCGGAG
CAGCGATACGGC
Found at i:566500 original size:5 final size:5
Alignment explanation
Indices: 566490--566514 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
566480 GGAATAGGAT
566490 GTGGG GTGGG GTGGG GTGGG GTGGG
1 GTGGG GTGGG GTGGG GTGGG GTGGG
566515 AGAATGGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GTGGG
Found at i:566914 original size:17 final size:16
Alignment explanation
Indices: 566894--566967 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 16
566884 TAAATTATTA
566894 ATTTTAATTTGTTATAT
1 ATTTTAATTT-TTATAT
*
566911 ATTTAAATTTTTAT-T
1 ATTTTAATTTTTATAT
* * *
566926 TTTTTAAATTATATAT
1 ATTTTAATTTTTATAT
*
566942 AATTTTAATTTTTATTTT
1 -ATTTTAATTTTTA-TAT
566960 ATTTTAAT
1 ATTTTAAT
566968 ATAATGTCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 11 0.24
16 5 0.11
17 27 0.60
18 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (16 bp):
ATTTTAATTTTTATAT
Found at i:566924 original size:16 final size:16
Alignment explanation
Indices: 566875--566956 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
566865 AAATTACGTA
*
566875 TTTAT-TATATAAATT
1 TTTATATATTTAAATT
*
566890 ATTA-AT-TTT-AATT
1 TTTATATATTTAAATT
566903 TGTTATATATTTAAATT
1 T-TTATATATTTAAATT
* *
566920 TTTATTTTTTTAAA-T
1 TTTATATATTTAAATT
* *
566935 TATATATAATTTTAATT
1 TTTATAT-ATTTAAATT
566952 TTTAT
1 TTTAT
566957 TTTATTTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 12 0.24
16 19 0.38
17 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (16 bp):
TTTATATATTTAAATT
Found at i:567210 original size:20 final size:20
Alignment explanation
Indices: 567173--567209 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
567163 TATTTACCTA
*
567173 TATTTTATAACTTTTATATT
1 TATTTTATAACTTATATATT
567193 TATTTTA-AACTTA-ATAT
1 TATTTTATAACTTATATAT
567210 ACTTTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 5 0.31
20 7 0.44
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTATAACTTATATATT
Found at i:570090 original size:18 final size:18
Alignment explanation
Indices: 570036--570081 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
570026 TGAGAAACCA
570036 ATAAAT-AAATA-AAAAT
1 ATAAATAAAATATAAAAT
**
570052 A-ACCTAAAATATAAAAT
1 ATAAATAAAATATAAAAT
570069 ATAAATAAAATAT
1 ATAAATAAAATAT
570082 TTAATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.09
16 6 0.26
17 6 0.26
18 9 0.39
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAATAAAATATAAAAT
Found at i:571225 original size:12 final size:11
Alignment explanation
Indices: 571208--571249 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
571198 TAAATAAATA
571208 TATAATATAATT
1 TATAATATAA-T
*
571220 TATAATATAAA
1 TATAATATAAT
571231 TAT-ATAT-AT
1 TATAATATAAT
571240 TATAATATAA
1 TATAATATAA
571250 GGACGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 8 0.31
11 4 0.15
12 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATAATATAAT
Found at i:571235 original size:20 final size:20
Alignment explanation
Indices: 571204--571249 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
571194 CCTGTAAATA
571204 AATATATAATATA-AT-TTAT
1 AATATA-AATATATATATTAT
571223 AATATAAATATATATATTAT
1 AATATAAATATATATATTAT
571243 AATATAA
1 AATATAA
571250 GGACGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 8 0.32
20 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAAATATATATATTAT
Found at i:571248 original size:25 final size:24
Alignment explanation
Indices: 571201--571249 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
571191 GGCCCTGTAA
571201 ATAAATATATAATATAATTTATAAT
1 ATAAATATATAATATAA-TTATAAT
571226 ATAAATATATATATTATAA-TATAA
1 ATAAATATATA-A-TATAATTATAA
571250 GGACGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 16 0.73
26 1 0.05
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAATATATAATATAATTATAAT
Found at i:571929 original size:105 final size:105
Alignment explanation
Indices: 571725--572391 Score: 1149
Period size: 105 Copynumber: 6.3 Consensus size: 105
571715 TGTTTCGTGG
* *** * *
571725 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAACCGGGAAAT-TACTTGTTGGCAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGT--TTGTTGACAACCA
* * *
571789 GCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGG-GC
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GGAGT
* *
571831 CCAATCTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTCGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
571896 GGCCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
571936 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
572001 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
572041 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTAGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
572106 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
572146 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTCGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
572211 GGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
572251 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
572316 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
572356 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
572392 GGTAAAACCT
Statistics
Matches: 537, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
104 2 0.00
105 492 0.92
106 42 0.08
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:572614 original size:1 final size:1
Alignment explanation
Indices: 572608--572636 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
572598 CACATTCTGG
572608 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
572637 GGAGATGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:573213 original size:1 final size:1
Alignment explanation
Indices: 573207--573237 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
573197 ACCCCAAACG
573207 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
573238 CAACTTAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:585003 original size:12 final size:11
Alignment explanation
Indices: 584986--585027 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
584976 TAAATAAATA
584986 TATAATATAATT
1 TATAATATAA-T
*
584998 TATAATATAAA
1 TATAATATAAT
585009 TAT-ATAT-AT
1 TATAATATAAT
585018 TATAATATAA
1 TATAATATAA
585028 GGACGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 8 0.31
11 4 0.15
12 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATAATATAAT
Found at i:585013 original size:20 final size:20
Alignment explanation
Indices: 584982--585027 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
584972 CCTGTAAATA
584982 AATATATAATATA-AT-TTAT
1 AATATA-AATATATATATTAT
585001 AATATAAATATATATATTAT
1 AATATAAATATATATATTAT
585021 AATATAA
1 AATATAA
585028 GGACGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 8 0.32
20 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAAATATATATATTAT
Found at i:585026 original size:25 final size:24
Alignment explanation
Indices: 584979--585027 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
584969 GGCCCTGTAA
584979 ATAAATATATAATATAATTTATAAT
1 ATAAATATATAATATAA-TTATAAT
585004 ATAAATATATATATTATAA-TATAA
1 ATAAATATATA-A-TATAATTATAA
585028 GGACGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 16 0.73
26 1 0.05
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAATATATAATATAATTATAAT
Found at i:587718 original size:19 final size:19
Alignment explanation
Indices: 587694--587737 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
587684 TTAGTTCATT
*
587694 GATGCATAAGGAGTGCATC
1 GATGCATAAGGACTGCATC
*
587713 GATGCATGAGGACTGCATC
1 GATGCATAAGGACTGCATC
587732 GATGCA
1 GATGCA
587738 CCTACTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.20
Consensus pattern (19 bp):
GATGCATAAGGACTGCATC
Found at i:588526 original size:20 final size:20
Alignment explanation
Indices: 588489--588526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
588479 TTCGGGATAT
*
588489 AGTGGTTCTTTGGAACAATC
1 AGTGGTTCTTCGGAACAATC
*
588509 AGTGGTTCTTCGGGACAA
1 AGTGGTTCTTCGGAACAA
588527 ATATTCAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
AGTGGTTCTTCGGAACAATC
Found at i:591171 original size:21 final size:21
Alignment explanation
Indices: 591147--591202 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
591137 GCCCCAAAAG
*
591147 AATTACAAGAATTAAAGATTT
1 AATTACAAGAATTAAAGATTC
591168 AATTACAAGAATTAAAGATTC
1 AATTACAAGAATTAAAGATTC
591189 AATTACAAGAATTA
1 AATTACAAGAATTA
591203 TTGGACAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (21 bp):
AATTACAAGAATTAAAGATTC
Found at i:594695 original size:19 final size:19
Alignment explanation
Indices: 594671--594720 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
594661 GAATGCAATT
594671 AGTGCATCGATGAATAAGG
1 AGTGCATCGATGAATAAGG
* * *
594690 AGTGCATCGAAGCATGAGG
1 AGTGCATCGATGAATAAGG
594709 AGTGCATCGATG
1 AGTGCATCGATG
594721 CACCTACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (19 bp):
AGTGCATCGATGAATAAGG
Found at i:595235 original size:24 final size:21
Alignment explanation
Indices: 595208--595265 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
595198 ATGTGAAATA
595208 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
595232 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
595254 ATGAAAAGTGAT
1 ATG-AAAGTGAT
595266 GAGAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:595509 original size:18 final size:18
Alignment explanation
Indices: 595486--595558 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
595476 AAACATATAC
595486 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
595504 AGTGGTTCTTCGGAATAAT
1 AGTGGTCCTTCGGGA-CAT
595523 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
595542 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
595559 AATATTCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:608809 original size:20 final size:21
Alignment explanation
Indices: 608708--608818 Score: 86
Period size: 20 Copynumber: 5.4 Consensus size: 21
608698 AAATAATCAA
* **
608708 CAAATTCGCAACGCGAACTTT
1 CAAATTCGCAACACGAGTTTT
* *
608729 -AATTTCGCAACA-TAGTTTT
1 CAAATTCGCAACACGAGTTTT
*
608748 CAAATTCGCAACACGAATTTTT
1 CAAATTCGCAACACG-AGTTTT
* * *
608770 CAGATTCGTAACTC-AGTTTT
1 CAAATTCGCAACACGAGTTTT
*
608790 AAAATTCGCAACACGA-TTTT
1 CAAATTCGCAACACGAGTTTT
*
608810 CTAATTCGC
1 CAAATTCGC
608819 GACGCTAATT
Statistics
Matches: 68, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
19 4 0.06
20 47 0.69
21 1 0.01
22 16 0.24
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
CAAATTCGCAACACGAGTTTT
Found at i:608875 original size:20 final size:20
Alignment explanation
Indices: 608812--608867 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
608802 ACGATTTTCT
*
608812 AATTCGCGACGCTAATTCCG
1 AATTCGCGACCCTAATTCCG
608832 AATTCGCGACCCTAATTCCG
1 AATTCGCGACCCTAATTCCG
608852 AATTCGCGACCCTAAT
1 AATTCGCGACCCTAAT
608868 ATCGAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (20 bp):
AATTCGCGACCCTAATTCCG
Found at i:608914 original size:27 final size:27
Alignment explanation
Indices: 608879--608958 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
608869 TCGAATTATA
*
608879 AAATC-GCGTTGCGAATCGTGAATTAG
1 AAATCAGCGTCGCGAATCGTGAATTAG
* * * *
608905 GAATTAGCGTCGCGAATTGTGAATTCG
1 AAATCAGCGTCGCGAATCGTGAATTAG
608932 AAATCAGCGTCGCGAATTCG-GAATTAG
1 AAATCAGCGTCGCGAA-TCGTGAATTAG
608959 CGTTGCGAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
26 3 0.07
27 38 0.88
28 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (27 bp):
AAATCAGCGTCGCGAATCGTGAATTAG
Found at i:608976 original size:20 final size:20
Alignment explanation
Indices: 608925--608968 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
608915 CGCGAATTGT
* *
608925 GAATTCGAAATCAGCGTCGC
1 GAATTCGGAATTAGCGTCGC
*
608945 GAATTCGGAATTAGCGTTGC
1 GAATTCGGAATTAGCGTCGC
608965 GAAT
1 GAAT
608969 CGCGAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
GAATTCGGAATTAGCGTCGC
Found at i:609285 original size:2 final size:2
Alignment explanation
Indices: 609278--609308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
609268 AATTGATTTA
609278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
609309 AAGAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:618361 original size:20 final size:19
Alignment explanation
Indices: 618338--618377 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
618328 CACACCGATG
618338 ATGATTCATTTGTAATTTTA
1 ATGATT-ATTTGTAATTTTA
* *
618358 ATGATTTTTTTTAATTTTA
1 ATGATTATTTGTAATTTTA
618377 A
1 A
618378 ATTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (19 bp):
ATGATTATTTGTAATTTTA
Found at i:622892 original size:32 final size:31
Alignment explanation
Indices: 622856--622923 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
622846 TAAAATAAAA
* *
622856 TAAGATACAATCATTTTACGTTTTTATTTAAT
1 TAAGATACAATCACTTT-CATTTTTATTTAAT
***
622888 TAAGATTTTATCACTTTCATTTTTATTTAAT
1 TAAGATACAATCACTTTCATTTTTATTTAAT
622919 TAAGA
1 TAAGA
622924 CGTGGTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (31 bp):
TAAGATACAATCACTTTCATTTTTATTTAAT
Found at i:623124 original size:15 final size:16
Alignment explanation
Indices: 623104--623138 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
623094 AAAATATTTT
623104 AAAT-AAGTTAATAAA
1 AAATAAAGTTAATAAA
623119 AAATAAAAGTTAATAAA
1 AAAT-AAAGTTAATAAA
623136 AAA
1 AAA
623139 AATACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
17 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATAAAGTTAATAAA
Found at i:629898 original size:20 final size:20
Alignment explanation
Indices: 629873--629910 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
629863 AAAAAAGAAC
629873 TAGTATCGATACTATACCAA
1 TAGTATCGATACTATACCAA
*
629893 TAGTATCGATACTTTACC
1 TAGTATCGATACTATACC
629911 GCAGAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
TAGTATCGATACTATACCAA
Found at i:639453 original size:12 final size:12
Alignment explanation
Indices: 639436--639460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
639426 ATATATGTGT
639436 GTGTGTGTGCGC
1 GTGTGTGTGCGC
639448 GTGTGTGTGCGC
1 GTGTGTGTGCGC
639460 G
1 G
639461 CGCGTGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (12 bp):
GTGTGTGTGCGC
Found at i:639453 original size:16 final size:16
Alignment explanation
Indices: 639432--639466 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
639422 ATATATATAT
* *
639432 GTGTGTGTGTGTGCGC
1 GTGTGTGTGCGCGCGC
639448 GTGTGTGTGCGCGCGC
1 GTGTGTGTGCGCGCGC
639464 GTG
1 GTG
639467 ATAACAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (16 bp):
GTGTGTGTGCGCGCGC
Found at i:639890 original size:5 final size:5
Alignment explanation
Indices: 639874--639923 Score: 84
Period size: 5 Copynumber: 10.0 Consensus size: 5
639864 CTACCACGTC
639874 CACGA CCACGA CACGA CACGA -ACGA CACGA CACGA CACGA CACGA CACGA
1 CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
639924 GACGGCGGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.09
5 34 0.79
6 5 0.12
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:640366 original size:6 final size:6
Alignment explanation
Indices: 640355--640435 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
640345 TCTCGTCTCG
640355 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
640403 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
640436 AATACGTGTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:641809 original size:16 final size:16
Alignment explanation
Indices: 641788--641820 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
641778 TCAAGCCAGG
641788 TGGAAGAGTACCCGAT
1 TGGAAGAGTACCCGAT
641804 TGGAAGAGTACCCGAT
1 TGGAAGAGTACCCGAT
641820 T
1 T
641821 TCCACAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (16 bp):
TGGAAGAGTACCCGAT
Found at i:649816 original size:20 final size:21
Alignment explanation
Indices: 649788--649826 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
649778 TAGATAAAAC
649788 AAATAATT-ATATAAAAATTT
1 AAATAATTAATATAAAAATTT
* *
649808 AAATTATTAATTTAAAAAT
1 AAATAATTAATATAAAAAT
649827 AAGATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATAATTAATATAAAAATTT
Found at i:652588 original size:30 final size:30
Alignment explanation
Indices: 652552--652626 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
652542 TAAGTGATAT
* *
652552 TTTATAT-AAGTTTAGGAGTTAAATTAACAC
1 TTTATATAAAATTTAGGA-TCAAATTAACAC
* *
652582 TTTATATAAAATTTAGGATCAAATTAATAT
1 TTTATATAAAATTTAGGATCAAATTAACAC
*
652612 TTTATCTAAAATTTA
1 TTTATATAAAATTTA
652627 ATCATTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 30 0.77
31 9 0.23
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTATATAAAATTTAGGATCAAATTAACAC
Found at i:652832 original size:17 final size:16
Alignment explanation
Indices: 652792--652832 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
652782 TTTGTCTACC
652792 AAAAATAAT-TATTTT
1 AAAAATAATATATTTT
*
652807 AATAA-AATATATTTTT
1 AAAAATAATATA-TTTT
652823 AAAAATAATA
1 AAAAATAATA
652833 AGGTAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.14
15 6 0.29
16 8 0.38
17 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATAATATATTTT
Found at i:661633 original size:50 final size:50
Alignment explanation
Indices: 661558--661663 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
661548 GAAGCTGAGA
661558 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
1 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
661608 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
1 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
661658 AAACTG
1 AAACTG
661664 TCTTTCTGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (50 bp):
AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
Found at i:665939 original size:21 final size:20
Alignment explanation
Indices: 665853--666010 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
665843 AAATGACCAA
**
665853 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
665872 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
665892 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
665912 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
665933 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
665954 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
665974 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
665995 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
666011 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:666020 original size:20 final size:20
Alignment explanation
Indices: 665977--666170 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
665967 CGATTTTCCA
* ** *
665977 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
665997 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
666017 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
666037 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
666057 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
666077 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
666097 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
666117 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
666137 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
666158 AAATCGCAACGCG
1 AAATCGCAACGCG
666171 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:666061 original size:60 final size:60
Alignment explanation
Indices: 665977--666170 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
665967 CGATTTTCCA
* ** * *
665977 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
* * ***
666037 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAA-TGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACT-CGTATCCGT
* ** *
666097 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACTCGTATCCGT
666158 AAATCGCAACGCG
1 AAATCGCAACGCG
666171 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.72
61 30 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
Found at i:666591 original size:33 final size:33
Alignment explanation
Indices: 666552--666622 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
666542 TTCACTTAGA
*
666552 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
666585 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
666618 TTTCA
1 TTTCA
666623 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:666759 original size:41 final size:41
Alignment explanation
Indices: 666701--666778 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
666691 TTGCAGAAGA
*
666701 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
666742 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
666779 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:666775 original size:21 final size:21
Alignment explanation
Indices: 666702--666777 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
666692 TGCAGAAGAG
*
666702 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
666723 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
666743 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
666764 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
666778 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:666781 original size:14 final size:14
Alignment explanation
Indices: 666762--666818 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
666752 GAGAAATGAA
666762 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
666776 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
666795 AATCGCAACGAGAG
1 AATCGCAACGAGAG
666809 AATCGCAACG
1 AATCGCAACG
666819 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:666797 original size:33 final size:33
Alignment explanation
Indices: 666757--666821 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
666747 AACGAGAGAA
666757 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
666790 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
666822 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:666830 original size:33 final size:33
Alignment explanation
Indices: 666760--666834 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
666750 GAGAGAAATG
* **
666760 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
666793 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
666826 AAAATCGCA
1 AAAATCGCA
666835 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:666852 original size:19 final size:19
Alignment explanation
Indices: 666830--666927 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
666820 GAAACCAAAA
*
666830 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
666849 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
666863 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
666882 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
666896 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
666915 TCGCGTTGCGATT
1 TCGCGTTGCGATT
666928 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:666871 original size:14 final size:14
Alignment explanation
Indices: 666852--666941 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
666842 TTTCATTTCG
666852 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
666866 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
666885 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
666899 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
666918 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
666932 CGTTGCGATT
1 CGTTGCGATT
666942 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:666877 original size:33 final size:33
Alignment explanation
Indices: 666835--666949 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
666825 CAAAATCGCA
666835 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
666868 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
666901 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
666934 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
666950 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:668805 original size:93 final size:93
Alignment explanation
Indices: 668646--669114 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
668636 TAGATTGCTT
* *
668646 AGTAAATTTATTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
668711 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
668739 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
668804 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
668832 AGTAAATTTGTTCGGTTGCCGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
668897 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
668925 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
668990 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
669018 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
669083 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
669110 AGTAA
1 AGTAA
669115 TGCAATCCAT
Statistics
Matches: 372, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 366 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:669202 original size:19 final size:19
Alignment explanation
Indices: 669162--669290 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
669152 TAGTTTACTT
* *
669162 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
669182 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
669201 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
669220 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
669234 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
669253 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
669267 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
669286 TCGCA
1 TCGCA
669291 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:669236 original size:33 final size:32
Alignment explanation
Indices: 669198--669290 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
669188 CGCGAAACCA
**
669198 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
669230 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
669263 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
669291 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:669288 original size:52 final size:52
Alignment explanation
Indices: 669162--669290 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
669152 TAGTTTACTT
* **
669162 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
669214 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
669267 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
669291 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:669308 original size:19 final size:19
Alignment explanation
Indices: 669286--669420 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
669276 GAAACCAAAA
*
669286 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
669305 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
669321 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
669338 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
669354 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
669371 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
669390 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
669410 TCGTGTTGCGA
1 TCGCGTTGCGA
669421 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:669327 original size:14 final size:14
Alignment explanation
Indices: 669308--669364 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
669298 TTTCATTTCG
669308 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
669322 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
669339 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
669355 CGTTGCGATT
1 CGTTGCGATT
669365 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:669333 original size:33 final size:33
Alignment explanation
Indices: 669291--669383 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
669281 CAAAATCGCA
*
669291 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
669324 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
669357 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
669384 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:671365 original size:14 final size:14
Alignment explanation
Indices: 671346--671381 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
671336 ATTGTTTAAT
671346 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
671360 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
671374 TGATTTGT
1 TGATTTGT
671382 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:671520 original size:19 final size:19
Alignment explanation
Indices: 671488--671585 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
671478 AAAAATGACT
671488 ATCGCAAT-CTGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
671507 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
671526 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
671540 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
671559 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
671579 ATCGCAA
1 ATCGCAA
671586 CGAGAGAATC
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 36 0.53
20 17 0.25
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:671617 original size:53 final size:53
Alignment explanation
Indices: 671488--671603 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
671478 AAAAATGACT
671488 ATCGCAAT-CTGAAATGAAAATCGCAATGC-GAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
*
671540 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
671593 ATCGCAATGCG
1 ATCGCAATGCG
671604 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
52 27 0.44
53 34 0.56
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
Found at i:671647 original size:33 final size:33
Alignment explanation
Indices: 671610--671900 Score: 220
Period size: 33 Copynumber: 8.5 Consensus size: 33
671600 TGCGTTTATA
671610 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
671643 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *
671683 -TTT-GCGATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGC-A-TTGCGATTCTCTCGTTGCGATTTTC
671714 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
671747 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
671787 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
* *
671818 ATTTCGCATTGCGATTCTATCGTTGCGATTTTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
671851 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
671885 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
671901 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 27, Indels: 52
0.72 0.10 0.18
Matches are distributed among these distances:
31 14 0.07
32 13 0.06
33 87 0.42
34 27 0.13
35 11 0.05
36 8 0.04
37 4 0.02
38 18 0.09
39 9 0.04
40 14 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:671656 original size:19 final size:19
Alignment explanation
Indices: 671632--671900 Score: 282
Period size: 19 Copynumber: 15.4 Consensus size: 19
671622 GATTCTCTCG
671632 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
671651 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
671670 TTGCGA--TTC---TCTCT
1 TTGCGATTTTCATTTCGCA
671684 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
671703 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
671722 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
671736 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
671755 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
671774 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
671788 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
671807 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
671826 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
*
671840 TTGCGATTTTTATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
671860 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
671874 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
671893 TTGCGATT
1 TTGCGATT
671901 GTAATTTCCG
Statistics
Matches: 210, Mismatches: 14, Indels: 52
0.76 0.05 0.19
Matches are distributed among these distances:
14 38 0.18
16 25 0.12
17 23 0.11
18 3 0.01
19 110 0.52
20 11 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:671667 original size:52 final size:52
Alignment explanation
Indices: 671610--671872 Score: 490
Period size: 52 Copynumber: 5.0 Consensus size: 52
671600 TGCGTTTATA
671610 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
671662 ATTTCGCATTGCGATTCTCTCTTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
671714 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
671766 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
671818 ATTTCGCATTGCGATTCTATCGTTGCGATTTTTATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
671871 AT
1 AT
671873 GTTGGGATTT
Statistics
Matches: 206, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
52 189 0.92
53 17 0.08
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:674193 original size:12 final size:12
Alignment explanation
Indices: 674176--674200 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
674166 TCTTCGGGGA
674176 CTTTTTCTTCTT
1 CTTTTTCTTCTT
674188 CTTTTTCTTCTT
1 CTTTTTCTTCTT
674200 C
1 C
674201 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:675128 original size:20 final size:20
Alignment explanation
Indices: 675100--675289 Score: 195
Period size: 20 Copynumber: 9.5 Consensus size: 20
675090 AAATTTCAGT
* * * *
675100 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
675120 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
675140 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
675160 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
675180 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
675200 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
675220 GTTGCGATTTACGGATACGA
1 GTTGCGATTTACGGATACGC
* *
675240 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
675260 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
675280 GTTGCGATTT
1 GTTGCGATTT
675290 TGGAAAATCG
Statistics
Matches: 144, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
19 2 0.01
20 140 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:675306 original size:21 final size:21
Alignment explanation
Indices: 675276--675358 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
675266 ATTTTCATAT
*
675276 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
675297 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
675318 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
675339 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
675359 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:675349 original size:42 final size:43
Alignment explanation
Indices: 675256--675354 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
675246 ATTTATGTGT
* *
675256 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
675297 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
675339 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
675355 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:679507 original size:20 final size:20
Alignment explanation
Indices: 679484--679523 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
679474 AATTTCTTAA
679484 GAAAATTAGTGAATA-ATTTT
1 GAAAATT-GTGAATATATTTT
*
679504 GAAAATTTTGAATATATTTT
1 GAAAATTGTGAATATATTTT
679524 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
GAAAATTGTGAATATATTTT
Found at i:687509 original size:12 final size:12
Alignment explanation
Indices: 687492--687516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
687482 TTTAGACATT
687492 AAAATATTTTTA
1 AAAATATTTTTA
687504 AAAATATTTTTA
1 AAAATATTTTTA
687516 A
1 A
687517 GCACTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATATTTTTA
Found at i:687975 original size:19 final size:18
Alignment explanation
Indices: 687951--688003 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
687941 TTATTTAATA
687951 TTAATTTTACAAATATTAT
1 TTAATTTTACAAA-ATTAT
**
687970 TTAATTATTTTAAAATTAT
1 TTAATT-TTACAAAATTAT
* *
687989 TTTATTTTAAAAAAT
1 TTAATTTTACAAAAT
688004 GAGAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 7 0.25
19 16 0.57
20 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTTACAAAATTAT
Found at i:687979 original size:22 final size:24
Alignment explanation
Indices: 687940--687985 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
687930 AATGTTTAGA
687940 ATTATTTAATATTAATTTTACAAAT
1 ATTATTTAATATTAATTTTA-AAAT
687965 ATTATTT-A-ATT-ATTTTAAAAT
1 ATTATTTAATATTAATTTTAAAAT
687986 TATTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 3 0.14
24 1 0.05
25 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATTTAATATTAATTTTAAAAT
Found at i:688482 original size:33 final size:33
Alignment explanation
Indices: 688440--688519 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
688430 ATAAATCATG
688440 CTTTGCCCCCTTATTTTTTTACAATTAATTATA
1 CTTTGCCCCCTTATTTTTTTACAATTAATTATA
* ***
688473 CTTTGCCCCCTCATTTTTTTATGGTTAATTATA
1 CTTTGCCCCCTTATTTTTTTACAATTAATTATA
*
688506 CTTTGTCCCTCTTA
1 CTTTG-CCCCCTTA
688520 AGTTGAAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 34 0.85
34 6 0.15
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.51
Consensus pattern (33 bp):
CTTTGCCCCCTTATTTTTTTACAATTAATTATA
Done.