Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007980.1 Hibiscus syriacus cultivar Beakdansim tig00110419_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: 1499237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:248851 original size:195 final size:196
Alignment explanation
Indices: 248452--248970 Score: 581
Period size: 195 Copynumber: 2.6 Consensus size: 196
248442 GTAAACATAC
*
248452 GTGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAA-ATCGAAACCGATAATTATAAAGTAAT
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * * *
248514 AGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATAATAGAATAGGTCAACATAATG
65 AGGTAAATTTAC-A---AACCGGTAGAAATATACCGATTTTATAAGAAAATAGGTCAACATAATA
* * *
248579 TATCGATACAAATTTAAAAAGTGTCGATACATTTTGTCTAGAATGAATGTCAAACGAGGTGCACG
126 TATCGACACAAATTTAAAAAGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACA
248644 CATAAA
191 CATAAA
*
248650 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
248715 GGTAAATTTAC-AACCTGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATATATC
66 GGTAAATTTACAAACC-GGTAGAAATATACCGATTTTATAAGAAAATAGGTCAACATAATATATC
** ** *
248779 GACAC-GTTTTAAATTTGTGTCGATAC-TTTTTTCCAGAATGAATGTGC-AACGAGGTGCACACA
130 GACACAAATTTAAA-AAGTGTCGATACATTTTGTCCAGAATGAATGT-CAAACGAGGTGCACACA
248841 TAAA
193 TAAA
* * * * *
248845 GTGTCGATACATTTA--AAATTGTATTGATCCCAAAAACATCAAAATCGATAATTATATTGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * *
248908 AGGTAAATTTGTA-ATATTATCGGTATAAATATACTGATTTAATTAGAAAATAGGTCAATATAA
65 AGGTAAA-TT-TACA-A--ACCGGTAGAAATATACCGATTTTATAAGAAAATAGGTCAACATAA
248971 GTGTTACCTA
Statistics
Matches: 275, Mismatches: 33, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
193 3 0.01
194 45 0.16
195 62 0.23
196 57 0.21
197 1 0.00
198 60 0.22
199 11 0.04
200 36 0.13
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAAACCGGTAGAAATATACCGATTTTATAAGAAAATAGGTCAACATAATATATCG
ACACAAATTTAAAAAGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACACATAA
A
Found at i:249043 original size:64 final size:64
Alignment explanation
Indices: 248975--249098 Score: 214
Period size: 64 Copynumber: 1.9 Consensus size: 64
248965 ATATAAGTGT
*
248975 TACCTAATATGTTATTATATTTGATAATATTTCCGGTTAAATG-TCTATTTTATTATATAAGCTC
1 TACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGAT-TATTTTATTATATAAGCTC
*
249039 TACCTAATATGTTATTGTAATTGATAATATTTCCGGTTAAATGATTATTTTATTATATAA
1 TACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGATTATTTTATTATATAA
249099 ATATTACCTA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 56 0.98
65 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (64 bp):
TACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGATTATTTTATTATATAAGCTC
Found at i:249107 original size:64 final size:63
Alignment explanation
Indices: 248965--249127 Score: 204
Period size: 64 Copynumber: 2.6 Consensus size: 63
248955 AAATAGGTCA
* *
248965 ATATAAGTGTTACCTAATATGTTATTATATTTGATAATATTTCCGGTTAAATGTCTATTTTATT
1 ATATAAAT-TTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGTCTATTTTATT
* * *
249029 ATATAAGCTCTACCTAATATGTTATTGTAATTGATAATATTTCCGGTTAAATGAT-TATTTTATT
1 ATATAA-ATTTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATG-TCTATTTTATT
* * *
249093 ATATAAATATTACCTATTATATTA-TATAAGTGATA
1 ATATAAAT-TTACCTAATATGTTATTATAATTGATA
249128 CCTAATATGT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 10 0.12
64 74 0.86
65 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (63 bp):
ATATAAATTTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGTCTATTTTATT
Found at i:255818 original size:33 final size:33
Alignment explanation
Indices: 255776--255842 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
255766 TCGTTTAAAG
255776 TGAAAATTAATGTGGGATCCAGCTCTAAATCTA
1 TGAAAATTAATGTGGGATCCAGCTCTAAATCTA
*
255809 TGAAAATTAATGTGGGGTCCAGCTCTAAATCTA
1 TGAAAATTAATGTGGGATCCAGCTCTAAATCTA
255842 T
1 T
255843 CTCTGAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (33 bp):
TGAAAATTAATGTGGGATCCAGCTCTAAATCTA
Found at i:266121 original size:51 final size:50
Alignment explanation
Indices: 266011--266133 Score: 128
Period size: 51 Copynumber: 2.4 Consensus size: 50
266001 TATTTTATAA
*
266011 ATTTAATA-TTAATAAAATATTTTAATATCATTTTAATCAAAATATTAATT
1 ATTTAATATTTAATAAAATATTTTAATAT-ATTTTAATAAAAATATTAATT
* *
266061 ATTAAAATATTTAA-AATATATTTATTAATAT-TTTTAATAATAAATATTATATT
1 ATT-TAATATTTAATAAAATA-TT-TTAATATATTTTAATAA-AAATATTA-ATT
266114 -TTTAATATTATAATAAAATA
1 ATTTAATATT-TAATAAAATA
266134 ATCAATTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
50 3 0.05
51 23 0.38
52 19 0.32
53 15 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (50 bp):
ATTTAATATTTAATAAAATATTTTAATATATTTTAATAAAAATATTAATT
Found at i:266144 original size:23 final size:23
Alignment explanation
Indices: 266118--266168 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
266108 TATATTTTTA
266118 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAAT-ATATT
*
266141 ATATTATAATAATATAATATATT
1 ATATTATAATAAAATAATATATT
266164 ATATT
1 ATATT
266169 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTATAATAAAATAATATATT
Found at i:266163 original size:55 final size:54
Alignment explanation
Indices: 266095--266265 Score: 156
Period size: 54 Copynumber: 3.1 Consensus size: 54
266085 TTAATATTTT
266095 TAATAATAA-ATATTATATTTTTAATATTATAATAAAATAATCAATTATATTATAA
1 TAAT-ATAATATATTATATTTTTAATATT-TAATAAAATAATCAATTATATTATAA
* * *
266150 TAATATAATATATTATATTTTT-AT-TTTAATAATGTATAATAAATTAT-TAATAA
1 TAATATAATATATTATATTTTTAATATTTAATAA--AATAATCAATTATATTATAA
* * * * *
266203 TGA-ATAATATTATTTATATATTTAATA-TTAATATAATAATCTAATAATATTTTAA
1 TAATATAATA-TA-TTATATTTTTAATATTTAATAAAATAATC-AATTATATTATAA
266258 TAAATATA
1 T-AATATA
266266 TTTAAAATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
52 12 0.13
53 16 0.17
54 31 0.33
55 30 0.32
56 1 0.01
57 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (54 bp):
TAATATAATATATTATATTTTTAATATTTAATAAAATAATCAATTATATTATAA
Found at i:266179 original size:26 final size:26
Alignment explanation
Indices: 266075--266180 Score: 67
Period size: 26 Copynumber: 4.0 Consensus size: 26
266065 AAATATTTAA
**
266075 AATATATT-TATTAATATTTTTAATAAT
1 AATATATTATATTTTTA-TTTTAAT-AT
*
266102 AA-ATATTATATTTTTAATATTATAATAA
1 AATATATTATATTTTT-AT-TT-TAATAT
* **
266130 AATA-ATCA-ATTATATTATAATAATAT
1 AATATATTATATT-T-TTATTTTAATAT
266156 AATATATTATATTTTTATTTTAATA
1 AATATATTATATTTTTATTTTAATA
266181 ATGTATAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 19
0.67 0.11 0.21
Matches are distributed among these distances:
26 23 0.38
27 15 0.25
28 15 0.25
29 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATATTATATTTTTATTTTAATAT
Found at i:266274 original size:23 final size:23
Alignment explanation
Indices: 266227--266299 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
266217 TATATATTTA
*
266227 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
266251 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
266274 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
266297 ATA
1 ATA
266300 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:266589 original size:15 final size:15
Alignment explanation
Indices: 266560--266595 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
266550 TAAACATCGT
266560 AAAATG-TTTTCCAG
1 AAAATGTTTTTCCAG
*
266574 AAAATGTTTTTTCAG
1 AAAATGTTTTTCCAG
266589 AAAATGT
1 AAAATGT
266596 AATCCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
AAAATGTTTTTCCAG
Found at i:266627 original size:14 final size:14
Alignment explanation
Indices: 266600--266661 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
266590 AAATGTAATC
* *
266600 CATTTATCGGAAAA
1 CATTTTTCGAAAAA
266614 CATTTTTCGAAAAA
1 CATTTTTCGAAAAA
*
266628 TATTTTTCGAAAAA
1 CATTTTTCGAAAAA
* * *
266642 TATTTTCCGAAAAC
1 CATTTTTCGAAAAA
266656 CATTTT
1 CATTTT
266662 CAACGAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (14 bp):
CATTTTTCGAAAAA
Found at i:266633 original size:13 final size:14
Alignment explanation
Indices: 266610--266654 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
266600 CATTTATCGG
*
266610 AAAACATTTTTCGA
1 AAAATATTTTTCGA
266624 AAAATATTTTTCGA
1 AAAATATTTTTCGA
*
266638 AAAATATTTTCCGA
1 AAAATATTTTTCGA
266652 AAA
1 AAA
266655 CCATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAATATTTTTCGA
Found at i:267075 original size:70 final size:70
Alignment explanation
Indices: 266938--267075 Score: 152
Period size: 70 Copynumber: 2.0 Consensus size: 70
266928 AGCTTAAGAG
* * * * * * * * * *
266938 TCACATTTGTTCTTGTAGTATATCAAATTTATTATTTCCGCTCTTATCGTATTTTTGTATTATTT
1 TCACATTTGTCCTTGTAGTAGATCAAATGTATCATTTCCGCCCTAATCGTATTTTCGCATCAATT
267003 TAAAT
66 TAAAT
* *
267008 TCACATTTGTCCCTT-TAGTAGATCAAATGTATCATTTTCGCCCTAATCTTATTTTCGCATCAAT
1 TCACATTTGT-CCTTGTAGTAGATCAAATGTATCATTTCCGCCCTAATCGTATTTTCGCATCAAT
267072 TTAA
65 TTAA
267076 CCTTAAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
70 52 0.95
71 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (70 bp):
TCACATTTGTCCTTGTAGTAGATCAAATGTATCATTTCCGCCCTAATCGTATTTTCGCATCAATT
TAAAT
Found at i:268491 original size:3 final size:3
Alignment explanation
Indices: 268476--268535 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
268466 TATGTAACAT
* * * *
268476 TAA TAA TAG TAA TAA TAA TATA TTA TAA T-A TAA TAG TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
268521 TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA T
268536 TTTAATATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:268496 original size:33 final size:34
Alignment explanation
Indices: 268459--268535 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
268449 GGGCCTGTAA
* *
268459 AATATAAT-ATGTAACA-TTAATAATAGTAATAAT
1 AATATAATAATATAACAGTT-ATAATAATAATAAT
*
268492 AATATATTATAATATAATAGTTATAATAATAATAAT
1 AATATA--ATAATATAACAGTTATAATAATAATAAT
268528 AATATAAT
1 AATATAAT
268536 TTTAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 6 0.16
34 2 0.05
35 2 0.05
36 25 0.68
37 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (34 bp):
AATATAATAATATAACAGTTATAATAATAATAAT
Found at i:268530 original size:39 final size:37
Alignment explanation
Indices: 268478--268555 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
268468 TGTAACATTA
*
268478 ATAATAGTAATAATAATAT-ATTATAATATAATAGTT
1 ATAATAATAATAATAATATAATTATAATATAATAGTT
* *
268514 ATAATAATAATAATAATATAATTTTAATATAATATTT
1 ATAATAATAATAATAATATAATTATAATATAATAGTT
268551 ATAAT
1 ATAAT
268556 CCGGACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 18 0.47
37 20 0.53
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (37 bp):
ATAATAATAATAATAATATAATTATAATATAATAGTT
Found at i:268761 original size:23 final size:24
Alignment explanation
Indices: 268730--268775 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
268720 AAGATATATT
*
268730 GATAGAATATATAATTA-ATCGAG
1 GATAAAATATATAATTATATCGAG
268753 GATAAAATATATAATTATATCGA
1 GATAAAATATATAATTATATCGA
268776 TTTTATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (24 bp):
GATAAAATATATAATTATATCGAG
Found at i:270810 original size:127 final size:127
Alignment explanation
Indices: 270584--270839 Score: 467
Period size: 127 Copynumber: 2.0 Consensus size: 127
270574 GCCTTGTGAA
* * *
270584 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGTGGCACAACACAAACTCTTGTTG
1 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAAAACAAACTCTTGTTA
* *
270649 ACGTTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
66 ACGCTATCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
270711 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAAAACAAACTCTTGTTA
1 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAAAACAAACTCTTGTTA
270776 ACGCTATCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
66 ACGCTATCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
270838 TG
1 TG
270840 CCCTAAGTTG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 124 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (127 bp):
TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAAAACAAACTCTTGTTA
ACGCTATCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
Found at i:271376 original size:127 final size:127
Alignment explanation
Indices: 271219--271474 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 127
271209 GCCTTGTGAA
* *
271219 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAACACAAACTCTTGTTG
1 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAACACAAACTCTTATAG
* *
271284 ACGTTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCGACAATTGACTGC
66 ACGCTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
271346 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAACACAAACTCTTATAG
1 TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAACACAAACTCTTATAG
271411 ACGCTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
66 ACGCTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
271473 TG
1 TG
271475 CCCTAAGTTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 125 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.23
Consensus pattern (127 bp):
TGGCTCAACGCGGGACTGTTGCACTTGCACCCTCATCATCTGCGGCACAACACAAACTCTTATAG
ACGCTGTCGGAATCGAGTTGCTCCTAATCCCCGTAGACGGCAGCGGTCCCACAATTGACTGC
Found at i:271784 original size:132 final size:133
Alignment explanation
Indices: 271540--271892 Score: 389
Period size: 132 Copynumber: 2.7 Consensus size: 133
271530 CATCAGAAAG
* * * * *
271540 AAAGAGGCAATGGTCCGACAGTCGACCGCTGGTTTAAGTTGTGAGCATTGGCACCAATGGAGA-A
1 AAAG-GGCAATGGTCCGACAGTCGACTGCTGGTTTACGTTGCGAGCATGGGTACCAATGGAGATA
* * * **
271604 AGGGTTTATATTTGTTTGTCTTAGCCTTGGTGACGTCGGATTCCAGTTGTTCACCT-TCGAT-TG
65 AGGGTTTCTATTTGTTTCTCTTGGCCTAAGTGACGTCGGATTCCAGTTGTTC-CCTGTCGATCT-
271667 GAACGA
128 GAACGA
* * * *
271673 AAATGGCAATGGTCGGACAGTCGACTGCTGGTCTACGTTGCGAGCACGGGTACCAATGGA-ATAA
1 AAAGGGCAATGGTCCGACAGTCGACTGCTGGTTTACGTTGCGAGCATGGGTACCAATGGAGATAA
* ** *
271737 GGGTTTCTATTTGTTTCTCTTGGCCTAATTGGTGTCGGATTCGAGTTGTTCCCTGTCGATCTGAA
66 GGGTTTCTATTTGTTTCTCTTGGCCTAAGTGACGTCGGATTCCAGTTGTTCCCTGTCGATCTGAA
271802 CGA
131 CGA
* * * *
271805 AACGGGCAGTGGTCCGATAGTCGACTGCTGATTTAACG-TGCGAGCATTGGGT-CCAATGGAGAT
1 AAAGGGCAATGGTCCGACAGTCGACTGCTGGTTT-ACGTTGCGAGCA-TGGGTACCAATGGAGAT
*
271868 -AGGG-TTCATATTTATTTCTCTTGGC
64 AAGGGTTTC-TATTTGTTTCTCTTGGC
271893 GGCAGTGTAG
Statistics
Matches: 186, Mismatches: 27, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
131 7 0.04
132 166 0.89
133 13 0.07
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (133 bp):
AAAGGGCAATGGTCCGACAGTCGACTGCTGGTTTACGTTGCGAGCATGGGTACCAATGGAGATAA
GGGTTTCTATTTGTTTCTCTTGGCCTAAGTGACGTCGGATTCCAGTTGTTCCCTGTCGATCTGAA
CGA
Found at i:272652 original size:21 final size:20
Alignment explanation
Indices: 272626--272744 Score: 114
Period size: 21 Copynumber: 5.8 Consensus size: 20
272616 ATCAGTTTCC
272626 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
272647 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
272668 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
272687 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* *
272710 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
272730 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
272745 ACACATAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.01
20 19 0.23
21 59 0.71
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:272683 original size:42 final size:41
Alignment explanation
Indices: 272621--272744 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
272611 CGCAAATCAG
272621 TTTCCAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGATT-TTGAAAATCGCAACGCGAT
* * ** **
272663 TCTT-GAAAATCGCAATGCGATAGT-ACAAATTCGCATTGCGAT
1 T-TTCCAAAATCGCAACGCGATTTTGA-AAA-TCGCAACGCGAT
* *
272705 TTTCCAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGA
272745 ACACATAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 45 0.70
43 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGAT
Found at i:272735 original size:20 final size:20
Alignment explanation
Indices: 272626--272763 Score: 84
Period size: 21 Copynumber: 6.7 Consensus size: 20
272616 ATCAGTTTCC
* *
272626 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
* *
272647 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
*
272668 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
** * * *
272686 TACAAATTCGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
272710 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
272730 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
272749 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
272764 TATCCGTAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 34 0.35
21 54 0.56
22 4 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:272887 original size:20 final size:20
Alignment explanation
Indices: 272711--272879 Score: 198
Period size: 20 Copynumber: 8.4 Consensus size: 20
272701 CGATTTTCCA
* ** *
272711 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
272731 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
272751 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
272771 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
272791 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
272811 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
272831 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
272851 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
272871 AAATCGCAA
1 AAATCGCAA
272880 GGAGAATCTG
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 124 0.97
21 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:272892 original size:20 final size:20
Alignment explanation
Indices: 272711--272900 Score: 148
Period size: 20 Copynumber: 9.5 Consensus size: 20
272701 CGATTTTCCA
* ** *
272711 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
272731 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
272751 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
272771 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * **
272791 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGAGAATCCGT
* * *
272811 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
272831 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
272851 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
* *
272871 AAATCGCAAGGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
272891 AAATCACAAC
1 AAATCGCAAC
272901 ACTGAAATTT
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 143 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:273622 original size:24 final size:24
Alignment explanation
Indices: 273583--273629 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
273573 AAATTTGGTC
273583 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
273607 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
273630 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:274967 original size:33 final size:33
Alignment explanation
Indices: 274916--275126 Score: 318
Period size: 33 Copynumber: 6.2 Consensus size: 33
274906 CGGAAATTAC
274916 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
274949 AATCCCAAC-ATGAAAATCGCAATGCGGAAATG-A
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
274982 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
275015 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
275053 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
275086 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
275119 AATCGCAA
1 AATCGCAA
275127 TGCGAAATTA
Statistics
Matches: 163, Mismatches: 6, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
32 7 0.04
33 114 0.70
34 8 0.05
35 2 0.01
36 2 0.01
37 1 0.01
38 29 0.18
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:275072 original size:14 final size:14
Alignment explanation
Indices: 275053--275107 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
275043 GCGAAATGAA
275053 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
275067 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
275086 AATCGCAACGAGAG
1 AATCGCAACGAGAG
275100 AATCGCAA
1 AATCGCAA
275108 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:275123 original size:52 final size:52
Alignment explanation
Indices: 274958--275134 Score: 245
Period size: 52 Copynumber: 3.4 Consensus size: 52
274948 AAATCCCAAC
274958 ATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
275010 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
*
275060 ACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
275114 ATGAAAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
275135 TATAAACGCA
Statistics
Matches: 108, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
50 7 0.06
51 13 0.12
52 74 0.69
53 7 0.06
54 7 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:275150 original size:19 final size:19
Alignment explanation
Indices: 274930--275134 Score: 218
Period size: 19 Copynumber: 11.8 Consensus size: 19
274920 GCAACGAGAG
274930 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
274949 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
274963 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
*
274982 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
274996 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
275015 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
275034 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
275053 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
275067 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
275086 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
275100 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
275119 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
275135 TATAAACGCA
Statistics
Matches: 156, Mismatches: 8, Indels: 44
0.75 0.04 0.21
Matches are distributed among these distances:
13 1 0.01
14 41 0.26
15 2 0.01
16 8 0.05
17 6 0.04
18 3 0.02
19 92 0.59
20 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:275150 original size:104 final size:104
Alignment explanation
Indices: 274930--275134 Score: 360
Period size: 104 Copynumber: 2.0 Consensus size: 104
274920 GCAACGAGAG
274930 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGA
274995 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
275034 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAACGA
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATG-AAATCGCAACGA
275097 GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
64 GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
275135 TATAAACGCA
Statistics
Matches: 97, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 6 0.06
104 90 0.93
105 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (104 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGA
GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:275253 original size:52 final size:53
Alignment explanation
Indices: 275141--275256 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
275131 AAATTATAAA
*
275141 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
275194 CGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
275246 CGCATTGCGAT
1 CGCATTGCGAT
275257 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:275264 original size:19 final size:19
Alignment explanation
Indices: 275159--275256 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
275149 GATTCTCTCG
275159 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
275179 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
275198 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
275212 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
275231 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
275250 TTGCGAT
1 TTGCGAT
275257 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:275382 original size:14 final size:13
Alignment explanation
Indices: 275354--275411 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
275344 TTATGTTCGC
*
275354 ATCAATTACACAA
1 ATCAATTATACAA
275367 ATCAACTTATACAA
1 ATCAA-TTATACAA
* *
275381 ATCATCTTTTACAA
1 ATCA-ATTATACAA
*
275395 ATCAATTAAAC-A
1 ATCAATTATACAA
275407 ATCAA
1 ATCAA
275412 AAAATAAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 9 0.24
14 22 0.59
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTATACAA
Found at i:275992 original size:20 final size:20
Alignment explanation
Indices: 275967--276140 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
275957 CTTTAAATAT
275967 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
275987 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
276009 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
276028 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
276048 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
276068 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
276088 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
276108 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
276128 CGCGTTGCGATTT
1 CGCGTTGCGATTT
276141 TGGAAAATCG
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 112 0.85
21 15 0.11
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:276157 original size:21 final size:21
Alignment explanation
Indices: 276127--276209 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
276117 ATTTTCATAT
*
276127 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
276148 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
276169 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
276190 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
276210 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:276200 original size:42 final size:43
Alignment explanation
Indices: 276107--276205 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
276097 ATTTATGTGT
* *
276107 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
276148 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
276190 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
276206 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:277539 original size:200 final size:200
Alignment explanation
Indices: 277184--278200 Score: 1178
Period size: 200 Copynumber: 5.1 Consensus size: 200
277174 GTAAGCAGAC
277184 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
277249 GGTAATTTTGTAATATAACTGGTATAAATATATTGGTTTTATGTAAGAATATGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * * *
277314 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGGATACACAAAATGGTGAACGC
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCAAAAAATGGTGCACGC
277379 ATAAA
196 ATAAA
* * * * * *
277384 GTGTCGATATATTTATAAAAAGTGTCGATCCCAGAGACATCGAACCCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
277449 GATAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATATGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * *
277514 ATTGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGAATGCCCAAAAAAATCGTGCA
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT--CC-AAAAAATGGTGCA
277579 CGCATAAA
193 CGCATAAA
* * * *
277587 GTGTTGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACTCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
277652 GGTAATTTT-TCAATGTAACC-G-------ATA-------TATGTGAGAATGGGTCTATATAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATG
* * * * * * *
277701 TATCGACACATTTGAAATTGGTGTTGATACTTTTTTTCCAGAATGAATGCC-CAAAATGGTGAAC
130 TATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCAAAAAATGGTGCAC
277765 GCATAAA
194 GCATAAA
* * * *
277772 GTGTTGATACATTTTTAAAAAGTGTCGATCCCAAAGACATCG-AACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
277836 GGTAATTTTGTAATATAACCAGTATAAATATATCGGTATTATGTGAG-ATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * *
277900 ATCGACACTTTTTAATTTTGTGTCGATACCTTTTGTCCATAACGAATGCCCAAAAAAATGGTGCA
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT--CC-AAAAAATGGTGCA
*
277965 CACATAAA
193 CGCATAAA
* * * * *
277973 GTTTCGAAACATTTATAAAAAGTATAGATCCCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
278038 GGTAATTTT-TCAATGTAACTGGTATAAATATACCGGTTTTATGCGAGAATAGGTCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATG
* * * * * *
278102 TATCGACAC-TTATAGAATTTGTGTCGATACTTTTTGTCTAGAAGGAATGC-TAAAAGGGTGCAC
130 TATCGACACTTTTTA-AATTTGTGTCGATACTTTTTGTCCAGAATGAATCCAAAAAATGGTGCAC
* *
278165 CCATTAA
194 GCATAAA
* *
278172 GTGTCGATACATTTTTAAAAAGTGTCGAT
1 GTGTCGATACATTTATAAAAAGTATCGAT
278201 ACATTTCTAA
Statistics
Matches: 688, Mismatches: 102, Indels: 55
0.81 0.12 0.07
Matches are distributed among these distances:
184 37 0.05
185 57 0.08
187 2 0.00
188 62 0.09
192 3 0.00
195 3 0.00
198 53 0.08
199 50 0.07
200 158 0.23
201 53 0.08
202 67 0.10
203 143 0.21
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCAAAAAATGGTGCACGC
ATAAA
Found at i:277814 original size:185 final size:190
Alignment explanation
Indices: 277294--278200 Score: 807
Period size: 203 Copynumber: 4.6 Consensus size: 190
277284 GTTTTATGTA
* * * * * *
277294 AGAATATGTCTACATAATGTATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGG
1 AGAATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGA
* * * * * * *
277359 ATACAC-AAAATGGTGAACGCATAAAGTGTCGATATATTTATAAAAAGTGTCGATCCCAGAGACA
66 ATGCCCAAAAATGGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAAACA
* * * * *
277423 TCGAACCCCATAATTATAATATAATAGATAATTTTGT-AATGTAACCGGTATAAATATATCGGTT
131 TCGAAACCCATGATTATAATGTAATAGGTAATTTT-TCAATGTAACC---A-GAATATATC-G--
277487 TTATATG
188 ---T-TG
*
277494 AGAATAGGTCTACATAATGTATTGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGA
1 AGAATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGA
*
277559 ATGCCCAAAAAAATCGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAAA
66 ATGCCC--AAAAATGGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAAA
*
277624 CATCGAAACTCATGATTATAATGTAATAGGTAATTTTTCAATGTAACC-G-ATATAT-G-TG
129 CATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACCAGAATATATCGTTG
* * * * * * * * *
277682 AGAATGGGTCTATATAATGTATCGACACATTTGAAATTGGTGTTGATACTTTTTTTCCAGAATGA
1 AGAATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGA
* * *
277747 ATGCCC-AAAATGGTGAACGCATAAAGTGTTGATACATTTTTAAAAAGTGTCGATCCCA-AAGAC
66 ATGCCCAAAAATGGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAA-AC
* *
277810 ATCG-AACCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACCAGTATAAATATATCGGT
130 ATCGAAACCCATGATTATAATGTAATAGGTAATTTT-TCAATGTAACCAG----AATATATC-G-
277873 ATTATG
188 --T-TG
* * * *
277879 TGAGATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACCTTTTGTCCATAACG
1 AGA-ATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATG
* * * *
277944 AATGCCCAAAAAAATGGTGCACACATAAAGT-TTCGAAACATTTATAAAAAGTATAGATCCCATA
65 AATGCCC--AAAAATGGTGCACGCATAAAGTGTT-GATACATTTATAAAAAGTATCGATCCCAGA
* * *
278008 AACATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACTGGTATAAATATACCG
127 AACATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAAC---CA-GAATATATC-
278073 GTTTTATGCG
187 G---T-T--G
* * * * * * *
278083 AGAATAGGTCTAGAAAATGTATCGACAC-TTATAGAATTTGTGTCGATACTTTTTGTCTAGAAGG
1 AGAATAGGTCTACATAATGTATCGACACTTTTTA-ATTTTGTGTCGATACATTTTGTCCAGAATG
* * * * * * *
278147 AATG--CTAAAAGGGTGCACCCATTAAGTGTCGATACATTTTTAAAAAGTGTCGAT
65 AATGCCCAAAAATGGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGAT
278201 ACATTTCTAA
Statistics
Matches: 592, Mismatches: 80, Indels: 71
0.80 0.11 0.10
Matches are distributed among these distances:
184 39 0.07
185 56 0.09
188 63 0.11
190 6 0.01
192 1 0.00
195 1 0.00
197 10 0.02
198 57 0.10
199 38 0.06
200 65 0.11
201 51 0.09
202 58 0.10
203 143 0.24
204 3 0.01
205 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (190 bp):
AGAATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGA
ATGCCCAAAAATGGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAAACA
TCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACCAGAATATATCGTTG
Found at i:278005 original size:201 final size:199
Alignment explanation
Indices: 277676--278194 Score: 591
Period size: 202 Copynumber: 2.6 Consensus size: 199
277666 GTAACCGATA
* * * * * *
277676 TATGTGAGAATGGGTCTATATAATGTATCGACACATTTGAAATTGGTGTTGATACTTTTTTTCCA
1 TATGTGAGAATAGGTCTACATAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCA
* * * * * *
277741 GAATGAATGCCCAAAATGGTGAACGCATAAAGTGTTGATACATTTTTAAAAAGTGTCGATCCCA-
65 GAACGAATGCCCAAAATGGTGAACACATAAAGTGTTGAAACATTTATAAAAAGTATAGATCCCAT
277805 AAGACATCG-AACCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACCAGTATAAATATA
130 AA-ACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCAGTATAAATATA
*
277868 TCGGTAT
193 CCGGTAT
* *
277875 TATGTGAG-ATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACCTTTTGTCCA
1 TATGTGAGAATAGGTCTACATAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCA
* *
277939 TAACGAATGCCCAAAAAAATGGTGCACACATAAAGT-TTCGAAACATTTATAAAAAGTATAGATC
65 GAACGAATGCCC---AAAATGGTGAACACATAAAGTGTT-GAAACATTTATAAAAAGTATAGATC
* * **
278003 CCATAAACATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACTGGTATAAATA
126 CCATAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCAGTATAAATA
*
278068 TACCGGTTT
191 TACCGGTAT
* * * * *
278077 TATGCGAGAATAGGTCTAGAAAATGTATCGACACTTATAGAATTTGTGTCGATACTTTTTGTCTA
1 TATGTGAGAATAGGTCTACATAATGTATCGACACTTTTA-AATTTGTGTCGATACTTTTTGTCCA
* * * * * * * * *
278142 GAAGGAATG-CTAAAAGGGTGCACCCATTAAGTGTCGATACATTTTTAAAAAGT
65 GAACGAATGCCCAAAATGGTGAACACATAAAGTGTTGAAACATTTATAAAAAGT
278195 GTCGATACAT
Statistics
Matches: 271, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
198 57 0.21
199 42 0.15
200 3 0.01
201 50 0.18
202 67 0.25
203 52 0.19
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (199 bp):
TATGTGAGAATAGGTCTACATAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAG
AACGAATGCCCAAAATGGTGAACACATAAAGTGTTGAAACATTTATAAAAAGTATAGATCCCATA
AACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCAGTATAAATATACCG
GTAT
Found at i:278014 original size:386 final size:388
Alignment explanation
Indices: 277301--278056 Score: 1239
Period size: 386 Copynumber: 2.0 Consensus size: 388
277291 GTAAGAATAT
* *
277301 GTCTACATAATGTATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGGATACACA
1 GTCTACATAATGTATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATACACA
* *
277366 AAATGGTGAACGCATAAAGTGTCGATATATTTATAAAAAGTGTCGATCCCAGAGACATCGAACCC
66 AAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAGACATCGAACCC
* * *
277431 CATAATTATAATATAATAGATAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATATGAG
131 CATAATTATAATATAATAGATAATTTTGTAATATAACCAGTATAAATATATCGGTATTATATGAG
* *
277496 AATAGGTCTACATAATGTATTGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGAAT
196 AATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAACGAAT
* * *
277561 GCCCAAAAAAATCGTGCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAGAAACA
261 GCCCAAAAAAATCGTGCACACATAAAGTGTTGAAACATTTATAAAAAGTATAGATCCCAGAAACA
*
277626 TCGAAACTCATGATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATATGTGAGAATGG
326 TCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATATGTGAGAATGG
* * * * *
277689 GTCTATATAATGTATCGACACATTTGAAATTGGTGTTGATACTTTTTTTCCAGAATGAATGCCCA
1 GTCTACATAATGTATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATACACA
* *
277754 AAATGGTGAACGCATAAAGTGTTGATACATTTTTAAAAAGTGTCGATCCCAAAGACATCGAA-CC
66 AAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAGACATCGAACCC
* * *
277818 CATAATTATAATGTAATAGGTAATTTTGTAATATAACCAGTATAAATATATCGGTATTATGTGAG
131 CATAATTATAATATAATAGATAATTTTGTAATATAACCAGTATAAATATATCGGTATTATATGAG
* *
277883 -ATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACCTTTTGTCCATAACGAAT
196 AATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAACGAAT
* *
277947 GCCCAAAAAAATGGTGCACACATAAAGT-TTCGAAACATTTATAAAAAGTATAGATCCCATAAAC
261 GCCCAAAAAAATCGTGCACACATAAAGTGTT-GAAACATTTATAAAAAGTATAGATCCCAGAAAC
278011 ATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAAC
325 ATCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAAC
278057 TGGTATAAAT
Statistics
Matches: 340, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
385 2 0.01
386 161 0.47
387 61 0.18
388 116 0.34
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (388 bp):
GTCTACATAATGTATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATACACA
AAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAGACATCGAACCC
CATAATTATAATATAATAGATAATTTTGTAATATAACCAGTATAAATATATCGGTATTATATGAG
AATAGGTCTACATAATGTATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAACGAAT
GCCCAAAAAAATCGTGCACACATAAAGTGTTGAAACATTTATAAAAAGTATAGATCCCAGAAACA
TCGAAACCCATGATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATATGTGAGAATGG
Found at i:278194 original size:21 final size:21
Alignment explanation
Indices: 278170--278221 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
278160 TGCACCCATT
*
278170 AAGTGTCGATACATTTTTAAA
1 AAGTGTCGATACATTTCTAAA
278191 AAGTGTCGATACATTTCTAAA
1 AAGTGTCGATACATTTCTAAA
278212 AAGTGTCGAT
1 AAGTGTCGAT
278222 CCCAAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AAGTGTCGATACATTTCTAAA
Found at i:278650 original size:15 final size:15
Alignment explanation
Indices: 278630--278658 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
278620 TCTTTCTCAA
278630 AGCTCTTCTCAACCC
1 AGCTCTTCTCAACCC
278645 AGCTCTTCTCAACC
1 AGCTCTTCTCAACC
278659 ACAACCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.45, G:0.07, T:0.28
Consensus pattern (15 bp):
AGCTCTTCTCAACCC
Found at i:279001 original size:2 final size:2
Alignment explanation
Indices: 278994--279039 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
278984 ATGGGGAAAG
278994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279036 AT AT
1 AT AT
279040 CTGGATACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281871 original size:199 final size:198
Alignment explanation
Indices: 281463--282230 Score: 1057
Period size: 199 Copynumber: 3.9 Consensus size: 198
281453 TAAAGTTTCC
*
281463 CATAAAGTGTCGATACATTTATAAAAGATATCGATCCAAAAAACATCGAAACTGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAG-TATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * *
281528 GTAATAGGTAAATTTACAATGTGACCGGTATAAATATACCGATTTTATGAGCAAATAGGTCAGCA
65 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * *** * *
281593 TAAAGTATCGACACCTTTTAAATTTGAGTCGATAC-TTTTTGTCCGAGCCT--TTGCTC-AACGA
130 TAATGTATCGACA-CTTTTAAATTTGTGTCGATACATTTTT-TCC-ATAATGAATGC-CAAACGG
* * *
281654 GCTTCATG
191 GGTACACG
*
281662 CATAAAAGTGTCGATACATTTA-AAATTGTATCGATCCAAAAAACATCGAAACCGAAAATTATAA
1 CAT-AAAGTGTCGATACATTTATAAA-AGTATCGATCCAAAAAACATCGAAACCGAAAATTATAA
* *
281726 TGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGT-ATA
64 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCA-A
*
281790 CATAATGTATCGACACTGTTTAAATTTGTGTTGATACATTTTTTCCATAATGAATGCCAAACGGG
128 CATAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTTTCCATAATGAATGCCAAACGGG
281855 GTACACG
192 GTACACG
* *
281862 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCTC-AAAAACATCGAAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTAT-AAAAGTATCGATC-CAAAAAACATCGAAACCGAAAATTATAA
** * * *
281926 TGTAATAGGTAAATTTACAATGTAACATGTATAAGTATATCG-TTTTATGAGAAAATAGGTGAAC
64 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAAC
* * *
281990 ATAATGTATCGACACTTTTTAGATTTGTGTCGATACATTTTGTCCATAATGAATGCAAAACGGGG
129 ATAATGTATCGACAC-TTTTAAATTTGTGTCGATACATTTTTTCCATAATGAATGCCAAACGGGG
*
282055 TGCACG
193 TACACG
282061 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTAT-AAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
** *
282126 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGCTTTATGAGAAAATAGGTTAACA
65 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* *
282191 TAGTGTATCGACACTTTTAAATTTATGTCGATACATTTTT
130 TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTTT
282231 AAATTACGCG
Statistics
Matches: 510, Mismatches: 44, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
198 6 0.01
199 355 0.70
200 145 0.28
201 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTATAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACAT
AATGTATCGACACTTTTAAATTTGTGTCGATACATTTTTTCCATAATGAATGCCAAACGGGGTAC
ACG
Found at i:282201 original size:399 final size:398
Alignment explanation
Indices: 281463--282230 Score: 1116
Period size: 399 Copynumber: 1.9 Consensus size: 398
281453 TAAAGTTTCC
*
281463 CATAAAGTGTCGATACATTTATAAAAGATATCGATCCAAAAAACATCGAAACTGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAGATATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * * *
281528 GTAATAGGTAAATTTACAATGTGACCGGTATAAATATACCGATTTTATGAGCAAATAGGTCAGCA
66 GTAATAGGTAAATTTACAATGTAACAGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* ** * ** *
281593 TAAAGTATCGACACCTTTTAAATTTGAGTCGATACTTTTTGTCCGAGCCTTTGCTCAACGAGCTT
131 TAAAGTATCGACACCTTTTAAATTTGAGTCGATACATTTTGTCCGAGAATATGCAAAACGAGCTG
* **
281658 CATGCATAAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACATCGAAACCGAAAATTA
196 CACGCATAAAAGTGTCGATACATTTAAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTA
*
281723 TAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGATTTTATGAGAAAATAGGTA
261 TAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGACTTTATGAGAAAATAGGTA
* *
281788 TACATAATGTATCGACACTGTTTAAATTTGTGTTGATACATTTTTTCCATAATGAATGCCAAACG
326 TACATAATGTATCGACACT-TTTAAATTTATGTCGATACATTTTTTCCATAATGAATGCCAAACG
281853 GGGTACACG
390 GGGTACACG
* *
281862 CATAAAGTGTCGATACATTTTTAAAA-AGTATCGATCTC-AAAAACATCGAAACCGATAATTATA
1 CATAAAGTGTCGATACATTTATAAAAGA-TATCGATC-CAAAAAACATCGAAACCGAAAATTATA
* * * *
281925 ATGTAATAGGTAAATTTACAATGTAACATGTATAAGTATATCG-TTTTATGAGAAAATAGGTGAA
64 ATGTAATAGGTAAATTTACAATGTAACAGGTATAAATATACCGATTTTATGAGAAAATAGGTCAA
* * * * * *
281989 CATAATGTATCGACACTTTTTAGATTTGTGTCGATACATTTTGTCC-ATAATGAATGCAAAACGG
129 CATAAAGTATCGACACCTTTTAAATTTGAGTCGATACATTTTGTCCGAGAAT--ATGCAAAACGA
*
282053 GGTGCACGCAT-AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAA
192 GCTGCACGCATAAAAGTGTCGATACATTTA-AAAAAGTATCGATCCAAAAAACATCGAAACCGAA
* * *
282117 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGCTTTATGAGAAAAT
256 AATTATAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGACTTTATGAGAAAAT
*
282182 AGGT-TAACATAGTGTATCGACACTTTTAAATTTATGTCGATACATTTTT
321 AGGTAT-ACATAATGTATCGACACTTTTAAATTTATGTCGATACATTTTT
282231 AAATTACGCG
Statistics
Matches: 328, Mismatches: 35, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
397 2 0.01
398 102 0.31
399 223 0.68
400 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (398 bp):
CATAAAGTGTCGATACATTTATAAAAGATATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACAGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACA
TAAAGTATCGACACCTTTTAAATTTGAGTCGATACATTTTGTCCGAGAATATGCAAAACGAGCTG
CACGCATAAAAGTGTCGATACATTTAAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTA
TAATGTAATAGGTAAATATACAATGTAACCGATATAAATATACCGACTTTATGAGAAAATAGGTA
TACATAATGTATCGACACTTTTAAATTTATGTCGATACATTTTTTCCATAATGAATGCCAAACGG
GGTACACG
Found at i:286406 original size:198 final size:199
Alignment explanation
Indices: 285905--286422 Score: 614
Period size: 200 Copynumber: 2.6 Consensus size: 199
285895 TGTCTAGAAT
** *
285905 ATAAAGTGTCGATACATTTATTAAAAGTATCAATCTCAATTACATCGAAACCGATAATTATAATA
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCAATCTCAAAAACATCGAAACCGATAATTATAATG
* * * * *
285970 TAATAGATAAATTTACAATGTAACAAATATAAATATATTGGTTTTATAAGAAAATAGGTTAGCAT
65 TAATAGGTAAATTTACAATGTTACAGATATAAATATACTGGTTTTATAAGAAAATAGGTTAGAAT
* * *
286035 AAAGTATCGATACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGGGGTG
130 AAAGTATCAATACTATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTG
*
286100 CACGC
195 CACAC
* * *
286105 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCTCATAAACATCGAAACCGATAATTACAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCAATCTCAAAAACATCGAAACCGATAATTATAATG
* * * * * *
286170 TGATATGTAAATTTACAATG-TACCCGATAGAAATATACTGGTTTTATGAGAAAATATGTTTA-A
65 TAATAGGTAAATTTACAATGTTA-CAGATATAAATATACTGGTTTTATAAGAAAATA-GGTTAGA
* * * * *
286233 ATAATGTATTAATACTTTTTAAGTTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGG
128 ATAAAGTATCAATACTATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGG
* *
286297 TGTATAC
193 TGCACAC
* **
286304 ATAAAGTGTCGATACATTTA-AAATTGTATCAATCAAAAAAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAA-AGTATCAATCTCAAAAACATCGAAACCGATAATTATAATG
** ** * * *
286368 TAATAGGTAAATTTGTAATGTTATTGGTATAAATATACT-GTTTTCTTAGAAAATA
65 TAATAGGTAAATTTACAATGTTACAGATATAAATATACTGGTTTTATAAGAAAATA
286423 AGTCAATATA
Statistics
Matches: 270, Mismatches: 44, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
197 17 0.06
198 62 0.23
199 47 0.17
200 140 0.52
201 4 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (199 bp):
ATAAAGTGTCGATACATTTATAAAAGTATCAATCTCAAAAACATCGAAACCGATAATTATAATGT
AATAGGTAAATTTACAATGTTACAGATATAAATATACTGGTTTTATAAGAAAATAGGTTAGAATA
AAGTATCAATACTATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGC
ACAC
Found at i:292316 original size:20 final size:19
Alignment explanation
Indices: 292290--292337 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
292280 TAATATACTT
* **
292290 TTAAAAATTATAATTAATA
1 TTAAAAATTAAAAAAAATA
292309 TTATAAAATTAAAAAAAATA
1 TTA-AAAATTAAAAAAAATA
292329 TTAAAAATT
1 TTAAAAATT
292338 GTACAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAATTAAAAAAAATA
Found at i:293324 original size:15 final size:15
Alignment explanation
Indices: 293305--293344 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
293295 CAGCTGGGGC
293305 CTTCTCGGCTGGCTTT
1 CTTCTCGGCTGG-TTT
293321 -TTCTCGGCTGGTTT
1 CTTCTCGGCTGGTTT
293335 CTTCTCGGCT
1 CTTCTCGGCT
293345 TTCGGTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.00, C:0.30, G:0.25, T:0.45
Consensus pattern (15 bp):
CTTCTCGGCTGGTTT
Found at i:294981 original size:33 final size:33
Alignment explanation
Indices: 294938--295002 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
294928 TCACCCCATA
* *
294938 AATCCGTAAAGTTAACTTAGAGCGAATTATAAG
1 AATCCCTAAAGTTAACTTAGAGCGAATGATAAG
*
294971 AATCCCTAAAGTTAACTTAGAGTGAATGATAA
1 AATCCCTAAAGTTAACTTAGAGCGAATGATAA
295003 AATTGAGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (33 bp):
AATCCCTAAAGTTAACTTAGAGCGAATGATAAG
Found at i:295243 original size:15 final size:16
Alignment explanation
Indices: 295223--295255 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
295213 AATTTTAGAA
295223 AAAAAATAATA-TTTT
1 AAAAAATAATACTTTT
295238 AAAAAATAATACTTTT
1 AAAAAATAATACTTTT
295254 AA
1 AA
295256 CTTTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAAATAATACTTTT
Found at i:297386 original size:42 final size:40
Alignment explanation
Indices: 297340--297509 Score: 96
Period size: 40 Copynumber: 4.2 Consensus size: 40
297330 AAAACGTTGT
297340 AATAGAGTTGACATATAGCGGCGTTTTTACAAAAAACGCCGC
1 AATAGAGTTGACATATAGCGGCGTTTTTAC--AAAACGCCGC
* *** * * *
297382 AATAG-GGTGGTTTATTGCGGCGTTTTTTACAAAACGTCGT
1 AATAGAGTTGACATATAGCGGCG-TTTTTACAAAACGCCGC
* * * * *
297422 AATAGAGTGGTAAAT-TAGCGGCGTTTATACCGCAAACGCTGC
1 AATAGAGTTG-ACATATAGCGGCGTTTTTA-C-AAAACGCCGC
* * * *
297464 AATATA-TTAACATATAGTGGCG-TTTTAGCCAAAATGCCGC
1 AATAGAGTTGACATATAGCGGCGTTTTTA--CAAAACGCCGC
297504 AATAGA
1 AATAGA
297510 TCGGTAAATT
Statistics
Matches: 93, Mismatches: 28, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
40 37 0.40
41 32 0.34
42 24 0.26
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (40 bp):
AATAGAGTTGACATATAGCGGCGTTTTTACAAAACGCCGC
Found at i:297432 original size:40 final size:41
Alignment explanation
Indices: 297329--297447 Score: 116
Period size: 40 Copynumber: 2.9 Consensus size: 41
297319 CGTTTGTCGT
* ** *
297329 AAAAACGTTGTAATAGAGTTGACATATAGCGGCG-TTTTTAC
1 AAAAACGTCGTAATAGAG-TGGTATATTGCGGCGTTTTTTAC
* * * *
297370 AAAAAACGCCGCAATAGGGTGGTTTATTGCGGCGTTTTTTAC
1 -AAAAACGTCGTAATAGAGTGGTATATTGCGGCGTTTTTTAC
*
297412 -AAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTT
1 AAAAACGTCGTAATAGAGTGGTATATT-GCGGCGTTT
297448 ATACCGCAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
40 21 0.34
41 20 0.32
42 21 0.34
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (41 bp):
AAAAACGTCGTAATAGAGTGGTATATTGCGGCGTTTTTTAC
Found at i:297443 original size:41 final size:42
Alignment explanation
Indices: 297329--297447 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
297319 CGTTTGTCGT
* * *
297329 AAAAACGTTGTAATAGAGTTG-ACATATAGCGGCG-TTTTTAC
1 AAAAACGTCGTAATAGAGTGGTAAAT-TAGCGGCGTTTTTTAC
* * * **
297370 AAAAAACGCCGCAATAGGGTGGTTTATT-GCGGCGTTTTTTAC
1 -AAAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTTTTTAC
297412 -AAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTT
1 AAAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTT
297448 ATACCGCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
40 21 0.34
41 15 0.24
42 24 0.39
43 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (42 bp):
AAAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTTTTTAC
Found at i:297486 original size:82 final size:83
Alignment explanation
Indices: 297400--297567 Score: 234
Period size: 82 Copynumber: 2.0 Consensus size: 83
297390 GGTTTATTGC
** * * *
297400 GGCGTTTTTTACAAAACGTCGTAATAGAGT-GGTAAATTAGCGGCGTTTATACCGCAAACG-CTG
1 GGCGTTTTAGACAAAACGCCGCAATAGA-TCGGTAAATTAGCGGCGTTTATACCACAAACGAC-G
297463 CAATATATTA-ACATATAGT
64 CAATATATTACACATATAGT
* *
297482 GGCGTTTTAGCCAAAATGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGACGCA
1 GGCGTTTTAGACAAAACGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGACGCA
297547 ATATATTACACATATAGT
66 ATATATTACACATATAGT
297565 GGC
1 GGC
297568 ATTTATTCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 1 0.01
82 62 0.82
83 13 0.17
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (83 bp):
GGCGTTTTAGACAAAACGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGACGCA
ATATATTACACATATAGT
Found at i:297549 original size:42 final size:40
Alignment explanation
Indices: 297355--297549 Score: 125
Period size: 41 Copynumber: 4.8 Consensus size: 40
297345 AGTTGACATA
* * * * **
297355 TAGCGGCGTTTTTACAAAAAACGCCGCAATAGGGTGGTTTAT
1 TAGCGGCGTTTATACCACAAACG-CGCAATA-GATGGTAAAT
* *
297397 T-GCGGCGTTTTTTA-CA-AAACGTCGTAATAGAGTGGTAAAT
1 TAGCGGCG-TTTATACCACAAACG-CGCAATAGA-TGGTAAAT
* *
297437 TAGCGGCGTTTATACCGCAAACGCTGCAATATAT--TAACAT
1 TAGCGGCGTTTATACCACAAACGC-GCAATAGATGGTAA-AT
* *
297477 ATAGTGGCGTTT-TAGCCA-AAATGCCGCAATAGATCGGTAAAT
1 -TAGCGGCGTTTATA-CCACAAACG-CGCAATAGAT-GGTAAAT
297519 TAGCGGCGTTTATACCACAAACGACGCAATA
1 TAGCGGCGTTTATACCACAAACG-CGCAATA
297550 TATTACACAT
Statistics
Matches: 121, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
39 4 0.03
40 39 0.32
41 42 0.35
42 33 0.27
43 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (40 bp):
TAGCGGCGTTTATACCACAAACGCGCAATAGATGGTAAAT
Found at i:297573 original size:42 final size:40
Alignment explanation
Indices: 297441--297573 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 40
297431 GTAAATTAGC
*
297441 GGCGTTTATACCGCAAACGCTGCAATATATTAACATATAGT
1 GGCGTTTATACCACAAACGC-GCAATATATTAACATATAGT
* * *
297482 GGCGTTT-TAGCCA-AAATGCCGCAATAGATCGGTAA-AT-TAGC
1 GGCGTTTATA-CCACAAACG-CGCAATATAT---TAACATATAGT
297523 GGCGTTTATACCACAAACGACGCAATATATTACACATATAGT
1 GGCGTTTATACCACAAACG-CGCAATATATTA-ACATATAGT
*
297565 GGCATTTAT
1 GGCGTTTAT
297574 TCTTAAAACG
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
39 2 0.03
40 15 0.21
41 25 0.34
42 28 0.38
43 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (40 bp):
GGCGTTTATACCACAAACGCGCAATATATTAACATATAGT
Found at i:297634 original size:43 final size:43
Alignment explanation
Indices: 297579--297741 Score: 192
Period size: 41 Copynumber: 3.9 Consensus size: 43
297569 TTTATTCTTA
* * * *
297579 AAACGCCGCAATAGTGATAATAAATAGTGGTGTGTTTTTAGAC
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTGTTTTTAGAC
* *
297622 AAACGCCACAATAGTGTTAATCACTAGTGGC--GTTTTTAGAA
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTGTTTTTAGAC
* * *
297663 AAACGCCGCAATAGTTTTAATCAATAGTAGCGT-TTTTTA-AC
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTGTTTTTAGAC
* *
297704 AAACGCCATAATAGTG-TAATCAATAGTGGCGTTTTTTT
1 AAACGCCACAATAGTGTTAATCAATAGTGGCGTGTTTTT
297742 TATAAATGCC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
40 15 0.15
41 55 0.54
42 6 0.06
43 26 0.25
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (43 bp):
AAACGCCACAATAGTGTTAATCAATAGTGGCGTGTTTTTAGAC
Found at i:297753 original size:82 final size:84
Alignment explanation
Indices: 297560--297755 Score: 236
Period size: 84 Copynumber: 2.3 Consensus size: 84
297550 TATTACACAT
* * * *
297560 ATAGTGGCATTTATTCTTAAAACGCCGCAATAGTGATAATAAATAGTGGTGTGTTTTTAGACAAA
1 ATAGTGGCGTTT-TTTTTAAAACGCCGCAATAGTGATAATAAATAGTAGCGTGTTTTTAGACAAA
297625 CGCCACAATAGTGTTAATCA
65 CGCCACAATAGTGTTAATCA
* *** ** *
297645 CTAGTGGCGTTTTTAGAAAAACGCCGCAATAGTTTTAATCAATAGTAGCGT-TTTTTA-ACAAAC
1 ATAGTGGCGTTTTTTTTAAAACGCCGCAATAGTGATAATAAATAGTAGCGTGTTTTTAGACAAAC
*
297708 GCCATAATAGTG-TAATCA
66 GCCACAATAGTGTTAATCA
*
297726 ATAGTGGCGTTTTTTTTATAAATGCCGCAA
1 ATAGTGGCGTTTTTTTTA-AAACGCCGCAA
297756 AATGTTAAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
81 20 0.21
82 27 0.29
83 6 0.06
84 31 0.33
85 10 0.11
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (84 bp):
ATAGTGGCGTTTTTTTTAAAACGCCGCAATAGTGATAATAAATAGTAGCGTGTTTTTAGACAAAC
GCCACAATAGTGTTAATCA
Found at i:299362 original size:41 final size:42
Alignment explanation
Indices: 299280--299362 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 42
299270 GCCGCTAAAA
* * ** *
299280 AGTTGTACTTTAGTGGTGTTTTTGACATAAACGTCGTAATAG
1 AGTTGTAATTTAGTGGTCTTTTTGACATAAACACCGCAATAG
299322 AGTTGTAATTTAGTGG-CTTTTTGTA-ATAAACACCGCAATAG
1 AGTTGTAATTTAGTGGTCTTTTTG-ACATAAACACCGCAATAG
299363 TGTGTCCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 19 0.54
42 16 0.46
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (42 bp):
AGTTGTAATTTAGTGGTCTTTTTGACATAAACACCGCAATAG
Found at i:307411 original size:21 final size:21
Alignment explanation
Indices: 307394--307443 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
307384 TGAAGCAAGG
307394 GAAGCAGAGAGAGCAGCAACA
1 GAAGCAGAGAGAGCAGCAACA
** *
307415 GAAGCAGCTAGAGCAGCAGCA
1 GAAGCAGAGAGAGCAGCAACA
*
307436 AAAGCAGA
1 GAAGCAGA
307444 TAAAGAAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.32, T:0.02
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAGCAACA
Found at i:307462 original size:21 final size:21
Alignment explanation
Indices: 307447--307513 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
307437 AAGCAGATAA
*
307447 AGAAGTAACGGCAGCACAAAG
1 AGAAGTAACGACAGCACAAAG
* *
307468 AGAAGTAACGACAGCATAGAG
1 AGAAGTAACGACAGCACAAAG
* * * *
307489 AGAAGCAGCGGCAACACAAAG
1 AGAAGTAACGACAGCACAAAG
307510 AGAA
1 AGAA
307514 ACAACATATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.49, C:0.18, G:0.28, T:0.04
Consensus pattern (21 bp):
AGAAGTAACGACAGCACAAAG
Found at i:307992 original size:43 final size:43
Alignment explanation
Indices: 307930--308223 Score: 245
Period size: 43 Copynumber: 6.9 Consensus size: 43
307920 TGTTTTTAGC
* *
307930 AAAAACGCC-AAAAAAATCAATACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
* * *
307972 AAAAATGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTG-G
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
* * *
308014 AATAAACGCCGCAAAACATCAAAATCTACTGCGGCGTTTGTG-G
1 AA-AAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
* * * * * * *
308057 GAAAACGCCGAAAAACATCAACACCTACTACGGCGTTTATCTA-
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGT-GAG
* * * * * **
308100 AAAAACACCGCTAAATATCAATACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
* * * * * * * *
308143 ACAAACGTCGCTAAATATCAACACCTATTACGGCGTTTGTCAC
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
* * *
308186 ACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTT
308224 TTTGTTTTTA
Statistics
Matches: 209, Mismatches: 38, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
42 44 0.21
43 165 0.79
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAATACCTATTGCGGCGTTTGTGAG
Found at i:321794 original size:2 final size:2
Alignment explanation
Indices: 321787--321814 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
321777 CTTGAACTTA
321787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321815 TTGGTTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322531 original size:64 final size:63
Alignment explanation
Indices: 322404--322632 Score: 173
Period size: 64 Copynumber: 3.6 Consensus size: 63
322394 TTTTCAAAGG
* * * * *
322404 CATGCACCGATGCA-TCAATACCATGCATCGATGCATTAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACT-CTGATTTAATTAAAACATCGAATGCA
322468 TT
62 TT
*
322470 CCATGCACCGATGCACTCTCTATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCA-TT
* * * *** * *
322535 GATGCATCGATACACAAGCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TG--ATTTAATTAAAACATCGAATGCA-
322597 TT
62 TT
* *
322599 CATGCATCGATGCACTCT-TAGTGCA-CGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
322633 AGGAGTCCAA
Statistics
Matches: 133, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
63 10 0.08
64 85 0.64
65 17 0.13
66 5 0.04
67 14 0.11
68 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATT
Found at i:322613 original size:17 final size:19
Alignment explanation
Indices: 322585--322632 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
322575 ATTTTTCAAA
322585 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
322603 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
322622 CA-CGATGCACT
1 CATCGATGCACT
322633 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:331932 original size:150 final size:150
Alignment explanation
Indices: 331661--331960 Score: 591
Period size: 150 Copynumber: 2.0 Consensus size: 150
331651 AGGCCACTGG
331661 AAACTGGAACAACAAGCGGCAGAGTCCTCCAAGTTACAATGCACATTTGGCTTAACTAAAATAAA
1 AAACTGGAACAACAAGCGGCAGAGTCCTCCAAGTTACAATGCACATTTGGCTTAACTAAAATAAA
*
331726 TTATGCTCAAAACAAGGATCAATCTGGAAAACGTATGAATATCTTGTCTGCTCTGTAAAGATATA
66 TTATGCTCAAAACAAGGATCAATCTGGAAAACGTATGAATATATTGTCTGCTCTGTAAAGATATA
331791 GGCATGTAGATAAAAGTACA
131 GGCATGTAGATAAAAGTACA
331811 AAACTGGAACAACAAGCGGCAGAGTCCTCCAAGTTACAATGCACATTTGGCTTAACTAAAATAAA
1 AAACTGGAACAACAAGCGGCAGAGTCCTCCAAGTTACAATGCACATTTGGCTTAACTAAAATAAA
331876 TTATGCTCAAAACAAGGATCAATCTGGAAAACGTATGAATATATTGTCTGCTCTGTAAAGATATA
66 TTATGCTCAAAACAAGGATCAATCTGGAAAACGTATGAATATATTGTCTGCTCTGTAAAGATATA
331941 GGCATGTAGATAAAAGTACA
131 GGCATGTAGATAAAAGTACA
331961 TATGCACATA
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (150 bp):
AAACTGGAACAACAAGCGGCAGAGTCCTCCAAGTTACAATGCACATTTGGCTTAACTAAAATAAA
TTATGCTCAAAACAAGGATCAATCTGGAAAACGTATGAATATATTGTCTGCTCTGTAAAGATATA
GGCATGTAGATAAAAGTACA
Found at i:334228 original size:31 final size:31
Alignment explanation
Indices: 334193--334254 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
334183 TATTCAGGTC
334193 GGATTTTTTAAAAAAAATTCGGGATCGGGTT
1 GGATTTTTTAAAAAAAATTCGGGATCGGGTT
* * *
334224 GGATTTTTTATAAAAATTTCGGGTTCGGGTT
1 GGATTTTTTAAAAAAAATTCGGGATCGGGTT
334255 AGGTCGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.06, G:0.26, T:0.40
Consensus pattern (31 bp):
GGATTTTTTAAAAAAAATTCGGGATCGGGTT
Found at i:334306 original size:38 final size:39
Alignment explanation
Indices: 334248--334322 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
334238 AATTTCGGGT
* * * *
334248 TCGGGTTAGGTCGAGTTTTTTTTAAGTTTGATATTCGTA
1 TCGGGTCAGGTCGAGGTTTTTTTAAATGTGATATTCGTA
334287 TCGGGTCAGGTCG-GGTTTTTTTAAATGTGATATTCG
1 TCGGGTCAGGTCGAGGTTTTTTTAAATGTGATATTCG
334323 GGTCGAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 20 0.62
39 12 0.38
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.45
Consensus pattern (39 bp):
TCGGGTCAGGTCGAGGTTTTTTTAAATGTGATATTCGTA
Found at i:348074 original size:28 final size:29
Alignment explanation
Indices: 348032--348100 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
348022 AAAATATGTT
348032 TTCGTCCCCTAAAA-TTTTATAAGTTCAAG
1 TTCG-CCCCTAAAATTTTTATAAGTTCAAG
* *
348061 TTCGCCCCTGAAATTTTTATAAGTTTAAG
1 TTCGCCCCTAAAATTTTTATAAGTTCAAG
*
348090 TTCTCCCCTAA
1 TTCGCCCCTAA
348101 CTTAAAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (29 bp):
TTCGCCCCTAAAATTTTTATAAGTTCAAG
Found at i:359939 original size:2 final size:2
Alignment explanation
Indices: 359932--359959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
359922 ATAATTCTAG
359932 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
359960 CTTACTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:361624 original size:24 final size:24
Alignment explanation
Indices: 361587--361670 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
361577 AATATATTTT
* *
361587 TATTTTGATTTTAATTTTAAAAATA
1 TATTTTTA-TTTAACTTTAAAAATA
*
361612 T-TTTTTATCTTAACTTAAAAAATA
1 TATTTTTAT-TTAACTTTAAAAATA
361636 TATACTTTTA-TTAACTTTAAAAATA
1 TAT--TTTTATTTAACTTTAAAAATA
361661 TATTTGTTAT
1 TATTT-TTAT
361671 ATCTTAACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
23 3 0.06
24 22 0.45
25 19 0.39
27 5 0.10
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTTTTATTTAACTTTAAAAATA
Found at i:361633 original size:25 final size:25
Alignment explanation
Indices: 361605--361680 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 25
361595 TTTTAATTTT
361605 AAAAATATTTTTTATCTTAACTTAA
1 AAAAATATTTTTTATCTTAACTTAA
*
361630 AAAATATATACTTTTA--TTAACTTTAA
1 AAAA-ATAT-TTTTTATCTTAAC-TTAA
*
361656 AAATATATTTGTTATATCTTAACTT
1 AAAAATATTT-TT-TATCTTAACTT
361681 CAAATATCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
24 1 0.02
25 15 0.37
26 13 0.32
27 7 0.17
28 5 0.12
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (25 bp):
AAAAATATTTTTTATCTTAACTTAA
Found at i:361743 original size:32 final size:32
Alignment explanation
Indices: 361707--361783 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 32
361697 CCTTAACCTC
* *
361707 AAATATATATTTTTATT-CTTTATTAACTTAAA
1 AAATATATATTTTTATTACTTAATTAA-TAAAA
*
361739 AAATA-AT-TTATTATTAACTTAATTAATAAAA
1 AAATATATATTTTTATT-ACTTAATTAATAAAA
361770 ATAATATATATTTT
1 A-AATATATATTTT
361784 AAAATTAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
30 7 0.19
31 7 0.19
32 17 0.47
33 2 0.06
34 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (32 bp):
AAATATATATTTTTATTACTTAATTAATAAAA
Found at i:361831 original size:2 final size:2
Alignment explanation
Indices: 361824--361865 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
361814 AAATTAAAAT
361824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
361866 AGCTAAGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:362584 original size:16 final size:17
Alignment explanation
Indices: 362553--362589 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
362543 TCATTTAATG
*
362553 TTTAAAGTTGTTATGTT
1 TTTAAAATTGTTATGTT
362570 TTTAAAATT-TTATGTT
1 TTTAAAATTGTTATGTT
362586 TTTA
1 TTTA
362590 GACCTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (17 bp):
TTTAAAATTGTTATGTT
Found at i:369522 original size:33 final size:33
Alignment explanation
Indices: 369485--369551 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
369475 TATAAAATTC
369485 ATATTCATATTCAAAATTTAAATGATCAAAACA
1 ATATTCATATTCAAAATTTAAATGATCAAAACA
*
369518 ATATTCATATTCAAGATTTAAATGATCAAAACA
1 ATATTCATATTCAAAATTTAAATGATCAAAACA
369551 A
1 A
369552 GGACTCGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (33 bp):
ATATTCATATTCAAAATTTAAATGATCAAAACA
Found at i:371915 original size:24 final size:24
Alignment explanation
Indices: 371869--371920 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
371859 AAATAAAAAT
* *
371869 GAACACAAATGAACGAACGTAAAC
1 GAACACAAACGAACGAACATAAAC
* * *
371893 GAACACAAACGGACGATCATAAAT
1 GAACACAAACGAACGAACATAAAC
371917 GAAC
1 GAAC
371921 GTAAACTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.21, G:0.17, T:0.10
Consensus pattern (24 bp):
GAACACAAACGAACGAACATAAAC
Found at i:372128 original size:14 final size:14
Alignment explanation
Indices: 372105--372181 Score: 67
Period size: 14 Copynumber: 5.8 Consensus size: 14
372095 TTGAAAGAAC
*
372105 ATAAACGAACGAAA
1 ATAAATGAACGAAA
372119 ATAAATGAAC-AAA
1 ATAAATGAACGAAA
372132 CATAAATGAAC-AAA
1 -ATAAATGAACGAAA
*
372146 CATAAATG---G-AT
1 -ATAAATGAACGAAA
*
372157 ATAAATGAACGAAC
1 ATAAATGAACGAAA
372171 ATAAATGAACG
1 ATAAATGAACG
372182 GATTACACAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
10 7 0.13
11 1 0.02
13 4 0.07
14 42 0.78
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.16
Consensus pattern (14 bp):
ATAAATGAACGAAA
Found at i:372184 original size:28 final size:28
Alignment explanation
Indices: 372105--372184 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
372095 TTGAAAGAAC
* * ** *
372105 ATAAACGAACGAAAATAAATGAACAAAC
1 ATAAATGAACGAACATAAATGAACGGAT
*
372133 ATAAATGAACAAACATAAAT----GGAT
1 ATAAATGAACGAACATAAATGAACGGAT
372157 ATAAATGAACGAACATAAATGAACGGAT
1 ATAAATGAACGAACATAAATGAACGGAT
372185 TACACAACGT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
24 20 0.49
28 21 0.51
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (28 bp):
ATAAATGAACGAACATAAATGAACGGAT
Found at i:380752 original size:21 final size:21
Alignment explanation
Indices: 380726--380766 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
380716 TTAAAGTCCC
380726 AAGTTTGACTGAAGAAGATGT
1 AAGTTTGACTGAAGAAGATGT
380747 AAGTTTGACTGAAGAAGATG
1 AAGTTTGACTGAAGAAGATG
380767 GATTCTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (21 bp):
AAGTTTGACTGAAGAAGATGT
Found at i:381684 original size:24 final size:24
Alignment explanation
Indices: 381657--381702 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
381647 CTAGAAGGCC
381657 GGTTGATTTTCAAACTAAGGGGAT
1 GGTTGATTTTCAAACTAAGGGGAT
*
381681 GGTTGATTTTCAAATTAAGGGG
1 GGTTGATTTTCAAACTAAGGGG
381703 CTGCTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (24 bp):
GGTTGATTTTCAAACTAAGGGGAT
Found at i:382272 original size:2 final size:2
Alignment explanation
Indices: 382265--382308 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
382255 ATCAAGTGCT
382265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
382307 TA
1 TA
382309 CGAAAGAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:395080 original size:29 final size:29
Alignment explanation
Indices: 395038--395155 Score: 227
Period size: 29 Copynumber: 4.1 Consensus size: 29
395028 ATACAGTGGT
395038 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
395067 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
395096 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
395125 CTTGGAGGTCACCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
395154 CT
1 CT
395156 GTGTGTATTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:395229 original size:15 final size:15
Alignment explanation
Indices: 395209--395289 Score: 83
Period size: 15 Copynumber: 5.2 Consensus size: 15
395199 GGACGTGGGA
395209 ATGCATGGGGAGGGG
1 ATGCATGGGGAGGGG
395224 ATGCAT-GGGACGTGGG
1 ATGCATGGGGA-G-GGG
* *
395240 AATGCATGGGGTGGGA
1 -ATGCATGGGGAGGGG
* *
395256 ATGCATGGGGTGGGA
1 ATGCATGGGGAGGGG
395271 ATGCATGGGGGAGGGG
1 ATGCAT-GGGGAGGGG
395287 ATG
1 ATG
395290 GTGCATTGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.07
15 28 0.49
16 15 0.26
17 7 0.12
18 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.54, T:0.17
Consensus pattern (15 bp):
ATGCATGGGGAGGGG
Found at i:395231 original size:32 final size:32
Alignment explanation
Indices: 395195--395307 Score: 149
Period size: 32 Copynumber: 3.5 Consensus size: 32
395185 ATGCAATCAA
395195 CATGGGACGTGGGAATGCATGGGGAGGGGATG
1 CATGGGACGTGGGAATGCATGGGGAGGGGATG
* *
395227 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGGATG
395259 CATGGG--GTGGGAATGCATGGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGGA---TG
*
395293 CATTGGACGTGGGAA
1 CATGGGACGTGGGAA
395308 AACCTTCCTC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.17
31 8 0.11
32 36 0.51
34 7 0.10
36 7 0.10
ACGTcount: A:0.21, C:0.09, G:0.52, T:0.18
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGGATG
Found at i:395883 original size:21 final size:21
Alignment explanation
Indices: 395858--395901 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
395848 AATCTAGTTA
395858 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
395879 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
395900 AT
1 AT
395902 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:395911 original size:28 final size:30
Alignment explanation
Indices: 395878--395940 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
395868 TAGTATAAAT
*
395878 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
395906 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
395936 TATTA
1 TATTA
395941 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:396488 original size:20 final size:21
Alignment explanation
Indices: 396444--396488 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
396434 AAATATTGTG
**
396444 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
396465 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
396485 TTTA
1 TTTA
396489 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:396777 original size:26 final size:25
Alignment explanation
Indices: 396748--396806 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
396738 AAATCATGTT
*
396748 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
396774 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
396800 ATTATTA
1 ATTATTA
396807 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:399704 original size:14 final size:14
Alignment explanation
Indices: 399687--399730 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
399677 GATGATTTAG
399687 TAATGATTTGATAA
1 TAATGATTTGATAA
* *
399701 TAATCA-TT-ATAG
1 TAATGATTTGATAA
399713 TAATGATTTGATAA
1 TAATGATTTGATAA
399727 TAAT
1 TAAT
399731 CATTAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:399713 original size:26 final size:26
Alignment explanation
Indices: 399684--400103 Score: 278
Period size: 26 Copynumber: 17.2 Consensus size: 26
399674 TTTGATGATT
399684 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
399710 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
399736 -A-TAATGA-TT--TAGTAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
399757 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * * *
399778 TA-AAAT--TTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
399802 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
399828 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
399854 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
399880 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * * *
399902 TA--AAT-TTTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
399926 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
399952 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
399978 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * *
400004 TAAAAATGATTTAATAATGAT--TTAA
1 TAGTAATGATTTGATAATAATCATT-A
* *
400029 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
*
400049 TAGTAATGATTTGATAACAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
400075 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
400100 TAGT
1 TAGT
400104 TATTATTTAG
Statistics
Matches: 326, Mismatches: 35, Indels: 67
0.76 0.08 0.16
Matches are distributed among these distances:
19 10 0.03
20 11 0.03
21 17 0.05
22 23 0.07
23 14 0.04
24 26 0.08
25 31 0.10
26 183 0.56
27 11 0.03
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:399781 original size:21 final size:21
Alignment explanation
Indices: 399714--399783 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
399704 TCATTATAGT
*
399714 AATGATTTGATAATAATCATTAA
1 AATGATTTAATAATAAT--TTAA
* *
399737 TAATGATTTAGTAATCATTATAA
1 -AATGATTTAATAATAATT-TAA
*
399760 AATGATTTAATAATGATTTAA
1 AATGATTTAATAATAATTTAA
399781 AAT
1 AAT
399784 TTTAATGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.15
22 17 0.43
23 3 0.08
24 14 0.35
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (21 bp):
AATGATTTAATAATAATTTAA
Found at i:399808 original size:19 final size:18
Alignment explanation
Indices: 399761--399816 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
399751 TCATTATAAA
399761 ATGATTTAATAATGATTT-
1 ATGATTT-ATAATGATTTG
**
399779 AAAATTT-TAATGATTTG
1 ATGATTTATAATGATTTG
399796 ATGATTTAGTAATGATTTG
1 ATGATTTA-TAATGATTTG
399815 AT
1 AT
399817 AATAATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (18 bp):
ATGATTTATAATGATTTG
Found at i:399932 original size:19 final size:19
Alignment explanation
Indices: 399885--399940 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
399875 CATTATAAAA
399885 ATGATTTAATAATGATTT-
1 ATGATTTAATAATGATTTG
* *
399903 A-AATTT-TTAATGATTTG
1 ATGATTTAATAATGATTTG
*
399920 ATGATTTAGTAATGATTTG
1 ATGATTTAATAATGATTTG
399939 AT
1 AT
399941 AATAATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
ATGATTTAATAATGATTTG
Found at i:399952 original size:124 final size:124
Alignment explanation
Indices: 399631--400095 Score: 829
Period size: 124 Copynumber: 3.8 Consensus size: 124
399621 TGTATTTATT
399631 ATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
1 ATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
399696 GATAATAATCATTATAGTAATGATTTGATAATAATCA-T-TAATAATGATTTAG---TA
66 GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
399750 ATCATTAT-AAAATGATTTAATAATGATTTAAA-ATTTTAATGATTTGATGATTTAGTAATGATT
1 ATCATTATAAAAATGATTTAATAATGATTTAAATA-TTTAATGATTTGATGATTTAGTAATGATT
399813 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
65 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
*
399873 ATCATTATAAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATGATTTAGTAATGATTT
1 ATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
399938 GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
66 GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
399997 ATCATTATAAAAATGATTTAATAATGATTT-AATATTTAATGATTTGATGATTTAGTAATGATTT
1 ATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
* * *
400061 GATAACAATCATTATAATAATGATTTTATAATAAT
66 GATAATAATCATTATAGTAATGATTTGATAATAAT
400096 TATTTAGTTA
Statistics
Matches: 333, Mismatches: 5, Indels: 12
0.95 0.01 0.03
Matches are distributed among these distances:
117 1 0.00
118 91 0.27
119 9 0.03
120 14 0.04
123 75 0.23
124 143 0.43
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (124 bp):
ATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
Found at i:400041 original size:8 final size:8
Alignment explanation
Indices: 400018--400050 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
400008 AATGATTTAA
400018 TAATGATT
1 TAATGATT
400026 TAAT-ATT
1 TAATGATT
400033 TAATGATT
1 TAATGATT
*
400041 TGATGATT
1 TAATGATT
400049 TA
1 TA
400051 GTAATGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:400328 original size:17 final size:17
Alignment explanation
Indices: 400303--400335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
400293 ACTAAATATT
*
400303 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
400320 TAATGATTTGATACTA
1 TAATGATTTGATACTA
400336 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:400328 original size:25 final size:23
Alignment explanation
Indices: 400249--400328 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
400239 GATTTATTGT
400249 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
400270 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
400297 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
400319 GTAATGATTT
1 -TAAT-ATTT
400329 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:402624 original size:34 final size:32
Alignment explanation
Indices: 402561--402642 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 32
402551 GCTAAACCCT
*
402561 TAAAC-AACTAATAAAATATTCTTCTATATAA
1 TAAACTAACTAATAAACTATTCTTCTATATAA
*
402592 CTAAAACTAACTAATAAACTATT-TTTTCATATAA
1 -T-AAACTAACTAATAAACTATTCTTCT-ATATAA
*
402626 TATACT-ACTAATAAACT
1 TAAACTAACTAATAAACT
402643 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 11 0.25
32 5 0.11
33 8 0.18
34 20 0.45
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAACTAACTAATAAACTATTCTTCTATATAA
Found at i:402734 original size:42 final size:40
Alignment explanation
Indices: 402687--402808 Score: 110
Period size: 43 Copynumber: 3.0 Consensus size: 40
402677 CAAATATAAC
402687 TTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 TTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
*
402727 ATATAACTAACTATTAAC-AA-ACAAACTAATT-AAT--TATTTT
1 -T-TAACT-A-T-TTAACTAACACAAACTAATTAAATAATTTTTT
* *
402767 TTAACTATATAACTATCAACATATACTAATTAAATAATTTTT
1 TTAACTATTTAACTAAC-ACA-A-ACTAATTAAATAATTTTT
402809 AATTTATGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
35 4 0.06
36 2 0.03
37 1 0.02
38 8 0.12
39 2 0.03
40 12 0.18
41 4 0.06
42 8 0.12
43 16 0.25
44 3 0.05
45 5 0.08
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (40 bp):
TTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
Found at i:402773 original size:38 final size:45
Alignment explanation
Indices: 402680--402769 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 45
402670 CAACAAACAA
*
402680 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAAT-ATATTTT
* *
402727 ATATAACTAACTA-TTAAC-AA-ACAAACTAATTAATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATATATTTT
402769 A
1 A
402770 ACTATATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 8 0.19
43 14 0.33
44 2 0.05
45 5 0.12
46 6 0.14
47 7 0.17
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATATATTTT
Found at i:402998 original size:21 final size:21
Alignment explanation
Indices: 402974--403024 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
402964 TTCTTCTTAC
402974 TTTCCTTTCTCCCTTTCTTTA
1 TTTCCTTTCTCCCTTTCTTTA
*
402995 TTTCCTTTCTCCCTTTCTTTC
1 TTTCCTTTCTCCCTTTCTTTA
403016 TTT-CTTTCT
1 TTTCCTTTCT
403025 TTCTTTCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTCCTTTCTCCCTTTCTTTA
Found at i:403016 original size:4 final size:4
Alignment explanation
Indices: 402959--403032 Score: 62
Period size: 4 Copynumber: 18.5 Consensus size: 4
402949 CCTTATCTCC
* ** * **
402959 CTTT C-TT C-TT CTTA CTTT CCTTT CTCC CTTT CTTT ATTT CCTTT CTCC
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT CTTT
403007 CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT
403033 CGGCTGCAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
3 6 0.11
4 42 0.76
5 7 0.13
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:403066 original size:23 final size:23
Alignment explanation
Indices: 403036--403081 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
403026 TCTTTCTCGG
403036 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
403059 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
403082 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:403122 original size:25 final size:25
Alignment explanation
Indices: 403094--403145 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
403084 TTTCTTTTAT
403094 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
403119 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
403144 AA
1 AA
403146 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:403335 original size:13 final size:13
Alignment explanation
Indices: 403317--403348 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
403307 GGCTGCATGT
403317 GAATGGATGATGG
1 GAATGGATGATGG
403330 GAATGGATGATGG
1 GAATGGATGATGG
403343 GAATGG
1 GAATGG
403349 CGCCGGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (13 bp):
GAATGGATGATGG
Found at i:403382 original size:29 final size:29
Alignment explanation
Indices: 403349--403457 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
403339 ATGGGAATGG
403349 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
403378 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
403407 CGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
403436 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
403458 CTCTATTCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 73 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:403516 original size:26 final size:26
Alignment explanation
Indices: 403480--403535 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
403470 GCATGGCCAC
*
403480 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATAG
403506 CTCGCATGGGGAGAACGCTCGTATAG
1 CTCGCATGGGGAGAACGCTCGTATAG
403532 CTCG
1 CTCG
403536 TATGCATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCGTATAG
Found at i:403561 original size:35 final size:35
Alignment explanation
Indices: 403522--403609 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
403512 TGGGGAGAAC
*
403522 GCTCGTATAGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
*
403557 GCTCGTATGGCTCGTATGCATGGGGAGAACTATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
403592 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
403610 TCACCCCGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:403621 original size:12 final size:12
Alignment explanation
Indices: 403604--403645 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
403594 TCGTATGGCT
403604 CGTATGTCACCC
1 CGTATGTCACCC
*
403616 CGTATGTCAACC
1 CGTATGTCACCC
403628 CGTATGTCACCC
1 CGTATGTCACCC
403640 CGTATG
1 CGTATG
403646 GCCACCTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:403688 original size:30 final size:32
Alignment explanation
Indices: 403654--403719 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 32
403644 TGGCCACCTC
403654 GCATGGGGAGAA-C-GCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
403684 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACC--T-GCTCGTATGGCTCGTAT
403719 G
1 G
403720 TATGTCGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 12 0.39
31 1 0.03
35 18 0.58
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (32 bp):
GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
Found at i:404191 original size:10 final size:10
Alignment explanation
Indices: 404176--404203 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
404166 ACCTAAGCAT
404176 AAATGAAACA
1 AAATGAAACA
404186 AAATGAAACA
1 AAATGAAACA
404196 AAATGAAA
1 AAATGAAA
404204 TGGCTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.07, G:0.11, T:0.11
Consensus pattern (10 bp):
AAATGAAACA
Found at i:404730 original size:3 final size:3
Alignment explanation
Indices: 404702--404754 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
404692 CCGGTGAGCA
* *
404702 TTC TTT TTC TTC TCTC TCTC TCTC TTC TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC TTC TTC T-TC T-TC T-TC TTC TTC TTC TTC TTC TTC TTC TTC
404750 TTC TT
1 TTC TT
404755 TTTCGGGTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 34 0.76
4 11 0.24
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:410966 original size:18 final size:19
Alignment explanation
Indices: 410945--410996 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 19
410935 TTGGTAACGG
410945 TTGGTATCTTTTTAA-CAA
1 TTGGTATCTTTTTAATCAA
410963 TTGGTATCCTTTTGTAATCAA
1 TTGGTAT-CTTTT-TAATCAA
410984 TTGGTATCTTTTT
1 TTGGTATCTTTTT
410997 CATTAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 8 0.26
21 10 0.32
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (19 bp):
TTGGTATCTTTTTAATCAA
Found at i:411284 original size:22 final size:22
Alignment explanation
Indices: 411248--411306 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
411238 AGACCCATAT
*
411248 CAATACCTCTTATGAACGGGTAC
1 CAATACC-CCTATGAACGGGTAC
* * *
411271 CGATACCCCTATGAATGGGTAT
1 CAATACCCCTATGAACGGGTAC
411293 CAATACCCC-ATGAA
1 CAATACCCCTATGAA
411307 GGCTCAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 5 0.16
22 20 0.65
23 6 0.19
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (22 bp):
CAATACCCCTATGAACGGGTAC
Found at i:414006 original size:120 final size:118
Alignment explanation
Indices: 413757--414038 Score: 334
Period size: 120 Copynumber: 2.3 Consensus size: 118
413747 GAAAAAAAAA
* * * * ** *
413757 TTAGGTACTAAAACGAAGAAAACTAATAGTTTAGGTACTAAACTCGTTACGTTTTTAATGACGGG
1 TTAGGTACTAAAA-AAAGAAAACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTTAACAACAGG
* **
413822 TACTAAAATGAAATGAAAACTAAACGTTATGTATGATTTATAAAAAATTAAAAGT
65 TACTAAAATGAAA-GAAAACTAAAAGTTAAATATGATTTATAAAAAATTAAAAGT
* *
413877 TTAGATACTAAAATAAAGTAAAACTGATAATTTAGGTACTAAACGCGTTAAGTTTTTAACAACAA
1 TTAGGTACTAAAA-AAAG-AAAACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTTAACAAC-A
* * *
413942 TGTACTAAAATGAAA-AAAAGTAAAAGTTAAATATGATTTGA-AAAAAATTGAAAGT
63 GGTACTAAAATGAAAGAAAACTAAAAGTTAAATATGATTT-ATAAAAAATTAAAAGT
**
413997 TTAGGTACTAAAAAGAACCAAACTGATAGTTTAGGTACTAAA
1 TTAGGTACTAAAAA-AAGAAAACTGATAGTTTAGGTACTAAA
414039 TGCATAATTT
Statistics
Matches: 138, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
119 23 0.17
120 62 0.45
121 39 0.28
122 14 0.10
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (118 bp):
TTAGGTACTAAAAAAAGAAAACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTTAACAACAGGT
ACTAAAATGAAAGAAAACTAAAAGTTAAATATGATTTATAAAAAATTAAAAGT
Found at i:414883 original size:22 final size:22
Alignment explanation
Indices: 414838--414942 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 22
414828 ATGCGTAAGA
* *
414838 AAAATATA-TAAATAAAAAAAAT
1 AAAATATAGT-AATAAATATAAT
414860 AAAATATGAGTAATATATATATAAT
1 AAAATAT-AGTAATA-A-ATATAAT
414885 -AAA-ATAGTAATAAATATAAT
1 AAAATATAGTAATAAATATAAT
* ** * *
414905 ATAATATAACATTAATAAATAAT
1 AAAATATAGTAATAA-ATATAAT
*
414928 AAAATATAATAATAA
1 AAAATATAGTAATAA
414943 TAATAGTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.11
21 3 0.05
22 21 0.32
23 25 0.38
24 5 0.08
25 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAATATAGTAATAAATATAAT
Found at i:414901 original size:20 final size:22
Alignment explanation
Indices: 414868--414947 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 22
414858 ATAAAATATG
414868 AGTAATATATATATAATAAAAT
1 AGTAATATATATATAATAAAAT
*
414890 AGTAATA-A-ATATAATATAAT
1 AGTAATATATATATAATAAAAT
* *
414910 A-TAACATTAATAAATAATAAAAT
1 AGTAATA-T-ATATATAATAAAAT
414933 A-TAATA-ATA-ATAATA
1 AGTAATATATATATAATA
414948 GTTTAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 10 0.20
20 15 0.31
21 1 0.02
22 8 0.16
23 15 0.31
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
AGTAATATATATATAATAAAAT
Found at i:414906 original size:25 final size:25
Alignment explanation
Indices: 414871--414944 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
414861 AAATATGAGT
414871 AATATATATATAATAAAATAGTAATA
1 AATATA-ATATAATAAAATAGTAATA
* * *
414897 AATATAATATAATATAACATTAATA
1 AATATAATATAATAAAATAGTAATA
414922 AATAATAAAATATAATAATAATA
1 AAT-AT--AATATAATAA-AATA
414945 ATAGTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 19 0.49
26 8 0.21
28 9 0.23
29 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (25 bp):
AATATAATATAATAAAATAGTAATA
Done.