Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_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: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:472585 original size:67 final size:67
Alignment explanation
Indices: 472472--472796 Score: 287
Period size: 67 Copynumber: 5.0 Consensus size: 67
472462 TTTGAGATTG
* * * *
472472 TTTCATTTGATACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTTTCTCTTAGGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTAAGAT
472537 AA
66 AA
* *
472539 TTTCTTTTGAAACAAAAATCTGTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTAAGAT
472604 AA
66 AA
* * * * *
472606 TTTCTTTTGAAA-AAAAATCTTTGAGTC-GTTTCCCTT-CAAAC-GAATTTTGTCTCT-TGAA-A
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTT-CTTTGGAAACAAAATGTTGTCTCTCTTAAGA
* *
472665 CAT
65 TAA
* * * * * * * * * *
472668 TTTCTCTTAAAACAAGATCATCTTTGAGTTTGTTTCTCTGGAAAC--AAGGTTTTATCGCTTAAA
1 TTTCTTTTGAAACAA-A-AATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTAAG
* *
472731 ACAG
64 ATAA
* * *
472735 TTTCTTTTG-AAGAAAAATC--TGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCAC-TAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTAAGAT
472796 A
66 A
472797 CAATTTTCTG
Statistics
Matches: 208, Mismatches: 40, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
62 31 0.15
63 10 0.05
64 24 0.12
65 28 0.13
66 32 0.15
67 83 0.40
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTAAGAT
AA
Found at i:472781 original size:129 final size:129
Alignment explanation
Indices: 472471--472787 Score: 297
Period size: 129 Copynumber: 2.4 Consensus size: 129
472461 CTTTGAGATT
* * *
472471 GTTTCATTTGATACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATGTTGTTTCTCTTAGGA
1 GTTTCTTTTGA-AAAAAAATC-TTGAGTCTGTTTCTTTGGAAACAAAAT-TT-TGTCTCTTA-GA
* * * * * * *
472536 TAATTTCTTTTGAAACAAAAATCTGTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAA
61 AAATTTCTCTTAAAACAAAAATCTGTGAGTCTGTTTCTCTGGAAACAAAAGTTTGTATCGCTTAA
* *
472601 GATA
126 AACA
* * * *
472605 ATTTCTTTTGAAAAAAAATCTTTGAGTC-GTTTCCCTT-CAAAC-GAATTTTGTCTCTT-GAAAC
1 GTTTCTTTTGAAAAAAAATC-TTGAGTCTGTTT-CTTTGGAAACAAAATTTTGTCTCTTAGAAA-
* * * *
472666 ATTTTCTCTTAAAACAAGATCATCTTTGAGTTTGTTTCTCTGGAAAC-AAGGTTT-TATCGCTTA
63 A-TTTCTCTTAAAACAA-A-AATCTGTGAGTCTGTTTCTCTGGAAACAAAAGTTTGTATCGCTTA
472729 AAACA
125 AAACA
*
472734 GTTTCTTTTGAAGAAAAATC-TGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTC
1 GTTTCTTTTGAAAAAAAATCTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTC
472788 ACTAAGATAC
Statistics
Matches: 150, Mismatches: 25, Indels: 21
0.77 0.13 0.11
Matches are distributed among these distances:
127 12 0.08
128 9 0.06
129 59 0.39
130 8 0.05
131 26 0.17
132 8 0.05
133 19 0.13
134 9 0.06
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (129 bp):
GTTTCTTTTGAAAAAAAATCTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTAGAAAATT
TCTCTTAAAACAAAAATCTGTGAGTCTGTTTCTCTGGAAACAAAAGTTTGTATCGCTTAAAACA
Found at i:473158 original size:28 final size:28
Alignment explanation
Indices: 473119--473180 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
473109 TAAAAATATC
*
473119 ATCTTTGAGTTTATTT-TTCTTGAAATAA
1 ATCTTTGAGTTTATTTCTT-TTGAAACAA
* *
473147 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAGTTTATTTCTTTTGAAACAA
473175 ATCTTT
1 ATCTTT
473181 AATTTGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (28 bp):
ATCTTTGAGTTTATTTCTTTTGAAACAA
Found at i:473287 original size:40 final size:40
Alignment explanation
Indices: 473226--473710 Score: 289
Period size: 40 Copynumber: 11.4 Consensus size: 40
473216 TGGCCAGCCG
* * * *
473226 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGATC
* *
473266 TCCTCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-TC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC
* * * *
473308 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATC
* *
473355 TCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGATC
* * * *
473395 TCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC
* * * *
473437 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATC
* *
473484 TCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGATC
* * * * * *
473524 TCTTCATCACTTATGAGCCATGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC
* * * *
473566 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGATC
* * *
473613 TCTTCATCACGTATGAGCCATGTCATTCCC-CGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGATC
*
473653 TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-TC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGATC
473694 GTCCTCATCACGTATGA
1 -TCCTCATCACGTATGA
473711 ACTGAGTTAT
Statistics
Matches: 346, Mismatches: 60, Indels: 76
0.72 0.12 0.16
Matches are distributed among these distances:
38 3 0.01
39 1 0.00
40 124 0.36
41 2 0.01
42 24 0.07
43 91 0.26
44 3 0.01
45 4 0.01
46 89 0.26
47 5 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGATC
Found at i:473364 original size:46 final size:45
Alignment explanation
Indices: 473259--473768 Score: 286
Period size: 40 Copynumber: 11.7 Consensus size: 45
473249 CATCCCCAGA
* * * **
473259 CCAGATCTCCTCATCACGTATGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * * * *
473302 CCAG-TCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCACC-TTAGATGG
*
473348 CCAGAACTCTTCATCACGTATGAGCCGTGTCATC-CC-CAGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * **
473388 CCAGATCTCTTCATCACGTATGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * * * *
473431 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCACC-TTAGATGG
*
473477 CCAGAACTCTTCATCACGTATGAGCCGTGTCATC-CC-CAGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * * * **
473517 CCAGATCTCTTCATCACTTATGAGCCATGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * * * *
473560 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCACC-TTAGATGG
* *
473606 CCAGAACTCTTCATCACGTATGAGCCATGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCA-TCACCTTAGATGG
* **
473646 CCAGATCTCTTCATCACGTATGAGCCGTGTCA-C-CC-TAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
* * * * * * *
473688 CCAG-TCGTCCTCATCACGTATGAACTGAGTTATCATCCACCCTTAGACGA
1 CCAGAAC-TCTTCATCACGTATGAGC--CG-TGTCAT-CA-CCTTAGATGG
* *
473738 CCAGACCTCTTCATCACGTATGAGCAGTGTC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTC
473769 GTCCCCACCA
Statistics
Matches: 365, Mismatches: 62, Indels: 76
0.73 0.12 0.15
Matches are distributed among these distances:
38 3 0.01
39 6 0.02
40 96 0.26
41 2 0.01
42 24 0.07
43 82 0.22
44 1 0.00
45 17 0.05
46 95 0.26
47 9 0.02
48 2 0.01
49 2 0.01
50 25 0.07
51 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (45 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCTTAGATGG
Found at i:473376 original size:89 final size:85
Alignment explanation
Indices: 473219--473637 Score: 322
Period size: 89 Copynumber: 4.9 Consensus size: 85
473209 CTAAAGATGG
* * * *
473219 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CCCAGA-CCAGATCTCCTCATCACGTATGA
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTAGATCCAGAACTCTTCATCACGTATGA
473282 GCCGTGTCAACCATAGATAA
66 GCCGTGTCAACCATAGATAA
* *
473302 CCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC--TAGAT--CCAGAACTCTTCATCACGT
* **
473367 ATGAGCCGTGTCATCCCCAG---A
62 ATGAGCCGTGTCAACCATAGATAA
* * * * * *
473388 CCAGATC-TCTTCATCACGTATGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTCATCACG
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCACC-TAGAT--CCAGAAC-TCTTCATCACG
* * * * **
473449 TAGGAACCGTGTTATCACCTTTAGATGG
61 TATGAGCCGTGTCA--ACC-ATAGATAA
* * * * * * *
473477 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCATC-CCCAGA-CCAGATCTCTTCATCACTTATG
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCACCTAGATCCAGAACTCTTCATCACGTATG
*
473539 AGCCATGTCAACCATAGATAA
65 AGCCGTGTCAACCATAGATAA
*
473560 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC--TAGAT--CCAGAACTCTTCATCACGT
*
473625 ATGAGCCATGTCA
62 ATGAGCCGTGTCA
473638 TTCCCCGACC
Statistics
Matches: 267, Mismatches: 45, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
82 2 0.01
83 93 0.35
84 10 0.04
85 2 0.01
86 57 0.21
87 3 0.01
89 98 0.37
90 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (85 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTAGATCCAGAACTCTTCATCACGTATGA
GCCGTGTCAACCATAGATAA
Found at i:473443 original size:129 final size:129
Alignment explanation
Indices: 473229--473775 Score: 864
Period size: 129 Copynumber: 4.2 Consensus size: 129
473219 CCAGCCGTCC
* * * *
473229 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTATGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
473294 ATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
473358 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
473423 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* *
473487 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACTTATGAGCCATGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
473552 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
473616 TCATCACGTATGAGCCATGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTC-AC
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
* * * * * * * * *
473679 CCTAGATAACCAGTCGTCCTCATCACGTATGAACTGAGTTATCATCCACCCTTAGACGACCAGAC
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTG-T-T-AT-CACCTTTAGATGGCCAGAA
473744 CTCT
126 CTCT
* *
473748 TCATCACGTATGAGCAGTGTCGTCCCCA
1 TCATCACGTATGAGCCGTGTCATCCCCA
473776 CCAACACGCA
Statistics
Matches: 390, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
128 35 0.09
129 304 0.78
130 6 0.02
131 7 0.02
132 38 0.10
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:473933 original size:3 final size:3
Alignment explanation
Indices: 473927--473991 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
473917 TTTATATATA
* *
473927 TAT TAT TAT TAT TGT TAT TTT TAT TAT TAT TATT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
473972 TAT TCAT TAT CAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT T
473992 TACATATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:473964 original size:31 final size:30
Alignment explanation
Indices: 473912--473993 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
473902 TTTTGTCCGG
* *
473912 TTTTTTTTA-TATATATATTATTATTATTGTTA
1 TTTTTATTATTAT-TAT-TTATTATTATT-ATA
473944 TTTTTATTATTATTATTTATTATTATTATA
1 TTTTTATTATTATTATTTATTATTATTATA
* *
473974 TTCATTATCATTATTATTTA
1 TT-TTTATTATTATTATTTA
473994 CATATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 4 0.09
31 26 0.59
32 11 0.25
33 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTTTATTATTATTATTTATTATTATTATA
Found at i:474467 original size:12 final size:11
Alignment explanation
Indices: 474445--474472 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
474435 GGGTTTCCAG
474445 AAAAGAAAAAA
1 AAAAGAAAAAA
474456 AAAAGAAAAAA
1 AAAAGAAAAAA
474467 AAAAGA
1 AAAAGA
474473 GAGTCAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:479183 original size:19 final size:19
Alignment explanation
Indices: 479159--479197 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
479149 TCGAATGCAT
479159 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
479178 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
479197 T
1 T
479198 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:479265 original size:45 final size:46
Alignment explanation
Indices: 479180--479285 Score: 153
Period size: 45 Copynumber: 2.3 Consensus size: 46
479170 ATGCACTCTC
*
479180 CATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
* **
479226 GATGCATCGATGCA-TCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTT
479271 CATGCATCGATGCAC
1 CATGCATCGATGCAC
479286 ACTTGGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
45 35 0.66
46 18 0.34
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (46 bp):
CATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:485101 original size:20 final size:21
Alignment explanation
Indices: 485076--485125 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
485066 GCTTCAGTAC
485076 CGATGCAT-TT-AACAATGCAT
1 CGATGCATCTTGAA-AATGCAT
*
485096 CGATGCATCCTTGAATATGCAT
1 CGATGCAT-CTTGAAAATGCAT
485118 CGATGCAT
1 CGATGCAT
485126 AAGACCATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
CGATGCATCTTGAAAATGCAT
Found at i:486700 original size:21 final size:21
Alignment explanation
Indices: 486658--486701 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
486648 GCCCTGGGAG
*
486658 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
486679 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
486700 CT
1 CT
486702 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:487732 original size:19 final size:19
Alignment explanation
Indices: 487708--487746 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
487698 TCGAATGCAT
487708 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
487727 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
487746 T
1 T
487747 GAATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:487762 original size:64 final size:63
Alignment explanation
Indices: 487694--487852 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 63
487684 GAATTAATTG
* *** *
487694 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TG-AATTTTTCA
1 AACATCGAATGCATT-CATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCAATTTTTC-
487757 A
63 A
* *
487758 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCA
1 AACATCGAATGCA-TTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCAATTTTTCA
487822 AACATCGAATGCATTCATGCATCGATGCACA
1 AACATCGAATGCATTCATGCATCGATGCACA
487853 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 19 0.23
64 56 0.67
65 9 0.11
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCAATTTTTCA
Found at i:490302 original size:13 final size:13
Alignment explanation
Indices: 490284--490311 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
490274 GAAAAAGACA
490284 AGAGAGAAGGTTG
1 AGAGAGAAGGTTG
490297 AGAGAGAAGGTTG
1 AGAGAGAAGGTTG
490310 AG
1 AG
490312 CCGCTGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.46, T:0.14
Consensus pattern (13 bp):
AGAGAGAAGGTTG
Found at i:490865 original size:12 final size:12
Alignment explanation
Indices: 490848--490876 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
490838 TTATTTCTTG
490848 TATTTATGAAGA
1 TATTTATGAAGA
490860 TATTTATGAAGA
1 TATTTATGAAGA
490872 TATTT
1 TATTT
490877 TAAACAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (12 bp):
TATTTATGAAGA
Found at i:490931 original size:2 final size:2
Alignment explanation
Indices: 490924--490952 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
490914 TTCCCCGCAT
490924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
490953 GACACGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492562 original size:11 final size:11
Alignment explanation
Indices: 492546--492575 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
492536 ATTGAATCTT
492546 AGAGGAAATAA
1 AGAGGAAATAA
492557 AGAGGAAATAA
1 AGAGGAAATAA
492568 AGAGGAAA
1 AGAGGAAA
492576 CTCACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (11 bp):
AGAGGAAATAA
Found at i:493865 original size:99 final size:99
Alignment explanation
Indices: 493694--493891 Score: 387
Period size: 99 Copynumber: 2.0 Consensus size: 99
493684 GCAACTAGGT
493694 TGGTAAGGTTTTAAAGTTCATGTGGATATTATTGTGGTGATAACAACCACTCCATAGAGAATTAT
1 TGGTAAGGTTTTAAAGTTCATGTGGATATTATTGTGGTGATAACAACCACTCCATAGAGAATTAT
493759 TGGATCTTAAGATTAAAGGTTTGAAACTTTATCA
66 TGGATCTTAAGATTAAAGGTTTGAAACTTTATCA
*
493793 TGGTAAGGTTTTAAAGTTCATGTGGATATTATTGTGGTGATTACAACCACTCCATAGAGAATTAT
1 TGGTAAGGTTTTAAAGTTCATGTGGATATTATTGTGGTGATAACAACCACTCCATAGAGAATTAT
493858 TGGATCTTAAGATTAAAGGTTTGAAACTTTATCA
66 TGGATCTTAAGATTAAAGGTTTGAAACTTTATCA
493892 CTGAAGGGTC
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (99 bp):
TGGTAAGGTTTTAAAGTTCATGTGGATATTATTGTGGTGATAACAACCACTCCATAGAGAATTAT
TGGATCTTAAGATTAAAGGTTTGAAACTTTATCA
Found at i:495884 original size:25 final size:25
Alignment explanation
Indices: 495842--495897 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
495832 TTTTAAAAAA
495842 CTTTC-TCAAACATTTTTCAAAATT
1 CTTTCATCAAACATTTTTCAAAATT
*
495866 CTTTCATCCAACATTTTTCAAAATT
1 CTTTCATCAAACATTTTTCAAAATT
495891 CTTTCAT
1 CTTTCAT
495898 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.46
Consensus pattern (25 bp):
CTTTCATCAAACATTTTTCAAAATT
Found at i:500672 original size:16 final size:17
Alignment explanation
Indices: 500644--500675 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
500634 CATCTTTAGA
500644 GTAGAGATAGAGATGAC
1 GTAGAGATAGAGATGAC
500661 GTAGAG-TAGAGATGA
1 GTAGAGATAGAGATGA
500676 GGGCTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.03, G:0.38, T:0.19
Consensus pattern (17 bp):
GTAGAGATAGAGATGAC
Found at i:511361 original size:21 final size:20
Alignment explanation
Indices: 511327--511365 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
511317 AATTTCTAGA
*
511327 TTTTTTTTGGCTTTTTATCT
1 TTTTTTTTGCCTTTTTATCT
511347 TTTTTTATTGCCTTTTTAT
1 TTTTTT-TTGCCTTTTTAT
511366 TTCCTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.08, C:0.10, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTTTTTGCCTTTTTATCT
Found at i:518052 original size:15 final size:15
Alignment explanation
Indices: 518027--518055 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
518017 ACTTCGCGCA
518027 CAACTTCTTCTCTCT
1 CAACTTCTTCTCTCT
518042 CAACTTCTTCTCTC
1 CAACTTCTTCTCTC
518056 CTTTTAATAT
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:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (15 bp):
CAACTTCTTCTCTCT
Found at i:523483 original size:19 final size:19
Alignment explanation
Indices: 523443--523485 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
523433 TTAATATATC
523443 AAATACAATTTAAATTTAT
1 AAATACAATTTAAATTTAT
523462 AAATAC-ATTTAGATATTT-T
1 AAATACAATTTA-A-ATTTAT
523481 AAATA
1 AAATA
523486 AGATATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATACAATTTAAATTTAT
Found at i:547297 original size:19 final size:20
Alignment explanation
Indices: 547259--547297 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
547249 AATGGTGACC
*
547259 AATCGAACTAAATTATTTTT
1 AATCGAACTAAATAATTTTT
*
547279 AATCGAA-TTAATAATTTTT
1 AATCGAACTAAATAATTTTT
547298 TTTTCTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (20 bp):
AATCGAACTAAATAATTTTT
Found at i:552704 original size:15 final size:15
Alignment explanation
Indices: 552684--552715 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
552674 AAGGCATGAT
552684 AATAAAATGAAACAA
1 AATAAAATGAAACAA
552699 AATAAAATGAAACAA
1 AATAAAATGAAACAA
552714 AA
1 AA
552716 AATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (15 bp):
AATAAAATGAAACAA
Found at i:552770 original size:28 final size:27
Alignment explanation
Indices: 552712--552776 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
552702 AAAATGAAAC
*
552712 AAAAAA-TAAATATTACGTATGATTTT
1 AAAAAATTAAATATTACGTATGATTTA
*
552738 AAAAAATTAAATGTTACGTATGATTTAA
1 AAAAAATTAAATATTACGTATGATTT-A
552766 AAAAAATTAAA
1 AAAAAATTAAA
552777 AGTTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 6 0.17
27 18 0.51
28 11 0.31
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (27 bp):
AAAAAATTAAATATTACGTATGATTTA
Found at i:553683 original size:29 final size:28
Alignment explanation
Indices: 553644--553703 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
553634 CACACCTAAA
553644 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
553672 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
553701 TTA
1 TTA
553704 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:558348 original size:29 final size:28
Alignment explanation
Indices: 558312--558370 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
558302 CCTAAATTAA
558312 TTTTATGTCATTGCTTACATCAATTTAG
1 TTTTATGTCATTGCTTACATCAATTTAG
558340 TTTTGATGTCATTGCTTACATCAATTTAG
1 TTTT-ATGTCATTGCTTACATCAATTTAG
558369 TT
1 TT
558371 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTTATGTCATTGCTTACATCAATTTAG
Found at i:564771 original size:23 final size:23
Alignment explanation
Indices: 564729--564790 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
564719 TCAGTGTAGA
*
564729 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATACCCCCTTTGAAG
*
564751 GGGAACCGATCCCCCCTTTGAAG
1 GGGAACCGATACCCCCTTTGAAG
*
564774 GGGAACCGATTCCCCCT
1 GGGAACCGATACCCCCT
564791 GTAGAGAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.18
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTGAAG
Found at i:566367 original size:18 final size:18
Alignment explanation
Indices: 566341--566376 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
566331 GCCGACTCTG
*
566341 ACGATGAACAAGAACAAC
1 ACGAGGAACAAGAACAAC
*
566359 ACGAGGAACAAGCACAAC
1 ACGAGGAACAAGAACAAC
566377 CAAAGGAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.19, T:0.03
Consensus pattern (18 bp):
ACGAGGAACAAGAACAAC
Found at i:568647 original size:81 final size:81
Alignment explanation
Indices: 568542--569427 Score: 1280
Period size: 81 Copynumber: 11.1 Consensus size: 81
568532 TATTCTAAAA
* * * *
568542 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGTCAGTTAGATGAAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
568607 GTTAAATACCTTAT-AG
66 GTTAAATACCTT-TGAG
* *
568623 TAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
568688 GCTAAATACATTTGAAG
66 GTTAAATACCTTTG-AG
* * *
568705 -AAAAGATTAATGGCCTATCTGTGCATTTGACAGAAATGTATCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
568769 CTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
568785 TAAAAGATTAATGGCCTAACTTTGCATCTGACAGAAATGTGTCAATTATG-C-----------AG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
568838 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
568854 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATTTGTTAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
568919 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* * *
568935 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTATATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
569000 GTTAAATACCTTTCAA
66 GTTAAATACCTTTGAG
569016 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
569081 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
569097 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
569162 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
*
569178 TAAAAGATTAATGGCCTAGCTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
569243 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
569259 TAAAATATTAATGACCTAGTTGTGCATTTTATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
569324 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
569340 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGGAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
569405 GCTAAATGCCTTT-AGG
66 GTTAAATACCTTTGA-G
569421 TAAAAGA
1 TAAAAGA
569428 CTAAATGCTT
Statistics
Matches: 729, Mismatches: 60, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
69 61 0.08
70 1 0.00
80 5 0.01
81 660 0.91
82 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:569419 original size:22 final size:22
Alignment explanation
Indices: 569394--569435 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
569384 ATCATGCAAG
* *
569394 TTAGATGAAAGGCTAAATGCCT
1 TTAGATAAAAGACTAAATGCCT
*
569416 TTAGGTAAAAGACTAAATGC
1 TTAGATAAAAGACTAAATGC
569436 TTAACAGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (22 bp):
TTAGATAAAAGACTAAATGCCT
Found at i:570752 original size:20 final size:23
Alignment explanation
Indices: 570699--570752 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 23
570689 TTTGAAATTA
570699 CTCCCCTTACTCTAACACTTCTCTC
1 CTCCCCTTACTCTAACA--TCTCTC
570724 CTCCCCCTTACTCTAACA-CT-T-
1 CT-CCCCTTACTCTAACATCTCTC
570745 CTCCCCTT
1 CTCCCCTT
570753 TAAAACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 1 0.04
23 2 0.07
25 2 0.07
26 15 0.54
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (23 bp):
CTCCCCTTACTCTAACATCTCTC
Found at i:571080 original size:15 final size:16
Alignment explanation
Indices: 571062--571100 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
571052 TCAAATATCC
571062 AACAA-CCAAAGTAAA
1 AACAATCCAAAGTAAA
571077 AACAATCCAAAGT-AA
1 AACAATCCAAAGTAAA
571092 AACAATCCA
1 AACAATCCA
571101 TGAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.62, C:0.23, G:0.05, T:0.10
Consensus pattern (16 bp):
AACAATCCAAAGTAAA
Found at i:572652 original size:23 final size:23
Alignment explanation
Indices: 572599--572680 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 23
572589 CAGAACCCGT
*
572599 GGGGGTATCGATTCCC--T-AAA
1 GGGGGAATCGATTCCCATTCAAA
*
572619 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCATTCAAA
*
572643 GGGGGAATCGATTCCCTTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
*
572665 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
572681 TCTGCACTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 17 0.32
23 17 0.32
24 5 0.09
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:576031 original size:22 final size:21
Alignment explanation
Indices: 575993--576045 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
575983 AGATATATCA
575993 AAAACATAAT-TAAATGAGA-
1 AAAACATAATCTAAATGAGAT
576012 AACATACATAATCTAAATGAGAT
1 AA-A-ACATAATCTAAATGAGAT
576035 AAAACATAATC
1 AAAACATAATC
576046 ATTTAGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.07
20 1 0.03
21 15 0.50
22 10 0.33
23 2 0.07
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.23
Consensus pattern (21 bp):
AAAACATAATCTAAATGAGAT
Found at i:576676 original size:117 final size:117
Alignment explanation
Indices: 576458--576677 Score: 284
Period size: 117 Copynumber: 1.9 Consensus size: 117
576448 ATTTCAAATC
* *
576458 AAATTTTTTTTTCAATACTTTTAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCA
1 AAATTTCTTTTTCAATACTTTTAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCA
* *
576523 TTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTGA
66 TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGA
* * *
576575 AAATTTCTTTTTCAA-AGTTTTCATATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACATTT
1 AAATTTCTTTTTCAATACTTTT-AAATTTTATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTT
* * * **
576638 CATTTTTATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
576678 ATCATTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 6 0.07
117 78 0.89
118 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (117 bp):
AAATTTCTTTTTCAATACTTTTAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCA
TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGA
Found at i:582598 original size:30 final size:30
Alignment explanation
Indices: 582562--582621 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
582552 ACAATTTAAG
582562 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
582592 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
582622 ATTCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:582730 original size:13 final size:13
Alignment explanation
Indices: 582712--582770 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
582702 AGTGCATCCA
582712 TGCATCCCTGCAG
1 TGCATCCCTGCAG
582725 TGCATCCCTGCAG
1 TGCATCCCTGCAG
582738 TGCAT--C--CA-
1 TGCATCCCTGCAG
582746 TGCATCCCTGCAG
1 TGCATCCCTGCAG
*
582759 TGCATCCATGCA
1 TGCATCCCTGCA
582771 TCTGCACTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 1 0.03
11 1 0.03
12 2 0.05
13 29 0.73
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:582745 original size:34 final size:34
Alignment explanation
Indices: 582702--582770 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
582692 AGGGTGTCAA
*
582702 AGTGCATCCATGCATCCCTGCAGTGCATCCCTGC
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGC
582736 AGTGCATCCATGCATCCCTGCAGTGCATCCATGC
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGC
582770 A
1 A
582771 TCTGCACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.23
Consensus pattern (34 bp):
AGTGCATCCATGCATCCCTGCAGTGCATCCATGC
Found at i:582749 original size:21 final size:21
Alignment explanation
Indices: 582725--582772 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
582715 ATCCCTGCAG
582725 TGCATCCCTGCAGTGCATCCA
1 TGCATCCCTGCAGTGCATCCA
582746 TGCATCCCTGCAGTGCATCCA
1 TGCATCCCTGCAGTGCATCCA
582767 TGCATC
1 TGCATC
582773 TGCACTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (21 bp):
TGCATCCCTGCAGTGCATCCA
Found at i:582864 original size:21 final size:21
Alignment explanation
Indices: 582838--582910 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
582828 CAATTAGTGC
*
582838 ATCGATGCATCCTTGCCATTA
1 ATCGATGCATCCTTGCCATGA
*
582859 ATCGATGCATCCTTGCCATGC
1 ATCGATGCATCCTTGCCATGA
*
582880 ATCGATGCATCC-TGCCATGC
1 ATCGATGCATCCTTGCCATGA
*
582900 ATCCATGCATC
1 ATCGATGCATC
582911 AAGGCTGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 18 0.37
21 31 0.63
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (21 bp):
ATCGATGCATCCTTGCCATGA
Found at i:586137 original size:30 final size:30
Alignment explanation
Indices: 586101--586160 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
586091 ACAATTTAAG
586101 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
586131 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
586161 ATTCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:586267 original size:21 final size:21
Alignment explanation
Indices: 586241--586298 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
586231 AGGGTGTCAA
586241 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
586262 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
586283 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
586299 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:586387 original size:21 final size:21
Alignment explanation
Indices: 586361--586436 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
586351 ATGCAATTAG
*
586361 TGCATCGATGTATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
586382 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
586403 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
586423 TGCATCCATGCATC
1 TGCATCGATGCATC
586437 AAGGCTGCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 18 0.34
21 35 0.66
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:590038 original size:17 final size:18
Alignment explanation
Indices: 590013--590047 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
590003 TATGAATTCA
*
590013 TTAATATGA-ACATATGT
1 TTAACATGATACATATGT
590030 TTAACATGATACATATGT
1 TTAACATGATACATATGT
590048 GTTATTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (18 bp):
TTAACATGATACATATGT
Found at i:590533 original size:22 final size:22
Alignment explanation
Indices: 590505--590547 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
590495 TCCTTCAGTT
*
590505 ATATACAGAGGTCCTTAAGGAC
1 ATATACACAGGTCCTTAAGGAC
*
590527 ATATACACAGGTCCTTTAGGA
1 ATATACACAGGTCCTTAAGGA
590548 AAAATCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (22 bp):
ATATACACAGGTCCTTAAGGAC
Found at i:595317 original size:22 final size:22
Alignment explanation
Indices: 595289--595343 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
595279 GGTCTACGCA
*
595289 GTCCTTCGGGACATATACAGAG
1 GTCCTTCGGGACATATACACAG
595311 GTCCTTCGGGACATATACACAG
1 GTCCTTCGGGACATATACACAG
*
595333 GTCATTCGGGA
1 GTCCTTCGGGA
595344 TAAATTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTCCTTCGGGACATATACACAG
Found at i:595353 original size:22 final size:22
Alignment explanation
Indices: 595293--595353 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
595283 TACGCAGTCC
* * *
595293 TTCGGGACATATACAGAGGTCC
1 TTCGGGACAAATACACAGGTCA
*
595315 TTCGGGACATATACACAGGTCA
1 TTCGGGACAAATACACAGGTCA
* *
595337 TTCGGGATAAATTCACA
1 TTCGGGACAAATACACA
595354 TGCCCCTAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (22 bp):
TTCGGGACAAATACACAGGTCA
Found at i:598144 original size:17 final size:17
Alignment explanation
Indices: 598099--598152 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
598089 TGACCGGTCA
*
598099 CGACCCGACCCGTTAACC
1 CGACCCGACCCGTTGA-C
* * *
598117 CAACCCAACCCATTGAC
1 CGACCCGACCCGTTGAC
598134 CGACCCGACCCGTTGAC
1 CGACCCGACCCGTTGAC
598151 CG
1 CG
598153 TTGACCGATG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.24, C:0.48, G:0.17, T:0.11
Consensus pattern (17 bp):
CGACCCGACCCGTTGAC
Found at i:605120 original size:18 final size:18
Alignment explanation
Indices: 605097--605168 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 18
605087 TTTAACCGGT
*
605097 CACGACCCGGCCCGTTGA
1 CACGACCCGACCCGTTGA
* *
605115 CACGACCCGAGCCGTTAA
1 CACGACCCGACCCGTTGA
* * *
605133 CCCGACCTGACCTGTTGA
1 CACGACCCGACCCGTTGA
*
605151 C-CGACCCGACCTGTTGA
1 CACGACCCGACCCGTTGA
605168 C
1 C
605169 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 16 0.36
18 29 0.64
ACGTcount: A:0.19, C:0.42, G:0.24, T:0.15
Consensus pattern (18 bp):
CACGACCCGACCCGTTGA
Found at i:605180 original size:7 final size:7
Alignment explanation
Indices: 605158--605190 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
605148 TGACCGACCC
605158 GACCTGTT
1 GACC-GTT
605166 GA-CGTT
1 GACCGTT
605172 GACCGTT
1 GACCGTT
605179 GACCGTT
1 GACCGTT
605186 GACCG
1 GACCG
605191 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.21
7 17 0.71
8 2 0.08
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:612348 original size:18 final size:18
Alignment explanation
Indices: 612325--612395 Score: 81
Period size: 18 Copynumber: 4.0 Consensus size: 18
612315 AACCGGTCAC
*
612325 GACCCGGCCCGTTAACCG
1 GACCCGACCCGTTAACCG
*
612343 GACCCGACCCGTTAACCC
1 GACCCGACCCGTTAACCG
* * *
612361 GACCTGACCTGTTGACC-
1 GACCCGACCCGTTAACCG
*
612378 GACCCGACCCGTTGACCG
1 GACCCGACCCGTTAACCG
612396 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 15 0.33
18 30 0.67
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTAACCG
Found at i:619529 original size:18 final size:18
Alignment explanation
Indices: 619503--619573 Score: 90
Period size: 18 Copynumber: 4.0 Consensus size: 18
619493 TGACCGGTCA
619503 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
* *
619521 CGTCCCGACCCGTTAACC
1 CGACCCGACCCGTTGACC
* **
619539 CGACCTGACCTATTGA-C
1 CGACCCGACCCGTTGACC
619556 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
619574 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
17 14 0.33
18 28 0.67
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.15
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:624266 original size:13 final size:13
Alignment explanation
Indices: 624244--624291 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
624234 GAGGAAAGAA
624244 AGGATGAAGGAAG
1 AGGATGAAGGAAG
*
624257 AGGGTGAAGGAAG
1 AGGATGAAGGAAG
*
624270 AGGATAAAGGAAG
1 AGGATGAAGGAAG
*
624283 AGGAAGAAG
1 AGGATGAAG
624292 ACAAAGGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.46, T:0.06
Consensus pattern (13 bp):
AGGATGAAGGAAG
Found at i:627597 original size:35 final size:35
Alignment explanation
Indices: 627544--627635 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
627534 AAACATATAC
* ** * *
627544 GCACACACAGTGCTATCACATCAGAAT-TGTGATAT
1 GCACACAAAGTGAAATCACATCAGAATCAG-AATAT
627579 GCACACAAAGTGAAATCACATCAGAATCAGAATAT
1 GCACACAAAGTGAAATCACATCAGAATCAGAATAT
*
627614 GCACACAAAGTGTAATCACATC
1 GCACACAAAGTGAAATCACATC
627636 GAAAATATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 49 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (35 bp):
GCACACAAAGTGAAATCACATCAGAATCAGAATAT
Found at i:627714 original size:35 final size:35
Alignment explanation
Indices: 627675--627752 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
627665 ACCACAATAT
*
627675 ATCACTTCAGAATC-GTAATATGCACACAAAGTGAA
1 ATCACATCAGAATCAG-AATATGCACACAAAGTGAA
**
627710 ATCACATCAGAATCAGAATATGCACACAAAGTGCT
1 ATCACATCAGAATCAGAATATGCACACAAAGTGAA
627745 ATCACATC
1 ATCACATC
627753 GAAAATATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (35 bp):
ATCACATCAGAATCAGAATATGCACACAAAGTGAA
Found at i:627763 original size:117 final size:117
Alignment explanation
Indices: 627557--628030 Score: 797
Period size: 117 Copynumber: 4.1 Consensus size: 117
627547 CACACAGTGC
* * *
627557 TATCACATCAGAATTGTGATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
1 TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
*
627622 AGTGTAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAATA
66 AGTGTAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAGTA
627674 TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
1 TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
*
627739 AGTGCT-ATCACATCGAAAATATACTAGTGTACCTTCATGTAACACCACAGTA
66 AGTG-TAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAGTA
* * *
627791 TATCACTTCAGAATTGTAATATGCACACAAAGTGCAATCACATCAGAATCAGAATATGTACACAA
1 TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
* * *
627856 AGTGCAATCACATCGAAAATATACTAGTGTACCTTTAGGTAACACCACAGTT
66 AGTGTAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAGTA
* * *
627908 TATCACTTCAGAATCGTAATATGCACACAGAGTGCAATCACATCAGAATTAGAATATGCACACAA
1 TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
*
627973 AGTGTAATCACATCGAAAATATATTAGTGTACCTTCAGGTAACACCACAGTA
66 AGTGTAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAGTA
628025 TATCAC
1 TATCAC
628031 AATCACTCCA
Statistics
Matches: 335, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
117 334 1.00
118 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (117 bp):
TATCACTTCAGAATCGTAATATGCACACAAAGTGAAATCACATCAGAATCAGAATATGCACACAA
AGTGTAATCACATCGAAAATATACTAGTGTACCTTCAGGTAACACCACAGTA
Found at i:637083 original size:21 final size:21
Alignment explanation
Indices: 637043--637083 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
637033 ATAAAATTTT
*
637043 GAAAAATTGAAAGGTCAGAAA
1 GAAAAATTGAAAGATCAGAAA
* *
637064 GAAAAATTGAGAGATGAGAA
1 GAAAAATTGAAAGATCAGAA
637084 TTTTACACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (21 bp):
GAAAAATTGAAAGATCAGAAA
Found at i:642325 original size:27 final size:27
Alignment explanation
Indices: 642287--642338 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
642277 TTCAGAGGAA
* *
642287 GTTAGGCGGTTAGGAAACTGTTGAGAG
1 GTTAGGCAGTTAGGAAACGGTTGAGAG
*
642314 GTTAGGCAGTTAGGAAGCGGTTGAG
1 GTTAGGCAGTTAGGAAACGGTTGAG
642339 CTTCTGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (27 bp):
GTTAGGCAGTTAGGAAACGGTTGAGAG
Found at i:646922 original size:27 final size:27
Alignment explanation
Indices: 646884--646935 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
646874 TTCAGAGGAA
* *
646884 GTTAGGCGGTTAGGAAACTGTTGAGAG
1 GTTAGGCAGTTAGGAAACGGTTGAGAG
*
646911 GTTAGGCAGTTAGGAAGCGGTTGAG
1 GTTAGGCAGTTAGGAAACGGTTGAG
646936 CTTCTGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (27 bp):
GTTAGGCAGTTAGGAAACGGTTGAGAG
Found at i:648841 original size:28 final size:28
Alignment explanation
Indices: 648797--648851 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
648787 TTATATAACA
648797 AACAATATATATATTGTATCTTAGTAAG
1 AACAATATATATATTGTATCTTAGTAAG
*
648825 AACAATATATATCTTGTATCTTAGTAA
1 AACAATATATATATTGTATCTTAGTAA
648852 ATTTTTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (28 bp):
AACAATATATATATTGTATCTTAGTAAG
Found at i:649003 original size:20 final size:20
Alignment explanation
Indices: 648978--649030 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
648968 TTTTATATTA
648978 TATATAGATATATTAATAGT
1 TATATAGATATATTAATAGT
648998 TATATAGATATATTAATAGT
1 TATATAGATATATTAATAGT
*
649018 TATATATATATAT
1 TATATAGATATAT
649031 ATATAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATAGATATATTAATAGT
Found at i:649045 original size:20 final size:20
Alignment explanation
Indices: 648974--649045 Score: 54
Period size: 24 Copynumber: 3.3 Consensus size: 20
648964 ATAATTTTAT
* *
648974 ATTATATATAGATATATTAA
1 ATTATATATATATATAATAA
* *
648994 TAGTTATATAGATATATTAATAGTT
1 -A-TTATATATATATA-TAATA--A
649019 ATATATATATATATATAATAA
1 AT-TATATATATATATAATAA
649040 ATTATA
1 ATTATA
649046 ATTTAATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.10
21 3 0.08
22 11 0.28
23 10 0.25
24 12 0.30
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
ATTATATATATATATAATAA
Found at i:649177 original size:30 final size:30
Alignment explanation
Indices: 649141--649292 Score: 89
Period size: 30 Copynumber: 5.0 Consensus size: 30
649131 TTAAGTTAAT
649141 ATATTTTAAAAATTAAGATAAAAATAAAAA
1 ATATTTTAAAAATTAAGATAAAAATAAAAA
* * * * * *
649171 ATATTTTTTAAGA-GAATATAGAGATAAAATA
1 ATA-TTTTAAAAATTAAGATAAAAATAAAA-A
* * * *
649202 TATATTTT-TACATTAAAATAAAAATAAAAT
1 -ATATTTTAAAAATTAAGATAAAAATAAAAA
** *
649232 ATA-TTTAATAGGTTAAGGA-AAAAATAAAAT
1 ATATTTTAA-AAATTAA-GATAAAAATAAAAA
*
649262 ATA-TTTAACAAGTTAAGATAAAAATAAAAA
1 ATATTTTAA-AAATTAAGATAAAAATAAAAA
649292 A
1 A
649293 AATAAAAATT
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
28 3 0.03
29 5 0.05
30 58 0.62
31 25 0.27
32 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.32
Consensus pattern (30 bp):
ATATTTTAAAAATTAAGATAAAAATAAAAA
Found at i:649389 original size:28 final size:27
Alignment explanation
Indices: 649322--649389 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
649312 AGAATTAAGA
*
649322 TATATAAAATATTATATTCATATTTTT
1 TATATAAAATATTATATTCATATTTAT
*
649349 TATTATAAAATATTATATTCGTATTATAT
1 TA-TATAAAATATTATATTCATATT-TAT
649378 TA-ATAAATATAT
1 TATATAAA-ATAT
649390 ATAATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 7 0.19
28 25 0.69
29 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
TATATAAAATATTATATTCATATTTAT
Found at i:651077 original size:24 final size:24
Alignment explanation
Indices: 651050--651101 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
651040 AACGGATATA
*
651050 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
651074 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
651098 TCAA
1 TCAA
651102 GTAACAGATC
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:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:651102 original size:24 final size:24
Alignment explanation
Indices: 651066--651191 Score: 150
Period size: 24 Copynumber: 5.2 Consensus size: 24
651056 ATCAAAACAT
*
651066 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
651090 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
* *
651114 AATTCAAGTCAAGTATCAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
651138 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAGATCAG
*
651162 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
651186 AAATCA
1 AAATCA
651192 AATCGAAAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
23 4 0.04
24 82 0.90
25 5 0.05
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:652317 original size:18 final size:18
Alignment explanation
Indices: 652296--652331 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
652286 CTTCCATCCG
*
652296 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
652314 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
652332 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:653657 original size:8 final size:8
Alignment explanation
Indices: 653644--653678 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
653634 GGTCAACTCC
653644 GGTCAACG
1 GGTCAACG
653652 GGTCAACG
1 GGTCAACG
653660 GGTCAAC-
1 GGTCAACG
653667 GGTCAACG
1 GGTCAACG
653675 GGTC
1 GGTC
653679 GGGTCAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:653672 original size:15 final size:16
Alignment explanation
Indices: 653644--653678 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
653634 GGTCAACTCC
653644 GGTCAACGGGTCAACG
1 GGTCAACGGGTCAACG
653660 GGTCAAC-GGTCAACG
1 GGTCAACGGGTCAACG
653675 GGTC
1 GGTC
653679 GGGTCAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (16 bp):
GGTCAACGGGTCAACG
Found at i:653694 original size:13 final size:13
Alignment explanation
Indices: 653678--653721 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
653668 GTCAACGGGT
653678 CGGGTCAGGTAAA
1 CGGGTCAGGTAAA
*
653691 CGGGTCGGGTAAA
1 CGGGTCAGGTAAA
653704 CGGGTCAGGTAAA
1 CGGGTCAGGTAAA
653717 CGGGT
1 CGGGT
653722 TGTGACCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.43, T:0.16
Consensus pattern (13 bp):
CGGGTCAGGTAAA
Found at i:655671 original size:2 final size:2
Alignment explanation
Indices: 655666--655698 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
655656 TTTTTAAAAC
655666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
655699 CCCCCATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:655916 original size:24 final size:24
Alignment explanation
Indices: 655889--655940 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
655879 AACGGATATA
*
655889 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
655913 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
655937 TCAA
1 TCAA
655941 GTAACAGATC
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:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:655941 original size:24 final size:24
Alignment explanation
Indices: 655905--656030 Score: 150
Period size: 24 Copynumber: 5.2 Consensus size: 24
655895 ATCAAAACAT
*
655905 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
655929 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
* *
655953 AATTCAAGTCAAGTATCAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
655977 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAGATCAG
*
656001 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
656025 AAATCA
1 AAATCA
656031 AATCGAAAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
23 4 0.04
24 82 0.90
25 5 0.05
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:657155 original size:18 final size:18
Alignment explanation
Indices: 657134--657169 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
657124 CTTCCATCCG
*
657134 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
657152 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
657170 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:658494 original size:8 final size:8
Alignment explanation
Indices: 658481--658528 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
658471 GGTCAACTCC
658481 GGTCAACG
1 GGTCAACG
658489 GGTCAACG
1 GGTCAACG
658497 GGTCAAC-
1 GGTCAACG
658504 GGTCAACG
1 GGTCAACG
658512 GGT---CG
1 GGTCAACG
658517 GGTCAACG
1 GGTCAACG
658525 GGTC
1 GGTC
658529 GGGTAGGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.14
7 7 0.19
8 24 0.67
ACGTcount: A:0.21, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:658522 original size:13 final size:13
Alignment explanation
Indices: 658508--658571 Score: 74
Period size: 13 Copynumber: 4.5 Consensus size: 13
658498 GTCAACGGTC
*
658508 AACGGGTCGGGTC
1 AACGGGTCGGGTA
658521 AACGGGTCGGGTAGGGTA
1 AACGGGTC--G--G-GTA
658539 AACGGGTCGGGTA
1 AACGGGTCGGGTA
658552 AACGGGTCGGGTA
1 AACGGGTCGGGTA
658565 AACGGGT
1 AACGGGT
658572 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
13 31 0.69
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 10 0.22
ACGTcount: A:0.22, C:0.16, G:0.47, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:658563 original size:18 final size:18
Alignment explanation
Indices: 658510--658551 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
658500 CAACGGTCAA
* *
658510 CGGGTCGGGTCAACGGGT
1 CGGGTAGGGTAAACGGGT
658528 CGGGTAGGGTAAACGGGT
1 CGGGTAGGGTAAACGGGT
658546 CGGGTA
1 CGGGTA
658552 AACGGGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTAGGGTAAACGGGT
Found at i:664287 original size:14 final size:14
Alignment explanation
Indices: 664268--664323 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
664258 CGTTCATGAA
664268 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
664282 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
664296 CG-T---TTATGTT
1 CGTTCAGTTATGTT
* *
664306 TGTTCGGTTATGTT
1 CGTTCAGTTATGTT
664320 CGTT
1 CGTT
664324 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:664296 original size:24 final size:24
Alignment explanation
Indices: 664275--664343 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
664265 GAACGTTCAG
664275 TTATGTTCGTTCAGTTATGTTCGT
1 TTATGTTCGTTCAGTTATGTTCGT
* *
664299 TTATGTTTGTTCGGTTATGTTCGT
1 TTATGTTCGTTCAGTTATGTTCGT
* *
664323 TTATGTTCATTCATTTATGTT
1 TTATGTTCGTTCAGTTATGTT
664344 TAAGCCAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTCAGTTATGTTCGT
Found at i:665013 original size:10 final size:10
Alignment explanation
Indices: 664998--665071 Score: 68
Period size: 10 Copynumber: 7.6 Consensus size: 10
664988 GGTCTCCAAT
664998 GTTTATGTTC
1 GTTTATGTTC
665008 GTTTATGTTC
1 GTTTATGTTC
*
665018 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
*
665030 GTTTGTGTTC
1 GTTTATGTTC
665040 GTTTATG-T-
1 GTTTATGTTC
665048 -TTT-TGTTC
1 GTTTATGTTC
665056 GTTTATGTTC
1 GTTTATGTTC
665066 GTTTAT
1 GTTTAT
665072 TTATTAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.04
7 4 0.08
9 4 0.08
10 30 0.58
11 8 0.15
12 4 0.08
ACGTcount: A:0.09, C:0.08, G:0.20, T:0.62
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:665022 original size:16 final size:16
Alignment explanation
Indices: 665003--665067 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
664993 CCAATGTTTA
665003 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
665019 TGTTCATTTATGTTTG
1 TGTTCGTTTATGTTCG
**
665035 TGTTCGTTTATGTTTT
1 TGTTCGTTTATGTTCG
665051 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
665067 T
1 T
665068 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.09, G:0.22, T:0.62
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:665039 original size:32 final size:32
Alignment explanation
Indices: 664996--665064 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
664986 AGGGTCTCCA
664996 ATGTTTATGTTCGTTTATGTTCGTGTTCATTT
1 ATGTTTATGTTCGTTTATGTTCGTGTTCATTT
* ** *
665028 ATGTTTGTGTTCGTTTATGTTTTTGTTCGTTT
1 ATGTTTATGTTCGTTTATGTTCGTGTTCATTT
665060 ATGTT
1 ATGTT
665065 CGTTTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.10, C:0.07, G:0.20, T:0.62
Consensus pattern (32 bp):
ATGTTTATGTTCGTTTATGTTCGTGTTCATTT
Found at i:665161 original size:16 final size:16
Alignment explanation
Indices: 665136--665176 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
665126 AAAAACATTT
665136 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
665152 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
665168 T-TT-ATTTAT
1 TGTTCATTTAT
665177 TAAATGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:666111 original size:12 final size:12
Alignment explanation
Indices: 666085--666118 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
666075 AGCTCGATTG
666085 AAGCTCGAGACTC
1 AAGCTCGA-ACTC
666098 AAGCTCGAACTC
1 AAGCTCGAACTC
*
666110 AAACTCGAA
1 AAGCTCGAA
666119 TTTGAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (12 bp):
AAGCTCGAACTC
Found at i:668866 original size:156 final size:156
Alignment explanation
Indices: 668582--668894 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 156
668572 GACCTGTTAT
668582 ATTTGTAATCTTCTGATTTCGTCATTAATCAAGGTTTACGTTTTTATATTCGGGTTATTAATTTA
1 ATTTGTAATCTTCTGATTTCGTCATTAATCAAGGTTTACGTTTTTATATTCGGGTTATTAATTTA
668647 TTTTTATTTTATGTTTTGATCACCATTTGTTTTGATAATGGACCTATTAATTGATTTGACCAAGT
66 TTTTTATTTTATGTTTTGATCACCATTTGTTTTGATAATGGACCTATTAATTGATTTGACCAAGT
668712 GTGATTTATTAGTTTATTTACATATA
131 GTGATTTATTAGTTTATTTACATATA
*
668738 ATTTGTAATCTTTTGATTTCGTCATTAATCAAGGTTTACGTTTTTATATTCGGGTTATTAATTTA
1 ATTTGTAATCTTCTGATTTCGTCATTAATCAAGGTTTACGTTTTTATATTCGGGTTATTAATTTA
*
668803 TTTTTATTTTATGTTTTGATCACCATTTGTTTTGATAATGGACCTATTGATTGATTTGACCAAGT
66 TTTTTATTTTATGTTTTGATCACCATTTGTTTTGATAATGGACCTATTAATTGATTTGACCAAGT
668868 GTGATTTATTAGTTTATTTACATATA
131 GTGATTTATTAGTTTATTTACATATA
668894 A
1 A
668895 ACCCTTGTTA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (156 bp):
ATTTGTAATCTTCTGATTTCGTCATTAATCAAGGTTTACGTTTTTATATTCGGGTTATTAATTTA
TTTTTATTTTATGTTTTGATCACCATTTGTTTTGATAATGGACCTATTAATTGATTTGACCAAGT
GTGATTTATTAGTTTATTTACATATA
Found at i:668997 original size:7 final size:7
Alignment explanation
Indices: 668983--669056 Score: 78
Period size: 7 Copynumber: 10.7 Consensus size: 7
668973 AATCTGATTA
668983 AGGGTTT
1 AGGGTTT
*
668990 ATGGTTT
1 AGGGTTT
*
668997 AGGGCTT
1 AGGGTTT
669004 AGGGTTT
1 AGGGTTT
* *
669011 AAGATTT
1 AGGGTTT
*
669018 AGTGTTT
1 AGGGTTT
*
669025 A-AGTTT
1 AGGGTTT
669031 AGGGTTT
1 AGGGTTT
*
669038 AGGGTCT
1 AGGGTTT
669045 AGGGTTT
1 AGGGTTT
669052 AGGGT
1 AGGGT
669057 GTAATCTAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
6 5 0.09
7 48 0.91
ACGTcount: A:0.19, C:0.03, G:0.36, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:669123 original size:32 final size:32
Alignment explanation
Indices: 669080--669147 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
669070 TGCTTAATTA
*
669080 AATGGTCTTTTATTTTTCTTTTAGTAATATAC
1 AATGGTATTTTATTTTTCTTTTAGTAATATAC
669112 AATGGTATTTTATTTTTCTTTTAGTAATATAC
1 AATGGTATTTTATTTTTCTTTTAGTAATATAC
669144 AATG
1 AATG
669148 TAACAATTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.54
Consensus pattern (32 bp):
AATGGTATTTTATTTTTCTTTTAGTAATATAC
Found at i:669226 original size:11 final size:11
Alignment explanation
Indices: 669210--669268 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
669200 GTATTATAGA
669210 ATTTTTAATAT
1 ATTTTTAATAT
669221 ATTTTTAA-A-
1 ATTTTTAATAT
669230 ATTTTATAAT-T
1 ATTTT-TAATAT
** *
669241 ATTAATAATGT
1 ATTTTTAATAT
*
669252 ATTTTTAATAA
1 ATTTTTAATAT
669263 ATTTTT
1 ATTTTT
669269 TATAATGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 25 0.66
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:669388 original size:11 final size:11
Alignment explanation
Indices: 669374--669405 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
669364 TCGTTACGAA
669374 CTCGAGTCGAG
1 CTCGAGTCGAG
669385 CTCGAGTCGAG
1 CTCGAGTCGAG
669396 -TCGAGTCGAG
1 CTCGAGTCGAG
669406 TCTATTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:669394 original size:5 final size:5
Alignment explanation
Indices: 669375--669407 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
669365 CGTTACGAAC
669375 TCGAG TCGAG CTCGAG TCGAG TCGAG TCGAG TC
1 TCGAG TCGAG -TCGAG TCGAG TCGAG TCGAG TC
669408 TATTTGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.21
Consensus pattern (5 bp):
TCGAG
Found at i:669622 original size:4 final size:4
Alignment explanation
Indices: 669615--669643 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
669605 AAAAGATTGA
669615 TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
669644 ATATTGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:671909 original size:2 final size:2
Alignment explanation
Indices: 671902--671935 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
671892 AACCACATCT
671902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
671936 ATGTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:674362 original size:13 final size:13
Alignment explanation
Indices: 674344--674368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
674334 TAAGGATTTA
674344 TTATTACAACTCC
1 TTATTACAACTCC
674357 TTATTACAACTC
1 TTATTACAACTC
674369 TGGGTTAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (13 bp):
TTATTACAACTCC
Found at i:678329 original size:24 final size:24
Alignment explanation
Indices: 678302--678359 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
678292 CCTTTTATAA
* *
678302 CAGCCCCACAAGGTTCTGTTTTTC
1 CAGCCCCACAAGGTGCAGTTTTTC
678326 CAGCCCCACAAGGTGCAGTTTTTC
1 CAGCCCCACAAGGTGCAGTTTTTC
678350 CAGCCCCACA
1 CAGCCCCACA
678360 GTCATTTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGCCCCACAAGGTGCAGTTTTTC
Found at i:680259 original size:24 final size:25
Alignment explanation
Indices: 680209--680268 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
680199 TTCACAACTA
680209 CTACATCACTACCACCATCTCAATCAT
1 CTACATCACTACCACCATCT--ATCAT
*
680236 CTACATCACTACCATCATCT-TCAT
1 CTACATCACTACCACCATCTATCAT
*
680260 CTCCATCAC
1 CTACATCAC
680269 CATCACCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 12 0.39
27 19 0.61
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (25 bp):
CTACATCACTACCACCATCTATCAT
Found at i:680271 original size:6 final size:6
Alignment explanation
Indices: 680257--680309 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
680247 CCATCATCTT
* * *
680257 CATCTC CATCAC CATCAC CACTTCTAC CATCTC CATCTC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CA--TC-AC CATCAC CATCAC CATCAC CATCAC
680308 CA
1 CA
680310 CCACTGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 33 0.80
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.26, C:0.49, G:0.00, T:0.25
Consensus pattern (6 bp):
CATCAC
Found at i:680276 original size:27 final size:28
Alignment explanation
Indices: 680246--680306 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
680236 CTACATCACT
*
680246 ACCATCATCT-TCATCTCCATCACCATC
1 ACCATCATCTACCATCTCCATCACCATC
* *
680273 ACCA-CTTCTACCATCTCCATCTCCATC
1 ACCATCATCTACCATCTCCATCACCATC
680300 ACCATCA
1 ACCATCA
680307 CCACCACTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.14
27 23 0.82
28 1 0.04
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.28
Consensus pattern (28 bp):
ACCATCATCTACCATCTCCATCACCATC
Found at i:680312 original size:27 final size:27
Alignment explanation
Indices: 680257--680312 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
680247 CCATCATCTT
* *
680257 CATCTCCATCACCATCACCACTTCTAC
1 CATCTCCATCACCATCACCACTACCAC
*
680284 CATCTCCATCTCCATCACCA-TCACCAC
1 CATCTCCATCACCATCACCACT-ACCAC
680311 CA
1 CA
680313 CTGTCACGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (27 bp):
CATCTCCATCACCATCACCACTACCAC
Found at i:689789 original size:18 final size:17
Alignment explanation
Indices: 689754--689804 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
689744 AAAGGAAATT
689754 AAATGAATAA-AATGAAAA
1 AAAT-AATAATAAT-AAAA
689772 GAAATAATAATAATAAAA
1 -AAATAATAATAATAAAA
*
689790 ATACTAATAATAATA
1 A-AATAATAATAATA
689805 TAAACTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.03
18 21 0.72
19 7 0.24
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATAATAATAATAAAA
Found at i:689791 original size:15 final size:15
Alignment explanation
Indices: 689773--689802 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
689763 AAATGAAAAG
689773 AAATAATAATAATAA
1 AAATAATAATAATAA
*
689788 AAATACTAATAATAA
1 AAATAATAATAATAA
689803 TATAAACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:689821 original size:16 final size:16
Alignment explanation
Indices: 689776--689824 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
689766 TGAAAAGAAA
*
689776 TAATAATAATAAAAATAC
1 TAATAATAAT-ATAA-AC
689794 TAATAATAATATAAAC
1 TAATAATAATATAAAC
689810 TATATAATATATATA
1 TA-ATAATA-ATATA
689825 TCTCAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 15 0.54
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAATATAAAC
Found at i:689926 original size:32 final size:31
Alignment explanation
Indices: 689886--689952 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
689876 ACTATATACC
689886 ATATAGTTTTCAAAAATGA-TTTTAAAA-TATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAACTA-T
*
689917 ATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAACTAT
689949 ATAT
1 ATAT
689953 TATATAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.16
32 25 0.78
33 2 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAACTAT
Found at i:689954 original size:37 final size:35
Alignment explanation
Indices: 689912--690104 Score: 112
Period size: 37 Copynumber: 5.3 Consensus size: 35
689902 TGATTTTAAA
*
689912 ATATTATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATTATATAA-TTTT-CAAAATAGTTTTAAAACTAT
*
689949 ATATTATATAAATTTTTCAAAA-ATGTTTTTTTTAAACTAT
1 ATATTATAT-AA-TTTTCAAAATA-G---TTTTAAAACTAT
* * * *
689989 ACA-T-TAT-ATTTTAAAAAT-GATTTCAAAAATAT
1 ATATTATATAATTTTCAAAATAG-TTTTAAAACTAT
* *
690021 ATGTTATATAATTTTCAAAAT-GTTTTAAAACTTCT
1 ATATTATATAATTTTCAAAATAGTTTTAAAAC-TAT
**
690056 ATATTGTATATAAGTTTTCAAAA-ACGTTTTAAAAAAACT
1 ATA-T-TATATAA-TTTTCAAAATA-GTTTTAAAACTA-T
690095 ATATTATATA
1 ATATTATATA
690105 TATATTTTCG
Statistics
Matches: 121, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
32 10 0.08
33 1 0.01
34 11 0.09
35 23 0.19
36 3 0.02
37 27 0.22
38 19 0.16
39 14 0.12
40 13 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATTATATAATTTTCAAAATAGTTTTAAAACTAT
Found at i:690097 original size:39 final size:37
Alignment explanation
Indices: 690013--690156 Score: 114
Period size: 39 Copynumber: 3.8 Consensus size: 37
690003 AAATGATTTC
*
690013 AAAAA-TATATGTTATATAATTTTC-AAAATGTTTTAA
1 AAAAACTATATG-TATATAATTTTCAAAAACGTTTTAA
***
690049 AACTTCTATATTGTATATAAGTTTTCAAAAACGTTTTAA
1 AAAAACTATA-TGTATATAA-TTTTCAAAAACGTTTTAA
* * * **
690088 AAAAACTATATTATATATATATTTTCGGAAACCGTTTTTT
1 AAAAACTATA-TGTATATA-ATTTTC-AAAAACGTTTTAA
* *
690128 GAAAACTATATGT-TATATTTTTCAAAAAC
1 AAAAACTATATGTATATAATTTTCAAAAAC
690157 ACTTTCAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
36 6 0.07
37 16 0.19
38 11 0.13
39 33 0.39
40 19 0.22
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (37 bp):
AAAAACTATATGTATATAATTTTCAAAAACGTTTTAA
Found at i:692210 original size:21 final size:22
Alignment explanation
Indices: 692163--692204 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
692153 GGGTATAATT
*
692163 ATAAATTAGTTTAAAATTTAAG
1 ATAAATTAGTTTAAAATTAAAG
692185 ATAAATTA-TTTAAAA-TAAAG
1 ATAAATTAGTTTAAAATTAAAG
692205 GGTAAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAAATTAGTTTAAAATTAAAG
Found at i:692654 original size:23 final size:23
Alignment explanation
Indices: 692626--692680 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
692616 TTTACCCTTT
692626 ATTTTAAATAATTTATC-TTTAAA
1 ATTTTAAATAATTT-TCTTTTAAA
* *
692649 TTTTTAACTAATTTTCTTTTAAA
1 ATTTTAAATAATTTTCTTTTAAA
692672 ATTTTAAAT
1 ATTTTAAAT
692681 CTTTATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTAAATAATTTTCTTTTAAA
Found at i:694623 original size:2 final size:2
Alignment explanation
Indices: 694616--694651 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
694606 TTCCTTTTTC
694616 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
694652 TACTAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:697385 original size:256 final size:253
Alignment explanation
Indices: 697079--697655 Score: 692
Period size: 256 Copynumber: 2.3 Consensus size: 253
697069 CTTATTCATA
697079 TATTGAATAAAAATATTTTTTTATTATTTC--G--G-GTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAAT--AAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTC-GGT
* * *
697139 CGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCGGGTAGGTTTTTTAAAGTGTGATATTC-
63 CGGGTCAGGTAGGGTGAAACTTTATTTTAGTCGGGTCGGGTAGGTTTTTTAAAGTATGATATTCG
697203 G-GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAATCCGACCCGAAAATATATATAATT
128 GAGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCC-A----A----AAAATATATA-AATT
697267 TACC-T-TATATTTA-GAAATAATTACAAT-ATA-CCCTCTATATATAATTTTTTTCAATTAAGT
183 TACCTTATATATTTATG-AATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGT
697327 -C-TTTT
247 ACGTTTT
697332 TATTGAAT-AAT-TTTTTTTATT-TCGGTTCGGGTCGAGTCGGGTTTCTAATTCATATA-T---T
1 TATTGAATAAATATTTTTTTATTAT---TTCGGGTCGAGTCGGGTTTCTAATTCATATATTCGGT
* * *
697390 CGGGTCAGGTAGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCG
63 CGGGTCAGGTAGGGTGAAACTTTATTTTAGTCGGGTCGGGTAGGTTTTTTAAAGTATGATATTC-
* *
697455 GGTCAGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAATATATAATTTTACCTTA
127 GG--AGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAATATATAAATTTACCTTA
697520 TATATTTATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTT
190 TATATTTATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGT-AC-GTTT
697585 T
253 T
* *
697586 TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGGTTTCTAATTCATATATTCTGGT
1 TATTGAAT--AAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTC-GGT
697651 CGGGT
63 CGGGT
697656 GAAACTTTAT
Statistics
Matches: 282, Mismatches: 10, Indels: 56
0.81 0.03 0.16
Matches are distributed among these distances:
246 7 0.02
247 11 0.04
248 21 0.07
249 14 0.05
250 33 0.12
251 63 0.22
252 1 0.00
253 10 0.04
254 12 0.04
255 3 0.01
256 86 0.30
257 4 0.01
258 10 0.04
259 1 0.00
261 6 0.02
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (253 bp):
TATTGAATAAATATTTTTTTATTATTTCGGGTCGAGTCGGGTTTCTAATTCATATATTCGGTCGG
GTCAGGTAGGGTGAAACTTTATTTTAGTCGGGTCGGGTAGGTTTTTTAAAGTATGATATTCGGAG
GTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAATATATAAATTTACCTTATATATT
TATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTACGTTTT
Found at i:697661 original size:251 final size:244
Alignment explanation
Indices: 697079--697684 Score: 688
Period size: 251 Copynumber: 2.4 Consensus size: 244
697069 CTTATTCATA
697079 TATTGAATAAAAATATTTTTTTATTA--TT---TCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGGTTTCTAATTCATATA-T----T
* * *
697139 CGGGTCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCGGGTAGGTTTTTTAAAGTGTGATATTCG
61 C--GTC-GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTAAAGTATGATATTCG
697204 GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAATCCGACCCGAAAATATATATAATTTA
123 GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAA--C-A--C-AAAATATATATAATTTA
697269 CCTTATATTTAGAAATAATTACAATATACCCTCTATATATAATTTTTTTCAATTAAGTCTTTT
182 CCTTATATTTAGAAATAATTACAATATACCCTCTATATATAATTTTTTTCAATTAAGTCTTTT
* *
697332 TATTGAAT---AAT-TTTTTTTATT-TCGGTTCGGGTCGAGTCGGGTTTCTAATTCATATATTCG
1 TATTGAATAAAAATATTTTTTTATTAT---TTTGGGTCGGGTCGGGTTTCTAATTCATATATTC-
* *
697392 GGTCAGGTAGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGG
62 -GTC-GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTAAAGTATGATATTC--G
* *
697457 TCAGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCC-A-A-AAAATATATA-ATTTTACCT
123 ---GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAACACAAAATATATATAATTTACC-
697518 TATATATTTATG-AATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTG
184 T-TATATTTA-GAAATAATTACAAT-ATA-CCCTCTATATATAATTTTTTTCAATTAAGT--C--
697582 TTTT
241 TTTT
697586 TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGGTTTCTAATTCATATATTC-T-G
1 TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGGTTTCTAATTCATATATTCGTCG
**
697649 GTCGGGTGAAACTTTATTTTGGTCAAGTCGGGTCGG
66 GTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGG
697685 ATGGAGGTTC
Statistics
Matches: 311, Mismatches: 15, Indels: 56
0.81 0.04 0.15
Matches are distributed among these distances:
246 7 0.02
247 11 0.04
248 20 0.06
249 14 0.05
250 33 0.11
251 94 0.30
252 1 0.00
253 11 0.04
254 12 0.04
255 2 0.01
256 92 0.30
257 3 0.01
258 10 0.03
259 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (244 bp):
TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGGGTTTCTAATTCATATATTCGTCG
GTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTAAAGTATGATATTCGGGTCGAGT
TCGGGTTTAGGGTGAAAAATACCCGACCCAACACAAAATATATATAATTTACCTTATATTTAGAA
ATAATTACAATATACCCTCTATATATAATTTTTTTCAATTAAGTCTTTT
Found at i:698082 original size:18 final size:17
Alignment explanation
Indices: 698046--698091 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
698036 ATGGAATTGA
*
698046 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAG
698063 ATTCCAATTCCTTCACAG
1 ATTCCAATTCC-TCACAG
698081 ATTCCAATTCC
1 ATTCCAATTCC
698092 CTCATAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (17 bp):
ATTCCAATTCCTCACAG
Found at i:705282 original size:37 final size:37
Alignment explanation
Indices: 705232--705332 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
705222 TTCTTCCTAA
* * *
705232 TAGGATTCAAACTCCTAAAAATAGGATATAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
705269 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
** * *
705306 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
705333 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:705755 original size:21 final size:22
Alignment explanation
Indices: 705729--705773 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
705719 ACCCTTATAT
705729 TTATATGTATATATATA-TTAA
1 TTATATGTATATATATATTTAA
* * *
705750 TTATATTTATTTATTTATTTAA
1 TTATATGTATATATATATTTAA
705772 TT
1 TT
705774 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATATGTATATATATATTTAA
Found at i:706001 original size:23 final size:22
Alignment explanation
Indices: 705974--706072 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 22
705964 TATTTTCATT
705974 TATTTTATTATTATTACTAT-TA
1 TATTTTATTATTATTA-TATATA
705996 GTATTTTATTA-TATTATATATA
1 -TATTTTATTATTATTATATATA
* *
706018 TATTTTTTTA-TATTTTATATA
1 TATTTTATTATTATTATATATA
* * * *
706039 TTTTTTTTTATTTTTTTATATA
1 TATTTTATTATTATTATATATA
706061 CTA-TTTATTATT
1 -TATTTTATTATT
706073 TCATCATGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
21 31 0.46
22 25 0.37
23 11 0.16
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (22 bp):
TATTTTATTATTATTATATATA
Found at i:706038 original size:19 final size:19
Alignment explanation
Indices: 705997--706052 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
705987 TTACTATTAG
*
705997 TATTTTATTATATTATATATA
1 TATTTTTTTATATT-T-TATA
706018 TATTTTTTTATATTTTATA
1 TATTTTTTTATATTTTATA
*
706037 TATTTTTTTTTATTTT
1 TATTTTTTTATATTTT
706053 TTTATATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
20 1 0.03
21 13 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTTTTATATTTTATA
Found at i:706073 original size:22 final size:22
Alignment explanation
Indices: 706030--706073 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
706020 TTTTTTTATA
* * *
706030 TTTTATATATTTTTTTTTATTT
1 TTTTATATACTATTTATTATTT
706052 TTTTATATACTATTTATTATTT
1 TTTTATATACTATTTATTATTT
706074 CATCATGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATATACTATTTATTATTT
Done.