Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007710.1 Hibiscus syriacus cultivar Beakdansim tig00109925_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: 668603
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:323678 original size:32 final size:31
Alignment explanation
Indices: 323527--323677 Score: 146
Period size: 32 Copynumber: 4.7 Consensus size: 31
323517 TCAGTTCAGA
* *
323527 TCAATATCATATC-AGTTGATTTTTGGACCGGG
1 TCAATATCAGATCGA-TTGA-TTTTGGATCGGG
* * * *
323559 TCAATATCAAATCAATTAGATTTTGGGTCAGG
1 TCAATATCAGATCGATT-GATTTTGGATCGGG
*
323591 TCAATATC-GAATCGATTAGATTTTGGGTCGGG
1 TCAATATCAG-ATCGATT-GATTTTGGATCGGG
*
323623 TCAATATC-GAATCGATTGATTTTCGGATTGGG
1 TCAATATCAG-ATCGATTGATTTT-GGATCGGG
323655 TCAATATCAGATCGATTGATTTT
1 TCAATATCAGATCGATTGATTTT
323678 CAGTTTGGGT
Statistics
Matches: 105, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
31 6 0.06
32 95 0.90
33 4 0.04
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (31 bp):
TCAATATCAGATCGATTGATTTTGGATCGGG
Found at i:324510 original size:135 final size:134
Alignment explanation
Indices: 324354--324597 Score: 407
Period size: 135 Copynumber: 1.8 Consensus size: 134
324344 TTTTTATTAA
*
324354 TTTTGTAACTTTGTTTAAATTAATTTATTATTCAAAATAATTTTCATTGTCCGAATTAAACTATT
1 TTTTGTAACTTTGTTTAAATTAATTTATTATTCAAAATAATTTTCATCGTCCGAATTAAACTATT
* * *
324419 ATCAAAAAGTTGATATTGATATTCCTTAAACTATTATCATAGTTTAATATATCTATTATAAATCT
66 ATCAAAAA-ATGATATTGATATTCATTAAACTATTACCATAGTTTAATATATCTATTATAAATCT
324484 AATAT
130 AATAT
* * *
324489 TTTTTTAACTTTGTTTAAATTAATTTATTATTCAAACTAATTTTCATCGTTCGAATTAAACTATT
1 TTTTGTAACTTTGTTTAAATTAATTTATTATTCAAAATAATTTTCATCGTCCGAATTAAACTATT
*
324554 ATCAAAAAATGATATTGATATTCATTACACTATTACCATAGTTT
66 ATCAAAAAATGATATTGATATTCATTAAACTATTACCATAGTTT
324598 GTGTTTAACT
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 32 0.32
135 69 0.68
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.47
Consensus pattern (134 bp):
TTTTGTAACTTTGTTTAAATTAATTTATTATTCAAAATAATTTTCATCGTCCGAATTAAACTATT
ATCAAAAAATGATATTGATATTCATTAAACTATTACCATAGTTTAATATATCTATTATAAATCTA
ATAT
Found at i:327730 original size:8 final size:8
Alignment explanation
Indices: 327712--327742 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
327702 TATTGGATTA
327712 ATGGTAATT
1 ATGG-AATT
327721 ATGGAATT
1 ATGGAATT
327729 ATGGAATT
1 ATGGAATT
327737 ATGGAA
1 ATGGAA
327743 GGGATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (8 bp):
ATGGAATT
Found at i:328409 original size:45 final size:45
Alignment explanation
Indices: 328334--328436 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
328324 CATATTGAAT
* *
328334 GTGCATCGATGCA-CTCTTTAAAGAAAAAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCTTTAAAGAAAAAACATCGAAGGCAATTG
* * *
328378 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTT
1 GTGCATCGATGCATCCCTTTAAAGA-AAAAACATCGAAGGCAATTG
*
328423 GTGTATCGATGCAT
1 GTGCATCGATGCAT
328437 GAGTAGTACA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 14 0.27
45 37 0.73
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (45 bp):
GTGCATCGATGCATCCCTTTAAAGAAAAAACATCGAAGGCAATTG
Found at i:328488 original size:20 final size:20
Alignment explanation
Indices: 328463--328500 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
328453 CACATGTTAA
328463 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
328483 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
328501 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:332475 original size:45 final size:45
Alignment explanation
Indices: 332378--332480 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
332368 CATATTGAAT
* *
332378 GTGCATCGATGCA-CTCTTTAAAGAAGAAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCTTTAAAGAAGAAACATCGAAGGCAATTG
* * *
332422 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTT
1 GTGCATCGATGCATCCCTTTAAAGAAG-AAACATCGAAGGCAATTG
* *
332467 TTGTATCGATGCAT
1 GTGCATCGATGCAT
332481 GAGTAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 15 0.30
45 35 0.70
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (45 bp):
GTGCATCGATGCATCCCTTTAAAGAAGAAACATCGAAGGCAATTG
Found at i:332536 original size:20 final size:22
Alignment explanation
Indices: 332487--332544 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
332477 GCATGAGTAG
332487 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
332511 TACATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
332531 TGCATCGATGCACT
1 TGCATCGATGCACT
332545 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:333184 original size:31 final size:31
Alignment explanation
Indices: 333146--333206 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
333136 GAGTTGAGGG
*
333146 TTTACCTATG-TCTTTCGAGACATATGGACAA
1 TTTACCTAGGTTC-TTCGAGACATATGGACAA
* *
333177 TTTACCTAGGTTCTTCGGGACCTATGGACA
1 TTTACCTAGGTTCTTCGAGACATATGGACA
333207 GTTGTCGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTACCTAGGTTCTTCGAGACATATGGACAA
Found at i:334499 original size:20 final size:20
Alignment explanation
Indices: 334476--334513 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
334466 AGTTTGGTTA
334476 GTAG-GTTGGGTGTTTGGATG
1 GTAGTGTTGGGT-TTTGGATG
*
334496 GTAGTTTTGGGTTTTGGA
1 GTAGTGTTGGGTTTTGGA
334514 GGATGAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (20 bp):
GTAGTGTTGGGTTTTGGATG
Found at i:336070 original size:64 final size:63
Alignment explanation
Indices: 335965--336083 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 63
335955 GAATCGCATA
* *
335965 CCAAATCATGTCTTTTTAAATTTTTATTTAAAAAGATGTACCCCAGGTTTTCAACCTACCTAAT
1 CCAAATCACGTCTTTTTAAATTTTTATTTAAAAAGACGTACCCCAGGTTTT-AACCTACCTAAT
* *
336029 CCAAATCCCGTCTTTTTAAATTTTTATTTAAAAAGGCGTACCCCAGGTTTTAACC
1 CCAAATCACGTCTTTTTAAATTTTTATTTAAAAAGACGTACCCCAGGTTTTAACC
336084 CCAGGTTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 4 0.08
64 47 0.92
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (63 bp):
CCAAATCACGTCTTTTTAAATTTTTATTTAAAAAGACGTACCCCAGGTTTTAACCTACCTAAT
Found at i:356786 original size:23 final size:23
Alignment explanation
Indices: 356746--356789 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
356736 CTTGAAGAAT
*
356746 AAAAGAAAATAAATAATAAAAGA
1 AAAAGAAAATAAAAAATAAAAGA
356769 AAAAGAAAA-AAGAAAATAAAA
1 AAAAGAAAATAA-AAAATAAAA
356790 AGGGGTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAAGAAAATAAAAAATAAAAGA
Found at i:357485 original size:15 final size:15
Alignment explanation
Indices: 357467--357531 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
357457 GAAAGAAATG
357467 ATAAAAAGAGAAAAA
1 ATAAAAAGAGAAAAA
357482 AT--AAAGAGAAAAA
1 ATAAAAAGAGAAAAA
357495 ATAAAATA-AGAAAATA
1 ATAAAA-AGAGAAAA-A
* *
357511 AGAAAAAGA-AAAAG
1 ATAAAAAGAGAAAAA
357525 ATAAAAA
1 ATAAAAA
357532 CCAAAGTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 13 0.31
14 6 0.14
15 15 0.36
16 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
ATAAAAAGAGAAAAA
Found at i:357487 original size:13 final size:13
Alignment explanation
Indices: 357471--357499 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
357461 GAAATGATAA
357471 AAAGAGAAAAAAT
1 AAAGAGAAAAAAT
357484 AAAGAGAAAAAAT
1 AAAGAGAAAAAAT
357497 AAA
1 AAA
357500 ATAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAGAGAAAAAAT
Found at i:359804 original size:20 final size:20
Alignment explanation
Indices: 359775--359817 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
359765 ATCCCACCAC
*
359775 ATGCAACTACATGCTTCTAA
1 ATGCAACTACATGCTCCTAA
* *
359795 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
359815 ATG
1 ATG
359818 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:370664 original size:90 final size:90
Alignment explanation
Indices: 370558--370725 Score: 309
Period size: 90 Copynumber: 1.9 Consensus size: 90
370548 TATTTAATTT
*
370558 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGCGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGCGTAACT
370623 TGGATATAAAAGGATTATTAAACTC
66 TGGATATAAAAGGATTATTAAACTC
*
370648 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGCGTAACT
*
370713 TGGCTATAAAAGG
66 TGGATATAAAAGG
370726 GTGTGTTAGG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (90 bp):
CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGCGTAACT
TGGATATAAAAGGATTATTAAACTC
Found at i:374189 original size:43 final size:43
Alignment explanation
Indices: 374070--374316 Score: 282
Period size: 43 Copynumber: 5.8 Consensus size: 43
374060 ACGCCGCAAA
* * * *
374070 ATCTATAGCAGTGTTTTTGCA-ACAAACGCCACAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
** * * *
374112 ATCTATAGCGGTATTTTTTTGATATAAATGCCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGT-ATACAAACGCCGCAAAAGGTCAT
* * *
374156 ATCTATAGTGGCGTTTTTGTATACAAACGCCGCAAAAAGTCAG
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
** *
374199 ATCTATAGCGGCGTTTTTGTATACAAACGTTGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
* * * * *
374242 ATCTATAACAGCATTTTTGGATACAAACGACGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
*
374285 ATCTATAGCAGCGTTTTT-TATACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGTATACAAACGCCGC
374317 TAATTTCAAT
Statistics
Matches: 172, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.16
43 110 0.64
44 34 0.20
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAT
Found at i:374281 original size:129 final size:128
Alignment explanation
Indices: 374070--374316 Score: 325
Period size: 129 Copynumber: 1.9 Consensus size: 128
374060 ACGCCGCAAA
* * * * * *
374070 ATCTATAGCAGTGTTTTTGCAACAAACGCCACAAAAGGTCATATCTATAGCGGTATTTTTTTGAT
1 ATCTATAGCAGCGTTTTTGCAACAAACGCCACAAAAGGTCAAATCTATAACAGCATTTTTTGGAT
* * * **
374135 ATAAATGCCGCAAAAGGTCATATCTATAGTGGCGTTTTTGTATACAAACGCCGCAAAAAGTCAG
66 ACAAACGACGCAAAAGGTCATATCTATAGCAGCGTTTTT-TATACAAACGCCGCAAAAAGTCAG
* * ***
374199 ATCTATAGCGGCGTTTTTGTATACAAACGTTGCAAAAGGTCAAATCTATAACAGCA-TTTTTGGA
1 ATCTATAGCAGCGTTTTTGCA-ACAAACGCCACAAAAGGTCAAATCTATAACAGCATTTTTTGGA
374263 TACAAACGACGCAAAAGGTCATATCTATAGCAGCGTTTTTTATACAAACGCCGC
65 TACAAACGACGCAAAAGGTCATATCTATAGCAGCGTTTTTTATACAAACGCCGC
374317 TAATTTCAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
128 14 0.14
129 60 0.59
130 27 0.27
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (128 bp):
ATCTATAGCAGCGTTTTTGCAACAAACGCCACAAAAGGTCAAATCTATAACAGCATTTTTTGGAT
ACAAACGACGCAAAAGGTCATATCTATAGCAGCGTTTTTTATACAAACGCCGCAAAAAGTCAG
Found at i:378104 original size:41 final size:41
Alignment explanation
Indices: 378051--378256 Score: 200
Period size: 41 Copynumber: 5.0 Consensus size: 41
378041 TTTGTAAACT
* *
378051 CAAGTGTATAGCGACGATTGAATAAAAACGCCACTAAAGTA
1 CAAGTCTATAGCGACGATTGTATAAAAACGCCACTAAAGTA
* *
378092 -AGAGTCTTTAGCGGC-ATTTGTATAAAAACGCCACTAAAGTA
1 CA-AGTCTATAGCGACGA-TTGTATAAAAACGCCACTAAAGTA
* * * * * *
378133 CAATTGTATAACGACGTTTATATAAAAAAGCCACTAAAGTA
1 CAAGTCTATAGCGACGATTGTATAAAAACGCCACTAAAGTA
* * * *
378174 CAATTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTA
1 CAAGTCTATAGCGACGATTGTATAAAAACGCCACTAAAGTA
* * ** * *
378215 CGAGTCTTTAGCGTTGTTTGTATAAAAATGCCACTAAAGTA
1 CAAGTCTATAGCGACGATTGTATAAAAACGCCACTAAAGTA
378256 C
1 C
378257 TACTCTTTTG
Statistics
Matches: 136, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.01
41 133 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (41 bp):
CAAGTCTATAGCGACGATTGTATAAAAACGCCACTAAAGTA
Found at i:378264 original size:41 final size:41
Alignment explanation
Indices: 378072--378292 Score: 239
Period size: 41 Copynumber: 5.4 Consensus size: 41
378062 CGACGATTGA
*
378072 ATAAAAACGCCACTAAAGTA-AGAGTCTTTAGCGGCATTTGT
1 ATAAAAACGCCACTAAAGTACA-AGTCTTTAGCGGCGTTTGT
* * * * * *
378113 ATAAAAACGCCACTAAAGTACAATTGTATAACGACGTTTAT
1 ATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGT
* * *
378154 ATAAAAAAGCCACTAAAGTACAATTCTATAGCGGCGTTTGT
1 ATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGT
* * **
378195 ATAAAAACACCACTAAAGTACGAGTCTTTAGCGTTGTTTGT
1 ATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGT
* * * *
378236 ATAAAAATGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT
1 ATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGT
378277 -TGAAAAAACGCCACTA
1 AT--AAAAACGCCACTA
378293 TCGATGAACC
Statistics
Matches: 150, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.01
41 136 0.91
42 13 0.09
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (41 bp):
ATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGT
Found at i:378723 original size:3 final size:3
Alignment explanation
Indices: 378715--378744 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
378705 TTAATCTGAG
378715 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
378745 TTTTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:383848 original size:16 final size:17
Alignment explanation
Indices: 383792--383853 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
383782 ACCTATTCAT
*
383792 AATACAAAATAATATTA
1 AATAAAAAATAATATTA
*
383809 AATAAAAAATACAT-GTA
1 AATAAAAAATA-ATATTA
383826 AATAAAAAATAATATTA
1 AATAAAAAATAATATTA
*
383843 TA-AAAAAATAA
1 AATAAAAAATAA
383854 AAAATATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 11 0.28
17 26 0.67
18 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAAAAAATAATATTA
Found at i:384163 original size:197 final size:199
Alignment explanation
Indices: 383897--384299 Score: 668
Period size: 197 Copynumber: 2.0 Consensus size: 199
383887 AGAAAAAAGG
* *
383897 GTGTAAGTAAAAGTAGTAAATCATGTAGTAGATGATGTAGGTGTGTAAGAAAGTATTGAAGCAAA
1 GTGTAAGTAAAAGTAGTAAATCATGTAGTAGATGATGTAGGTGTGTAAGAAAGTACTAAAGCAAA
* *
383962 TAGTAGAGAATTT-TTTGGAAGTGTT-AAAATAATCGAAAAAAATGAATTTAAAAATCAAAATAT
66 TAGTAGAGAATTTGTTTGAAAGTGTTAAAAATAATCG-AAAAAAGGAATTTAAAAATCAAAATAT
* * * *
384025 TAAAAAA-TCACAATCAAAGTAAGAAGTAAATAAGGCAATGGGAGGAAGCATAGAAACTCTAGTT
130 TAAAAAATTCACAACCAAAGTAAGAAGTAAAGAAGGCAATGGGAGGAAACAGAGAAACTCTAGTT
384089 TCAAA
195 TCAAA
384094 GTGTAAGTAAAAGTAGTAAATCATGTAGTAGATGATGTAGGTGTGTAAGAAAGTACTAAAGCAAA
1 GTGTAAGTAAAAGTAGTAAATCATGTAGTAGATGATGTAGGTGTGTAAGAAAGTACTAAAGCAAA
*
384159 TAGTAGAGAATTTGTTTGAAAGTGTTAAAAATAATTGAAAAAAGGAATTTAAAAATCAAAATATT
66 TAGTAGAGAATTTGTTTGAAAGTGTTAAAAATAATCGAAAAAAGGAATTTAAAAATCAAAATATT
* *
384224 AAAAAATTTCACAACCAAAGTAAGAAGTAAAGATGGCAATGGGAGGAAACAGAGAAACTTTAGTT
131 AAAAAA-TTCACAACCAAAGTAAGAAGTAAAGAAGGCAATGGGAGGAAACAGAGAAACTCTAGTT
384289 TCAAA
195 TCAAA
384294 GTGTAA
1 GTGTAA
384300 ACCTTTCATC
Statistics
Matches: 191, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
197 76 0.40
198 44 0.23
199 9 0.05
200 62 0.32
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.26
Consensus pattern (199 bp):
GTGTAAGTAAAAGTAGTAAATCATGTAGTAGATGATGTAGGTGTGTAAGAAAGTACTAAAGCAAA
TAGTAGAGAATTTGTTTGAAAGTGTTAAAAATAATCGAAAAAAGGAATTTAAAAATCAAAATATT
AAAAAATTCACAACCAAAGTAAGAAGTAAAGAAGGCAATGGGAGGAAACAGAGAAACTCTAGTTT
CAAA
Found at i:388047 original size:6 final size:6
Alignment explanation
Indices: 388036--388085 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
388026 TCCGCAGCAT
*
388036 CCGCAA CCGCAA CCGCGACA CCGCAA CCGCAACA CCGCAA CCGTAA CCGC
1 CCGCAA CCGCAA CCGC-A-A CCGCAA CCGC-A-A CCGCAA CCGCAA CCGC
388086 GACAGATGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 24 0.63
7 4 0.11
8 10 0.26
ACGTcount: A:0.30, C:0.50, G:0.18, T:0.02
Consensus pattern (6 bp):
CCGCAA
Found at i:388060 original size:14 final size:14
Alignment explanation
Indices: 388041--388078 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
388031 AGCATCCGCA
*
388041 ACCGCAACCGCGAC
1 ACCGCAACCGCAAC
388055 ACCGCAACCGCAAC
1 ACCGCAACCGCAAC
388069 ACCGCAACCG
1 ACCGCAACCG
388079 TAACCGCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (14 bp):
ACCGCAACCGCAAC
Found at i:389156 original size:41 final size:41
Alignment explanation
Indices: 389079--389174 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
389069 AACTAAAACC
389079 TATTTTATTAATA-TTTTTATAACATGACATCAATTAGTAT
1 TATTTTATTAATATTTTTTATAACATGACATCAATTAGTAT
* ** * *
389119 TATTTTATTAATATTTTTTATGATGTGGCATCTATTAGTAT
1 TATTTTATTAATATTTTTTATAACATGACATCAATTAGTAT
389160 TATTTTATTAATATT
1 TATTTTATTAATATT
389175 GTTATTACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.26
41 37 0.74
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.55
Consensus pattern (41 bp):
TATTTTATTAATATTTTTTATAACATGACATCAATTAGTAT
Found at i:390020 original size:32 final size:30
Alignment explanation
Indices: 389984--390050 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
389974 AAACAAATAC
**
389984 ATTAAAATAAAAAGTAATTTAAACTTTGAGTT
1 ATTAAAATAAAAA-TAAAATAAA-TTTGAGTT
**
390016 ATTAAAATATTAATAAAATAAATTTGAGTT
1 ATTAAAATAAAAATAAAATAAATTTGAGTT
390046 ATTAA
1 ATTAA
390051 TAGATGTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 13 0.42
31 7 0.23
32 11 0.35
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.39
Consensus pattern (30 bp):
ATTAAAATAAAAATAAAATAAATTTGAGTT
Found at i:400875 original size:15 final size:17
Alignment explanation
Indices: 400844--400876 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
400834 ATATAAAAAC
400844 ATAAAATATAGGATAAT
1 ATAAAATATAGGATAAT
400861 ATAAAA-ATA-GATAAT
1 ATAAAATATAGGATAAT
400876 A
1 A
400877 AATGAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
ATAAAATATAGGATAAT
Found at i:401496 original size:37 final size:36
Alignment explanation
Indices: 401453--401554 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
401443 ATAGTAGAAC
401453 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
401490 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
401524 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
401555 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:402401 original size:105 final size:104
Alignment explanation
Indices: 402104--402819 Score: 1048
Period size: 105 Copynumber: 6.8 Consensus size: 104
402094 TTGTTCCAAT
* * * ** * * *
402104 TCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTG-GAACCGGGAAATTGTTTGTTGACAACC
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGAGAAGTTG-TTGTTGACAAGC
* * *
402168 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAG
**
402210 TCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-TGA-AA-TT-TTGTTGACAAGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
402270 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAG
* *
402310 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
*
402375 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAG
* *
402415 TCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
402480 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG-AG
* *
402520 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGACAAGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
402585 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAG
*
402625 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGAC-A--AG
*
402690 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG-AG
* * * * *
402733 TCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTATTGACAGGCAG
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
402798 CGGTCCCTTCGTCGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTG
402820 TGATCCACTC
Statistics
Matches: 567, Mismatches: 31, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
100 84 0.15
101 1 0.00
102 4 0.01
103 4 0.01
104 4 0.01
105 335 0.59
106 35 0.06
107 2 0.00
108 98 0.17
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (104 bp):
TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAG
Found at i:403332 original size:68 final size:65
Alignment explanation
Indices: 403242--403634 Score: 213
Period size: 72 Copynumber: 5.8 Consensus size: 65
403232 AAGATATCTG
* **
403242 TTGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-GTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA
403306 TTT
64 -TT
* * *
403309 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
403374 T
65 T
* ** * * * *
403375 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TAGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-A
** *
403439 GACAAA-ACT
56 TTCAAAGATT
* * * ** * * * * * *
403448 TAGTTCCAA-AGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
403512 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--ATCTCAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAA-TAAAT-TC---A-
*
403575 AGACGAAAT
60 A-A-G-ATT
* * *
403584 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAA
403635 CTGTCTCAAG
Statistics
Matches: 255, Mismatches: 47, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
63 5 0.02
64 11 0.04
65 74 0.29
66 7 0.03
67 24 0.09
68 32 0.13
69 2 0.01
70 2 0.01
71 2 0.01
72 81 0.32
73 10 0.04
74 5 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:403375 original size:67 final size:66
Alignment explanation
Indices: 403242--403399 Score: 212
Period size: 68 Copynumber: 2.4 Consensus size: 66
403232 AAGATATCTG
* **
403242 TTGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-GTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
403306 TTT
65 -TT
* * *
403309 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
403373 TT
65 TT
*
403375 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
403400 ATAGACGAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
65 22 0.27
66 3 0.04
67 24 0.30
68 31 0.38
69 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:403426 original size:36 final size:35
Alignment explanation
Indices: 403375--403654 Score: 254
Period size: 36 Copynumber: 8.0 Consensus size: 35
403365 TTCAAAGATT
* *
403375 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
403411 TAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
403446 CTTAGTTCCAA-AGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
403483 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
403512 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
403547 TTTATTTCAAGGGAAACTATCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
403584 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
403619 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
403655 CTCTTATAGT
Statistics
Matches: 200, Mismatches: 28, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 16 0.08
36 146 0.73
37 13 0.06
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:403484 original size:137 final size:136
Alignment explanation
Indices: 403316--403635 Score: 428
Period size: 137 Copynumber: 2.3 Consensus size: 136
403306 TTTTGTGTTT
* * * *
403316 CAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTT
* *
403381 CAAGGGAAACTGTCTCAAGATAGACGAAAA-TAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
66 CAAGGGAAACTGTCTCAAGAGAGAC-AAAATTA-TTTCAAGAGAAACTATCTCAAGAGAGACAAA
403445 ACTTAGTTC
129 A-TTAGTTC
** * * * *
403454 CAA-AGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTT
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTT
* * *
403518 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGATAGACGAAA
66 CAAGGGAAACTGTCTCAAGAGAGACAAAA-TTATTTCAAGAGAAACTATCTCAAGAGAGACAAAA
* *
403583 TTTGTTT
130 TTAGTTC
*
403590 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
403636 TGTCTCAAGA
Statistics
Matches: 157, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
136 12 0.08
137 140 0.89
138 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (136 bp):
CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTT
CAAGGGAAACTGTCTCAAGAGAGACAAAATTATTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
TAGTTC
Found at i:403518 original size:101 final size:102
Alignment explanation
Indices: 403413--403598 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
403403 GACGAAAATA
* *
403413 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AGAAACTGTCTCAAGGGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAGAGAAACTATCTCAAGAGAGA
*
403477 CGGAATTTGTTTCAA-AGAAAACATATTCAAATATTTT
65 CGAAATTTGTTTCAAGAGAAAACATATTCAAATATTTT
* * * * *
403514 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGATAGAC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAGAGAAACTATCTCAAGAGAGAC
403579 GAAATTTGTTTCAAGAGAAA
66 GAAATTTGTTTCAAGAGAAA
403599 CTGTCTCAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 5 0.07
101 65 0.87
102 5 0.07
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (102 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAGAGAAACTATCTCAAGAGAGAC
GAAATTTGTTTCAAGAGAAAACATATTCAAATATTTT
Found at i:403696 original size:71 final size:72
Alignment explanation
Indices: 403517--403696 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 72
403507 ATATTTTGTT
* * * *
403517 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTATCTCAAGATAGACGAA
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
* *
403582 ATTTGTT
66 ATCTGTA
*
403589 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
403654 ACTCT-TA
66 A-TCTGTA
* * *
403661 T--AGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
403697 TAAGAAAAAC
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
70 7 0.07
71 23 0.24
72 63 0.66
73 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (72 bp):
TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
ATCTGTA
Found at i:404162 original size:18 final size:18
Alignment explanation
Indices: 404135--404170 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
404125 TGTTGAATCC
* *
404135 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
404153 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
404171 TTGATATTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:404611 original size:22 final size:22
Alignment explanation
Indices: 404585--404633 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
404575 TTGTGTTTGG
*
404585 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
404607 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
404629 TCAAA
1 TCAAA
404634 AGATTGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:404640 original size:22 final size:22
Alignment explanation
Indices: 404593--404640 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
404583 GGTCAAAGGT
* * *
404593 TTGACATTTGATGCTCAAAGGT
1 TTGACATTGGATGCTCAAAAGA
404615 TTGACATTGGATGCTCAAAAGA
1 TTGACATTGGATGCTCAAAAGA
404637 TTGA
1 TTGA
404641 TGGGGTAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (22 bp):
TTGACATTGGATGCTCAAAAGA
Found at i:405311 original size:21 final size:20
Alignment explanation
Indices: 405268--405315 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
405258 TTTGTCCCCT
* *
405268 TTTTTTATTTTTGTTCTTTC
1 TTTTTTGTTCTTGTTCTTTC
*
405288 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTGTTCTTGTTCTTT-C
405309 TTTTTTG
1 TTTTTTG
405316 CTTATTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTTGTTCTTGTTCTTTC
Found at i:408580 original size:16 final size:18
Alignment explanation
Indices: 408548--408582 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
408538 AATATAAAAC
408548 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
408566 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
408582 A
1 A
408583 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:409195 original size:37 final size:36
Alignment explanation
Indices: 409152--409253 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
409142 ATAGTATAAC
409152 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
409189 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
409223 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
409254 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:413085 original size:12 final size:13
Alignment explanation
Indices: 413068--413096 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
413058 CTTAATTGCG
413068 AAAATTAAAAT-T
1 AAAATTAAAATAT
413080 AAAATTAAAATAT
1 AAAATTAAAATAT
413093 AAAA
1 AAAA
413097 ATACGAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATAT
Found at i:415349 original size:124 final size:124
Alignment explanation
Indices: 415171--415663 Score: 756
Period size: 124 Copynumber: 4.0 Consensus size: 124
415161 GGCATTACTG
* * * * *
415171 CTGGTGGGCACAATTCCCTTCGTCGTGAAGTTGAAACCGTAGAGGGACCATTCGTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCCTTCGTTGTGAAGTTG
* *
415236 AGCCTTGAATTGGATACCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTA
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * *
415295 CTGGTGAGAACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTAAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCCTTCGTTGTGAAGTTG
* *
415360 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGTTG
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * * * ** *
415419 CTGGTGAGCACGATACCATTCATCGTGAAGTTGAAACTGT-GAATG-CCCTTCTTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCCTTCGTTGTGAAGTTG
*
415482 ATCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
* * * *
415541 CTGGTGAGCACGATTCCCTTCGTCATGAAGTTAAAACAGTGTAGGGCCCCTTCGTTGTGAAGTTG
1 CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCCTTCGTTGTGAAGTTG
415606 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
66 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
415664 GCTTTGAGTC
Statistics
Matches: 332, Mismatches: 35, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
122 106 0.32
123 5 0.02
124 221 0.67
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (124 bp):
CTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGAGGGCCCCTTCGTTGTGAAGTTG
AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTA
Found at i:415659 original size:246 final size:248
Alignment explanation
Indices: 415169--415699 Score: 793
Period size: 246 Copynumber: 2.2 Consensus size: 248
415159 ATGGCATTAC
* * * * *
415169 TGCTGGTGGGCACAATTCCCTTCGTCGTGAAGTTGAAACCGTAGAGGGACCATTCGTTGTGAAGT
1 TGCTGGTGAGCACAATACCATTCATCGTGAAGTTGAAACCGTAGAAGGACCATTCGTTGTGAAGT
415234 TGAGCCTTGAATTGGATACCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTACTGG
66 TGAGCCTTGAATTGGATACCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTACTGG
* * * *
415299 TGAGAACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTAAAGTTGAGCC
131 TGAGAACGATTCCCTTCGTCATGAAGTTAAAACAGTGGAGGGCCCCTTCGTTGTAAAGTTGAGCC
415364 TTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGT
196 TTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGT
* * * * *
415417 TGCTGGTGAGCACGATACCATTCATCGTGAAGTTGAAACTGT-GAATG-CCCTTCTTTGTGAAGT
1 TGCTGGTGAGCACAATACCATTCATCGTGAAGTTGAAACCGTAGAAGGACCATTCGTTGTGAAGT
* * *
415480 TGATCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGG
66 TGAGCCTTGAATTGGATACCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTACTGG
* * *
415545 TGAGCACGATTCCCTTCGTCATGAAGTTAAAACAGTGTAGGGCCCCTTCGTTGTGAAGTTGAGCC
131 TGAGAACGATTCCCTTCGTCATGAAGTTAAAACAGTGGAGGGCCCCTTCGTTGTAAAGTTGAGCC
*
415610 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGT
196 TTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGT
* * *
415663 TGCT-TTGAGTC-CAATATCC-TTCGTCGTGAAGATGAAA
1 TGCTGGTGAG-CACAATA-CCATTCATCGTGAAGTTGAAA
415700 TTGGCTCTTA
Statistics
Matches: 256, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
245 24 0.09
246 193 0.75
247 3 0.01
248 36 0.14
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (248 bp):
TGCTGGTGAGCACAATACCATTCATCGTGAAGTTGAAACCGTAGAAGGACCATTCGTTGTGAAGT
TGAGCCTTGAATTGGATACCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATGTTACTGG
TGAGAACGATTCCCTTCGTCATGAAGTTAAAACAGTGGAGGGCCCCTTCGTTGTAAAGTTGAGCC
TTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGT
Found at i:416063 original size:244 final size:241
Alignment explanation
Indices: 415549--416275 Score: 971
Period size: 244 Copynumber: 3.0 Consensus size: 241
415539 TACTGGTGAG
* * * *
415549 CACGAT-TCCCTTCGTCATGAAGTT-AAAACAGTGTAGGGCCCCTTCGTTGTGAAGTTGAGCCTT
1 CACGATAT-CCTTCGTCATGAAGTTGAAATCA-TGGACGGCCCATTCGTTGTGAAGTTGAGCCTT
* * * *
415612 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTT-GAGTCCA
64 GACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-----TG--TATTG-TTTCGAGTCCA
*
415676 ATATCCTTCGTCGTGAAGATGAAATTGGCTCTT-AATGAAACTGGGAAGCCCA-TTCGCCGTGAA
121 ATATCCTTCGTCGTGAAGTTGAAATTGGCT-TTGAATGAAACTGGGAAGCCCACTTCGCCGTGAA
* * * *
415739 GTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATTCAATCTAGAGTTGG
185 GTTGATCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
** **
415796 CACGATATTATTCGTTGTGAAGTTGAAATCATGGACGGCCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCATGAAGTTGAAATCATGGACGGCCCATTCGTTGTGAAGTTGAGCCTTGA
*
415861 CTTGAATATCCTTCGTTGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* *
415926 CCGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCAGCCCTTTGCCGTGAAGTTGATCT
131 TCGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCA---CTTCGCCGTGAAGTTGATCT
415991 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
193 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
* * * * *
416040 CACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCATTCATTGTCAAGTTGAGCCTAGA
1 CACGATATCCTTCGTCATGAAGTTGAAATCATGGACGGCCCATTCGTTGTGAAGTTGAGCCTTGA
** *
416105 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATTATTCA
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* * * * * * *
416170 TCGTGAAGTTGAAATTGGCTCTGAATGAAAATGGGAAACACA-TTCACCATGAAGTTGATCTATG
131 TCGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCACTTCGCCGTGAAGTTGATCTTTG
416234 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAG
196 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAG
416276 AAAGTTGGTT
Statistics
Matches: 430, Mismatches: 42, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
239 5 0.01
240 118 0.27
242 2 0.00
244 217 0.50
247 82 0.19
248 6 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (241 bp):
CACGATATCCTTCGTCATGAAGTTGAAATCATGGACGGCCCATTCGTTGTGAAGTTGAGCCTTGA
CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
TCGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCACTTCGCCGTGAAGTTGATCTTTG
AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTTGA
Found at i:420406 original size:9 final size:9
Alignment explanation
Indices: 420388--420442 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
420378 TTAGAAGAGG
*
420388 AATAATAAA
1 AATAAAAAA
420397 AATAAAAAA
1 AATAAAAAA
*
420406 AGTAAAAAA
1 AATAAAAAA
420415 AATAAAATAA
1 AATAAAA-AA
420425 AA-AATAAAA
1 AATAA-AAAA
420434 AATAAAAAA
1 AATAAAAAA
420443 TGTCAAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 32 0.80
10 8 0.20
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:420412 original size:7 final size:7
Alignment explanation
Indices: 420394--420443 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
420384 GAGGAATAAT
420394 AAAAATAA
1 AAAAAT-A
420402 AAAAAGTA
1 AAAAA-TA
420410 AAAAA-A
1 AAAAATA
420416 ATAAAATA
1 A-AAAATA
420424 AAAAATA
1 AAAAATA
420431 AAAAATA
1 AAAAATA
420438 AAAAAT
1 AAAAAT
420444 GTCAAATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.05
7 23 0.59
8 13 0.33
9 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:422769 original size:20 final size:21
Alignment explanation
Indices: 422723--422769 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
422713 AAGCCGCCGA
*
422723 ATAATTTTATTTTAATAAAATT
1 ATAATTTTA-TTTAATAAAAGT
422745 ATAATTTTA-TTAACTAAAAGT
1 ATAATTTTATTTAA-TAAAAGT
422766 -TAAT
1 ATAAT
422770 CCAACAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAATTTTATTTAATAAAAGT
Found at i:425879 original size:3 final size:3
Alignment explanation
Indices: 425871--425896 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
425861 TATCCGCCCT
425871 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
425897 TTGTGGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:428029 original size:12 final size:12
Alignment explanation
Indices: 428012--428036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
428002 AACTCAATCT
428012 TATAGATAGAGA
1 TATAGATAGAGA
428024 TATAGATAGAGA
1 TATAGATAGAGA
428036 T
1 T
428037 TGACATCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TATAGATAGAGA
Found at i:430797 original size:18 final size:18
Alignment explanation
Indices: 430774--430809 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
430764 CCACTATGAA
*
430774 ATGTCCCGAATGACCACT
1 ATGTCCCGAAGGACCACT
430792 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
430810 GTATATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:445260 original size:19 final size:18
Alignment explanation
Indices: 445234--445269 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
445224 ATACTATCCA
445234 TTTCTTATAAATTTATCT
1 TTTCTTATAAATTTATCT
*
445252 TTTCATTATAATTTTATC
1 TTTC-TTATAAATTTATC
445270 ATTTAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTATAAATTTATCT
Found at i:445909 original size:15 final size:15
Alignment explanation
Indices: 445889--445918 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
445879 TTGTTTATAA
445889 TTAATTATTATTATT
1 TTAATTATTATTATT
445904 TTAATTATTATTATT
1 TTAATTATTATTATT
445919 ATTTCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTATTATTATT
Found at i:445915 original size:18 final size:19
Alignment explanation
Indices: 445886--445922 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
445876 TAATTGTTTA
445886 TAATTAATTATTATTATTT
1 TAATTAATTATTATTATTT
445905 TAATT-ATTATTATTATTT
1 TAATTAATTATTATTATTT
445923 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTAATTATTATTATTT
Found at i:449015 original size:35 final size:35
Alignment explanation
Indices: 448976--449043 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
448966 TTTAATTTAA
*
448976 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTAAAGTATTTTAGAATTTGG
* * *
449011 GGTTTAGAATGTAATTGAAGTGTTTTAGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTAGAATTT
449044 TGAACATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTAGAATTTGG
Found at i:453516 original size:2 final size:2
Alignment explanation
Indices: 453509--453560 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
453499 TGACTTAATA
453509 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
453551 AT AT AT AT AT
1 AT AT AT AT AT
453561 GTTTTTTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458480 original size:504 final size:504
Alignment explanation
Indices: 457533--458545 Score: 2026
Period size: 504 Copynumber: 2.0 Consensus size: 504
457523 TTTAAGTGTA
457533 TAAATGATGAGCTGATGAGCCATTTTGTGATATCAGCAAGTAATATATGTAGCAAAATGTATAAA
1 TAAATGATGAGCTGATGAGCCATTTTGTGATATCAGCAAGTAATATATGTAGCAAAATGTATAAA
457598 TTTCCCTCTGTTGGAAAGAGTTGCTGCATTTTAGCTAGTGACAGGTTTTGTGTATAATCGCACCA
66 TTTCCCTCTGTTGGAAAGAGTTGCTGCATTTTAGCTAGTGACAGGTTTTGTGTATAATCGCACCA
457663 AGTTTGATACTTTCCGAAAGCGTTAGTCTCGTTACTTATGTTCATTTCGCTTCCACCCTTCTCTT
131 AGTTTGATACTTTCCGAAAGCGTTAGTCTCGTTACTTATGTTCATTTCGCTTCCACCCTTCTCTT
457728 GCTTAGAAGGACAAAATAGTAATTATAAAGAGAGATTGAAGAAATTTGGGGATTTTATTGTTGCG
196 GCTTAGAAGGACAAAATAGTAATTATAAAGAGAGATTGAAGAAATTTGGGGATTTTATTGTTGCG
457793 GAATACGGCTATCGGATAGAGCAAAATGACAACTGATAATTTGAGAAAATAAAAAATAAAGATAA
261 GAATACGGCTATCGGATAGAGCAAAATGACAACTGATAATTTGAGAAAATAAAAAATAAAGATAA
457858 ATAAGATACAAAATTTACGTATAAAACTCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTA
326 ATAAGATACAAAATTTACGTATAAAACTCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTA
457923 GAAGAATTTCACTATAAGAAAATAAGAATTACAATTTCTCTCAATCTACCAAGGAAAAAATAATG
391 GAAGAATTTCACTATAAGAAAATAAGAATTACAATTTCTCTCAATCTACCAAGGAAAAAATAATG
457988 ATAATTCTCTCTTGATAAAAAGGAGAAAACAACTCTCAAGAAAACTCTC
456 ATAATTCTCTCTTGATAAAAAGGAGAAAACAACTCTCAAGAAAACTCTC
458037 TAAATGATGAGCTGATGAGCCATTTTGTGATATCAGCAAGTAATATATGTAGCAAAATGTATAAA
1 TAAATGATGAGCTGATGAGCCATTTTGTGATATCAGCAAGTAATATATGTAGCAAAATGTATAAA
458102 TTTCCCTCTGTTGGAAAGAGTTGCTGCATTTTAGCTAGTGACAGGTTTTGTGTATAATCGCACCA
66 TTTCCCTCTGTTGGAAAGAGTTGCTGCATTTTAGCTAGTGACAGGTTTTGTGTATAATCGCACCA
458167 AGTTTGATACTTTCCGAAAGCGTTAGTCTCGTTACTTATGTTCATTTCGCTTCCACCCTTCTCTT
131 AGTTTGATACTTTCCGAAAGCGTTAGTCTCGTTACTTATGTTCATTTCGCTTCCACCCTTCTCTT
458232 GCTTAGAAGGACAAAATAGTAATTATAAAGAGAGATTGAAGAAATTTGGGGATTTTATTGTTGCG
196 GCTTAGAAGGACAAAATAGTAATTATAAAGAGAGATTGAAGAAATTTGGGGATTTTATTGTTGCG
458297 GAATACGGCTATCGGATAGAGCAAAATGACAACTGATAATTTGAGAAAATAAAAAATAAAGATAA
261 GAATACGGCTATCGGATAGAGCAAAATGACAACTGATAATTTGAGAAAATAAAAAATAAAGATAA
458362 ATAAGATACAAAATTTACGTATAAAACTCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTA
326 ATAAGATACAAAATTTACGTATAAAACTCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTA
458427 GAAGAATTTCACTATAAGAAAATAAGAATTACAATTTCTCTCAATCTACCAAGGAAAAAATAATG
391 GAAGAATTTCACTATAAGAAAATAAGAATTACAATTTCTCTCAATCTACCAAGGAAAAAATAATG
458492 ATAATTCTCTCTTGATAAAAAGGAGAAAACAACTCTCAAGAAAACTCTC
456 ATAATTCTCTCTTGATAAAAAGGAGAAAACAACTCTCAAGAAAACTCTC
458541 TAAAT
1 TAAAT
458546 TTTCTAGTAT
Statistics
Matches: 509, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
504 509 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (504 bp):
TAAATGATGAGCTGATGAGCCATTTTGTGATATCAGCAAGTAATATATGTAGCAAAATGTATAAA
TTTCCCTCTGTTGGAAAGAGTTGCTGCATTTTAGCTAGTGACAGGTTTTGTGTATAATCGCACCA
AGTTTGATACTTTCCGAAAGCGTTAGTCTCGTTACTTATGTTCATTTCGCTTCCACCCTTCTCTT
GCTTAGAAGGACAAAATAGTAATTATAAAGAGAGATTGAAGAAATTTGGGGATTTTATTGTTGCG
GAATACGGCTATCGGATAGAGCAAAATGACAACTGATAATTTGAGAAAATAAAAAATAAAGATAA
ATAAGATACAAAATTTACGTATAAAACTCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTA
GAAGAATTTCACTATAAGAAAATAAGAATTACAATTTCTCTCAATCTACCAAGGAAAAAATAATG
ATAATTCTCTCTTGATAAAAAGGAGAAAACAACTCTCAAGAAAACTCTC
Found at i:464434 original size:22 final size:22
Alignment explanation
Indices: 464403--464502 Score: 155
Period size: 22 Copynumber: 4.5 Consensus size: 22
464393 TGACCATTAT
* *
464403 GTCCCAAAGGACCACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
*
464425 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
464447 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
464469 GTCCCGAAGGATCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
464491 GTCTCGAAGGAC
1 GTCCCGAAGGAC
464503 TAATATACCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:465115 original size:19 final size:19
Alignment explanation
Indices: 465091--465161 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
465081 TTTAAGCAGG
*
465091 TGCATCGATTCACTCCTTA
1 TGCATCGATGCACTCCTTA
465110 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
465129 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
465148 TGCATCGATGCACT
1 TGCATCGATGCACT
465162 AATGGAATTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:465172 original size:102 final size:103
Alignment explanation
Indices: 465027--465226 Score: 248
Period size: 102 Copynumber: 1.9 Consensus size: 103
465017 CCTTGACGGG
* **
465027 TGCATCGATGCACTACCCATGCATCGGTGCATAAATCTTATTCGATGTT-TGTATTTT-AA-GCA
1 TGCATCGATGCACTACCCATGCATCGATGCATAAATCGAATTCGATGTTATGTATTTTAAATG-A
* *
465089 GGTGCATCGATTCACTCCTTATGCATCGATGCACTCCTTA
65 -GTGCATCGATACACTCCATATGCATCGATGCACTCCTTA
* * *
465129 TGCATCGATGCACT-CCTTATGCATCGATGCACT-AATGGAATTCGATGTTCATTTATTTTAAAT
1 TGCATCGATGCACTACC-CATGCATCGATGCA-TAAATCGAATTCGATGTT-ATGTATTTTAAAT
465192 GAGTGCATCGATACACTCCATATGCATCGATGCAC
63 GAGTGCATCGATACACTCCATATGCATCGATGCAC
465227 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
101 2 0.02
102 39 0.46
103 1 0.01
104 38 0.45
105 3 0.04
106 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (103 bp):
TGCATCGATGCACTACCCATGCATCGATGCATAAATCGAATTCGATGTTATGTATTTTAAATGAG
TGCATCGATACACTCCATATGCATCGATGCACTCCTTA
Found at i:470788 original size:20 final size:20
Alignment explanation
Indices: 470759--470803 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
470749 TATTATTCAT
*
470759 AGTTTGGAAACTTCTGTAAG
1 AGTTTGGAAACTTCAGTAAG
*
470779 AGTTTTGAAACTTCAGTAAG
1 AGTTTGGAAACTTCAGTAAG
470799 AGTTT
1 AGTTT
470804 CAAAACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (20 bp):
AGTTTGGAAACTTCAGTAAG
Found at i:470809 original size:20 final size:20
Alignment explanation
Indices: 470766--470811 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
470756 CATAGTTTGG
* **
470766 AAACTTCTGTAAGAGTTTTG
1 AAACTTCAGTAAGAGTTTCA
470786 AAACTTCAGTAAGAGTTTCA
1 AAACTTCAGTAAGAGTTTCA
470806 AAACTT
1 AAACTT
470812 TGCACCCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
AAACTTCAGTAAGAGTTTCA
Found at i:472177 original size:19 final size:20
Alignment explanation
Indices: 472153--472201 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
472143 AATGATTTTC
* *
472153 TTTTGAAAATCAAAGTG-GA
1 TTTTGAAAAACAAAATGAGA
472172 TTTTGAAAAACAAAATGAGA
1 TTTTGAAAAACAAAATGAGA
472192 TTTTGAAAAA
1 TTTTGAAAAA
472202 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAGA
Found at i:474056 original size:20 final size:20
Alignment explanation
Indices: 474033--474071 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
474023 AATTAAATCA
474033 TGTTTAAAG-TGTTTAAAATG
1 TGTTTAAAGCT-TTTAAAATG
474053 TGTTTAAAGCTTTTAAAAT
1 TGTTTAAAGCTTTTAAAAT
474072 ATGAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTTTAAAGCTTTTAAAATG
Found at i:474231 original size:40 final size:40
Alignment explanation
Indices: 474140--474232 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
474130 TATTGTTCAT
* *
474140 AGTTTGGAAACTTTTGTAAAAGTTTCCAAACTTCTGTAAG
1 AGTTTCGAAACTTCTGTAAAAGTTTCCAAACTTCTGTAAG
* *
474180 AGTTTCCAAACTTCTGTAAGAGTTTCCAAACTTCTGTAAG
1 AGTTTCGAAACTTCTGTAAAAGTTTCCAAACTTCTGTAAG
*
474220 AGTTTTGAAACTT
1 AGTTTCGAAACTT
474233 TGCACCTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (40 bp):
AGTTTCGAAACTTCTGTAAAAGTTTCCAAACTTCTGTAAG
Found at i:474232 original size:20 final size:20
Alignment explanation
Indices: 474147--474224 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
474137 CATAGTTTGG
* *
474147 AAACTTTTGTAAAAGTTTCC
1 AAACTTCTGTAAGAGTTTCC
474167 AAACTTCTGTAAGAGTTTCC
1 AAACTTCTGTAAGAGTTTCC
474187 AAACTTCTGTAAGAGTTTCC
1 AAACTTCTGTAAGAGTTTCC
474207 AAACTTCTGTAAGAGTTT
1 AAACTTCTGTAAGAGTTT
474225 TGAAACTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (20 bp):
AAACTTCTGTAAGAGTTTCC
Found at i:474384 original size:20 final size:20
Alignment explanation
Indices: 474341--474388 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
474331 AGTGTGTTTA
474341 AAAGTTTC-GATACTTTCAC
1 AAAGTTTCAGATACTTTCAC
*
474360 AAAGTTTCAGA-ACTTTCTCC
1 AAAGTTTCAGATACTTTC-AC
474380 AAAGTTTCA
1 AAAGTTTCA
474389 AAATTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (20 bp):
AAAGTTTCAGATACTTTCAC
Found at i:474587 original size:20 final size:20
Alignment explanation
Indices: 474544--474587 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
474534 AACCACTATG
* **
474544 TCCCGAAGGACCACAGTTTG
1 TCCCGAAGGACCACAGATAA
*
474564 TCCCGAAGGACCACTGATAA
1 TCCCGAAGGACCACAGATAA
474584 TCCC
1 TCCC
474588 TCGACTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.18
Consensus pattern (20 bp):
TCCCGAAGGACCACAGATAA
Found at i:478036 original size:3 final size:3
Alignment explanation
Indices: 478028--478098 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
478018 TGTTCTCACC
478028 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
478076 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
478099 GGACAAATTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:486897 original size:3 final size:3
Alignment explanation
Indices: 486889--486938 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
486879 ATATGTAAAA
* *
486889 AAT AAT AATT AAT AAT AA- AAA AAT AAA AAT AAT AAT AATT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
486935 AAT A
1 AAT A
486939 TACATATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:486904 original size:10 final size:10
Alignment explanation
Indices: 486889--486937 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
486879 ATATGTAAAA
486889 AATAATAATT
1 AATAATAATT
**
486899 AATAATAAAAA
1 AATAAT-AATT
*
486910 AATAA-AAAT
1 AATAATAATT
486919 AATAATAATT
1 AATAATAATT
486929 AATAATAAT
1 AATAATAAT
486938 ATACATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.24
10 18 0.55
11 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATT
Found at i:487139 original size:32 final size:32
Alignment explanation
Indices: 487085--487269 Score: 207
Period size: 32 Copynumber: 5.8 Consensus size: 32
487075 AGTCGAGGAT
* *
487085 TTACCTATGT-TCTACGGAACATATGGACAGAA
1 TTACCTATGTCT-TTCGGGACATATGGACAGAA
* *
487117 TTACTTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* * ** *
487149 TTATCTATGTCTTTCGGGATATATGGGTAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
487181 TTACCTATGTCTTTTGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
*
487213 TTACCTATGTTTTTCGGGACATATGGACAG--
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
487243 TTACCTATGT-TCTTAGGAACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
487270 TAGGTCCTTC
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
29 1 0.01
30 23 0.17
32 107 0.81
33 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:487974 original size:12 final size:12
Alignment explanation
Indices: 487954--488000 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
487944 ACTGTAGTAG
487954 GGTACTGTTCAC
1 GGTACTGTTCAC
*
487966 GGTATTGTTCAC
1 GGTACTGTTCAC
* * *
487978 GATATTGTTCAT
1 GGTACTGTTCAC
487990 GGTACTGTTCA
1 GGTACTGTTCA
488001 GACCGTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (12 bp):
GGTACTGTTCAC
Found at i:488299 original size:16 final size:16
Alignment explanation
Indices: 488278--488332 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
488268 CATTTAATAA
*
488278 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
488294 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
488310 ATAAATGAACACAAAC
1 ATAAACGAACACGAAC
488326 ATAAACG
1 ATAAACG
488333 TTGGAGACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:489428 original size:20 final size:20
Alignment explanation
Indices: 489403--489440 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
489393 AAGATTGGGT
489403 TAAACATAA-ATAAATGAACA
1 TAAACA-AACATAAATGAACA
489423 TAAACAAACATAAATGAA
1 TAAACAAACATAAATGAA
489441 TGAACATAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (20 bp):
TAAACAAACATAAATGAACA
Found at i:492646 original size:32 final size:32
Alignment explanation
Indices: 492605--492757 Score: 179
Period size: 32 Copynumber: 4.8 Consensus size: 32
492595 GTCAAAGGGT
* *
492605 TTACCTATGT-TCTACGGAACATATGGACAGAA
1 TTACCTATGTCT-TTCGGGACATATGGACAGAA
* * *
492637 TTACCTATGTCTTTCGGGATATATAGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
492669 TTACCTATGTCTTTCGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
492701 TTATCTATGTCTTTCGGGACATATGGATAG--
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
492731 TTACCTATGT-TCTTAGGAACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
492758 TAGGTCCTTC
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.01
30 22 0.21
32 82 0.77
33 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:492692 original size:64 final size:62
Alignment explanation
Indices: 492605--492757 Score: 209
Period size: 64 Copynumber: 2.4 Consensus size: 62
492595 GTCAAAGGGT
* *
492605 TTACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGATATATAGACAG
1 TTACCTATGTTCTTCGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATAGACAG
* * * *
492667 TATTACCTATG-TCTTTCGGGACATATGGACAGAATTATCTATGTCTTTCGGGACATATGGATAG
1 --TTACCTATGTTC-TTCGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATAGACAG
*
492731 TTACCTATGTTCTTAGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
492758 TAGGTCCTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
62 22 0.28
63 4 0.05
64 53 0.67
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATAGACAG
Found at i:495371 original size:34 final size:32
Alignment explanation
Indices: 495309--495378 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
495299 CCTTACAAAC
* *
495309 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
495341 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
495375 TCCC
1 TCCC
495379 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:495687 original size:21 final size:21
Alignment explanation
Indices: 495661--495702 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
495651 CCAGAATGGG
*
495661 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
495682 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
495703 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:495865 original size:21 final size:21
Alignment explanation
Indices: 495836--495887 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
495826 TGAACAGTGA
495836 GGGAATCGGTACCCCCTTGGG
1 GGGAATCGGTACCCCCTTGGG
*
495857 GGTAATCGGTACCCCCTTGGG
1 GGGAATCGGTACCCCCTTGGG
495878 GGGAATCGGT
1 GGGAATCGGT
495888 TACTGTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTTGGG
Found at i:499540 original size:23 final size:20
Alignment explanation
Indices: 499489--499548 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
499479 TTTTGGTGCA
*
499489 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
499508 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
499529 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
499549 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:503567 original size:11 final size:11
Alignment explanation
Indices: 503553--503604 Score: 86
Period size: 11 Copynumber: 4.7 Consensus size: 11
503543 ATGTTTTACG
503553 GAAGTACTGTA
1 GAAGTACTGTA
503564 GAAGTACTGTA
1 GAAGTACTGTA
*
503575 GCAGTACTGTA
1 GAAGTACTGTA
503586 GAAGTACTGTA
1 GAAGTACTGTA
*
503597 GCAGTACT
1 GAAGTACT
503605 ATAGTAGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (11 bp):
GAAGTACTGTA
Found at i:503580 original size:22 final size:22
Alignment explanation
Indices: 503555--503604 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
503545 GTTTTACGGA
503555 AGTACTGTAGAAGTACTGTAGC
1 AGTACTGTAGAAGTACTGTAGC
503577 AGTACTGTAGAAGTACTGTAGC
1 AGTACTGTAGAAGTACTGTAGC
503599 AGTACT
1 AGTACT
503605 ATAGTAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (22 bp):
AGTACTGTAGAAGTACTGTAGC
Found at i:503718 original size:22 final size:22
Alignment explanation
Indices: 503690--503731 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
503680 CTGTAGTAGG
*
503690 TTACTGTTCACGGTACTGTTTA
1 TTACTGTTCAAGGTACTGTTTA
*
503712 TTACTGTTCAATGTACTGTT
1 TTACTGTTCAAGGTACTGTT
503732 CATACCGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TTACTGTTCAAGGTACTGTTTA
Found at i:506005 original size:47 final size:47
Alignment explanation
Indices: 505917--506015 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
505907 TTGGAGTCCG
* * * *
505917 AATTTCTTTATACTAGTTGTTTATTTTACTGAATGTACCCACCCTGT
1 AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGACCCACCCTGA
*
505964 AATTTCTTTATACTAGTTGTTCACTTTACTGAA-GGAGCCCACTCTGA
1 AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGA-CCCACCCTGA
506011 AATTT
1 AATTT
506016 TATTCATGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 2 0.04
47 44 0.96
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (47 bp):
AATTTCTTTATACTAGTTGTTCACTTTACTGAATGGACCCACCCTGA
Found at i:508111 original size:17 final size:17
Alignment explanation
Indices: 508089--508127 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
508079 AAAGGTTAAA
508089 GTCAAGCACAAAGGAAC
1 GTCAAGCACAAAGGAAC
508106 GTCAAGCACAAAGGAAC
1 GTCAAGCACAAAGGAAC
508123 GTCAA
1 GTCAA
508128 TCTTTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (17 bp):
GTCAAGCACAAAGGAAC
Found at i:508572 original size:43 final size:40
Alignment explanation
Indices: 508519--508598 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
508509 GTGGAAAGGT
* *
508519 TTTGAAAAATATATATTATACTATTAAATATAAACATAAATGA
1 TTTGAAAAATA-ACATT-TAATATTAAATATAAA-ATAAATGA
* *
508562 TTTGACAAATAACATTTAATATTAACTATAAAATAAA
1 TTTGAAAAATAACATTTAATATTAAATATAAAATAAA
508599 ATGTTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 5 0.15
41 14 0.42
42 4 0.12
43 10 0.30
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (40 bp):
TTTGAAAAATAACATTTAATATTAAATATAAAATAAATGA
Found at i:511347 original size:12 final size:12
Alignment explanation
Indices: 511330--511361 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
511320 TGGTGATTTT
511330 GAAGAAGAGGAA
1 GAAGAAGAGGAA
511342 GAAGAAGAGGAA
1 GAAGAAGAGGAA
511354 GAAGAAGA
1 GAAGAAGA
511362 CGATGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
GAAGAAGAGGAA
Found at i:511378 original size:12 final size:12
Alignment explanation
Indices: 511363--511393 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
511353 AGAAGAAGAC
511363 GATGATGATGCA
1 GATGATGATGCA
511375 GATGATGATGCA
1 GATGATGATGCA
511387 GATGATG
1 GATGATG
511394 GATCTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (12 bp):
GATGATGATGCA
Found at i:513621 original size:68 final size:70
Alignment explanation
Indices: 513508--513647 Score: 221
Period size: 68 Copynumber: 2.0 Consensus size: 70
513498 TTGGTATAAC
*
513508 TAAGAGTAATCAACATGGGATCTTTTCTCTCTCAAAAATTTATTGCTGAAACATAACACGTATCT
1 TAAGAGTAATCAACATGGGATCTTTTCTCTCT-AAAAATTTATTGCAGAAACATAACACGTATCT
513573 GTAGCA
65 GTAGCA
* * *
513579 TAAGAGTAATCGACATGGGATC-TTTCTCTCT-AAAATTTATTGCAGAAGCATAACATGTATCTG
1 TAAGAGTAATCAACATGGGATCTTTTCTCTCTAAAAATTTATTGCAGAAACATAACACGTATCTG
513642 TAGCA
66 TAGCA
513647 T
1 T
513648 CTGTTAAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 35 0.54
70 9 0.14
71 21 0.32
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (70 bp):
TAAGAGTAATCAACATGGGATCTTTTCTCTCTAAAAATTTATTGCAGAAACATAACACGTATCTG
TAGCA
Found at i:514774 original size:10 final size:10
Alignment explanation
Indices: 514759--514800 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
514749 TGAACTAAAT
514759 AAATATTATA
1 AAATATTATA
514769 AAATATTATA
1 AAATATTATA
*
514779 AAAAATT-TA
1 AAATATTATA
*
514788 AAA-GTTATA
1 AAATATTATA
514797 AAAT
1 AAAT
514801 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 2 0.07
9 10 0.36
10 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAATATTATA
Found at i:515151 original size:18 final size:18
Alignment explanation
Indices: 515121--515155 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
515111 TCTAGTTAAT
515121 ATATATTTAATTTTTTTA
1 ATATATTTAATTTTTTTA
515139 ATAT-TTTATATTTTTTT
1 ATATATTTA-ATTTTTTT
515156 CTCAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATATATTTAATTTTTTTA
Found at i:524160 original size:2 final size:2
Alignment explanation
Indices: 524153--524178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
524143 TTTTGTAAGA
524153 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
524179 GAAAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:539095 original size:20 final size:20
Alignment explanation
Indices: 539069--539121 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
539059 ATAATACAAA
* *
539069 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTATGACT
*
539089 TTCGCAACGAGATTATGACT
1 ATCGCAACGAGATTATGACT
539109 ATCGCAACGAGAT
1 ATCGCAACGAGAT
539122 AATACAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTATGACT
Found at i:539106 original size:61 final size:61
Alignment explanation
Indices: 539028--539143 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
539018 AGTTTTCAGA
* * * *
539028 TTCGCAAGACGATTATGATTATCGTAATGCGATAATACAAAATCGCAACGCGATTCTGACT
1 TTCGCAAGACGATTATGACTATCGCAACGAGATAATACAAAATCGCAACGCGATTCTGACT
* * *
539089 TTCGCAACGA-GATTATGACTATCGCAACGAGATAATACAGAATCGTAATGCGATT
1 TTCGCAA-GACGATTATGACTATCGCAACGAGATAATACAAAATCGCAACGCGATT
539144 TTCAAAATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 45 0.96
62 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (61 bp):
TTCGCAAGACGATTATGACTATCGCAACGAGATAATACAAAATCGCAACGCGATTCTGACT
Found at i:539673 original size:14 final size:14
Alignment explanation
Indices: 539654--539683 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
539644 TCATTTGACT
*
539654 ATCGCAACGGGAAA
1 ATCGCAACGCGAAA
539668 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
539682 AT
1 AT
539684 GACTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:539692 original size:34 final size:34
Alignment explanation
Indices: 539649--539755 Score: 124
Period size: 40 Copynumber: 3.0 Consensus size: 34
539639 GACATTCATT
539649 TGACTATCGCAACGGGAAAATCGCAACGCGAAAA
1 TGACTATCGCAACGGGAAAATCGCAACGCGAAAA
*
539683 TGACTATCGCAACGCGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACG-GGAAA-----ATCGCAACGCGAAAA
* * *
539723 TGGCTATCGCAACGAGAAAATCGCAATGCGAAA
1 TGACTATCGCAACGGGAAAATCGCAACGCGAAA
539756 TGAAAATCGC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
34 27 0.44
35 4 0.06
39 3 0.05
40 28 0.45
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (34 bp):
TGACTATCGCAACGGGAAAATCGCAACGCGAAAA
Found at i:539693 original size:20 final size:20
Alignment explanation
Indices: 539668--539743 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
539658 CAACGGGAAA
*
539668 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
539688 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
539708 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
539728 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
539744 CGCAATGCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:539809 original size:19 final size:19
Alignment explanation
Indices: 539762--539902 Score: 211
Period size: 19 Copynumber: 7.7 Consensus size: 19
539752 GAAATGAAAA
539762 TCGCATTGCGATTTT-A--
1 TCGCATTGCGATTTTCATT
*
539778 TCG--TTGCGCTTTTCATT
1 TCGCATTGCGATTTTCATT
539795 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
539814 TCGCATTGCGATTTTCTTT
1 TCGCATTGCGATTTTCATT
*
539833 TCGCATTGCGCTTTTCATT
1 TCGCATTGCGATTTTCATT
*
539852 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
539871 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
539890 TCGCATTGCGATT
1 TCGCATTGCGATT
539903 CTCTCGTTGC
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 3 0.03
17 3 0.03
19 96 0.86
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:540061 original size:14 final size:14
Alignment explanation
Indices: 540042--540079 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
540032 CATCAATTAA
540042 ACAAATCAATATTT
1 ACAAATCAATATTT
* *
540056 ACAAATCATTTTTT
1 ACAAATCAATATTT
540070 ACAAATCAAT
1 ACAAATCAAT
540080 TAAACAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
ACAAATCAATATTT
Found at i:541919 original size:20 final size:20
Alignment explanation
Indices: 541894--541946 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
541884 GAAGAATAGT
*
541894 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
541914 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
541934 TGACTATCGCAAC
1 TTACTTTCGCAAC
541947 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:541944 original size:40 final size:38
Alignment explanation
Indices: 541900--542005 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 38
541890 TAGTTTACTT
* * **
541900 TCGCAACACGAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGAAA-TGACTATCGCAACGCG-AAATGAAAA
* *
541940 TCGCAACGCGGAAATGGCTATCGCAACGCGAAATGAAAA
1 TCGCAACAC-GAAATGACTATCGCAACGCGAAATGAAAA
* **
541979 TCGCAATACGAAATGAAAATCGCAACG
1 TCGCAACACGAAATGACTATCGCAACG
542006 ACAAAATCGC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
38 15 0.28
39 14 0.26
40 21 0.39
41 4 0.07
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (38 bp):
TCGCAACACGAAATGACTATCGCAACGCGAAATGAAAA
Found at i:541947 original size:20 final size:20
Alignment explanation
Indices: 541900--541972 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
541890 TAGTTTACTT
* * * *
541900 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
541920 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
541940 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
541960 TCGCAACGCGAAA
1 TCGCAACGCGAAA
541973 TGAAAATCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:541981 original size:19 final size:19
Alignment explanation
Indices: 541920--542039 Score: 97
Period size: 19 Copynumber: 6.5 Consensus size: 19
541910 AAACTTACTT
**
541920 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
541940 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
541960 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
541979 TCGCAATACGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
541998 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
542012 TCGCAATGCAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
542031 TCGCAACGC
1 TCGCAACGC
542040 AAAACACAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 42 0.50
20 26 0.31
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:542017 original size:33 final size:32
Alignment explanation
Indices: 541975--542043 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
541965 ACGCGAAATG
*
541975 AAAATCGCAATACGAAATGAAAATCGCAACGAC
1 AAAATCGCAATACAAAATGAAAATCGCAACG-C
*
542008 AAAATCGCAATGCAAAATGAAAATCGCAACGC
1 AAAATCGCAATACAAAATGAAAATCGCAACGC
542040 AAAA
1 AAAA
542044 CACAAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (32 bp):
AAAATCGCAATACAAAATGAAAATCGCAACGC
Found at i:542050 original size:19 final size:19
Alignment explanation
Indices: 541959--542054 Score: 69
Period size: 19 Copynumber: 5.3 Consensus size: 19
541949 GGAAATGGCT
* *
541959 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCAAAATCAAA
** * *
541978 ATCGCAATACGAAATGAAA
1 ATCGCAACGCAAAATCAAA
541997 ATCGCAACG----A-CAAA
1 ATCGCAACGCAAAATCAAA
* *
542011 ATCGCAATGCAAAATGAAA
1 ATCGCAACGCAAAATCAAA
542030 ATCGCAACGCAAAA-CACAA
1 ATCGCAACGCAAAATCA-AA
542049 ATCGCA
1 ATCGCA
542055 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
18 2 0.03
19 48 0.77
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCAAAATCAAA
Found at i:542072 original size:19 final size:19
Alignment explanation
Indices: 542050--542146 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
542040 AAAACACAAA
542050 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
542069 TCGCGTTACGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
542085 TCG--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
542102 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
542118 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
542135 TCGCATTGCGAT
1 TCGCATTGCGAT
542147 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 10 0.17
15 6 0.10
16 8 0.14
17 8 0.14
18 6 0.10
19 21 0.36
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:542101 original size:33 final size:33
Alignment explanation
Indices: 542055--542146 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
542045 ACAAATCGCA
*
542055 TTGCGATTTTCATTTCGCGTTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTACGATTTTGTCG
* *
542088 TTGTGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTACGATTTTGTCG
*
542121 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTACGAT
542147 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTACGATTTTGTCG
Found at i:542165 original size:20 final size:19
Alignment explanation
Indices: 542131--542185 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
542121 TTGCGATTTT
*
542131 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
542150 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
542170 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
542186 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:542749 original size:18 final size:18
Alignment explanation
Indices: 542726--542773 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
542716 CGGGTCGATC
542726 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
542744 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
542762 AGGTGATGGCTC
1 AGGTGATGGCTC
542774 CTGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:544098 original size:20 final size:20
Alignment explanation
Indices: 544073--544115 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
544063 AATAGTTTCT
544073 GAAAATGAA-AATCGCAACAC
1 GAAAAT-AACAATCGCAACAC
*
544093 GAAAATAACAATCGCAACGC
1 GAAAATAACAATCGCAACAC
544113 GAA
1 GAA
544116 TTTGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.09
Consensus pattern (20 bp):
GAAAATAACAATCGCAACAC
Found at i:544412 original size:22 final size:22
Alignment explanation
Indices: 544385--544428 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
544375 GATGGAGATA
544385 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
544407 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
544429 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:544640 original size:20 final size:20
Alignment explanation
Indices: 544615--544728 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
544605 GATTATGTAT
*
544615 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
544635 TATCTCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
544655 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
544675 TATCGCGTTACGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
544696 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
544716 TGTCGCATTGCGA
1 TATCGCGTTGCGA
544729 TTTTCCCAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:544732 original size:41 final size:41
Alignment explanation
Indices: 544595--544730 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
544585 CACTTTGAAA
*
544595 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
544636 ATCTCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * *
544676 ATCGCGTTACGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
*
544717 GTCGCATTGCGATT
1 ATCGCATTGCGATT
544731 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:544743 original size:41 final size:41
Alignment explanation
Indices: 544655--544750 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
544645 CGAAAGTAAG
* * ** *
544655 TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAA
* *
544696 TATCGCGTTGCGATAGTCAGTGTCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTT-CCAA
544738 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
544751 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAA
Found at i:544811 original size:21 final size:22
Alignment explanation
Indices: 544759--544811 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
544749 ATTTACTTAT
544759 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
544780 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
544801 TCGCATTGCGA
1 TCGCATTGCGA
544812 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:545627 original size:20 final size:20
Alignment explanation
Indices: 545598--545639 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
545588 ACACCAAATC
* *
545598 CAAATCCTCTCAACTTCTCT
1 CAAATACTCTCAAATTCTCT
*
545618 CAAATACTCTTAAATTCTCT
1 CAAATACTCTCAAATTCTCT
545638 CA
1 CA
545640 TAGCTCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAATACTCTCAAATTCTCT
Found at i:545676 original size:17 final size:18
Alignment explanation
Indices: 545654--545687 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
545644 TCTTTAAGGT
545654 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
545671 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
545688 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:545698 original size:33 final size:32
Alignment explanation
Indices: 545655--545730 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 32
545645 CTTTAAGGTA
* *
545655 TATTTTATTATATTTAATATTTTGTTAGT-ATTT
1 TATTTAATTATATTTAAT-TTTT-TTAATAATTT
545688 TATTTAA-T-TATTTAATTTTTTTAATAATTT
1 TATTTAATTATATTTAATTTTTTTAATAATTT
545718 T-TTTAATTA-ATTT
1 TATTTAATTATATTT
545731 TTTACAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 9 0.24
30 14 0.37
31 8 0.21
32 1 0.03
33 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (32 bp):
TATTTAATTATATTTAATTTTTTTAATAATTT
Found at i:545712 original size:17 final size:18
Alignment explanation
Indices: 545684--545717 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
545674 TTTTGTTAGT
*
545684 ATTTTATTTAATTATTTA
1 ATTTTATTTAATAATTTA
545702 ATTTT-TTTAATAATTT
1 ATTTTATTTAATAATTT
545718 TTTTAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTATTTAATAATTTA
Done.