Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008909.1 Hibiscus syriacus cultivar Beakdansim tig00112206_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: 2327114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:448040 original size:14 final size:17
Alignment explanation
Indices: 448027--448060 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
448017 AAAATTTATA
448027 TATATATT-TTTATAAT
1 TATATATTATTTATAAT
448043 TATATATTATTTA-AAT
1 TATATATTATTTATAAT
448059 TA
1 TA
448061 ATTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATTATTTATAAT
Found at i:448990 original size:31 final size:32
Alignment explanation
Indices: 448944--449014 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
448934 TTTATTTTAT
* *
448944 TTTAGTACCCCCGCCGTTAAAATCTTAATGCG
1 TTTAGTACCCCCGCCGTTAAAAACTTAATGCA
*
448976 TTTAGTA-TCCCGCCGTTAAAAACTTAATGCA
1 TTTAGTACCCCCGCCGTTAAAAACTTAATGCA
449007 TTTAGTAC
1 TTTAGTAC
449015 ATAAACTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (32 bp):
TTTAGTACCCCCGCCGTTAAAAACTTAATGCA
Found at i:452574 original size:2 final size:2
Alignment explanation
Indices: 452567--452594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
452557 ACCCTAACAC
452567 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
452595 TCCATACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454106 original size:15 final size:14
Alignment explanation
Indices: 454077--454111 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
454067 AATATTGTTT
454077 TTAATT-AAATTAA
1 TTAATTAAAATTAA
454090 TTAATTAAAATTTAA
1 TTAATTAAAA-TTAA
454105 TTAATTA
1 TTAATTA
454112 GGTCTCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTAAAATTAA
Found at i:459956 original size:29 final size:29
Alignment explanation
Indices: 459924--459990 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
459914 AATAAGTACT
* * *
459924 TAAATTATTTTTTAGTTAAAATAGATATC
1 TAAAGTATATTTTAGTCAAAATAGATATC
*
459953 TAAAGTATATTTTGGTCAAAATAGATATCC
1 TAAAGTATATTTTAGTCAAAATAGATAT-C
*
459983 TAATGTAT
1 TAAAGTAT
459991 TTAATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (29 bp):
TAAAGTATATTTTAGTCAAAATAGATATC
Found at i:469775 original size:19 final size:18
Alignment explanation
Indices: 469733--469775 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
469723 AATATATTAT
*
469733 TTAATTATTATAAATATA
1 TTAATTATTAAAAATATA
**
469751 GAAATTATTACAAAATATA
1 TTAATTATTA-AAAATATA
469770 TTAATT
1 TTAATT
469776 TAATTATTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAATTATTAAAAATATA
Found at i:469809 original size:42 final size:42
Alignment explanation
Indices: 469723--469814 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
469713 TTATATCATT
**
469723 AATATATT-ATTTAATTATTATAAATATAGAAATTATTACAA
1 AATATATTAATTTAATTATTATAAATATAGAAACAATTACAA
* *
469764 AATATATTAATTTAATTATT-TAAAATATAATAAACAATTA-TA
1 AATATATTAATTTAATTATTAT-AAATAT-AGAAACAATTACAA
469806 AATATATTA
1 AATATATTA
469815 TTATAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 9 0.20
42 27 0.61
43 8 0.18
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (42 bp):
AATATATTAATTTAATTATTATAAATATAGAAACAATTACAA
Found at i:469817 original size:14 final size:14
Alignment explanation
Indices: 469800--469843 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
469790 ATAATAAACA
469800 ATTATAAATATATT
1 ATTATAAATATATT
469814 ATTATAAATTATATT
1 ATTATAAA-TATATT
* *
469829 ATTTTAATTATATT
1 ATTATAAATATATT
469843 A
1 A
469844 AAATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:470142 original size:9 final size:9
Alignment explanation
Indices: 470130--470163 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
470120 TATATTTTTA
470130 ATATAAAAT
1 ATATAAAAT
470139 ATATAAAAAT
1 ATAT-AAAAT
*
470149 ATTTAAAAT
1 ATATAAAAT
470158 ATATAA
1 ATATAA
470164 TAATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATATAAAAT
Found at i:470169 original size:17 final size:18
Alignment explanation
Indices: 470128--470169 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
470118 AATATATTTT
*
470128 TAATATAAAATATATAAA
1 TAATTTAAAATATATAAA
*
470146 AATATTTAAAATATAT-AA
1 TA-ATTTAAAATATATAAA
470164 TAATTT
1 TAATTT
470170 TATATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTTAAAATATATAAA
Found at i:470614 original size:16 final size:15
Alignment explanation
Indices: 470593--470622 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
470583 GAATCAAAAT
470593 TATTAAATATTATATA
1 TATTAAATA-TATATA
470609 TATTAAATATATAT
1 TATTAAATATATAT
470623 TTTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATATATATA
Found at i:472914 original size:337 final size:335
Alignment explanation
Indices: 472274--472946 Score: 1296
Period size: 337 Copynumber: 2.0 Consensus size: 335
472264 GCACCAGCAA
472274 GGTGCTCGAGAGCGAGAAGCAGTTCTATACTTTGGTGAAAGTTTGAGACAGCCATTGGCAGATGA
1 GGTGCTCGAGAGCGAGAAGCAGTTCTATACTTTGGTGAAAGTTTGAGACAGCCATTGGCAGATGA
472339 TTTGCACGAAAGGCTTTCCTCCCGATAAGTTGAGAACTTTTTGAGAAGAGGTTGATTTTTTAACC
66 TTTGCACGAAAGGCTTTCCTCCCGATAAGTTGAGAACTTTTTGAGAAGAGGTTGATTTTTTAACC
472404 TTGTGGTATCTGTATGAATATGTATTTGAGTAGCTCTAACATGGCTAGATAACATGTGTGATTTC
131 TTGTGGTATCTGTATGAATATGTATTTGAGTAGCTCTAACATGGCTAGATAACATGTGTGATTTC
472469 ATGTCATCCTCATTTTAGTAGCAGCAGAAGTAGATTTTCGTGTTGAAGTAACATGTGCGATTTCA
196 ATGTCATCCTCATTTTAGTAGCAGCAGAAGTAGATTTTCGTGTTGAAGTAACATGTGCGATTTCA
472534 CTTGTATTATTAATTGCTGTGGCAAACTAACCTGGTATTTGTGGAAACTAA-AATGTTCTGATTT
261 CTTGTATTATTAATTGCTGTGGCAAACTAACCTGGTATTTGTGGAAACTAAGAATGTTCTGATTT
472598 TAAGAAACTG
326 TAAGAAACTG
472608 GGTGCTCGAGAGCGAGAAGCAGTTCTATTACTTTGGTGAAAGTTTGAGACAGCCATTGGCAGATG
1 GGTGCTCGAGAGCGAGAAGCAGTTCTA-TACTTTGGTGAAAGTTTGAGACAGCCATTGGCAGATG
472673 ATTTGCACGAAAGGCTTTCCTCCCGATAAGTTGAGAACTTTTTTGAGAAGAGGTTGATTTTTTAA
65 ATTTGCACGAAAGGCTTTCCTCCCGATAAGTTGAGAAC-TTTTTGAGAAGAGGTTGATTTTTTAA
472738 CCTTGTGGTATCTGTATGAATATGTATTTGAGTAGCTCTAACATGGCTAAGATAACATGTGTGAT
129 CCTTGTGGTATCTGTATGAATATGTATTTGAGTAGCTCTAACATGGCT-AGATAACATGTGTGAT
472803 TTCATGTCATCCTCATTTTAGTTAGCAGCAGAAGTAGA-TTTCGTGTTGAAGTAACATGTGCGAT
193 TTCATGTCATCCTCATTTTAG-TAGCAGCAGAAGTAGATTTTCGTGTTGAAGTAACATGTGCGAT
472867 TTCACTTGTATTATTAATTGCTGTGGCAAACTAACCTGGTATTTGTGGAAACTAAGAATGTTCTG
257 TTCACTTGTATTATTAATTGCTGTGGCAAACTAACCTGGTATTTGTGGAAACTAAGAATGTTCTG
472932 ATTTTAAGAAACTG
322 ATTTTAAGAAACTG
472946 G
1 G
472947 CATTGGAAAT
Statistics
Matches: 334, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
334 27 0.08
335 75 0.22
336 74 0.22
337 118 0.35
338 40 0.12
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (335 bp):
GGTGCTCGAGAGCGAGAAGCAGTTCTATACTTTGGTGAAAGTTTGAGACAGCCATTGGCAGATGA
TTTGCACGAAAGGCTTTCCTCCCGATAAGTTGAGAACTTTTTGAGAAGAGGTTGATTTTTTAACC
TTGTGGTATCTGTATGAATATGTATTTGAGTAGCTCTAACATGGCTAGATAACATGTGTGATTTC
ATGTCATCCTCATTTTAGTAGCAGCAGAAGTAGATTTTCGTGTTGAAGTAACATGTGCGATTTCA
CTTGTATTATTAATTGCTGTGGCAAACTAACCTGGTATTTGTGGAAACTAAGAATGTTCTGATTT
TAAGAAACTG
Found at i:475197 original size:84 final size:84
Alignment explanation
Indices: 475083--475250 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 84
475073 TGCAGTTCAG
475083 CCACTTTTTGGAAGAAGGCCATCCTTGGCCATTGCCGTTAGCACATTGAAAACTACATCCATGTT
1 CCACTTTTTGGAAGAAGGCCATCCTTGGCCATTGCCGTTAGCACATTGAAAACTACATCCATGTT
*
475148 CCCTTCTTTATGATTTATT
66 CCCCTCTTTATGATTTATT
* *
475167 CCACTTTTTGGAAGGAGGCCGTCCTTGGCCATTGCCGTTAGCACATTGAAAACTACATCCATGTT
1 CCACTTTTTGGAAGAAGGCCATCCTTGGCCATTGCCGTTAGCACATTGAAAACTACATCCATGTT
475232 CCCCTCTTTATGATTTATT
66 CCCCTCTTTATGATTTATT
475251 ATGATTTAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.35
Consensus pattern (84 bp):
CCACTTTTTGGAAGAAGGCCATCCTTGGCCATTGCCGTTAGCACATTGAAAACTACATCCATGTT
CCCCTCTTTATGATTTATT
Found at i:480605 original size:28 final size:28
Alignment explanation
Indices: 480573--480630 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
480563 ATAAAAACAT
480573 TACAAAT-TAAATAATAAAAACAATTAAA
1 TACAAATGT-AATAATAAAAACAATTAAA
* **
480601 TACAAATGTTATAATTCAAACAATTAAA
1 TACAAATGTAATAATAAAAACAATTAAA
480629 TA
1 TA
480631 ATAAAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (28 bp):
TACAAATGTAATAATAAAAACAATTAAA
Found at i:480668 original size:25 final size:25
Alignment explanation
Indices: 480626--480706 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
480616 TCAAACAATT
480626 AAAT-AATAAAAACATTATGAAACA
1 AAATAAATAAAAACATTATGAAACA
* *
480650 AAATAAATAAAAA-GTT-T---A-T
1 AAATAAATAAAAACATTATGAAACA
* *
480669 AATTAAATAAAAACATTAAGAAACA
1 AAATAAATAAAAACATTATGAAACA
480694 AAATAAATAAAAA
1 AAATAAATAAAAA
480707 GTATAATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
19 12 0.28
20 3 0.07
23 1 0.02
24 7 0.16
25 20 0.47
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATAAATAAAAACATTATGAAACA
Found at i:480725 original size:42 final size:43
Alignment explanation
Indices: 480630--480748 Score: 213
Period size: 42 Copynumber: 2.8 Consensus size: 43
480620 ACAATTAAAT
*
480630 AATAAAAACATTATGAAACAAAATAAATAAAAAGTTTATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAG-TTATAATTA
480674 AATAAAAACATTAAGAAACAAAATAAATAAAAAG-TATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTATAATTA
480716 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
480749 CAAATCCATT
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 41 0.55
44 33 0.45
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (43 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTATAATTA
Found at i:481148 original size:21 final size:21
Alignment explanation
Indices: 481122--481189 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
481112 AAACAATGTG
481122 GTGGTGGCATTTGAAATGGTT
1 GTGGTGGCATTTGAAATGGTT
* *
481143 GTGGTGGCA-TCGAAAATGGCT
1 GTGGTGGCATTTG-AAATGGTT
* * *
481164 GTGGTGCCATCTGAAATTGTT
1 GTGGTGGCATTTGAAATGGTT
*
481185 CTGGT
1 GTGGT
481190 AGCTATTGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.92
22 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.35, T:0.34
Consensus pattern (21 bp):
GTGGTGGCATTTGAAATGGTT
Found at i:483248 original size:60 final size:59
Alignment explanation
Indices: 483092--483252 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 59
483082 CGCGCCTTTT
* * *** *
483092 GCCAGCTCGGACGGAACCCCACGAAGGCGCGCTTCATGATCCGCGCCTTCCATTGTAGT
1 GCCAGCTCGGACAGAACCCCACGAAGGCGCGCTTCATGATTCGCGCCTTCCAACATAGC
* ** * * *
483151 GCCAGCTCAGACAGAACCCCGTGAAGGTGC-ATGTCATGATTCGCGCCTTTCCAACATGGC
1 GCCAGCTCGGACAGAACCCCACGAAGGCGCGCT-TCATGATTCGCGCC-TTCCAACATAGC
* *
483211 GTCAGCTCGGACAGAATCCCACGAAGGCGCGCTTCATGATTC
1 GCCAGCTCGGACAGAACCCCACGAAGGCGCGCTTCATGATTC
483253 ACTCTTTGTC
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
58 1 0.01
59 38 0.47
60 40 0.50
61 1 0.01
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (59 bp):
GCCAGCTCGGACAGAACCCCACGAAGGCGCGCTTCATGATTCGCGCCTTCCAACATAGC
Found at i:485411 original size:42 final size:42
Alignment explanation
Indices: 485345--485444 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
485335 ACCCAATTCA
* * *
485345 AATATA-TTTATAATTATTTATTATATTTTAAACAGTTAAAAT
1 AATATATTTTATAATAAATTATTATATTTTAAACAATT-AAAT
* * *
485387 AATATGTTTTATAATAAATT-TTATATTTTTAATAATTAAAT
1 AATATATTTTATAATAAATTATTATATTTTAAACAATTAAAT
485428 AATATATTTTAATAATA
1 AATATATTTT-ATAATA
485445 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 13 0.27
42 25 0.51
43 11 0.22
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (42 bp):
AATATATTTTATAATAAATTATTATATTTTAAACAATTAAAT
Found at i:485421 original size:21 final size:21
Alignment explanation
Indices: 485383--485444 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
485373 TAAACAGTTA
*
485383 AAATAATAT-GTTTT-ATAAT
1 AAATAATATATTTTTAATAAT
**
485402 AAATTTTATATTTTTAATAATT
1 AAATAATATATTTTTAATAA-T
485424 AAATAATATA-TTTTAATAAT
1 AAATAATATATTTTTAATAAT
485444 A
1 A
485445 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.20
20 6 0.17
21 13 0.37
22 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATAATATATTTTTAATAAT
Found at i:485482 original size:2 final size:2
Alignment explanation
Indices: 485475--485508 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
485465 TTCTTAAATA
485475 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
485509 TAACTGGGTC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488748 original size:17 final size:17
Alignment explanation
Indices: 488726--488759 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
488716 ATACTTACTC
488726 TAAATTAATAAAAAAAT
1 TAAATTAATAAAAAAAT
* *
488743 TAAATTTATCAAAAAAT
1 TAAATTAATAAAAAAAT
488760 AATATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTAATAAAAAAAT
Found at i:489270 original size:42 final size:42
Alignment explanation
Indices: 489211--489294 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
489201 TCATTGTCTT
489211 ATGAATTATAACTCCATGGATGGATGATGATGGCCATTAGTG
1 ATGAATTATAACTCCATGGATGGATGATGATGGCCATTAGTG
489253 ATGAATTATAACTCCATGGATGGATGATGATGGCCATTAGTG
1 ATGAATTATAACTCCATGGATGGATGATGATGGCCATTAGTG
489295 TATGTATGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (42 bp):
ATGAATTATAACTCCATGGATGGATGATGATGGCCATTAGTG
Found at i:490515 original size:176 final size:175
Alignment explanation
Indices: 490282--490882 Score: 707
Period size: 176 Copynumber: 3.4 Consensus size: 175
490272 CATACATGTA
* * * *
490282 ATTTCATTTGTTAGGAGGAATGAACTTCTAAAATTTGATGAGTGATCGAATTTATAAAATACAAC
1 ATTTCATATGTTAGGAGGAATGAAATTCTAAAATTTGATGAGTGAACGAACTTATAAAATACAAC
*
490347 CATTTGTCCTTTTTATGACAAGTTTAGATCAATCTATAGGATATACATATATCACATGGTTAAAA
66 CATTTGT-CTTTTTATGACAAGTTTAGATCAATCTATACGATATACATATATCACATGGTTAAAA
** * *
490412 GGGTTTTTAGTGCATGTCGTTTATGGTAGGCTGAGCCAGACGCATG
130 GAATTTTTAGTACATGTCGTTTATGGTAGGTTGAGCCAGACGCATG
* * *
490458 ATTTCATATGTTAAGAGGGAT-AAATTACTAAAATTTGATGAATGAACGAACTTATAAAATACAA
1 ATTTCATATGTTAGGAGGAATGAAATT-CTAAAATTTGATGAGTGAACGAACTTATAAAATACAA
* * * *
490522 CCATTTCTCTTTTTCCATTACAAGTTTAGATCAA--TATATG-TGAT--ATATATCACATGATT-
65 CCATTTGTCTTTTT--ATGACAAGTTTAGATCAATCTATACGAT-ATACATATATCACATGGTTA
* * * *
490581 AAAGTATTTTTAGTACATATCGTACATCGTTTGTGGCAGGTTGAGACAGACGCATG
127 AAAGAATTTTTAGTAC--AT-G----TCGTTTATGGTAGGTTGAGCCAGACGCATG
* * * *
490637 ATTTCATGTGTTAGGAGGAATGAACTTCTAAAATTTGATGAGTGATCAAACTTATAAAATACAAC
1 ATTTCATATGTTAGGAGGAATGAAATTCTAAAATTTGATGAGTGAACGAACTTATAAAATACAAC
* * *
490702 CAATTGTTCTTTTCATGACAAGTTTAGATCAATCTATACAATATACATATATCACATGGTTAAAA
66 CATTTG-TCTTTTTATGACAAGTTTAGATCAATCTATACGATATACATATATCACATGGTTAAAA
* ** * *
490767 AAAAATTTAGTACATGCCGTTTATGGTAGGTTGAGCCAGACACATG
130 GAATTTTTAGTACATGTCGTTTATGGTAGGTTGAGCCAGACGCATG
490813 ATTTCATATGTTAGGA-GAGAT-AAACTTCTAAAATTTGATGAGTGAACGAACTTATAAAATACA
1 ATTTCATATGTTAGGAGGA-ATGAAA-TTCTAAAATTTGATGAGTGAACGAACTTATAAAATACA
*
490876 ACTATTT
64 ACCATTT
490883 TTTTAATTAT
Statistics
Matches: 357, Mismatches: 47, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
172 13 0.04
173 14 0.04
174 3 0.01
175 22 0.06
176 142 0.40
177 17 0.05
178 17 0.05
179 83 0.23
180 17 0.05
181 3 0.01
182 14 0.04
183 12 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (175 bp):
ATTTCATATGTTAGGAGGAATGAAATTCTAAAATTTGATGAGTGAACGAACTTATAAAATACAAC
CATTTGTCTTTTTATGACAAGTTTAGATCAATCTATACGATATACATATATCACATGGTTAAAAG
AATTTTTAGTACATGTCGTTTATGGTAGGTTGAGCCAGACGCATG
Found at i:495536 original size:28 final size:28
Alignment explanation
Indices: 495504--495561 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
495494 GCATTTTATG
* *
495504 TTAAGGG-TTAATTTGAACTTTTTAAAAT
1 TTAAGGGATAAATTTGAAC-TTATAAAAT
495532 TTAAGGGATAAATTTGAACTTATAAAAT
1 TTAAGGGATAAATTTGAACTTATAAAAT
495560 TT
1 TT
495562 CTTGATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (28 bp):
TTAAGGGATAAATTTGAACTTATAAAAT
Found at i:496945 original size:60 final size:60
Alignment explanation
Indices: 496823--496938 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
496813 AACACAATCA
* * * ** *
496823 ATAGTTGAGTGACCATTTTGTAACTTTTAATAGTCGTTGGACTCAACAAAATAATATCCT
1 ATAGTTAAGGGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAATATCCT
* * *
496883 ATAGTTAAGGGACCATTTTATAACTTTTAATATTTGAGGGACTCAATAAAACAATA
1 ATAGTTAAGGGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAATA
496939 CTCTATAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (60 bp):
ATAGTTAAGGGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAATATCCT
Found at i:497386 original size:23 final size:22
Alignment explanation
Indices: 497326--497369 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
497316 ACAATCTGAT
* *
497326 AATTTCAAAAAAAATTATTTAA
1 AATTTAAAAAAAAATTATATAA
497348 AATTTAAAAATAAAATTATATA
1 AATTTAAAAA-AAAATTATATA
497370 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTTAAAAAAAAATTATATAA
Found at i:498735 original size:24 final size:24
Alignment explanation
Indices: 498704--498759 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
498694 AGAGAGAGAT
*
498704 AAAAAAGATTATAGCTTTATTATA
1 AAAAAAGATTATAGCTTTATCATA
498728 AAAAAAGATTATAGCTTTATCATA
1 AAAAAAGATTATAGCTTTATCATA
498752 AAAAAAGA
1 AAAAAAGA
498760 AAGAAAGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (24 bp):
AAAAAAGATTATAGCTTTATCATA
Found at i:499849 original size:168 final size:168
Alignment explanation
Indices: 499571--499908 Score: 523
Period size: 168 Copynumber: 2.0 Consensus size: 168
499561 TGAAGTTCAA
** * * *
499571 TTTGTTGCTGCAAATTTCAATTTCTTGATTCATAGTTTAGATTTTGTTACGTAAATGGTATTGAA
1 TTTGTTGCTGCAAATTTCAATTTCTTGATTCATACATTAGATTTTATCACATAAATGGTATTGAA
* *
499636 TTTAGAAATTCATTTGGGACGGCATGTATCGAACTCGATGAGCTCTAGTTGATTATCGTTATCGT
66 TTTAGAAATGCATTTGGGACGGCATGTATCGAACTCGATGAGCTCTAGTTGATTATCGTTATCAT
* **
499701 GTTTAATTATGAAGCTGCAAAGTTTGTCTATGAAGAAT
131 GCTTAATTATGAAGCTGCAAAGCGTGTCTATGAAGAAT
*
499739 TTTGTTGCTGCAAATTTCAGTTTCTTGATTCATACATTAGATTTTATCACATAAATGGTATTGAA
1 TTTGTTGCTGCAAATTTCAATTTCTTGATTCATACATTAGATTTTATCACATAAATGGTATTGAA
* ***
499804 TTTGGAAATGCATTTGGTTTGGCATGTATCGAACTCGATGAGCTCTAGTTGATTATCGTTATCAT
66 TTTAGAAATGCATTTGGGACGGCATGTATCGAACTCGATGAGCTCTAGTTGATTATCGTTATCAT
* *
499869 GCTTAATTATGAAGTTGCAAAGCGTGTCTGTGAAGAAT
131 GCTTAATTATGAAGCTGCAAAGCGTGTCTATGAAGAAT
499907 TT
1 TT
499909 ATCAGTTTGA
Statistics
Matches: 153, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
168 153 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (168 bp):
TTTGTTGCTGCAAATTTCAATTTCTTGATTCATACATTAGATTTTATCACATAAATGGTATTGAA
TTTAGAAATGCATTTGGGACGGCATGTATCGAACTCGATGAGCTCTAGTTGATTATCGTTATCAT
GCTTAATTATGAAGCTGCAAAGCGTGTCTATGAAGAAT
Found at i:505620 original size:21 final size:21
Alignment explanation
Indices: 505581--505620 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
505571 TTACTTCTAA
*
505581 CTTAAACCCTAAATTATAAAT
1 CTTAAACCCTAAATCATAAAT
* *
505602 CTTAAGCCCTAACTCATAA
1 CTTAAACCCTAAATCATAA
505621 CTACATAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (21 bp):
CTTAAACCCTAAATCATAAAT
Found at i:506877 original size:18 final size:20
Alignment explanation
Indices: 506826--506879 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
506816 ATATCACATC
*
506826 AATAACAAATTAAAATATTTT
1 AATAA-AAAGTAAAATATTTT
* *
506847 AATCAAAATTAAAATA-TTT
1 AATAAAAAGTAAAATATTTT
506866 AA-AAAAAGTAAAAT
1 AATAAAAAGTAAAAT
506880 TAAAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 11 0.37
21 4 0.13
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAAGTAAAATATTTT
Found at i:515009 original size:31 final size:31
Alignment explanation
Indices: 514965--515055 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
514955 ATAACTTTTA
* * * *
514965 ATAGTCAAAGGACTTAATAAAGCATTATCAT
1 ATAGTTAAGGGACTCAATAAAACATTATCAT
*
514996 ATAGTTAAGGGACTCAATAAAATATTATCAT
1 ATAGTTAAGGGACTCAATAAAACATTATCAT
* *
515027 ATAATTAAGGGACTCGATAAAACATTATC
1 ATAGTTAAGGGACTCAATAAAACATTATC
515056 CTATTGTCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (31 bp):
ATAGTTAAGGGACTCAATAAAACATTATCAT
Found at i:519350 original size:49 final size:49
Alignment explanation
Indices: 519278--519579 Score: 335
Period size: 49 Copynumber: 6.3 Consensus size: 49
519268 ACTATGATGA
* * * *
519278 GAAACATTAACCGGTACACCAACCATCCATCATTCCATAGATCATATAG
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATAG
*
519327 GAAATATTAACTGATACATCAACCATCCATCATTCCATTGATCATATAG
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATAG
* * * *
519376 GAAATATTAACTGATGCATCATA-CATCAATCA-TCCATCA-TTC-CATA-
1 GAAATATTAACTGATACATCA-ACCATCCATCATTCCAT-AGATCATATAG
* * * *
519422 GATCATA-TATAC--AT-CAACCATCCAT-CA---TTCTATAGATCATATAG
1 GA-AATATTA-ACTGATAC-ATCAACCATCCATCATTCCATAGATCATATAG
519466 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATAT-G
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATAG
*
519514 GAAATATTAACTGATACATCAACCATCCATCATTCTATAGATCATATAG
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATAG
519563 GAAATATTAACTGATAC
1 GAAATATTAACTGATAC
519580 TTGTCTTCTC
Statistics
Matches: 212, Mismatches: 22, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
41 1 0.00
42 6 0.03
43 8 0.04
44 6 0.03
45 17 0.08
46 7 0.03
47 8 0.04
48 54 0.25
49 104 0.49
50 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (49 bp):
GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATAG
Found at i:519435 original size:34 final size:34
Alignment explanation
Indices: 519396--519464 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
519386 CTGATGCATC
*
519396 ATACATCAATCATCCATCATTCCATAGATCATAT
1 ATACATCAACCATCCATCATTCCATAGATCATAT
*
519430 ATACATCAACCATCCATCATTCTATAGATCATAT
1 ATACATCAACCATCCATCATTCCATAGATCATAT
519464 A
1 A
519465 GGAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (34 bp):
ATACATCAACCATCCATCATTCCATAGATCATAT
Found at i:519619 original size:97 final size:96
Alignment explanation
Indices: 519278--519579 Score: 363
Period size: 90 Copynumber: 3.2 Consensus size: 96
519268 ACTATGATGA
* * * * *
519278 GAAACATTAACCGGTACACCAACCATCCATCATTCCATAGATCATATAGGAAATATTAACTGATA
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGA-CATA-GGGAAATATTAACTGATA
* *
519343 CATCAACCATCCATCATTCCATTGATCATATAG
64 CATCAACCATCCATCATTCTATAGATCATATAG
* * **
519376 GAAATATTAACTGATGCATCATA-CATCAATCA-TCCATCATTCCATA--G--ATCA-T-A-T-A
1 GAAATATTAACTGATACATCA-ACCATCCATCATTCCAT-A-GACATAGGGAAAT-ATTAACTGA
519431 TACATCAACCATCCATCATTCTATAGATCATATAG
62 TACATCAACCATCCATCATTCTATAGATCATATAG
*
519466 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGATCATATGGAAATATTAACTGATAC
1 GAAATATTAACTGATACATCAACCATCCATCATTCCATAGA-CATAGGGAAATATTAACTGATAC
519531 ATCAACCATCCATCATTCTATAGATCATATAG
65 ATCAACCATCCATCATTCTATAGATCATATAG
519563 GAAATATTAACTGATAC
1 GAAATATTAACTGATAC
519580 TTGTCTTCTC
Statistics
Matches: 175, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
89 1 0.01
90 67 0.38
91 6 0.03
92 2 0.01
93 4 0.02
94 4 0.02
95 2 0.01
96 1 0.01
97 58 0.33
98 29 0.17
99 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (96 bp):
GAAATATTAACTGATACATCAACCATCCATCATTCCATAGACATAGGGAAATATTAACTGATACA
TCAACCATCCATCATTCTATAGATCATATAG
Found at i:520255 original size:2 final size:2
Alignment explanation
Indices: 520248--520277 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
520238 AATAAAAATA
520248 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
520278 TTGTATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:520635 original size:17 final size:15
Alignment explanation
Indices: 520604--520641 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
520594 ATAATTAAAT
520604 TAATATATTTTATAA
1 TAATATATTTTATAA
520619 TAATATA-TTTATAA
1 TAATATATTTTATAA
520633 TAATA-ATTT
1 TAATATATTT
520642 ACTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 14 0.64
15 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATATTTTATAA
Found at i:522827 original size:21 final size:21
Alignment explanation
Indices: 522789--522838 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
522779 CAATGAATTA
*
522789 TCACGTCAACATCGTAAACTG
1 TCACGTCAACATCATAAACTG
*
522810 TCACGTCAACA-CTATAAATTG
1 TCACGTCAACATC-ATAAACTG
*
522831 TTACGTCA
1 TCACGTCA
522839 GTATCATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (21 bp):
TCACGTCAACATCATAAACTG
Found at i:526371 original size:27 final size:27
Alignment explanation
Indices: 526341--526396 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
526331 ATATTGGTGT
*
526341 TATTTTTAAACTCTTAAGTTACATTAA
1 TATTTTTAAACCCTTAAGTTACATTAA
526368 TATTTTTAAACCCTTAAGTTACATTAA
1 TATTTTTAAACCCTTAAGTTACATTAA
526395 TA
1 TA
526397 ATGACGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (27 bp):
TATTTTTAAACCCTTAAGTTACATTAA
Found at i:529712 original size:2 final size:2
Alignment explanation
Indices: 529707--529735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
529697 TCACAAAACA
529707 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 A
529736 ATGAAAAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:540634 original size:17 final size:18
Alignment explanation
Indices: 540607--540645 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
540597 TTACATCACT
540607 AAATAATTT-AAAATTACA
1 AAATAATTTAAAAATTA-A
540625 AAAT-ATTTAAAAATTAA
1 AAATAATTTAAAAATTAA
540642 AAAT
1 AAAT
540646 TGCATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATTTAAAAATTAA
Found at i:545957 original size:38 final size:38
Alignment explanation
Indices: 545885--545976 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 38
545875 TTAATTTTTT
* *
545885 ATTTATAA-TTCTCAAATTATTTCACTTTAAATTTTAA
1 ATTTATAATTTCTTAAATTATTTCACTATAAATTTTAA
545922 ATTTATAATTTCTTAAATT-TTATCAC-ATAACATTTTAA
1 ATTTATAATTTCTTAAATTATT-TCACTATAA-ATTTTAA
545960 ATTCT-TAATTTCTTAAA
1 ATT-TATAATTTCTTAAA
545977 AAAATTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
37 13 0.27
38 35 0.71
39 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTTATAATTTCTTAAATTATTTCACTATAAATTTTAA
Found at i:548041 original size:24 final size:24
Alignment explanation
Indices: 548014--548075 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
548004 GACGGGGCAA
548014 GGTTTGGGTATAATATTTCGGGTC
1 GGTTTGGGTATAATATTTCGGGTC
548038 GGTTTGGGTATAATATTTCGGGTC
1 GGTTTGGGTATAATATTTCGGGTC
548062 GGTTTGGGTATAAT
1 GGTTTGGGTATAAT
548076 TAAATATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.06, G:0.34, T:0.42
Consensus pattern (24 bp):
GGTTTGGGTATAATATTTCGGGTC
Found at i:552253 original size:22 final size:22
Alignment explanation
Indices: 552195--552256 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
552185 CTCTTAATGA
* *
552195 AACCGTTCAACGTTAAATGCTG
1 AACCGTTCAACATTCAATGCTG
*
552217 AACCGTTCAGCATTCAATGCTG
1 AACCGTTCAACATTCAATGCTG
552239 AACCGTTCAACATTCAAT
1 AACCGTTCAACATTCAAT
552257 ACGTTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (22 bp):
AACCGTTCAACATTCAATGCTG
Found at i:560286 original size:24 final size:24
Alignment explanation
Indices: 560242--560287 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
560232 TCGTCAAAGA
* *
560242 TCGAATACAAGGATCATAAACATC
1 TCGAATACAAGAATCAGAAACATC
560266 TCGAA-ACAAGAATCAAGAAACA
1 TCGAATACAAGAATC-AGAAACA
560288 AGGGGAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (24 bp):
TCGAATACAAGAATCAGAAACATC
Found at i:561305 original size:6 final size:6
Alignment explanation
Indices: 561272--561316 Score: 54
Period size: 6 Copynumber: 6.8 Consensus size: 6
561262 GAGTGAAGAT
561272 AAATTA AAATTTTA AAATTTA GAAATTA AAATTA AAATTA AAATT
1 AAATTA AAA--TTA AAA-TTA -AAATTA AAATTA AAATTA AAATT
561317 TTCAAAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 20 0.56
7 7 0.19
8 9 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (6 bp):
AAATTA
Found at i:561427 original size:31 final size:33
Alignment explanation
Indices: 561378--561456 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 33
561368 ATAATTATAC
*
561378 TTTTTAAAATTTAAAGA-GG-CTTAA-TAAGAA
1 TTTTTAAAAATTAAAGAGGGACTTAATTAAGAA
*
561408 TTTTTAAAAATTATGAGAGGGACTTAATTAAGAA
1 TTTTTAAAAATTA-AAGAGGGACTTAATTAAGAA
**
561442 TATTAAAAAAATTAA
1 T-TTTTAAAAATTAA
561457 TATAAATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 12 0.31
31 3 0.08
32 2 0.05
33 5 0.13
34 7 0.18
35 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (33 bp):
TTTTTAAAAATTAAAGAGGGACTTAATTAAGAA
Found at i:563129 original size:3 final size:3
Alignment explanation
Indices: 563121--563150 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
563111 TCCTGCGTCT
*
563121 CCG CCG CCG CCG CCG CCG CCG CCA CCG CCG
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG
563151 GGCATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.67, G:0.30, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:573919 original size:29 final size:29
Alignment explanation
Indices: 573865--573922 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
573855 GTGTTGGCCG
*
573865 TAGGTCGCCATGCCTTCCGGGTGACCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
*
573894 TAGGTCGCCATGTCTTCTC-GGCGACCTAC
1 TAGGTCGCCATGCCTTC-CGGGCGACCTAC
573923 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTAC
Found at i:573984 original size:14 final size:14
Alignment explanation
Indices: 573965--573997 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
573955 CGCTGGGCAT
573965 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
573979 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
573993 ACGAG
1 CCGAG
573998 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:574031 original size:33 final size:33
Alignment explanation
Indices: 573979--574063 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
573969 GGCCATCCGA
* * * *
573979 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
574012 CCGAGGGCAACCGTGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
574045 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
574064 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.28, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:574105 original size:23 final size:23
Alignment explanation
Indices: 574070--574125 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
574060 CGAGGGTAGG
*
574070 TCGCCCGGATTCCCTCGCATAGC
1 TCGCTCGGATTCCCTCGCATAGC
*
574093 TCGCTCGGTTTCCCTCGCATAGC
1 TCGCTCGGATTCCCTCGCATAGC
*
574116 TCGTTCGGAT
1 TCGCTCGGAT
574126 GGCCTCGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.38, G:0.23, T:0.29
Consensus pattern (23 bp):
TCGCTCGGATTCCCTCGCATAGC
Found at i:574131 original size:23 final size:23
Alignment explanation
Indices: 574070--574132 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
574060 CGAGGGTAGG
* *
574070 TCGCCCGGATTCCCTCGCATAGC
1 TCGCTCGGATGCCCTCGCATAGC
* *
574093 TCGCTCGGTTTCCCTCGCATAGC
1 TCGCTCGGATGCCCTCGCATAGC
* *
574116 TCGTTCGGATGGCCTCG
1 TCGCTCGGATGCCCTCG
574133 GTCGGATGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.10, C:0.38, G:0.25, T:0.27
Consensus pattern (23 bp):
TCGCTCGGATGCCCTCGCATAGC
Found at i:574137 original size:14 final size:14
Alignment explanation
Indices: 574115--574145 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
574105 CCTCGCATAG
*
574115 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
574129 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
574143 CTC
1 CTC
574146 AGATGCCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.32, G:0.35, T:0.26
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:580027 original size:17 final size:19
Alignment explanation
Indices: 580005--580046 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
579995 AAAATATAAT
580005 AATAATAG-AAAAAAATA-
1 AATAATAGTAAAAAAATAC
*
580022 AATAAT-GTAAATAAATAC
1 AATAATAGTAAAAAAATAC
580040 AATAATA
1 AATAATA
580047 AAGAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAGTAAAAAAATAC
Found at i:580330 original size:198 final size:194
Alignment explanation
Indices: 580024--580420 Score: 629
Period size: 200 Copynumber: 2.0 Consensus size: 194
580014 AAAAAATAAA
580024 TAATGTAAATAAATACAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATA-AATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
* * *
580089 TATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAA-TGTATA
65 TATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAAGTGTAAA
** *
580153 AAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
130 AAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
580218 TAATGTAAATAAAT-AATAATAAAGAAGTAAACAAATAGGGT-AAATACAAAATGTGTACATATA
1 TAATGTAAATAAATAAATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTGTAC-----
*
580281 TATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATACGAAT
60 -ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAA-
580346 GTGTAAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAA
123 GTGTAAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAA
580411 TTAAAAC
188 TTAAAAC
580418 TAA
1 TAA
580421 AATCCCGAGA
Statistics
Matches: 187, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
192 34 0.18
193 9 0.05
194 14 0.07
198 60 0.32
200 70 0.37
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (194 bp):
TAATGTAAATAAATAAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATAT
ATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAAGTGTAAAA
AAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
Found at i:581401 original size:3 final size:3
Alignment explanation
Indices: 581393--581421 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
581383 GTAAAGAGAA
581393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
581422 CAAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:582080 original size:105 final size:105
Alignment explanation
Indices: 581880--582755 Score: 1487
Period size: 105 Copynumber: 8.4 Consensus size: 105
581870 AAATTGTTCC
* ** * *
581880 GAGTCCAATATCCTCCGCCGTGAAGTCGAAATTGGCTCTGAAATTGAG--ATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
581943 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* * *
581983 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
582048 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
582088 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
582153 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* * * *
582193 GAGTCAAATATCCTTCGTCGTGAAGTTG-AATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
582257 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
582297 GAGTCAAATATCCTTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
1 GAGTCCAATATCC-TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
582361 CCAGCGGTCCCTTCGTCGTGAAGTTG-ACTTACGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
582401 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
582466 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
582506 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG-TTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
582570 CAGCGGTCCCTTCGTCGTGAAGTTG-ACTTACGTTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACG-TTGTCTG
* *
582610 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
582675 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
582715 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
582756 GTAAAACCTG
Statistics
Matches: 740, Mismatches: 24, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
103 55 0.07
104 288 0.39
105 390 0.53
106 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:582309 original size:209 final size:209
Alignment explanation
Indices: 581880--582755 Score: 1467
Period size: 209 Copynumber: 4.2 Consensus size: 209
581870 AAATTGTTCC
* ** * *
581880 GAGTCCAATATCCTCCGCCGTGAAGTCGAAATTGGCTCTGAAATTGAG--ATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
581943 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-CTGTGAA
66 CAGCGGTCCCTTCGTCGTGAAGTTG-ACTTACGTTGTCTGGAGTCCAATATCCTTCGTC-GTGAA
* *
582007 GTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
582072 GAACTTGCGTTGTCTG
194 GAACTTACGTTGTCTG
* *
582088 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
582153 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAAATATCCTTCGTCGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTG-ACTTACGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAG
* *
582218 TTG-AATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
582282 AACTTGCGTTGTCTG
195 AACTTACGTTGTCTG
*
582297 GAGTCAAATATCCTTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
1 GAGTCCAATATCC-TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
*
582361 CCAGCGGTCCCTTCGTCGTGAAGTTGACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGACTTACGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAG
582426 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
582491 AACTTACGTTGTCTG
195 AACTTACGTTGTCTG
582506 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG-TTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
582570 CAGCGGTCCCTTCGTCGTGAAGTTGACTTACGTTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGACTTACG-TTGTCTGGAGTCCAATATCCTTCGTCGTGAAG
* *
582635 TTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
582700 AACTTACGTTGTCTG
195 AACTTACGTTGTCTG
582715 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
582756 GTAAAACCTG
Statistics
Matches: 636, Mismatches: 25, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
208 129 0.20
209 425 0.67
210 81 0.13
211 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (209 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGACTTACGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTACGTTGTCTG
Found at i:583545 original size:1 final size:1
Alignment explanation
Indices: 583541--583565 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
583531 TTTTTCTCCC
583541 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
583566 CCAACTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:594240 original size:17 final size:19
Alignment explanation
Indices: 594218--594259 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
594208 AAAATATAAT
594218 AATAATAG-AAAAAAATA-
1 AATAATAGTAAAAAAATAC
*
594235 AATAAT-GTAAATAAATAC
1 AATAATAGTAAAAAAATAC
594253 AATAATA
1 AATAATA
594260 AAGAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAGTAAAAAAATAC
Found at i:594606 original size:188 final size:182
Alignment explanation
Indices: 594237--594614 Score: 557
Period size: 188 Copynumber: 2.0 Consensus size: 182
594227 AAAAAATAAA
594237 TAATGTAAATAAATACAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAAT--AATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
594302 TATATATAATATAACATATAAATGAAATAATATACTAATAATAAATGTATACGAATGTATAAAAA
64 TATATATAATATAACATATAAATGAAATAATATACTAATAAT-AA-GTATACGAATGTATAAAAA
* *
594367 CTAATAATAGTATAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
127 C-AAAAATAATATAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
594424 TAATGTAAATAAAT-ATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATATAT
1 TAATGTAAATAAATAATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTG--------T
* *
594488 ACATATATATATATAATATAACATATAAGTGAAATAATAATACTAATAAT-A-TATACGAATGTG
57 ACATATATATATATAATATAACATATAAATGAAATAAT-ATACTAATAATAAGTATACGAATGTA
594551 TAAAAA-AAAAATAATATAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
121 TAAAAACAAAAATAATATAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
594612 TAA
1 TAA
594615 AATCCCGAGA
Statistics
Matches: 177, Mismatches: 4, Indels: 19
0.88 0.02 0.09
Matches are distributed among these distances:
184 16 0.09
185 24 0.14
187 14 0.08
188 56 0.32
190 17 0.10
192 1 0.01
193 38 0.21
194 11 0.06
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (182 bp):
TAATGTAAATAAATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATATA
TATATAATATAACATATAAATGAAATAATATACTAATAATAAGTATACGAATGTATAAAAACAAA
AATAATATAAATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
Found at i:595594 original size:3 final size:3
Alignment explanation
Indices: 595586--595617 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
595576 GTAAAGAGAA
595586 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
595618 CAAATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:597831 original size:3 final size:3
Alignment explanation
Indices: 597823--597849 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
597813 AATAATCTTA
597823 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
597850 AAACTACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:608064 original size:28 final size:32
Alignment explanation
Indices: 608032--608100 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 32
608022 AAATTAAATC
*
608032 AATTAAAAT-AATTATTATT-T-TTAAAA-AA
1 AATTAAAATAAATTATAATTCTATTAAAAGAA
*
608060 AATTATAATTAAATTATAATTCTATTAAAAGTAA
1 AATTA-AAATAAATTATAATTCTATTAAAAG-AA
608094 AATTAAA
1 AATTAAA
608101 TTTTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 5 0.15
29 3 0.09
30 9 0.27
31 1 0.03
32 6 0.18
33 2 0.06
34 7 0.21
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
AATTAAAATAAATTATAATTCTATTAAAAGAA
Found at i:608437 original size:35 final size:34
Alignment explanation
Indices: 608378--608489 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
608368 AAAACATTCC
* *
608378 TCAATTTCATTATAAATCCCAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTTCAAAATAAT
*
608413 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTTCAAAATAAT
* *
608448 TCAATTACATTCTAAACCCCAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTTC-AAAATAAT
608483 TCAATTT
1 TCAATTT
608490 AAGGAGAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 5 0.07
35 59 0.88
36 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTTCAAAATAAT
Found at i:609519 original size:34 final size:34
Alignment explanation
Indices: 609444--609555 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
609434 AAAAAAGACA
* *
609444 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
609479 GTAATTGAATTATTTTGGAATTTAGGG-TTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
609513 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
609548 GAAATTGA
1 GAAATTGA
609556 GAATTGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 1 0.01
34 30 0.43
35 35 0.51
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:615962 original size:2 final size:2
Alignment explanation
Indices: 615955--615979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
615945 AAAACTGAAC
615955 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 A
615980 ATCATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:616497 original size:27 final size:25
Alignment explanation
Indices: 616447--616497 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
616437 CAATTAGATC
*
616447 CGACCCGAAAATTATACTCTCCACT
1 CGACCCGAAAATTATACCCTCCACT
*
616472 CGACTCGAAAATTATATACCCTCCAC
1 CGACCCGAAAA-T-TATACCCTCCAC
616498 CTAACCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.33, C:0.35, G:0.08, T:0.24
Consensus pattern (25 bp):
CGACCCGAAAATTATACCCTCCACT
Found at i:617090 original size:15 final size:15
Alignment explanation
Indices: 617070--617100 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
617060 ACATATACAT
617070 TTGTCATTTAGGAAC
1 TTGTCATTTAGGAAC
617085 TTGTCATTTAGGAAC
1 TTGTCATTTAGGAAC
617100 T
1 T
617101 GTATAGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TTGTCATTTAGGAAC
Found at i:623734 original size:2 final size:2
Alignment explanation
Indices: 623727--623755 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
623717 AATGCAATGA
623727 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 A
623756 CAAGACAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:625308 original size:32 final size:32
Alignment explanation
Indices: 625267--625347 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
625257 CATGACCGAG
625267 GGACTAAAATCGAACGGGAGTTAACGGTTAAA
1 GGACTAAAATCGAACGGGAGTTAACGGTTAAA
* *
625299 GGACTAAAATCGAACGAGAGTTAACGGTTAAG
1 GGACTAAAATCGAACGGGAGTTAACGGTTAAA
*
625331 GGACTAAAATCAAACGG
1 GGACTAAAATCGAACGG
625348 ATCGATATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (32 bp):
GGACTAAAATCGAACGGGAGTTAACGGTTAAA
Found at i:630552 original size:2 final size:2
Alignment explanation
Indices: 630545--630585 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
630535 TCAAATATGA
630545 AT AT AT AT 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 AT AT AT AT A
630586 GTCATAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:630673 original size:16 final size:16
Alignment explanation
Indices: 630652--630683 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
630642 ATTATTAGGT
630652 GTTTTGGTCTATTTTA
1 GTTTTGGTCTATTTTA
630668 GTTTTGGTCTATTTTA
1 GTTTTGGTCTATTTTA
630684 ATACATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.19, T:0.62
Consensus pattern (16 bp):
GTTTTGGTCTATTTTA
Found at i:635904 original size:212 final size:212
Alignment explanation
Indices: 635577--635979 Score: 594
Period size: 212 Copynumber: 1.9 Consensus size: 212
635567 TGTAATTGTT
* *
635577 TAGGCTGGTTCGTTTTTCGGTTTGATGAATTCAATTTGCATACACATAATCTTAATCCAGGCATT
1 TAGGCTGGTTCATTTTTCGGTTCGATGAATTCAATTTGCATACACATAATCTT-ATCCAGGCATT
* * * *
635642 GCTTGTATGCCTTGTAAGAATGAAATTAGGCAAATGCAGGCCCTTGAACCATAGTGATAAGCTTA
65 GCTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCA
** *
635707 TGTAAC-TCTAGCATTGGTTTTGATTTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTA
130 TGTAACTTC-AGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTA
635771 TGCGTTGATTTTCTGTGTG
194 TGCGTTGATTTTCTGTGTG
* * *
635790 TAGGTTGGTTCATTTTTCGGTTCGATGAATTCGATTTGCATACACATATTTCTT-TCCAGGCATT
1 TAGGCTGGTTCATTTTTCGGTTCGATGAATTCAATTTGCATACACATA-ATCTTATCCAGGCATT
* * * * * *
635854 GCTTGTATGCCTTGTATGCATGAAGTTGGGAAAATGTAGGCCATTGAACCATAATGCTAAGCTCA
65 GCTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCA
*
635919 TGTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCGTGTCGGTT
130 TGTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTT
635980 AAGCGCTGAT
Statistics
Matches: 169, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
212 119 0.70
213 46 0.27
214 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (212 bp):
TAGGCTGGTTCATTTTTCGGTTCGATGAATTCAATTTGCATACACATAATCTTATCCAGGCATTG
CTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCAT
GTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTATG
CGTTGATTTTCTGTGTG
Found at i:645588 original size:27 final size:27
Alignment explanation
Indices: 645550--645612 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
645540 TCGCGAACCG
645550 GAGTCGAATCTCTCAGCAGAGGGATAT
1 GAGTCGAATCTCTCAGCAGAGGGATAT
*
645577 GAGTCGAATCTCTCAGGAGAGGGATAT
1 GAGTCGAATCTCTCAGCAGAGGGATAT
*
645604 GAGCCGAAT
1 GAGTCGAAT
645613 GATCAACTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (27 bp):
GAGTCGAATCTCTCAGCAGAGGGATAT
Found at i:648869 original size:114 final size:114
Alignment explanation
Indices: 648542--649243 Score: 1064
Period size: 114 Copynumber: 6.0 Consensus size: 114
648532 AGCTGTGGGA
648542 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
648607 ATAGGAAAACCATAATCAAGCTTCATT-TTTTCAAATAAAACAATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
648655 ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
648720 ATAGGATTATAGGAAAACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTG
66 --------ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
648777 ACCACGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
648842 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
648891 ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
648956 ATAGGATTATAGGAAAACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACCACG
66 --------ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTT------G
649019 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
649084 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
649133 ACCATGCTATTCAGAGGCAAGAATGATTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* * * *
649198 ATAAGAAAACAATAATCAAGCTTCATTTTTTTTCATATAAAACAAT
66 ATAGGAAAACCATAACCAAGCTTCA-TTCTTTTCATATAAAACAAT
649244 CTCTCGAACA
Statistics
Matches: 544, Mismatches: 21, Indels: 46
0.89 0.03 0.08
Matches are distributed among these distances:
113 64 0.12
114 197 0.36
115 19 0.03
120 46 0.08
121 25 0.05
122 128 0.24
128 65 0.12
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (114 bp):
ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
Found at i:649169 original size:242 final size:239
Alignment explanation
Indices: 648542--649200 Score: 1227
Period size: 242 Copynumber: 2.8 Consensus size: 239
648532 AGCTGTGGGA
648542 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
648607 ATAGGAAAACCATAATCAAGCTTCATT-TTTTCAAATAAAACAATTTTGACCATGCTATTCAGAG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGAG
648671 GCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAA
131 GCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAA
648736 ACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACC
196 ACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACC
648780 A-C--GCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
648842 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGAG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGAG
648907 GCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAA
131 GCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAA
648972 ACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACCAC
196 ACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGA-C-C
649018 GACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAA
1 -ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAA
649083 CATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGA
65 CATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGA
* *
649148 GGCAAGAATGATTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATA
130 GGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATA
649201 AGAAAACAAT
Statistics
Matches: 410, Mismatches: 4, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
235 86 0.21
236 143 0.35
237 2 0.00
238 2 0.00
239 1 0.00
240 1 0.00
242 175 0.43
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (239 bp):
ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCATGCTATTCAGAG
GCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAA
ACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACC
Found at i:649501 original size:33 final size:30
Alignment explanation
Indices: 649464--649529 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
649454 TGACCTAGTA
*
649464 GGAGCATAAGAGAGGCGGCGGGACTGGAGGCGG
1 GGAGCAGAAGA-AGGCGG-GGGAC-GGAGGCGG
* *
649497 GGAGCAGAGGAAGTCGGGGGACGGAGGCGG
1 GGAGCAGAAGAAGGCGGGGGACGGAGGCGG
649527 GGA
1 GGA
649530 AGCGGCGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 11 0.37
31 5 0.17
32 5 0.17
33 9 0.30
ACGTcount: A:0.24, C:0.14, G:0.58, T:0.05
Consensus pattern (30 bp):
GGAGCAGAAGAAGGCGGGGGACGGAGGCGG
Found at i:649976 original size:12 final size:12
Alignment explanation
Indices: 649961--649985 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
649951 ACGGAGCTAC
649961 TTAAGGAGTGGG
1 TTAAGGAGTGGG
649973 TTAAGGAGTGGG
1 TTAAGGAGTGGG
649985 T
1 T
649986 GGGGTTCTTG
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:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (12 bp):
TTAAGGAGTGGG
Found at i:650317 original size:54 final size:52
Alignment explanation
Indices: 650254--650361 Score: 144
Period size: 52 Copynumber: 2.0 Consensus size: 52
650244 CACTCAGCCA
* ***
650254 TACACACAATCTTGTTTACATATTTGTGGGAGATTATTGACTAATCCCATTAAT
1 TACACACAATCTCGTTTAC--ATTTGCCAGAGATTATTGACTAATCCCATTAAT
* *
650308 TACACACAATCTCGTTTACATTTGCCATAGATTATTGACTAATCTCATTAAT
1 TACACACAATCTCGTTTACATTTGCCAGAGATTATTGACTAATCCCATTAAT
650360 TA
1 TA
650362 ATTTGCAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 30 0.62
54 18 0.38
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (52 bp):
TACACACAATCTCGTTTACATTTGCCAGAGATTATTGACTAATCCCATTAAT
Found at i:653230 original size:21 final size:22
Alignment explanation
Indices: 653192--653234 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
653182 AATGTCAGAG
*
653192 GGGAACTGATTCCCCTGCTACA
1 GGGAACTGATTACCCTGCTACA
653214 GGGAACTGA-TACCCTGCTACA
1 GGGAACTGATTACCCTGCTACA
653235 TTACTGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (22 bp):
GGGAACTGATTACCCTGCTACA
Found at i:653983 original size:31 final size:31
Alignment explanation
Indices: 653945--654038 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
653935 CCTGAAGGAC
* * *
653945 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
653976 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
654007 CAATCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
654038 C
1 C
654039 CCTCGACCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:657299 original size:35 final size:35
Alignment explanation
Indices: 657260--657341 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
657250 CTTTAAACCT
*
657260 TAAACCCTAAA-TCTTAAAACCTAAATAATAGATCC
1 TAAACCCTAAACTC-TAAAACATAAATAATAGATCC
* * * *
657295 TAAACCCTAGACTCTAAGACATGAATAATATATCC
1 TAAACCCTAAACTCTAAAACATAAATAATAGATCC
657330 TAAACCCTAAAC
1 TAAACCCTAAAC
657342 CTCGAATATC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 38 0.95
36 2 0.05
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (35 bp):
TAAACCCTAAACTCTAAAACATAAATAATAGATCC
Found at i:658240 original size:25 final size:24
Alignment explanation
Indices: 658188--658259 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
658178 AAGAGATCAA
* *
658188 ATTTTCATAAAATAAT-ATAAATT
1 ATTTTCATAAAATAATAAAAAAAT
658211 ATTTTCATAAAATAATAAAAAAAT
1 ATTTTCATAAAATAATAAAAAAAT
* *
658235 AGTTTTTAGAAAAT-ATAAATAAAAT
1 A-TTTTCATAAAATAATAAA-AAAAT
658260 TAAAGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.38
24 11 0.26
25 15 0.36
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTTTCATAAAATAATAAAAAAAT
Found at i:660887 original size:2 final size:2
Alignment explanation
Indices: 660880--660932 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
660870 AAAATACATC
660880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
660922 TA TA TA TA TA T
1 TA TA TA TA TA T
660933 TATTATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:661915 original size:26 final size:26
Alignment explanation
Indices: 661861--661915 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
661851 TTGTGTTGGT
* *
661861 TTTAGGGTGATTTCACCTTACTCGGA
1 TTTAGGGTGATTTCACCTAACTCGAA
*
661887 TTTAGGGTGATTTCATCTAA-TCCGAA
1 TTTAGGGTGATTTCACCTAACT-CGAA
661913 TTT
1 TTT
661916 GATCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (26 bp):
TTTAGGGTGATTTCACCTAACTCGAA
Found at i:671800 original size:49 final size:49
Alignment explanation
Indices: 671707--671800 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
671697 TATGTAAAAC
* * ** *
671707 AGGGGCGGACCTCCATGGTGCCCGGTGTATCCCGGGCAATCCCTCATCT
1 AGGGGCGGACCTCCATGGTACCCGGGGTATCCCAAGCAACCCCTCATCT
671756 AGGGGCGGACCTCCATGGTACCCGGGGTATCCCAAGCAACCCCTC
1 AGGGGCGGACCTCCATGGTACCCGGGGTATCCCAAGCAACCCCTC
671801 CACAAGTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (49 bp):
AGGGGCGGACCTCCATGGTACCCGGGGTATCCCAAGCAACCCCTCATCT
Found at i:673783 original size:60 final size:60
Alignment explanation
Indices: 673647--673785 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
673637 ATAGTCAGGT
* * * *
673647 GACCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGCAACATCCTATGGTCGAAG
1 GACCATTTTGTAACTTTTAATAGTTCAGGAACTAAACAAAGCAACATCCTATAGTCGAAG
* * * * *
673707 GACCATTTTATAACTTTTAATA-TTCATGGAACTAAATAAAGCAATATCCTATAGTTGGAG
1 GACCATTTTGTAACTTTTAATAGTTCA-GGAACTAAACAAAGCAACATCCTATAGTCGAAG
673767 GACCATTTGTGT-ACTTTTA
1 GACCATTT-TGTAACTTTTA
673786 CCCTTTTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.04
60 62 0.93
61 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTTCAGGAACTAAACAAAGCAACATCCTATAGTCGAAG
Found at i:674676 original size:28 final size:29
Alignment explanation
Indices: 674645--674702 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
674635 AAAATTGAAT
* * *
674645 ACTTTAGATACCTGTTTTG-ATCAAAAAC
1 ACTTTAGACACCTATTTTGAATAAAAAAC
*
674673 ACTTTAGGCACCTATTTTGAATAAAAAAC
1 ACTTTAGACACCTATTTTGAATAAAAAAC
674702 A
1 A
674703 AGTTTAGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (29 bp):
ACTTTAGACACCTATTTTGAATAAAAAAC
Found at i:677033 original size:25 final size:25
Alignment explanation
Indices: 677000--677054 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
676990 AAGGGTTGAG
* * *
677000 TGATACCGTATTTGAATTTGGTGTA
1 TGATGCCGTATTCGAACTTGGTGTA
677025 TGATGCCGTATTCGAACTTGGTGTA
1 TGATGCCGTATTCGAACTTGGTGTA
677050 TGATG
1 TGATG
677055 TCTATAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (25 bp):
TGATGCCGTATTCGAACTTGGTGTA
Found at i:679379 original size:14 final size:14
Alignment explanation
Indices: 679360--679390 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
679350 CGGGTCAAGT
679360 TATAAAGAGCTCGA
1 TATAAAGAGCTCGA
*
679374 TATAAAGAGTTCGA
1 TATAAAGAGCTCGA
679388 TAT
1 TAT
679391 CCCATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (14 bp):
TATAAAGAGCTCGA
Found at i:680467 original size:37 final size:37
Alignment explanation
Indices: 680417--680490 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
680407 AGGCAACAAG
680417 TATTCATCAAAGATAAAAAATAAGCCCCGAATTCGGC
1 TATTCATCAAAGATAAAAAATAAGCCCCGAATTCGGC
680454 TATTCATCAAAGATAAAAAATAAGCCCCGAATTCGGC
1 TATTCATCAAAGATAAAAAATAAGCCCCGAATTCGGC
680491 CACCCGCCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (37 bp):
TATTCATCAAAGATAAAAAATAAGCCCCGAATTCGGC
Found at i:681974 original size:31 final size:30
Alignment explanation
Indices: 681932--681998 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
681922 AAGATTCGTC
* *
681932 TAGTCCCTGATTTTAGCTACGT-TTCCCATAT
1 TAGTCCATGATTTTAGCTA--TATCCCCATAT
*
681963 TAGTCCATGATTTTGGCTATATCCCCATAT
1 TAGTCCATGATTTTAGCTATATCCCCATAT
681993 TAGTCC
1 TAGTCC
681999 CTGAGTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 14 0.44
31 17 0.53
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (30 bp):
TAGTCCATGATTTTAGCTATATCCCCATAT
Found at i:687041 original size:13 final size:13
Alignment explanation
Indices: 687023--687055 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
687013 TTGACGGACT
*
687023 CGACCCGTTTACC
1 CGACCCGGTTACC
687036 CGACCCGGTTACC
1 CGACCCGGTTACC
687049 CGACCCG
1 CGACCCG
687056 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
CGACCCGGTTACC
Found at i:687056 original size:18 final size:18
Alignment explanation
Indices: 686998--687071 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 18
686988 ACCGGTCACA
*
686998 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCGTTG
* * *
687016 A-CGGACTCGACCCGTTT
1 ACCCGACCCGACCCGTTG
687033 ACCCGACCCG----GTT-
1 ACCCGACCCGACCCGTTG
687046 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
687064 ACCCGACC
1 ACCCGACC
687072 TGTTGACCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.23
14 3 0.07
17 16 0.36
18 15 0.34
ACGTcount: A:0.19, C:0.47, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:687066 original size:13 final size:13
Alignment explanation
Indices: 687050--687079 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
687040 CCGGTTACCC
687050 GACCCGACCCGTT
1 GACCCGACCCGTT
*
687063 GACCCGACCTGTT
1 GACCCGACCCGTT
687076 GACC
1 GACC
687080 ATTGACTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:689545 original size:24 final size:24
Alignment explanation
Indices: 689480--689561 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
689470 AATTATGTTA
*
689480 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
689504 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* * *
689527 TGATACATGACCTGAATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
689551 TGATACTTGAC
1 TGATACTTGAC
689562 TTGATATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:691784 original size:13 final size:13
Alignment explanation
Indices: 691766--691798 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
691756 TTGACGGACT
*
691766 CGACCCGTTTACC
1 CGACCCGGTTACC
691779 CGACCCGGTTACC
1 CGACCCGGTTACC
691792 CGACCCG
1 CGACCCG
691799 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
CGACCCGGTTACC
Found at i:691799 original size:18 final size:18
Alignment explanation
Indices: 691741--691814 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 18
691731 ACCGGTCACA
*
691741 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCGTTG
* * *
691759 A-CGGACTCGACCCGTTT
1 ACCCGACCCGACCCGTTG
691776 ACCCGACCCG----GTT-
1 ACCCGACCCGACCCGTTG
691789 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
691807 ACCCGACC
1 ACCCGACC
691815 TGTTGACCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.23
14 3 0.07
17 16 0.36
18 15 0.34
ACGTcount: A:0.19, C:0.47, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:691809 original size:13 final size:13
Alignment explanation
Indices: 691793--691822 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
691783 CCGGTTACCC
691793 GACCCGACCCGTT
1 GACCCGACCCGTT
*
691806 GACCCGACCTGTT
1 GACCCGACCCGTT
691819 GACC
1 GACC
691823 ATTGACTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:694288 original size:24 final size:24
Alignment explanation
Indices: 694223--694304 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
694213 AATTATGTTA
*
694223 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
694247 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* * *
694270 TGATACATGACCTGAATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
694294 TGATACTTGAC
1 TGATACTTGAC
694305 TTGATATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:709740 original size:23 final size:23
Alignment explanation
Indices: 709698--709762 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
709688 CGAGAGTCTC
* * *
709698 CGAGGCCATCCGACCAAGCTATG
1 CGAGGGCATCCGAGCGAGCTATG
709721 CGAGGGCAGT-CGAGCGAGCTATG
1 CGAGGGCA-TCCGAGCGAGCTATG
709744 CGAGGGCATCCGAGCGAGC
1 CGAGGGCATCCGAGCGAGC
709763 GAGCAAGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.37, T:0.11
Consensus pattern (23 bp):
CGAGGGCATCCGAGCGAGCTATG
Found at i:709819 original size:29 final size:29
Alignment explanation
Indices: 709773--709828 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
709763 GAGCAAGGGT
* *
709773 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCACCCGGAGGGCATGGCGACCTACA
*
709802 AGGTCACCCGGAGGGCATGGTGACCTA
1 AGGTCACCCGGAGGGCATGGCGACCTA
709829 TGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.14
Consensus pattern (29 bp):
AGGTCACCCGGAGGGCATGGCGACCTACA
Found at i:710671 original size:18 final size:19
Alignment explanation
Indices: 710636--710671 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
710626 ATATGAGGGT
710636 TTTCAAAGTTTTGATGCTA
1 TTTCAAAGTTTTGATGCTA
*
710655 TTTCAAATTTTTG-TGCT
1 TTTCAAAGTTTTGATGCT
710672 TTTTAAATAT
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:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (19 bp):
TTTCAAAGTTTTGATGCTA
Found at i:711862 original size:27 final size:28
Alignment explanation
Indices: 711822--711881 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
711812 ACGAGTACTA
711822 AAATGAAACAAAAACTAAA-CTTAAGTAT
1 AAATGAAACAAAAA-TAAAGCTTAAGTAT
* *
711850 AAATTAAA-AAAAATAAAGTTTAAGTAT
1 AAATGAAACAAAAATAAAGCTTAAGTAT
711877 AAATG
1 AAATG
711882 TGTAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
27 17 0.61
28 7 0.25
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (28 bp):
AAATGAAACAAAAATAAAGCTTAAGTAT
Found at i:712154 original size:15 final size:16
Alignment explanation
Indices: 712127--712160 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
712117 GACAATTACA
712127 AAATATCATTTTAAAT
1 AAATATCATTTTAAAT
*
712143 AAATAT-ATTTTAATT
1 AAATATCATTTTAAAT
712158 AAA
1 AAA
712161 ATAGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATCATTTTAAAT
Found at i:712162 original size:16 final size:17
Alignment explanation
Indices: 712126--712163 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
712116 CGACAATTAC
712126 AAAATATCATTTTAAAT
1 AAAATATCATTTTAAAT
*
712143 -AAATAT-ATTTTAATT
1 AAAATATCATTTTAAAT
712158 AAAATA
1 AAAATA
712164 GATAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATATCATTTTAAAT
Found at i:712395 original size:30 final size:29
Alignment explanation
Indices: 712343--712437 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 29
712333 TTTAATTAAG
* *
712343 TACCTAAA--ATTTTTTA-TCAAAATAAA
1 TACCTAAATTATTTTTTAGTTAAAATAGA
*
712369 TACCTAAATTATCTTTTTAGTTAAAATAGG
1 TACCTAAATTAT-TTTTTAGTTAAAATAGA
* *
712399 TACCTAAAGTATTTTAT-G-TAAAATAGA
1 TACCTAAATTATTTTTTAGTTAAAATAGA
712426 TA-CTAAATTATT
1 TACCTAAATTATT
712438 CAAATTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 17 0.29
27 10 0.17
28 3 0.05
29 10 0.17
30 18 0.31
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.41
Consensus pattern (29 bp):
TACCTAAATTATTTTTTAGTTAAAATAGA
Found at i:715571 original size:20 final size:21
Alignment explanation
Indices: 715535--715573 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
715525 TATTAAAGCA
*
715535 TACTAAAATTGATAATTTAGG
1 TACTAAAATTCATAATTTAGG
715556 TACTAAAA-TCATAATTTA
1 TACTAAAATTCATAATTTA
715574 TCCAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
TACTAAAATTCATAATTTAGG
Found at i:716203 original size:10 final size:10
Alignment explanation
Indices: 716188--716245 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
716178 CACTTTTTTA
716188 AAAAATAAAT
1 AAAAATAAAT
716198 AAAAATAAAAT
1 AAAAAT-AAAT
716209 AAAAATAAAT
1 AAAAATAAAT
* *
716219 TAAAATGAAT
1 AAAAATAAAT
* *
716229 AAAATTCAAT
1 AAAAATAAAT
716239 AAAAATA
1 AAAAATA
716246 TAATGTAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 30 0.75
11 10 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:716323 original size:24 final size:26
Alignment explanation
Indices: 716293--716349 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 26
716283 TATTCTTTCT
*
716293 AATATTAATTTTA-AAAAAAT-ATTA
1 AATATTAATTTTATAAAAAATGAATA
*
716317 AATATTAATTTTATTAAAAATGAATA
1 AATATTAATTTTATAAAAAATGAATA
716343 AATATTA
1 AATATTA
716350 TTAACTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 13 0.45
25 6 0.21
26 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
AATATTAATTTTATAAAAAATGAATA
Found at i:716767 original size:31 final size:29
Alignment explanation
Indices: 716732--716800 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
716722 AATATGTGAT
716732 ATTTT-TTAGTTTTACATTATATTTTTATTGA
1 ATTTTATT-GTTTTA-ATT-TATTTTTATTGA
* *
716763 ATTTTATTTTTTTAATTTATTTTTATTGC
1 ATTTTATTGTTTTAATTTATTTTTATTGA
716792 ATATTTATT
1 AT-TTTATT
716801 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.38
30 9 0.26
31 10 0.29
32 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (29 bp):
ATTTTATTGTTTTAATTTATTTTTATTGA
Found at i:716775 original size:19 final size:19
Alignment explanation
Indices: 716748--716789 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
716738 TAGTTTTACA
*
716748 TTATATTTTT-ATTGAATT
1 TTATTTTTTTAATTGAATT
* *
716766 TTATTTTTTTAATTTATTT
1 TTATTTTTTTAATTGAATT
716785 TTATT
1 TTATT
716790 GCATATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTATTTTTTTAATTGAATT
Found at i:716799 original size:17 final size:16
Alignment explanation
Indices: 716751--716801 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 16
716741 TTTTACATTA
716751 TATTTTTATTGA-ATTT
1 TATTTTTATTGATA-TT
716767 TATTTTT-TT-A-ATT
1 TATTTTTATTGATATT
716780 TATTTTTATTGCATATT
1 TATTTTTATTG-ATATT
716797 TATTT
1 TATTT
716802 ATTTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.29
14 4 0.13
15 2 0.06
16 8 0.26
17 8 0.26
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (16 bp):
TATTTTTATTGATATT
Found at i:716801 original size:30 final size:30
Alignment explanation
Indices: 716741--716807 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
716731 TATTTTTTAG
716741 TTTTACATTATATTTTTATTGAATTTTATTT
1 TTTTA-ATTATATTTTTATTGAATTTTATTT
*
716772 TTTTAATT-TATTTTTATTGCATATTTATTT
1 TTTTAATTATATTTTTATTGAAT-TTTATTT
*
716802 ATTTAA
1 TTTTAA
716808 AAAAATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 13 0.39
30 15 0.45
31 5 0.15
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTTAATTATATTTTTATTGAATTTTATTT
Found at i:730651 original size:78 final size:78
Alignment explanation
Indices: 730522--730673 Score: 216
Period size: 78 Copynumber: 1.9 Consensus size: 78
730512 TGTCGGTGGA
* * *
730522 ATCTTCGTTTTTGAGATTCTCAGACTTCACTTCTTTGGGGAACAACGTTTCAGCGATGTTGTTCA
1 ATCTTCGTTTTTGAGATACTCAGACTTCACTTCTTCGGGGAACAACATTTCAGCGATGTTGTTCA
730587 AGCCACCTTTGGG
66 AGCCACCTTTGGG
* * ** *
730600 ATCTTCAG-TTTTGAGATACTCGGACTTCACTTCTTCGGGGAACGACATTTCAGCTTTGTTTTTC
1 ATCTTC-GTTTTTGAGATACTCAGACTTCACTTCTTCGGGGAACAACATTTCAGCGATGTTGTTC
730664 AAGCCACCTT
65 AAGCCACCTT
730674 CAGGGTCCCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
78 64 0.98
79 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (78 bp):
ATCTTCGTTTTTGAGATACTCAGACTTCACTTCTTCGGGGAACAACATTTCAGCGATGTTGTTCA
AGCCACCTTTGGG
Found at i:730813 original size:84 final size:84
Alignment explanation
Indices: 730684--730849 Score: 332
Period size: 84 Copynumber: 2.0 Consensus size: 84
730674 CAGGGTCCCG
730684 ATCCGATTCAATAACTTCATCCTCAATCCCTTGCTGCACTGCATCAGGTTGTTCCGAGACTAGTT
1 ATCCGATTCAATAACTTCATCCTCAATCCCTTGCTGCACTGCATCAGGTTGTTCCGAGACTAGTT
730749 CCGAGGTTTCAGAAGCTTC
66 CCGAGGTTTCAGAAGCTTC
730768 ATCCGATTCAATAACTTCATCCTCAATCCCTTGCTGCACTGCATCAGGTTGTTCCGAGACTAGTT
1 ATCCGATTCAATAACTTCATCCTCAATCCCTTGCTGCACTGCATCAGGTTGTTCCGAGACTAGTT
730833 CCGAGGTTTCAGAAGCT
66 CCGAGGTTTCAGAAGCT
730850 GCACTCTCTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (84 bp):
ATCCGATTCAATAACTTCATCCTCAATCCCTTGCTGCACTGCATCAGGTTGTTCCGAGACTAGTT
CCGAGGTTTCAGAAGCTTC
Found at i:734227 original size:38 final size:38
Alignment explanation
Indices: 734177--734251 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
734167 GACTCCGATC
734177 TTCTTTCTCGAATAGAGAACGGAAATCGGAAATCGGAT
1 TTCTTTCTCGAATAGAGAACGGAAATCGGAAATCGGAT
734215 TTCTTTCTCGAATAGAGAACGGAAATCGGAAATCGGA
1 TTCTTTCTCGAATAGAGAACGGAAATCGGAAATCGGA
734252 AGTAACGCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (38 bp):
TTCTTTCTCGAATAGAGAACGGAAATCGGAAATCGGAT
Found at i:735439 original size:261 final size:261
Alignment explanation
Indices: 734968--735439 Score: 773
Period size: 261 Copynumber: 1.8 Consensus size: 261
734958 CATGAAACCA
*
734968 GGGAACTCACATTGAAAAAGGTGAAAGTGGCCTTGGTGTTGGTTTGGTATCATGCTGTTCATCAC
1 GGGAACTCACATTGAAAAAGGTGAAAGTGGCCTTGGTGTTGGTTTGGTATCATGCTGCTCATCAC
*
735033 TTGGTTTATCTGCTACCGGAGGTTGAGGTGTGCTGTTTCCTGACAATGTAGCACCTTGGGACTCA
66 TTGGTTTATCTGCTACAGGAGGTTGAGGTGTGCTGTTTCCTGACAATGTAGCACCTTGGGACTCA
* * *
735098 CTATCCGTCGGTGCAGTCGTCGGCGCTCTAGGAGATGGTGATGAAGGGGGCTTAAGATCAGGATA
131 CTATCCGTCAGTGCAGTCGCCGGCGCTCTAGGAGATGGTGATGAAGGGGGCTTAAGATCAGCATA
*
735163 CTTGAAAAAGTTGGAGGGCCACAATGAATGACATGGTAAGAACTGGCCATAAACGAAGAAAACCC
196 CCTGAAAAAGTTGGAGGGCCACAATGAATGACATGGTAAGAACTGGCCATAAACGAAGAAAACCC
735228 G
261 G
* *
735229 GGGAACTCACATTGCAAAAGGTGAAAGTGGTCTTGGTGTTGGTTTGGTATCATGCTGCTCATCAC
1 GGGAACTCACATTGAAAAAGGTGAAAGTGGCCTTGGTGTTGGTTTGGTATCATGCTGCTCATCAC
* **
735294 TTGGTTTATCTGTTACAGGAGGTTGAGGTGTGCTGTTTCCTGACAATGTAGCACCTTGGGACTTG
66 TTGGTTTATCTGCTACAGGAGGTTGAGGTGTGCTGTTTCCTGACAATGTAGCACCTTGGGACTCA
* * * * * *
735359 TTGTCTGTCATTGCATTTGCCGGCGCTCTAGGAGATGGTGATGAAGGGGGCTTAAGATCAGCATA
131 CTATCCGTCAGTGCAGTCGCCGGCGCTCTAGGAGATGGTGATGAAGGGGGCTTAAGATCAGCATA
**
735424 CCTGAAATTGTTGGAG
196 CCTGAAAAAGTTGGAG
735440 CACTACCATG
Statistics
Matches: 192, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
261 192 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (261 bp):
GGGAACTCACATTGAAAAAGGTGAAAGTGGCCTTGGTGTTGGTTTGGTATCATGCTGCTCATCAC
TTGGTTTATCTGCTACAGGAGGTTGAGGTGTGCTGTTTCCTGACAATGTAGCACCTTGGGACTCA
CTATCCGTCAGTGCAGTCGCCGGCGCTCTAGGAGATGGTGATGAAGGGGGCTTAAGATCAGCATA
CCTGAAAAAGTTGGAGGGCCACAATGAATGACATGGTAAGAACTGGCCATAAACGAAGAAAACCC
G
Done.