Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 2 of 349
Found at i:425943 original size:22 final size:22
Alignment explanation
Indices: 425918--425963 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
425908 ATAAATTTAT
425918 TAGTCAATTAAAATAGTTAAAA
1 TAGTCAATTAAAATAGTTAAAA
* ***
425940 TAGTTAATTATTCTAGTTAAAA
1 TAGTCAATTAAAATAGTTAAAA
425962 TA
1 TA
425964 TTGATGTGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TAGTCAATTAAAATAGTTAAAA
Found at i:431889 original size:6 final size:6
Alignment explanation
Indices: 431878--431904 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
431868 AATCACTAAT
431878 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
431905 ACTGATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:432374 original size:43 final size:43
Alignment explanation
Indices: 432308--432404 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 43
432298 CTATAGATGG
* *
432308 CGCCGCTAAAGGTCGGGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGATCGGGACCTTTAGCAGCGCTTTTCCCACAAA
*
432351 CGCCTCTAAAGATCGGGACCTTTAGCAGCGCTTTTCCCACAAA
1 CGCCGCTAAAGATCGGGACCTTTAGCAGCGCTTTTCCCACAAA
432394 CGCCGCTAAAG
1 CGCCGCTAAAG
432405 GTCATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.21
Consensus pattern (43 bp):
CGCCGCTAAAGATCGGGACCTTTAGCAGCGCTTTTCCCACAAA
Found at i:436317 original size:25 final size:25
Alignment explanation
Indices: 436283--436346 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
436273 TCTGTAAAAT
436283 CAATTGAAACGGTGCGTGGT-GGAAA
1 CAATTGAAACGGTGCGTGGTAGG-AA
436308 CAATTGAAACGGTGCGTGGTAGGAA
1 CAATTGAAACGGTGCGTGGTAGGAA
436333 CAATTGAAACGGTG
1 CAATTGAAACGGTG
436347 AGTTTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (25 bp):
CAATTGAAACGGTGCGTGGTAGGAA
Found at i:437512 original size:7 final size:7
Alignment explanation
Indices: 437500--437628 Score: 64
Period size: 7 Copynumber: 18.1 Consensus size: 7
437490 ACTAATTAAT
437500 CTAAACC
1 CTAAACC
437507 CTAAACC
1 CTAAACC
*
437514 TCTTAACTC
1 -CTAAAC-C
*
437523 CT-ATCC
1 CTAAACC
*
437529 CATAAACA
1 C-TAAACC
437537 CTAAACC
1 CTAAACC
437544 CTAAACC
1 CTAAACC
* *
437551 TTTAACC
1 CTAAACC
*
437558 CTTAACC
1 CTAAACC
*
437565 CCAAACC
1 CTAAACC
*
437572 CTTACACC
1 C-TAAACC
* *
437580 TTAAACT
1 CTAAACC
437587 CT-AACC
1 CTAAACC
*
437593 CTAACCC
1 CTAAACC
*
437600 CTAAACA
1 CTAAACC
* *
437607 TTAAATC
1 CTAAACC
* *
437614 ATAATCC
1 CTAAACC
437621 CTAAACC
1 CTAAACC
437628 C
1 C
437629 ATAATTCATC
Statistics
Matches: 88, Mismatches: 28, Indels: 12
0.69 0.22 0.09
Matches are distributed among these distances:
6 7 0.08
7 66 0.75
8 14 0.16
9 1 0.01
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:437707 original size:46 final size:46
Alignment explanation
Indices: 437655--437748 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
437645 CTTCAAATAC
* * *
437655 TAGTTAACTCTTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
437701 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
437747 TA
1 TA
437749 AACCATAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (46 bp):
TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
Found at i:437722 original size:7 final size:7
Alignment explanation
Indices: 437666--437763 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
437656 AGTTAACTCT
*
437666 TAAACCT
1 TAAACCA
*
437673 TAAACCC
1 TAAACCA
437680 TAAACCA
1 TAAACCA
* * *
437687 TATATCT
1 TAAACCA
437694 TAAACCA
1 TAAACCA
437701 TAGTTAACTCA
1 TA---AAC-CA
437712 TAAACCA
1 TAAACCA
*
437719 TAAACCC
1 TAAACCA
437726 TAAACCA
1 TAAACCA
* *
437733 TATA-TA
1 TAAACCA
437739 TTAAACCA
1 -TAAACCA
437747 TAAACCA
1 TAAACCA
*
437754 TAAACTA
1 TAAACCA
437761 TAA
1 TAA
437764 TGATAATTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
6 1 0.01
7 58 0.83
8 4 0.06
10 3 0.04
11 4 0.06
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:437965 original size:41 final size:41
Alignment explanation
Indices: 437920--438221 Score: 311
Period size: 41 Copynumber: 7.4 Consensus size: 41
437910 GTTATATGAC
* * *
437920 TTTTAGCGGCGTTTTTCTAAAAGCGCGGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * * *
437961 TTTTAACGACGTTTTTCTAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * * *
438002 TTTTAACGGTGTTTTTCCAAAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
** * * * * *
438043 TTTTAGCGATGCTTTGCCAAAAACGCCGCTAATACTCTAAT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* *
438084 TTTTAGCGGCGCTTTGCCAAAAGCGCCGCTAATGCTCTGAT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
*
438125 TTTTAGCAGCGTTTTTCCAAAAGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * ** * * * *
438165 TTTTCGCGGCATTTTTGGTAAAAACGCTGCTATTGCTAT-AT
1 TTTTAGCGGCGTTTTT-CCAAAAGCGCCGCTAATGCTCTGAT
*
438206 TTTTAGTGGCGTTTTT
1 TTTTAGCGGCGTTTTT
438222 GGTAAAACGC
Statistics
Matches: 224, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 15 0.07
41 209 0.93
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
Found at i:438222 original size:41 final size:41
Alignment explanation
Indices: 438061--438243 Score: 138
Period size: 41 Copynumber: 4.5 Consensus size: 41
438051 ATGCTTTGCC
* * * ** **
438061 AAAAACGCCGCTAATACTCTAATTTTTAGCGGC-GCTTTGCC
1 AAAAACGCCGCTATTGCTAT-ATTTTTAGCGGCATTTTTGGT
* * * * * **
438102 AAAAGCGCCGCTAATGCTCTGATTTTTAGCAGCGTTTTT-CC
1 AAAAACGCCGCTATTGCTAT-ATTTTTAGCGGCATTTTTGGT
* * * *
438143 AAAAGCGCCGCTAATGCTCTATTTTTCGCGGCATTTTTGGT
1 AAAAACGCCGCTATTGCTATATTTTTAGCGGCATTTTTGGT
* * *
438184 AAAAACGCTGCTATTGCTATATTTTTAGTGGCGTTTTTGGT
1 AAAAACGCCGCTATTGCTATATTTTTAGCGGCATTTTTGGT
438225 -AAAACGCCGCTATTGCTAT
1 AAAAACGCCGCTATTGCTAT
438244 GTATTTTACA
Statistics
Matches: 121, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
40 33 0.27
41 85 0.70
42 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (41 bp):
AAAAACGCCGCTATTGCTATATTTTTAGCGGCATTTTTGGT
Found at i:443317 original size:20 final size:19
Alignment explanation
Indices: 443280--443321 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
443270 ATTCATTCAC
443280 AAATAAAATAATAAAAAGCA
1 AAATAAAATAATAAAAAG-A
443300 AAATAAAATAA-AATAAAGA
1 AAATAAAATAATAA-AAAGA
443319 AAA
1 AAA
443322 CAAGAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (19 bp):
AAATAAAATAATAAAAAGA
Found at i:446688 original size:20 final size:20
Alignment explanation
Indices: 446665--446722 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
446655 AATTCAAGTT
446665 TTTTAATTTAATAAATATAA
1 TTTTAATTTAATAAATATAA
* *
446685 TTTTAAATATAA-AAATATGA
1 TTTT-AATTTAATAAATATAA
446705 TTTT-ATTT--TAAATATAA
1 TTTTAATTTAATAAATATAA
446722 T
1 T
446723 AAGTAGAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 8 0.25
18 3 0.09
20 15 0.47
21 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAATTTAATAAATATAA
Found at i:450393 original size:238 final size:238
Alignment explanation
Indices: 449968--450503 Score: 742
Period size: 238 Copynumber: 2.3 Consensus size: 238
449958 ATAGTCCGAT
* * * *
449968 GGGGGAATATCAGGTTCATTTATAACAAACATGTCCAAAAGAGAAGCACATTAGAAGTATGTGTT
1 GGGGGAATATCGGGTTCATTTATACCAAACATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
* * * *
450033 AAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTTGGAACATGTTTTTGTTGAAGCA
66 AAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAGCA
* *
450098 TCACATCGAGTTTATTATCCATAGATTATAGCTTCTAAGAGTAATCACAGCAAATATCACATTTA
131 TCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATTTA
450163 ACTAGAACCCACTTCGGATTACG-AACATATTCAACAGTTTGAA
196 ACTAGAACCCACTTCGGATTA-GTAACATATTCAACAGTTTGAA
* * * * *
450206 GGGGGAATATTGGGTTCATTTATTCCGAACATATCCGAAAGAGAAGTACATTAGAAGTATG-GCT
1 GGGGGAATATCGGGTTCATTTATACCAAACATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
* * * *
450270 AGAATCTTATAGCGG-CAAAGCCATGTCAATGAGCCTAGATGCTCAGAAACGTGTTGTCGTTGAA
66 A-AATCTCATAACGGTC-AAGCCATGTCAACGAGCCTAGATGCT-AGAAACATGTTGTCGTTGAA
* * * *
450334 GCA-C-CATCGAGTTTATTGTCCATGGATCATACCTTCTAAGAGTAATTCACAGGAAATATCGCA
128 GCATCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAA-TCACAGCAAATATCACA
*
450397 TTTAACTAGAACCCACTTCGGATTAGTAACATATTCAACGGTTTGAA
192 TTTAACTAGAACCCACTTCGGATTAGTAACATATTCAACAGTTTGAA
* *
450444 GGGGGAATATCGGGTTCTTTTATACCTAAA-ATATCCAAAAGATAAGCACATTAGAAGTAT
1 GGGGGAATATCGGGTTCATTTATACC-AAACATATCCAAAAGAGAAGCACATTAGAAGTAT
450504 AATGGTAAAG
Statistics
Matches: 261, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
237 42 0.16
238 199 0.76
239 20 0.08
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (238 bp):
GGGGGAATATCGGGTTCATTTATACCAAACATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
AAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAGCA
TCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATTTA
ACTAGAACCCACTTCGGATTAGTAACATATTCAACAGTTTGAA
Found at i:451195 original size:31 final size:31
Alignment explanation
Indices: 451160--451220 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
451150 AGATAGTTCC
*
451160 ACTAACAGATACTATGAAGACATATGTATAG
1 ACTAACAGATACTACGAAGACATATGTATAG
451191 ACTAACAGATACTACGAAGACATATGTATA
1 ACTAACAGATACTACGAAGACATATGTATA
451221 TAGGCAATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (31 bp):
ACTAACAGATACTACGAAGACATATGTATAG
Found at i:451734 original size:16 final size:16
Alignment explanation
Indices: 451713--451752 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
451703 AAGATACATG
451713 CATGCATACATCCATC
1 CATGCATACATCCATC
*
451729 CATGCATCCATCCATC
1 CATGCATACATCCATC
*
451745 CATACATA
1 CATGCATA
451753 TACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (16 bp):
CATGCATACATCCATC
Found at i:457920 original size:167 final size:166
Alignment explanation
Indices: 457634--457968 Score: 580
Period size: 167 Copynumber: 2.0 Consensus size: 166
457624 TACATAAACT
* *
457634 AGTGGGAACTGACGTACTAAAAAATAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
1 AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
* *
457699 ATATCATATATCTAAGTTTCATATGTTATTATTTCATATCCATATATGGTAAAATTATATTTTGG
66 ATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTGG
457764 TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
131 TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
* *
457800 AGTGGGATCTGACATACTAAAAAACCAATTGTGCCAAAAAATTAGAATGATACTCATTTTCCTTT
1 AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAAT-ATACTCATTTTCCTTT
* *
457865 GATATCATATATCCAAGTTTCATATGTTATTATTTCATATCTATATATAGTAAAATTGTATTTTG
65 GATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTG
*
457930 GTCCCTAAAAATAAAAAGGTTTCTATTTATTTTTTTC
130 GTCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
457967 AG
1 AG
457969 AAGTGATGAA
Statistics
Matches: 159, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
166 44 0.28
167 115 0.72
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (166 bp):
AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
ATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTGG
TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
Found at i:459839 original size:16 final size:17
Alignment explanation
Indices: 459818--459850 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
459808 AAAACAATTA
459818 ATTTAATC-TAAACTTT
1 ATTTAATCTTAAACTTT
459834 ATTTAATCTTAAACTTT
1 ATTTAATCTTAAACTTT
459851 TAAGATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATCTTAAACTTT
Found at i:464098 original size:18 final size:20
Alignment explanation
Indices: 464075--464119 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
464065 GAAACCCAAC
464075 AAAATAAATC-AAACAT-GA
1 AAAATAAATCGAAACATGGA
464093 AAAATAAA-CGAAACATGGA
1 AAAATAAATCGAAACATGGA
464112 AAAA-AAAT
1 AAAATAAAT
464120 AAAAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 6 0.25
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAATAAATCGAAACATGGA
Found at i:466437 original size:96 final size:96
Alignment explanation
Indices: 466241--466442 Score: 219
Period size: 96 Copynumber: 2.1 Consensus size: 96
466231 GTTTCACCTC
* * * *
466241 CTTCAAAAGCGGTGGTCTCGATGTTCGAAGCAACTGTGGAACTTAGAACATTGAGTTCATTATAA
1 CTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATAA
* *
466306 AAAATTTCATCCTGCGAGAAGAACTGATCAC
66 AAAATTTCATCCTGCGAGAAGAACTGACCAA
* * * **
466337 CTTCAAAAGCGG-CGACGTCGATGTTCGAAGCAACTGTAGAATTTAGAACGCT-ATTTTGGTTAT
1 CTTCAAAAGCGGTCGAC-TCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGA-GTTCATTAT
* * * * *
466400 AAATATTTTCCTCCTGCGTGAAGAATTGACCAA
64 AAAAAATTTCATCCTGCGAGAAGAACTGACCAA
*
466433 CTTCATAAGC
1 CTTCAAAAGC
466443 AGTGGCGCCG
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
95 3 0.03
96 84 0.97
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (96 bp):
CTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATAA
AAAATTTCATCCTGCGAGAAGAACTGACCAA
Found at i:470014 original size:18 final size:18
Alignment explanation
Indices: 469993--470050 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
469983 GTGTTGGTTT
469993 TGGTTTTGGCGTCGGTGG
1 TGGTTTTGGCGTCGGTGG
*
470011 TGGTTTTGGCGTCGGTTG
1 TGGTTTTGGCGTCGGTGG
470029 TGGTTTTGGCGTCGGTGG
1 TGGTTTTGGCGTCGGTGG
470047 TGGT
1 TGGT
470051 GGAGGTGGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.00, C:0.10, G:0.48, T:0.41
Consensus pattern (18 bp):
TGGTTTTGGCGTCGGTGG
Found at i:476634 original size:21 final size:22
Alignment explanation
Indices: 476596--476638 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
476586 ATTTAAAAAC
*
476596 ATAAAAACTAATATTAAAACAA
1 ATAAAAACTAATACTAAAACAA
*
476618 ATAAAAA-TGATACTAAAACAA
1 ATAAAAACTAATACTAAAACAA
476639 TTTTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.21
Consensus pattern (22 bp):
ATAAAAACTAATACTAAAACAA
Found at i:478993 original size:102 final size:102
Alignment explanation
Indices: 478794--478986 Score: 280
Period size: 102 Copynumber: 1.9 Consensus size: 102
478784 ATTTATTACG
* * * * *
478794 AATTGAATGTAGACTTTTGATTTTTAGATTGAAAAATCAGTGATTATAAATTTTTAATTAGCTAA
1 AATTGAACGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTTTTAATTAGCTAA
*
478859 TAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
66 CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
* *
478896 AATTGAACGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTAT-CATTTGTTAATTAGCTA
1 AATTGAACGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTT-TTAATTAGCTA
* *
478960 CCAATCAGAGTGTTAAGCAGATAATTT
65 ACAATCAGAGTGATAAGCAGATAATTT
478987 TGTTATTTGG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 4 0.05
102 76 0.95
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (102 bp):
AATTGAACGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTTTTAATTAGCTAA
CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
Found at i:483843 original size:32 final size:32
Alignment explanation
Indices: 483798--483861 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
483788 TTTTAGGATT
483798 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
* *
483830 TTCTAGGGGAACTGGGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
483862 AGGAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (32 bp):
TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
Found at i:488447 original size:69 final size:69
Alignment explanation
Indices: 488336--488475 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
488326 CCGGAAGGTA
* ** *
488336 AACAAATTGAAAACTGAAATCGAAGTGTCACATTTTGCATGTACTAGGGTAAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
488401 GAAT
66 GAAT
* ** *
488405 AACAAATCGAAAACCAAAATCGAATTGTCATTTTTTGCATGTACTAGGATGAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
488470 GAAT
66 GAAT
488474 AA
1 AA
488476 TCTCTAGCGG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (69 bp):
AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
GAAT
Found at i:489548 original size:21 final size:21
Alignment explanation
Indices: 489524--489576 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
489514 GCATTCAGCT
*
489524 TACCCTCCACCACCTTCCGCA
1 TACCCTCCACCACCTTCCACA
489545 TACCCTCCACCACCTTCCACA
1 TACCCTCCACCACCTTCCACA
489566 TACCCTCCACC
1 TACCCTCCACC
489577 TCCGCCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.58, G:0.02, T:0.19
Consensus pattern (21 bp):
TACCCTCCACCACCTTCCACA
Found at i:489847 original size:25 final size:25
Alignment explanation
Indices: 489813--489862 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
489803 CCAAGGGTTT
*
489813 CACATGTCAACCAAATGCAAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
*
489838 CACATGTCAACCAAAAGCTAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
489863 AGAAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (25 bp):
CACATGTCAACCAAAAGCAAAAATG
Found at i:490093 original size:18 final size:18
Alignment explanation
Indices: 490070--490105 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
490060 TTGACCTAAG
490070 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
490088 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
490106 TAACTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
GCAGACTATTTATTATCC
Found at i:495449 original size:59 final size:59
Alignment explanation
Indices: 495381--495498 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
495371 AGAGTCCCCA
495381 ATCCTAAATGTTAGGTTGCATTTTAGTACTTTTACTAAAAAAATAGATAAATTAATTCT
1 ATCCTAAATGTTAGGTTGCATTTTAGTACTTTTACTAAAAAAATAGATAAATTAATTCT
495440 ATCCTAAATGTTAGGTTGCATTTTAGTACTTTTACTAAAAAAATAGATAAATTAATTCT
1 ATCCTAAATGTTAGGTTGCATTTTAGTACTTTTACTAAAAAAATAGATAAATTAATTCT
495499 TGCACGTTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (59 bp):
ATCCTAAATGTTAGGTTGCATTTTAGTACTTTTACTAAAAAAATAGATAAATTAATTCT
Found at i:496573 original size:23 final size:22
Alignment explanation
Indices: 496546--496600 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
496536 TAATTTTTTT
**
496546 ATTTAATTTTTTAAAAATTACA
1 ATTTAATTTCATAAAAATTACA
* * *
496568 TTTTTACTATCATAAAAATTACA
1 -ATTTAATTTCATAAAAATTACA
496591 ATTTAATTTC
1 ATTTAATTTC
496601 TCGCCCCCTA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAATTTCATAAAAATTACA
Found at i:498884 original size:15 final size:15
Alignment explanation
Indices: 498864--498971 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
498854 TTTATGGAAA
498864 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
498879 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
*
498893 AGTCAAAGATATAGGT
1 A-TCAAAGATATGGGT
* **
498909 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
498923 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
498939 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
498953 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
498969 ATC
1 ATC
498972 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:498893 original size:30 final size:30
Alignment explanation
Indices: 498857--498971 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
498847 ATCCATATTT
*
498857 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
498887 ATGGAAAGTCAAAGATATAGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
498917 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
498947 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
498972 GAGATATTGG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:505974 original size:13 final size:13
Alignment explanation
Indices: 505956--505983 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
505946 TAATAATTAA
505956 ATTGAATTAAATT
1 ATTGAATTAAATT
505969 ATTGAATTAAATT
1 ATTGAATTAAATT
505982 AT
1 AT
505984 AAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATTGAATTAAATT
Found at i:527844 original size:13 final size:12
Alignment explanation
Indices: 527826--527859 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
527816 ACATAAATTC
527826 AAACAAATAAGGA
1 AAACAAAT-AGGA
527839 AAACAAATAGGA
1 AAACAAATAGGA
527851 ACAACAAAT
1 A-AACAAAT
527860 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (12 bp):
AAACAAATAGGA
Found at i:528727 original size:121 final size:117
Alignment explanation
Indices: 528584--528839 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 117
528574 TTTATTTTTA
* *
528584 AGCTCAAGCTCGGCTTGAGATATAATC-AAGCTATTCGAGCAAGCTCAATTAAGCTCATTTATCT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAA-C---T-GAGCAAGCTCAATTAAGCTCATTTATCA
* *
528648 ATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTCATA-TGTATTAAATCTTG
61 ATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACT-TATTAAAGCTTG
** * * *
528705 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGCTCAAGCTCGATTCAGCTTATTTATCAATTTT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
* * * * * *
528770 TGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTCGTACTTATTAAAGCTTG
66 TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
*
528822 AGCTCGAGCTCAGCTTGA
1 AGCTCAAGCTCAGCTTGA
528840 TAATTAAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
117 86 0.74
118 2 0.02
121 27 0.23
122 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (117 bp):
AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
Found at i:528794 original size:117 final size:117
Alignment explanation
Indices: 528623--528839 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
528613 GCTATTCGAG
* *
528623 CAAGCTCAATTAAGCTCATTTATCTATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
*
528688 ATA-TGTATTAAATCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
66 ATACT-TATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
* * * * * * * *
528740 CAAGCTCGATTCAGCTTATTTATCAATTTTTGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
* *
528805 GTACTTATTAAAGCTTGAGCTCGAGCTCAGCTTGA
66 ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGA
528840 TAATTAAGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 85 0.99
118 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (117 bp):
CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
Found at i:533199 original size:22 final size:22
Alignment explanation
Indices: 533165--533206 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
533155 ACTATGATTT
*
533165 TTTTAATTATTTTAATTTATTA
1 TTTTAATTATTTTAAATTATTA
* *
533187 TTTTATTTCTTTTAAATTAT
1 TTTTAATTATTTTAAATTAT
533207 AATAGGAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTAATTATTTTAAATTATTA
Found at i:533336 original size:21 final size:20
Alignment explanation
Indices: 533312--533349 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
533302 ATTAAGCTTT
*
533312 TTATTTTTTTGAATATTTTAA
1 TTATATTTTT-AATATTTTAA
533333 TTATATTTTTAAT-TTTT
1 TTATATTTTTAATATTTT
533350 TTGAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 3 0.19
21 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTATATTTTTAATATTTTAA
Found at i:537926 original size:21 final size:21
Alignment explanation
Indices: 537900--537940 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
537890 AGACGAGCAA
* *
537900 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
537921 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
537941 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:550634 original size:21 final size:21
Alignment explanation
Indices: 550608--550648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
550598 AGACGAGCAA
* *
550608 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
550629 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
550649 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:553797 original size:19 final size:18
Alignment explanation
Indices: 553761--553800 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
553751 TTTAAAAAAA
* *
553761 TATAAATTTTAGATTTTT
1 TATAAATTTTAAAATTTT
553779 TATAAATATTTAAAATTTT
1 TATAAAT-TTTAAAATTTT
553798 TAT
1 TAT
553801 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAAATTTTAAAATTTT
Found at i:575797 original size:16 final size:17
Alignment explanation
Indices: 575784--575821 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
575774 TTTATTTTTG
575784 AATTTATATATTTTAGA
1 AATTTATATATTTTAGA
575801 AATTTATATATTTTA-A
1 AATTTATATATTTTAGA
575817 AATTT
1 AATTT
575822 TCAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTATATATTTTAGA
Found at i:577097 original size:20 final size:21
Alignment explanation
Indices: 577074--577113 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
577064 CGTGAAATTG
577074 CCTTTATT-ATTATT-ATTAAA
1 CCTTT-TTAATTATTAATTAAA
577094 CCTTTTTAATTATTAATTAA
1 CCTTTTTAATTATTAATTAA
577114 TCTTTGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.61
21 5 0.28
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
CCTTTTTAATTATTAATTAAA
Found at i:584760 original size:131 final size:130
Alignment explanation
Indices: 584510--584898 Score: 561
Period size: 131 Copynumber: 3.0 Consensus size: 130
584500 AATTGCTTTC
584510 CCTGTATGTCACGAATTTGGGTTTTATGTGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
1 CCTGTATGTCACGAATTTGGGTTTTA--TGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* ** * *
584575 TCGTCCTATCTTGTATCAAGAATCATAGACTTAGGATGTCTTTATACTGCTTATATCGGTTAATA
64 TCGTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAATA
584640 TA
129 TA
*
584642 TCTGTATGTCACGAATTTGGGTTTTATCCGTTCTTTTACCTGACTGCTAACTCA-ATCATTTTGC
1 CCTGTATGTCACGAATTTGGGTTTTAT--GTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
*
584706 TCATGCC-ATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAAT
64 TCGT-CCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAAT
584770 ATA
128 ATA
*
584773 CCTATATGTCACGAATCTT-GGTTTTATGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
1 CCTGTATGTCACGAAT-TTGGGTTTTATG-TTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* * * * *
584837 TCGTCCTGTTTCGTATTAAGAATCATAGACTGCAGATGTCTTTGTACTGCA-TATATCTGTTA
64 TCGTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTG-ATTATATCGGTTA
584899 TTCAAAAACT
Statistics
Matches: 234, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
129 1 0.00
130 27 0.12
131 151 0.65
132 55 0.24
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (130 bp):
CCTGTATGTCACGAATTTGGGTTTTATGTTCTTTTACCTGACTGCTAACTCATATCATTTTGCTC
GTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAATATA
Found at i:588661 original size:18 final size:18
Alignment explanation
Indices: 588638--588672 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
588628 AGTCAAAAAA
588638 ACAAATCAAACTTTTCTC
1 ACAAATCAAACTTTTCTC
588656 ACAAATCAAACTTTTCT
1 ACAAATCAAACTTTTCT
588673 AAGTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (18 bp):
ACAAATCAAACTTTTCTC
Found at i:595696 original size:171 final size:171
Alignment explanation
Indices: 595397--595715 Score: 530
Period size: 171 Copynumber: 1.9 Consensus size: 171
595387 AAAGCACCAA
**
595397 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTCCCTTTGGACAAGAAAAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
* * * *
595462 GACCTTCGGGCATAATCTTGGAGTCAAGGTGGCTTCTAAAGTTAACGGTGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGATAACGGGGAAAAATACACCATGA
595527 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
131 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
* * * *
595568 AAAGTTTGAACTTTGAACATGACAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAACAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
*
595633 GACCTTCAGGCCTAATCTTGGAGTCAAGGTGGCTTCAAAAGATAACGGGGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGATAACGGGGAAAAATACACCATGA
*
595698 TGAGAGCACTAAAATGTA
131 TAAGAGCACTAAAATGTA
595716 TTATGCTGCT
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
171 136 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (171 bp):
AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGATAACGGGGAAAAATACACCATGA
TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
Found at i:598734 original size:14 final size:14
Alignment explanation
Indices: 598715--598743 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
598705 GGTTATTCTG
598715 TCAGCCACTTTAGA
1 TCAGCCACTTTAGA
598729 TCAGCCACTTTAGA
1 TCAGCCACTTTAGA
598743 T
1 T
598744 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (14 bp):
TCAGCCACTTTAGA
Found at i:600723 original size:14 final size:14
Alignment explanation
Indices: 600701--600734 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
600691 GCCGTTTCGC
*
600701 TATTATATTGTTAT
1 TATTTTATTGTTAT
600715 TATTTTATTGTTAT
1 TATTTTATTGTTAT
*
600729 TGTTTT
1 TATTTT
600735 GATATTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:601167 original size:19 final size:20
Alignment explanation
Indices: 601129--601167 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
601119 ATATATTTAC
*
601129 TATATATTATAAAATATAAA
1 TATATATTAAAAAATATAAA
*
601149 TATAT-TTAAAAAATTTAAA
1 TATATATTAAAAAATATAAA
601168 AAATATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATATTAAAAAATATAAA
Found at i:605818 original size:13 final size:13
Alignment explanation
Indices: 605800--605863 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
605790 AATTCTTCAT
*
605800 TGCTTTTGAAATG
1 TGCTTTTGAAAAG
605813 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
605826 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
605839 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
605852 TGCTTTAGAAAA
1 TGCTTTTGAAAA
605864 ATTTAAGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 3 0.07
13 37 0.86
14 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:613927 original size:57 final size:57
Alignment explanation
Indices: 613859--614026 Score: 300
Period size: 57 Copynumber: 2.9 Consensus size: 57
613849 TCGGACATAA
613859 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* *
613916 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTTCTACAACAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* *
613973 CGAGTTCTGGGGATGCCTCCTCATCCTCGTTTTGTCCAACCACAAATTGGATTG
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTG
614027 AGAGCAACAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 105 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (57 bp):
CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
Found at i:616397 original size:29 final size:30
Alignment explanation
Indices: 616364--616437 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
616354 CTATGACTCT
**
616364 TATTTTAAATT-GGTCCTTAAACTTCAAAA
1 TATTTTAAATTACATCCTTAAACTTCAAAA
*
616393 TATTTT-AATTACATCCTTAAACTTTAAAA
1 TATTTTAAATTACATCCTTAAACTTCAAAA
*
616422 TGTTTT-AATTACATCC
1 TATTTTAAATTACATCC
616438 CGAAACTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 4 0.10
29 36 0.90
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (30 bp):
TATTTTAAATTACATCCTTAAACTTCAAAA
Found at i:616443 original size:29 final size:29
Alignment explanation
Indices: 616382--616444 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
616372 ATTGGTCCTT
**
616382 AAACTTCAAAATATTTTAATTACATCCTT
1 AAACTTCAAAATATTTTAATTACATCCCG
* *
616411 AAACTTTAAAATGTTTTAATTACATCCCG
1 AAACTTCAAAATATTTTAATTACATCCCG
616440 AAACT
1 AAACT
616445 ATCGATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (29 bp):
AAACTTCAAAATATTTTAATTACATCCCG
Found at i:617778 original size:57 final size:57
Alignment explanation
Indices: 617710--617877 Score: 291
Period size: 57 Copynumber: 2.9 Consensus size: 57
617700 TCGGACATAA
617710 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* * *
617767 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTTCTACAAAAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* *
617824 CGAGTTCTGGGGATGCCTCCTCATCCTCGTTTTGTCCAACCACAAATTGGATTG
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTG
617878 AGAGCAACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 103 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (57 bp):
CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
Found at i:623117 original size:41 final size:41
Alignment explanation
Indices: 623067--623324 Score: 390
Period size: 41 Copynumber: 6.3 Consensus size: 41
623057 AATTCATCAT
* *
623067 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* * *
623108 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAAACTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
623149 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
623190 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
623231 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
623272 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
623313 ATTCATATCACC
1 ATTCAGATCACC
623325 AATTCCAAAC
Statistics
Matches: 194, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 194 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:623210 original size:82 final size:82
Alignment explanation
Indices: 623073--623324 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
623063 TCATATTCGG
623073 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
*
623138 TTTATAAACTGATTCAT
66 TTTATAACCTGATTCAT
623155 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
623220 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
623237 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
623302 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
623319 ATCACC
1 ATCACC
623325 AATTCCAAAC
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:623560 original size:19 final size:19
Alignment explanation
Indices: 623536--623572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
623526 TTGTTCGATC
*
623536 CACACATATATATATATTA
1 CACACATATACATATATTA
623555 CACACATATACATATATT
1 CACACATATACATATATT
623573 CGCACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:630821 original size:19 final size:19
Alignment explanation
Indices: 630797--630835 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
630787 TTACAACACC
*
630797 TTTTTTACAATATTCATTT
1 TTTTTTAAAATATTCATTT
*
630816 TTTTTTAAAATTTTCATTT
1 TTTTTTAAAATATTCATTT
630835 T
1 T
630836 AAATTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAAAATATTCATTT
Found at i:633082 original size:5 final size:5
Alignment explanation
Indices: 633072--633105 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
633062 TTTGTTCAAC
633072 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
633106 GAATATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:633632 original size:24 final size:24
Alignment explanation
Indices: 633604--633661 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
633594 TAGTTCTTGC
633604 GAGCTTCTCGATTAATGCTCTCTT
1 GAGCTTCTCGATTAATGCTCTCTT
*
633628 GAGCTTCTCGATTAATGCTCTTTT
1 GAGCTTCTCGATTAATGCTCTCTT
633652 GAGCTTCTCG
1 GAGCTTCTCG
633662 TTTATGTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (24 bp):
GAGCTTCTCGATTAATGCTCTCTT
Found at i:638426 original size:44 final size:44
Alignment explanation
Indices: 638363--638473 Score: 206
Period size: 44 Copynumber: 2.5 Consensus size: 44
638353 AGAGTCATGC
638363 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
*
638407 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTTTTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
638451 TACTATGCGAATTTGTC-ATTTTC
1 TACTATGCGAATTTGTCAATTTTC
638474 CATTTTCAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
43 6 0.09
44 60 0.91
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (44 bp):
TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
Found at i:640686 original size:29 final size:30
Alignment explanation
Indices: 640643--640699 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
640633 GAATTTGATC
640643 AAATCAAAATCTCA-TGTATAAAATTGCACA
1 AAATCAAAATCTCATTG-ATAAAATTGCACA
* *
640673 AAATCAAAGT-TCATTGATACAATTGCA
1 AAATCAAAATCTCATTGATAAAATTGCA
640700 TATTGAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (30 bp):
AAATCAAAATCTCATTGATAAAATTGCACA
Found at i:641707 original size:30 final size:30
Alignment explanation
Indices: 641634--641837 Score: 203
Period size: 30 Copynumber: 6.8 Consensus size: 30
641624 TACTACAACT
* * *
641634 GCCGTTGGGTGAATTACCATAACCACCGCC
1 GCCGCTGGGTGAATAACCATAACCACTGCC
* *
641664 GCTGCTAGGGTGAATTACCATAACCACTGCC
1 GCCGCT-GGGTGAATAACCATAACCACTGCC
* * *
641695 ACCGCTGGGTGAATTACCATAACCACTACC
1 GCCGCTGGGTGAATAACCATAACCACTGCC
* * * * *
641725 ACCGCTAGGTGAATAACCATAACTATTGCT
1 GCCGCTGGGTGAATAACCATAACCACTGCC
*** *
641755 GCCGCTGGGTGAATAACCATAACTGTTGCT
1 GCCGCTGGGTGAATAACCATAACCACTGCC
*
641785 GCCG-TGGGGTGAATAACCATAACCACCGCC
1 GCCGCT-GGGTGAATAACCATAACCACTGCC
* *
641815 GCTGCTAGGTGAATAACCATAAC
1 GCCGCTGGGTGAATAACCATAAC
641838 TAAACCCATG
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
29 1 0.01
30 120 0.81
31 28 0.19
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (30 bp):
GCCGCTGGGTGAATAACCATAACCACTGCC
Found at i:642980 original size:19 final size:21
Alignment explanation
Indices: 642956--642995 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
642946 AGCTTGAAAT
*
642956 TTGGTT-AAGTTGG-GTGGTG
1 TTGGTTGAAATTGGTGTGGTG
642975 TTGGTTGAAATTGGTGTGGTG
1 TTGGTTGAAATTGGTGTGGTG
642996 ATCCAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.42
Consensus pattern (21 bp):
TTGGTTGAAATTGGTGTGGTG
Found at i:645604 original size:16 final size:17
Alignment explanation
Indices: 645574--645607 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
645564 TAAATTATAA
645574 AAAAATTTCATAAAAAT
1 AAAAATTTCATAAAAAT
*
645591 AAAAATTTTA-AAAAAT
1 AAAAATTTCATAAAAAT
645607 A
1 A
645608 TTTAACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTTCATAAAAAT
Found at i:687335 original size:21 final size:22
Alignment explanation
Indices: 687297--687338 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
687287 TTCACCCCAT
687297 ATGGCATTTTGCTTTACTTCCG
1 ATGGCATTTTGCTTTACTTCCG
687319 ATGGC-TTTT-CTTCTACTTCC
1 ATGGCATTTTGCTT-TACTTCC
687339 AGTGAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGCATTTTGCTTTACTTCCG
Found at i:688967 original size:378 final size:374
Alignment explanation
Indices: 688217--689089 Score: 1101
Period size: 378 Copynumber: 2.3 Consensus size: 374
688207 AAATTTAATG
* * *
688217 AAGGCAAAATTTGAATTACAAA-TTTCTAGGAGGGGTCAAAAATGCAATTTCACCGTTTTATCCA
1 AAGGCAAAATCTGAATTACAAATTTTC-AGGAGGGGTCAAAAATGAAATTTCACCATTTTAT-CA
* *
688281 AGGTGCCAAATCCAAAGCCTCTAG-TCCCTTTGGATTGGCCCTTTCTCTATCCTATTTTTTTACC
64 TGGTGCCAAATCCAAAGCCTCTAGCT-CCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTTACC
* * *
688345 GACTGTTTTCGGACATGGCGTATGAGATATGATCGGTCAAATTTGATCTTGGTCCTTCTTATTAT
128 GACTGTTTTCGGACATGGCGTATGAGATATGACCAGTCAAATTCGATCTTGGTCCTTCTTATTAT
* * * * * *
688410 ACTTAAATTTGATTTTTAGTCTTTATACTTTAATTTGATATTATTGGTTTTTCTTCTTTTATAAT
193 ACTAAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAATTGATTTTTCTACTTTTATAAT
* * * **
688475 ATCATTTGTCGGTTCAAATCATTAATTATTTTGATTAAAACATTATGATAAATATTCTTTTGGGA
258 ATCATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTTTTGGGA
* * **
688540 ATCGAGGTAAAAATATAAATTCAACTGGCTGAAGCTAAAAATTTAATGTTAA
323 ATCAAGGTAAAAATATAAATTCAACTGACCAAAGCTAAAAATTTAATGTTAA
*
688592 AAGGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATGTAT
1 AAGGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTAT-CAT
* * * * **
688657 CGTACCAAATCCGAAGCTTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGT-TTG
65 GGTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTT-TACCG
* * * * *
688721 ACCTGTTTTGGGACGTGGGGTATGAGATATGACCAGTCAAATTACGGTCTTGGTCCTTCTTATTG
129 A-CTGTTTTCGGACATGGCGTATGAGATATGACCAGTCAAATT-CGATCTTGGTCCTTCTTATTA
*
688786 TACTAAAATTTGATATTTAGTCTTTATAATTTATTTTGATATAATTTGATCTTTT-TACTTTTAT
192 TACTAAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAA-TTGAT-TTTTCTACTTTTAT
** * * *
688850 AATATTGTTGGTTAGTTCAAATCATTACCTATTCCGGTTAAAACATTATGATAAATATT-TTATT
255 AATATCATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTT-TT
* *
688914 GGGAATCAAGGTAAATATATATATTCAACTGACCAAAGCTAAAAATTTAATGTTAA
319 GGGAATCAAGGTAAAAATATAAATTCAACTGACCAAAGCTAAAAATTTAATGTTAA
* * * * * * * *
688970 AAGGTAAAA-CTTAAATTATAAATTTTTAGAAGGGGCCAAAAATGAAATTTCACTATTTTATCCT
1 AAGGCAAAATC-TGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATCAT
** * * *
689034 GGTGCCAAATCCAAAGCCAGTAGCCCCTTTGGGTTGGTCCTTTCTCTATACTATTT
65 GGTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTT
689090 CTGGGCATTG
Statistics
Matches: 427, Mismatches: 62, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
375 108 0.25
376 42 0.10
377 108 0.25
378 165 0.39
379 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (374 bp):
AAGGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATCATG
GTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTTACCGAC
TGTTTTCGGACATGGCGTATGAGATATGACCAGTCAAATTCGATCTTGGTCCTTCTTATTATACT
AAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAATTGATTTTTCTACTTTTATAATATC
ATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTTTTGGGAATC
AAGGTAAAAATATAAATTCAACTGACCAAAGCTAAAAATTTAATGTTAA
Found at i:689159 original size:14 final size:14
Alignment explanation
Indices: 689136--689175 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
689126 TTAATGACAT
689136 TATAAAATTAAAAA
1 TATAAAATTAAAAA
*
689150 TATCAAATT-AAAA
1 TATAAAATTAAAAA
689163 TATAAAGATTAAA
1 TATAAA-ATTAAA
689176 TCATCGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 11 0.50
15 2 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
TATAAAATTAAAAA
Found at i:689571 original size:18 final size:17
Alignment explanation
Indices: 689548--689583 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
689538 TGCTAACTAC
*
689548 AATTATATTCATATATTA
1 AATTATAATCATA-ATTA
689566 AATTATAATCATAATTA
1 AATTATAATCATAATTA
689583 A
1 A
689584 TGACTGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATAATCATAATTA
Found at i:691732 original size:25 final size:23
Alignment explanation
Indices: 691699--691748 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
691689 AAATTAATAT
691699 TTTAATTAATATTTATATTAAAAAA
1 TTTAATT-A-ATTTATATTAAAAAA
* *
691724 TTTATTTAATTTATTTTAAAAAA
1 TTTAATTAATTTATATTAAAAAA
691747 TT
1 TT
691749 AATGGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 1 0.04
25 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAATTAATTTATATTAAAAAA
Found at i:691786 original size:27 final size:26
Alignment explanation
Indices: 691731--691787 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
691721 AAATTTATTT
* * *
691731 AATTTATTTTAAAAAATTAATGGTCA
1 AATTTATTTTAAAAAATAAATGATAA
691757 AATTTATCTTTAAAAAAATAAAT-ATAA
1 AATTTAT-TTT-AAAAAATAAATGATAA
691784 AATT
1 AATT
691788 AACAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 9 0.35
28 10 0.38
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
AATTTATTTTAAAAAATAAATGATAA
Found at i:710639 original size:18 final size:18
Alignment explanation
Indices: 710616--710650 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
710606 CAAGGCATTC
710616 GGCTTTTGCGATAACATG
1 GGCTTTTGCGATAACATG
710634 GGCTTTTGCGATAACAT
1 GGCTTTTGCGATAACAT
710651 CTCTATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (18 bp):
GGCTTTTGCGATAACATG
Found at i:710687 original size:16 final size:16
Alignment explanation
Indices: 710666--710697 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
710656 TTTTCTCTCC
*
710666 CTCTTTCTAAGCTTTT
1 CTCTTTCCAAGCTTTT
710682 CTCTTTCCAAGCTTTT
1 CTCTTTCCAAGCTTTT
710698 AAAAATTGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.28, G:0.06, T:0.53
Consensus pattern (16 bp):
CTCTTTCCAAGCTTTT
Found at i:724888 original size:78 final size:78
Alignment explanation
Indices: 724800--725034 Score: 380
Period size: 78 Copynumber: 3.0 Consensus size: 78
724790 GTCAGGCAGA
* **
724800 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
724865 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
*
724878 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
724943 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * * * *
724956 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
*
725021 CAGCTTTCTGGAC
66 CGGCTTTCTGGAC
725034 G
1 G
725035 GCATGTCCGT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (78 bp):
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC
Found at i:726141 original size:192 final size:189
Alignment explanation
Indices: 725814--726189 Score: 524
Period size: 192 Copynumber: 2.0 Consensus size: 189
725804 AGTTTTTTGG
*
725814 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
* * * *
725879 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
* **
725944 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC
*
726006 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT
* * * * *
726069 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT
* * *
726133 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTCCATAGTAGAAGCTTCTTTATT
128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT
726190 ATATATAATC
Statistics
Matches: 164, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
189 14 0.09
190 28 0.17
191 33 0.20
192 79 0.48
193 10 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47
Consensus pattern (189 bp):
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC
Found at i:727630 original size:31 final size:31
Alignment explanation
Indices: 727595--727664 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
727585 TGCAAAATTT
* *
727595 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA
* *
727626 TTATTGAATTATTTGAAAGTTATATTTTAAG
1 TTATTGAGTTATTTGAAAGTTATATTTTAAA
727657 TTATTGAG
1 TTATTGAG
727665 CTGTTAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.53
Consensus pattern (31 bp):
TTATTGAGTTATTTGAAAGTTATATTTTAAA
Found at i:728055 original size:41 final size:41
Alignment explanation
Indices: 728009--728134 Score: 194
Period size: 35 Copynumber: 3.2 Consensus size: 41
727999 ACTAAATCAT
*
728009 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
728050 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
728085 AATATCTCATATAATACACTTAGATTTGTATGCTTGT-ATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
728125 AATATCTCAT
1 AATATCTCAT
728135 TTAGTAAGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
35 31 0.40
36 3 0.04
40 16 0.21
41 28 0.36
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (41 bp):
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
Found at i:730745 original size:55 final size:55
Alignment explanation
Indices: 730661--730771 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
730651 ACGTATATCT
*
730661 CCTATTGATGTATAAAAACTAGTTTTTCAATTGTAAAAATTGATAGAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAAAAATTGATAGAATTTTTAA
*
730716 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAGAAATTGATAGAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAAAAATTGATAGAATTTTTAA
730771 C
1 C
730772 GAAGAATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.41
Consensus pattern (55 bp):
CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAAAAATTGATAGAATTTTTAA
Found at i:736055 original size:123 final size:123
Alignment explanation
Indices: 735895--736123 Score: 336
Period size: 123 Copynumber: 1.9 Consensus size: 123
735885 TTTGCCTCAT
* * * *
735895 CTGGATTGTTGATGAAATTTGGGTTTGAAACTAAAAGCTTATTCGAGTTAGTAAGCGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
*
735960 AAGTCC-TTTCCATTCGTGTTTTAGCTT-TGTTCATCTTGTTTTTCCTCATATGGATTGC
66 AAGTCCTTTTCCATT-GTGTTGTAG-TTCTGTTCATCTTGTTTTTCCTCATATGGATTGC
* **
736018 CTGGATTGTTGACGAAATTCGGGTTTGAAACCGAAAGCTCATTCGAGTTAGTAATTGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
**
736083 AAGTCCTTTTTGATTGTGTTGTAGTTCTGTTCATCTTGTTT
66 AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTT
736124 AGATTGCTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 2 0.02
123 86 0.91
124 6 0.06
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (123 bp):
CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTTTTCCTCATATGGATTGC
Found at i:739873 original size:6 final size:6
Alignment explanation
Indices: 739858--739931 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
739848 TATGCTCCTT
* * * * *
739858 AGTAGG AGTAGT AGTAGG AGTAGG AGCAGG AGCAGG AGCAGG AGCAGG
1 AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG
* * * *
739906 AGCAGG AGCAGG AGCAGG AGCAGG AG
1 AGTAGG AGTAGG AGTAGG AGTAGG AG
739932 CTGCTGAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.49, T:0.07
Consensus pattern (6 bp):
AGTAGG
Found at i:739932 original size:6 final size:6
Alignment explanation
Indices: 739873--739932 Score: 111
Period size: 6 Copynumber: 10.0 Consensus size: 6
739863 GAGTAGTAGT
*
739873 AGGAGT AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
739921 AGGAGC AGGAGC
1 AGGAGC AGGAGC
739933 TGCTGAGTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.15, G:0.50, T:0.02
Consensus pattern (6 bp):
AGGAGC
Found at i:745619 original size:31 final size:31
Alignment explanation
Indices: 745584--745651 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
745574 GTGAAAACTT
745584 AATGACTTAAATAAAAAAATTCAAATAGTTC
1 AATGACTTAAATAAAAAAATTCAAATAGTTC
* ** * *
745615 AATGACTTAAATGAAAACTTTTAAATAGTTT
1 AATGACTTAAATAAAAAAATTCAAATAGTTC
745646 AATGAC
1 AATGAC
745652 CATTTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (31 bp):
AATGACTTAAATAAAAAAATTCAAATAGTTC
Found at i:755001 original size:135 final size:135
Alignment explanation
Indices: 754759--755026 Score: 500
Period size: 135 Copynumber: 2.0 Consensus size: 135
754749 TATAACCTTT
*
754759 TATCCGATGAAATGATATTCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCC
1 TATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCC
*
754824 TATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCC
66 TATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCACC
754889 GGTTA
131 GGTTA
**
754894 TATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAATTGCGCCGGCC
1 TATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCC
754959 TATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCACC
66 TATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCACC
755024 GGT
131 GGT
755027 GACTTCCCGA
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (135 bp):
TATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCC
TATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCACC
GGTTA
Found at i:756817 original size:19 final size:19
Alignment explanation
Indices: 756793--756831 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
756783 TATGAAAGTT
756793 TGTCTTATAACTATACTTA
1 TGTCTTATAACTATACTTA
756812 TGTCTTATAACTATACTTA
1 TGTCTTATAACTATACTTA
756831 T
1 T
756832 CAATAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (19 bp):
TGTCTTATAACTATACTTA
Found at i:757923 original size:2 final size:2
Alignment explanation
Indices: 757916--757956 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
757906 TCAGGTATTC
* *
757916 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT 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
757957 ATACAATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:757933 original size:12 final size:12
Alignment explanation
Indices: 757916--757956 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
757906 TCAGGTATTC
*
757916 ATATATATATAT
1 ATATATGTATAT
757928 ATATATGTATAT
1 ATATATGTATAT
757940 ATATATGTATAT
1 ATATATGTATAT
757952 ATATA
1 ATATA
757957 ATACAATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:759307 original size:29 final size:29
Alignment explanation
Indices: 759261--759317 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
759251 CACCTAATTA
*
759261 TGAAAAGTTACAAAATGATCATCCAACTG
1 TGAAAAGTTACAAAATGATCACCCAACTG
*
759290 TGAAAAGTTACAAGATGATCACCCAACT
1 TGAAAAGTTACAAAATGATCACCCAACT
759318 ATTCAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (29 bp):
TGAAAAGTTACAAAATGATCACCCAACTG
Found at i:765330 original size:16 final size:17
Alignment explanation
Indices: 765309--765351 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
765299 TTGAGATGAG
765309 AATAAATTT-TTAATTA
1 AATAAATTTATTAATTA
765325 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
765343 AA-AAATTTA
1 AATAAATTTA
765352 AATTAAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:765341 original size:18 final size:18
Alignment explanation
Indices: 765309--765357 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
765299 TTGAGATGAG
765309 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
765325 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
765343 AA-AAATTTAAATTAA
1 AATAAATTT-AATTAA
765358 GTACACATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.30
17 6 0.20
18 15 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:767580 original size:16 final size:16
Alignment explanation
Indices: 767556--767593 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
767546 TTTGGTTCGC
* *
767556 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
767572 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
767588 TGTAAT
1 TGTAAT
767594 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:767638 original size:45 final size:44
Alignment explanation
Indices: 767572--767666 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
767562 GGATTAGAGG
* *
767572 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
767617 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
767661 TGTAAT
1 TGTAAT
767667 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:767849 original size:18 final size:17
Alignment explanation
Indices: 767828--767862 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
767818 TTATTATTTA
*
767828 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
767846 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
767863 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:767856 original size:28 final size:27
Alignment explanation
Indices: 767786--767858 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
767776 TTTATTATCA
*
767786 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
767814 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
767841 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
767859 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:767996 original size:18 final size:17
Alignment explanation
Indices: 767975--768009 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
767965 TTATTATTAA
*
767975 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
767993 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
768010 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:768021 original size:147 final size:149
Alignment explanation
Indices: 767747--768021 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
767737 ATGATTATTG
*
767747 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
* *
767812 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
767877 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
767896 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
767959 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
768022 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:768053 original size:54 final size:54
Alignment explanation
Indices: 767995--768173 Score: 135
Period size: 54 Copynumber: 3.1 Consensus size: 54
767985 ATTAAAATAT
*
767995 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
* * * * * * * *
768049 ATAATTTATGATACTGTAAAATATAAAATAACATAATTATTATTAAATAT-AATATAATTAAAAT
1 ATAATTTA--ATA----AAATTCT-TAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA-
*
768113 AT
53 AC
*
768115 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
768169 ATAAT
1 ATAAT
768174 ATATGATACT
Statistics
Matches: 91, Mismatches: 20, Indels: 28
0.65 0.14 0.20
Matches are distributed among these distances:
54 13 0.14
55 10 0.11
56 6 0.07
57 6 0.07
58 3 0.03
59 5 0.05
60 10 0.11
61 5 0.05
62 3 0.03
63 6 0.07
64 6 0.07
65 10 0.11
66 8 0.09
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:768116 original size:18 final size:17
Alignment explanation
Indices: 768095--768129 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
768085 TTATTATTAA
768095 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
768113 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
768130 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:768244 original size:18 final size:17
Alignment explanation
Indices: 768205--768236 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
768195 TTTTAAATAA
768205 TTAATATTAAATATATT
1 TTAATATTAAATATATT
768222 TTAAT-TTAAATATAT
1 TTAATATTAAATATAT
768237 GATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTAAATATATT
Found at i:768261 original size:120 final size:119
Alignment explanation
Indices: 767959--768250 Score: 469
Period size: 120 Copynumber: 2.4 Consensus size: 119
767949 TCATATTTAA
767959 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
1 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
* *
768024 ATTCTTATATGAATTTACTCAAACCATAATTTATGATACTGTAAAATATAAAAT
66 ATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
* *
768078 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
768143 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA-AAATTTT
65 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAA--AT
* * *
768199 AAATAATTAATATTAAATATATTTTAATTTAAATATATGATTTAATAAAATT
1 AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
768251 TAAAATAATT
Statistics
Matches: 159, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
119 5 0.03
120 151 0.95
121 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (119 bp):
AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
ATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
Found at i:782640 original size:23 final size:22
Alignment explanation
Indices: 782597--782640 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
782587 GGTAGAGTGA
*
782597 TTTTATTTTTTTTCTTTAAAAG
1 TTTTATTTTTTTTCTTAAAAAG
*
782619 TTTTATTTTTTTATGTTAAAAA
1 TTTTATTTTTTT-TCTTAAAAA
782641 CTGTTGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTATTTTTTTTCTTAAAAAG
Found at i:785435 original size:2 final size:2
Alignment explanation
Indices: 785428--785460 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
785418 CAAAGTTTCT
785428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
785461 TTAAACTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:788304 original size:13 final size:14
Alignment explanation
Indices: 788271--788314 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
788261 CGAGCCAAAG
*
788271 ATTTAAAAACTAAAC
1 ATTT-AAAACTACAC
788286 ATTTAAAACTACA-
1 ATTTAAAACTACAC
788299 ATTTAAAACTACAC
1 ATTTAAAACTACAC
788313 AT
1 AT
788315 AACCTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.48
14 10 0.37
15 4 0.15
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTTAAAACTACAC
Found at i:788719 original size:30 final size:30
Alignment explanation
Indices: 788660--788724 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
788650 TATCCCAAAA
*
788660 AAATTGTTTTTAATAGGGAAAGAAATCTTG
1 AAATTGTTTCTAATAGGGAAAGAAATCTTG
* * *
788690 GAATTGTTTCTAATAGGGAAAGGACTCTTG
1 AAATTGTTTCTAATAGGGAAAGAAATCTTG
788720 AAATT
1 AAATT
788725 TTGCCTTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
AAATTGTTTCTAATAGGGAAAGAAATCTTG
Found at i:792055 original size:36 final size:36
Alignment explanation
Indices: 792015--792087 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
792005 GATAAATTGG
792015 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
1 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
* *
792051 AATATGAATTGTAAGCTAATAATTGGGAAATTTTAC
1 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
792087 A
1 A
792088 TTGTATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (36 bp):
AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
Found at i:792590 original size:37 final size:37
Alignment explanation
Indices: 792515--792608 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 37
792505 TTAGTGTTGA
* *
792515 GGCATGCTATTGGTTGGATTAGCTCCTTGGAGCATTT
1 GGCATGTTATTGGTTGGATTAGCTCCTTGAAGCATTT
* * *
792552 GGCGTGTTATTGGTTGGATTAGCT-CTTATAAGCGTTT
1 GGCATGTTATTGGTTGGATTAGCTCCTT-GAAGCATTT
*
792589 GGCATGTT-TTGGTTTGATTA
1 GGCATGTTATTGGTTGGATTA
792609 CTTGTGTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 14 0.29
37 35 0.71
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.43
Consensus pattern (37 bp):
GGCATGTTATTGGTTGGATTAGCTCCTTGAAGCATTT
Found at i:794070 original size:30 final size:30
Alignment explanation
Indices: 794011--794075 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
794001 CTATCCCAAA
794011 AAATTGTTTTTAATAGGGAAAGAAATCTTG
1 AAATTGTTTTTAATAGGGAAAGAAATCTTG
* * *
794041 GAATTGTTTTTAATAGGGAAAGGACTCTTG
1 AAATTGTTTTTAATAGGGAAAGAAATCTTG
794071 AAATT
1 AAATT
794076 TTTCCTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (30 bp):
AAATTGTTTTTAATAGGGAAAGAAATCTTG
Found at i:796952 original size:29 final size:30
Alignment explanation
Indices: 796919--796979 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
796909 CCAAAAAAAT
*
796919 TTGTTTTTAATA-GGAAAGAAATCTTGGAA
1 TTGTTTTTAATAGGGAAAGAAATCTTGAAA
* *
796948 TTGTTTTTAATAGGGAACGGAATCTTGAAA
1 TTGTTTTTAATAGGGAAAGAAATCTTGAAA
796978 TT
1 TT
796980 TTGCCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (30 bp):
TTGTTTTTAATAGGGAAAGAAATCTTGAAA
Found at i:806524 original size:30 final size:31
Alignment explanation
Indices: 806458--806539 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
806448 TGCCATTTGG
* *
806458 TTTAGATATCAAATTGAATATTAAAGCGAAA
1 TTTAAATATCAAATTGAATATTAAAACGAAA
* **
806489 CTTAAATATC-AATTGAATATTAAAATTAAA
1 TTTAAATATCAAATTGAATATTAAAACGAAA
*
806519 TTTAAATA-CAAAATGATATAT
1 TTTAAATATCAAATTGA-ATAT
806540 ATAAGATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 29 0.69
31 12 0.29
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (31 bp):
TTTAAATATCAAATTGAATATTAAAACGAAA
Found at i:806901 original size:10 final size:10
Alignment explanation
Indices: 806886--806923 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
806876 AGAGTAAAAA
806886 ATTTTCTTTC
1 ATTTTCTTTC
*
806896 ATTTTCCTTC
1 ATTTTCTTTC
806906 ATTTTCTTTC
1 ATTTTCTTTC
*
806916 GTTTTCTT
1 ATTTTCTT
806924 CTCTCTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (10 bp):
ATTTTCTTTC
Found at i:807902 original size:18 final size:18
Alignment explanation
Indices: 807844--807899 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
807834 GAGTCGTCTG
807844 AATTTAATTTAAATAATAT
1 AATTTAATTTAAA-AATAT
**
807863 AATTTTTTTTAAAAAT-T
1 AATTTAATTTAAAAATAT
807880 AATTTAATTCTAAAAATAT
1 AATTTAATT-TAAAAATAT
807899 A
1 A
807900 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.26
18 10 0.32
19 13 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTAATTTAAAAATAT
Found at i:808237 original size:41 final size:41
Alignment explanation
Indices: 808187--808272 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
808177 ACACTAAATT
808187 TATT-CTATTAATAAAATCATAAAAAATTCAAACATAATAA
1 TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
*
808227 TATTACTATTAATAAAATCATGAAAAATTCAAACATAATAA
1 TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
808268 TATTA
1 TATTA
808273 GCAATTCAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (41 bp):
TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
Found at i:818730 original size:17 final size:16
Alignment explanation
Indices: 818708--818764 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
818698 AAGAAACATA
818708 TTAAAAATATTAAAAAT
1 TTAAAAA-ATTAAAAAT
*
818725 TTAAAAAA-TAACATGAT
1 TTAAAAAATTAA-A-AAT
818742 TTAAAAAAATTAAAAAT
1 TT-AAAAAATTAAAAAT
*
818759 ATAAAA
1 TTAAAA
818765 TACTTGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 14 0.42
18 7 0.21
19 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAAATTAAAAAT
Found at i:824638 original size:13 final size:13
Alignment explanation
Indices: 824620--824644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
824610 TTAAAATTGG
824620 ACTTGATTTTTGA
1 ACTTGATTTTTGA
824633 ACTTGATTTTTG
1 ACTTGATTTTTG
824645 TTTTGCCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
ACTTGATTTTTGA
Found at i:829232 original size:27 final size:26
Alignment explanation
Indices: 829194--829306 Score: 136
Period size: 27 Copynumber: 4.2 Consensus size: 26
829184 CAGCATGGCT
* *
829194 ACCAGAACAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
829220 ACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
*
829248 ACCAGAACAGATATATGTGGTAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
829275 ACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
829302 ACCAG
1 ACCAG
829307 GACGCTTCCT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
26 6 0.08
27 54 0.70
28 17 0.22
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:829253 original size:54 final size:54
Alignment explanation
Indices: 829194--829306 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
829184 CAGCATGGCT
*
829194 ACCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCC
** * * *
829248 ACCAGAACAGATATATGTGGTAGAGCCACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCC
829302 ACCAG
1 ACCAG
829307 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 35 0.67
55 17 0.33
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (54 bp):
ACCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCC
Found at i:835481 original size:9 final size:8
Alignment explanation
Indices: 835454--835495 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
835444 AAAGGTTAGG
835454 TTTTTTT-
1 TTTTTTTA
* *
835461 TTTCTTCA
1 TTTTTTTA
835469 TTTTTTTA
1 TTTTTTTA
835477 TTTTTTTA
1 TTTTTTTA
835485 -TTTTTTA
1 TTTTTTTA
835492 TTTT
1 TTTT
835496 GGGTTGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:835844 original size:44 final size:44
Alignment explanation
Indices: 835786--836457 Score: 962
Period size: 44 Copynumber: 15.4 Consensus size: 44
835776 CCCGGTCTAA
* *
835786 TACAGAGACGCCAAATCCGTTATCTTCGATCTGCTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
835830 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTTCGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * **
835874 TACAGAGACGCCAAATCTATTATCTTTGATCTGCTCTCTTCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
835918 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCTGCCGT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
835962 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
836006 TACAGAGACGCCAAATCTGTTATCTTCAATCTG--CTCC-CCGTC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCG-C
* * * *
836048 TAATACAGACGCCAAATCCGTTATCTTCAATCTGCTCTCCGCCGC
1 T-ACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
836093 TACAGAGACGCTAAATCTGTTATCTTCAATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
836137 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
836181 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
836225 TACAGAGACGCCAAATCTGTTATCATCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
836269 TATAGAGACGCAAAATCTGTTATCTTCGATCTACTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
836313 TATAGAGACGCAAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
836357 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTGTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
836401 TACAAAGATGCCAAATC----ATCTTCGATTTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
836441 TACAGAGACGCCAAATC
1 TACAGAGACGCCAAATC
836458 ATCTTGGATT
Statistics
Matches: 573, Mismatches: 50, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
40 35 0.06
41 3 0.01
42 5 0.01
43 29 0.05
44 492 0.86
45 6 0.01
46 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:836570 original size:88 final size:88
Alignment explanation
Indices: 836419--836638 Score: 343
Period size: 88 Copynumber: 2.5 Consensus size: 88
836409 TGCCAAATCA
* * * * * * *
836419 TCTTCGATTTGCTCTCTGCC-GCTACAGAGACGCCAAATCATCTTGGATTTGCTTCAACGTAAAC
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACATAAAC
*
836483 ACGTGAAAGCCAAATCAGCTATG
66 ACGTAAAAGCCAAATCAGCTATG
836506 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACATAAAC
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACATAAAC
836571 ACGTAAAAGCCAAATCAGCTATG
66 ACGTAAAAGCCAAATCAGCTATG
* *
836594 TATTCGATCTGCTCCCCGCCTGATACAGAAATGCCAAATCATCTT
1 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTT
836639 CGATATCTTC
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
87 17 0.14
88 105 0.86
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACATAAAC
ACGTAAAAGCCAAATCAGCTATG
Found at i:836630 original size:47 final size:46
Alignment explanation
Indices: 836487--836634 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 46
836477 GTAAACACGT
836487 GAAA-GCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACA
1 GAAATGCCAAATCAGCTATGT-TTCGATCTGCTCCCCGCCTGATACA
* * * ** * *
836533 GAGATGCCAAATCATCT-TG----GATCTGCT-TCAACAT-AAACA
1 GAAATGCCAAATCAGCTATGTTTCGATCTGCTCCCCGCCTGATACA
*
836572 CGTAAAAGCCAAATCAGCTATGTATTCGATCTGCTCCCCGCCTGATACA
1 -G-AAATGCCAAATCAGCTATGT-TTCGATCTGCTCCCCGCCTGATACA
836621 GAAATGCCAAATCA
1 GAAATGCCAAATCA
836635 TCTTCGATAT
Statistics
Matches: 75, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
39 4 0.05
40 4 0.05
41 21 0.28
42 2 0.03
46 5 0.07
47 31 0.41
48 4 0.05
49 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (46 bp):
GAAATGCCAAATCAGCTATGTTTCGATCTGCTCCCCGCCTGATACA
Found at i:836874 original size:61 final size:64
Alignment explanation
Indices: 836752--836874 Score: 173
Period size: 61 Copynumber: 2.0 Consensus size: 64
836742 TTATGTATCC
836752 ATGCTTATGCCAAATAATTAGGATGCTATGATTAAAATGAATCAAATGCTCCTAACAAAATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATTAAAATGAATCAAATGCTCCTAACAAAATGTG
* * * *
836816 ATGCTTTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 ATGC-TTATGCCAAATAATTAGGATGCTATGATTAAAATGAATCAAATGCTCCTAACAAAATG
836875 AATGGTTATG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
61 27 0.50
62 1 0.02
63 1 0.02
64 5 0.09
65 20 0.37
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATTAAAATGAATCAAATGCTCCTAACAAAATGTG
Found at i:837585 original size:51 final size:51
Alignment explanation
Indices: 837491--837593 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
837481 CAAAAACCCC
* * * *
837491 TTTGGTCTCAAAGTGCCCTTTTGCGGGTTTTCACCTTGGCCTTTCCATTTTT
1 TTTGGTCTCAAAGCGCCCTTTTGCGAGTTTTCACCTCGACCTTTCC-TTTTT
837543 TTTGGTCTCAAAGCGCCC-TTTGCGAGTTTTCACCTCGACCTTTCCTTTTT
1 TTTGGTCTCAAAGCGCCCTTTTGCGAGTTTTCACCTCGACCTTTCCTTTTT
837593 T
1 T
837594 AGGTAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 6 0.13
51 24 0.51
52 17 0.36
ACGTcount: A:0.11, C:0.27, G:0.17, T:0.45
Consensus pattern (51 bp):
TTTGGTCTCAAAGCGCCCTTTTGCGAGTTTTCACCTCGACCTTTCCTTTTT
Found at i:849156 original size:13 final size:13
Alignment explanation
Indices: 849138--849162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
849128 ATCGTAAAAT
849138 AAATAAAAAATAA
1 AAATAAAAAATAA
849151 AAATAAAAAATA
1 AAATAAAAAATA
849163 CATAAAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAATAA
Done.