Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 22
Found at i:450409 original size:24 final size:24
Alignment explanation
Indices: 450373--450444 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
450363 AATAAAAATT
* *
450373 AGCCACCAATTTTGACAAACAACA
1 AGCCACCATTTTTGACAAACAAAA
*
450397 AGCCATCATTTTTGACAAACAAAA
1 AGCCACCATTTTTGACAAACAAAA
450421 ATGAACCACCATTTTTGACAAACA
1 A-G--CCACCATTTTTGACAAACA
450445 CAAATTGTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 22 0.54
25 1 0.02
27 18 0.44
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.22
Consensus pattern (24 bp):
AGCCACCATTTTTGACAAACAAAA
Found at i:450441 original size:27 final size:26
Alignment explanation
Indices: 450366--450449 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
450356 ATTTTGCAAT
* *
450366 AAAAATTAGCCACCAATTTTGACAAAC
1 AAAAATGA-CCACCATTTTTGACAAAC
* *
450393 AACAA-G-CCATCATTTTTGACAAAC
1 AAAAATGACCACCATTTTTGACAAAC
450417 AAAAATGAACCACCATTTTTGACAAAC
1 AAAAATG-ACCACCATTTTTGACAAAC
*
450444 ACAAAT
1 AAAAAT
450450 TGTGAGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 20 0.43
25 1 0.02
27 26 0.55
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.23
Consensus pattern (26 bp):
AAAAATGACCACCATTTTTGACAAAC
Found at i:451672 original size:21 final size:20
Alignment explanation
Indices: 451626--451678 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
451616 GTAGCCAAAC
**
451626 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
451646 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
451666 TTGTATCGATACA
1 TTGTATCGATACA
451679 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:455836 original size:13 final size:13
Alignment explanation
Indices: 455818--455846 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
455808 GAATAAATTG
455818 GAGAGGGAGGAGT
1 GAGAGGGAGGAGT
455831 GAGAGGGAGGAGT
1 GAGAGGGAGGAGT
455844 GAG
1 GAG
455847 CCTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.62, T:0.07
Consensus pattern (13 bp):
GAGAGGGAGGAGT
Found at i:455927 original size:24 final size:26
Alignment explanation
Indices: 455895--455960 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 26
455885 AAAATTAGCT
* *
455895 ACCAATTTTGACAAAC-AACAAG-CC
1 ACCATTTTTGACAAACAAAAAAGACC
*
455919 ACCATTTTTTACAAACAAAAAAGAACC
1 ACCATTTTTGACAAACAAAAAAG-ACC
455946 ACCATTTTTGACAAA
1 ACCATTTTTGACAAA
455961 TACAAAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.40
25 5 0.14
27 16 0.46
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.23
Consensus pattern (26 bp):
ACCATTTTTGACAAACAAAAAAGACC
Found at i:457754 original size:60 final size:60
Alignment explanation
Indices: 457679--457803 Score: 200
Period size: 60 Copynumber: 2.1 Consensus size: 60
457669 ATGATATAAA
* *
457679 TTTC-ACCGATATTATG-AGAAGTTTAGAGGATGAGTTCATTAGTAATAGGCAAAGCCTAT
1 TTTCAACCGATATTATGAAG-AGTTTAGAGGATGAGTTCATTAGCAATAGGCAAAACCTAT
*
457738 TTTCAACCGGTATTATGAAGAGTTTAGAGGATGAGTTCATTAGCAATAGGCAAAACCTAT
1 TTTCAACCGATATTATGAAGAGTTTAGAGGATGAGTTCATTAGCAATAGGCAAAACCTAT
457798 TTTCAA
1 TTTCAA
457804 TTCAAGTAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
59 4 0.07
60 55 0.90
61 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTCAACCGATATTATGAAGAGTTTAGAGGATGAGTTCATTAGCAATAGGCAAAACCTAT
Found at i:463526 original size:21 final size:23
Alignment explanation
Indices: 463477--463532 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
463467 TTTAAAAAGT
*
463477 AATTTTATATTAATATTTATATA
1 AATTTTATATTAATATTTAAATA
**
463500 TTTTTTA-ATTAA-ATTTAAATA
1 AATTTTATATTAATATTTAAATA
*
463521 AATTTTTTATTA
1 AATTTTATATTA
463533 TTAAATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTTATATTAATATTTAAATA
Found at i:463526 original size:22 final size:21
Alignment explanation
Indices: 463501--463560 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
463491 ATTTATATAT
463501 TTTTTAATTAAATTTAAATAAA
1 TTTTTAATTAAA-TTAAATAAA
*
463523 TTTTTTATT--ATTAAATAATA
1 TTTTTAATTAAATTAAATAA-A
* *
463543 ATTTAAATTAAATTAAAT
1 TTTTTAATTAAATTAAAT
463561 TAATCCGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 8 0.26
20 8 0.26
22 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAATTAAATTAAATAAA
Found at i:467730 original size:76 final size:78
Alignment explanation
Indices: 467629--467832 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
467619 GAGATAATAA
* * * * *
467629 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
467693 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
467705 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
467770 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
467784 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
467833 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:467824 original size:28 final size:28
Alignment explanation
Indices: 467784--467855 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
467774 GGAATAAAGC
** *
467784 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
467812 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
467840 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
467856 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:467913 original size:52 final size:50
Alignment explanation
Indices: 467844--468013 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
467834 AAATAACGAG
* * *
467844 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
467896 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
467949 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
468000 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
468014 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:468032 original size:28 final size:28
Alignment explanation
Indices: 467987--468068 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
467977 AGTGTTTTAA
* *
467987 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
468014 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
468041 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
468069 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:470509 original size:13 final size:13
Alignment explanation
Indices: 470491--470516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
470481 ACAAAGATCC
470491 ATGTATCGATACA
1 ATGTATCGATACA
470504 ATGTATCGATACA
1 ATGTATCGATACA
470517 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:470512 original size:33 final size:33
Alignment explanation
Indices: 470470--470536 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
470460 AAAATTTCCA
***
470470 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
470503 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
470536 A
1 A
470537 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:470580 original size:19 final size:18
Alignment explanation
Indices: 470556--470623 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
470546 CAGTAGCTAA
470556 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
470575 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
470590 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
470607 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
470624 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:470596 original size:13 final size:13
Alignment explanation
Indices: 470578--470602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470568 ACAATACTTA
470578 TGTATCGATACAT
1 TGTATCGATACAT
470591 TGTATCGATACA
1 TGTATCGATACA
470603 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:470600 original size:32 final size:32
Alignment explanation
Indices: 470559--470621 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
470549 TAGCTAATTA
*
470559 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
470591 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
470622 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:470703 original size:21 final size:21
Alignment explanation
Indices: 470679--470735 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
470669 CATTTGTAGG
470679 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
470700 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
470721 ATGTATCGATACATT
1 ATGTATCGATACATT
470736 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:470763 original size:15 final size:15
Alignment explanation
Indices: 470743--470772 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
470733 ATTTAAATTT
470743 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
470758 TTTTTTTTTTTTCAA
1 TTTTTTTTTTTTCAA
470773 ACACTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTTTCAA
Found at i:471585 original size:29 final size:29
Alignment explanation
Indices: 471536--471595 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
471526 TCGTTCGATG
471536 TAATTTCTTCTAAATTCTTGA-TTTAAAA
1 TAATTTCTTCTAAATTCTTGAGTTTAAAA
* * *
471564 TAATTTCTATTTAAATTTTTGAGTTTGAAA
1 TAATTTCT-TCTAAATTCTTGAGTTTAAAA
471594 TA
1 TA
471596 CAAGATTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 8 0.30
29 11 0.41
30 8 0.30
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (29 bp):
TAATTTCTTCTAAATTCTTGAGTTTAAAA
Found at i:471954 original size:15 final size:16
Alignment explanation
Indices: 471926--471958 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
471916 AAAAATTGAT
471926 TTTTTGAATCTTTAAA
1 TTTTTGAATCTTTAAA
471942 TTTTTGAAT-TTTAAA
1 TTTTTGAATCTTTAAA
471957 TT
1 TT
471959 ATTATGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTTGAATCTTTAAA
Found at i:473359 original size:2 final size:2
Alignment explanation
Indices: 473309--473339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
473299 GTTTATGCTT
473309 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 T
473340 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:475868 original size:31 final size:31
Alignment explanation
Indices: 475810--475869 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
475800 TATGAAGTAT
*
475810 AAATATAAATTTTTAAAGTTATAGATAAATA
1 AAATATAAATTTTTAAAGCTATAGATAAATA
* *
475841 AAATGTAAA-TTTTAAACGCTATGGATAAA
1 AAATATAAATTTTTAAA-GCTATAGATAAA
475870 AATGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (31 bp):
AAATATAAATTTTTAAAGCTATAGATAAATA
Found at i:478390 original size:22 final size:22
Alignment explanation
Indices: 478365--478412 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
478355 AATATTAAAT
478365 TTATTAAATGAATTTAAAAAAA
1 TTATTAAATGAATTTAAAAAAA
* ** *
478387 TTATTAAGTTCATTTAAAAAGA
1 TTATTAAATGAATTTAAAAAAA
478409 TTAT
1 TTAT
478413 GACATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (22 bp):
TTATTAAATGAATTTAAAAAAA
Found at i:479350 original size:52 final size:50
Alignment explanation
Indices: 479288--479384 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 50
479278 AAGTTTAAAT
*
479288 TATTATTTATAATTTAATAAAAATTAAAAATTATTTTTATATTATTAATTATA
1 TATTATTTATAATTAAAT-AAAATTAAAAA-TATTTTT-TATTATTAATTATA
**
479341 TATT-TTTATAATTAAATTTAATTAAAAATATTTTTTATTATTAA
1 TATTATTTATAATTAAATAAAATTAAAAATATTTTTTATTATTAA
479385 ATAATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 9 0.22
50 7 0.17
51 9 0.22
52 12 0.29
53 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (50 bp):
TATTATTTATAATTAAATAAAATTAAAAATATTTTTTATTATTAATTATA
Found at i:479711 original size:10 final size:10
Alignment explanation
Indices: 479696--479741 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
479686 GAGTATTAAA
*
479696 TATATAAATT
1 TATATATATT
479706 TATATATA-T
1 TATATATATT
479715 TATATATATT
1 TATATATATT
*
479725 T-TAATACATT
1 TAT-ATATATT
479735 TATATAT
1 TATATAT
479742 TTATATTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 10 0.33
10 19 0.63
11 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (10 bp):
TATATATATT
Found at i:479978 original size:20 final size:19
Alignment explanation
Indices: 479939--479977 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
479929 TACAAATATT
479939 TAAATTTTGACACATTATA
1 TAAATTTTGACACATTATA
*
479958 TAAATTTTGATACATT-TA
1 TAAATTTTGACACATTATA
479976 TA
1 TA
479978 TTGTGTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
TAAATTTTGACACATTATA
Found at i:480348 original size:6 final size:6
Alignment explanation
Indices: 480331--480381 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
480321 AAATATTAAT
* *
480331 TATTTA TA-TTA TTTTTA TA-TTA TATTTA TA-TTA TATTTA T-TATA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
480375 TATTTA T
1 TATTTA T
480382 CTAAATTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 18 0.49
6 19 0.51
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:480349 original size:11 final size:11
Alignment explanation
Indices: 480331--480381 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
480321 AAATATTAAT
480331 TATTTATATTA
1 TATTTATATTA
*
480342 TTTTTATATTA
1 TATTTATATTA
480353 TATTTATATTA
1 TATTTATATTA
480364 TATTTAT-TATA
1 TATTTATAT-TA
480375 TATTTAT
1 TATTTAT
480382 CTAAATTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 1 0.03
11 36 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:480378 original size:16 final size:16
Alignment explanation
Indices: 480330--480375 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
480320 AAAATATTAA
*
480330 TTAT-TTATATTATTT
1 TTATATTATATTATAT
480345 TTATATTATATT-TAT
1 TTATATTATATTATAT
480360 ATTATATT-TATTATAT
1 -TTATATTATATTATAT
480376 ATTTATCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATATTATAT
Found at i:480883 original size:23 final size:24
Alignment explanation
Indices: 480857--480904 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
480847 CCGTATAATG
480857 TTTAATT-TTTTTTCATGTTATAT
1 TTTAATTATTTTTTCATGTTATAT
* * *
480880 TTTACTTATTTTTTGATGTTGTAT
1 TTTAATTATTTTTTCATGTTATAT
480904 T
1 T
480905 CCTATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.69
Consensus pattern (24 bp):
TTTAATTATTTTTTCATGTTATAT
Found at i:482879 original size:18 final size:19
Alignment explanation
Indices: 482836--482887 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
482826 TGATAATAAT
482836 AAATATTTTTAA-TTTACTA
1 AAAT-TTTTTAAGTTTACTA
482855 ACTAATTTTTTAAGTTT-CTA
1 A--AATTTTTTAAGTTTACTA
482875 AAATTTTTTAAGT
1 AAATTTTTTAAGT
482888 CACAATGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.40
19 1 0.03
20 11 0.37
21 6 0.20
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (19 bp):
AAATTTTTTAAGTTTACTA
Found at i:484284 original size:2 final size:2
Alignment explanation
Indices: 484277--484325 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
484267 ATTTCTCATT
484277 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
484319 TA TA TA T
1 TA TA TA T
484326 TTGATAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:486036 original size:15 final size:13
Alignment explanation
Indices: 486018--486051 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
486008 CAGGTTAAAA
486018 AAAAAAGAGAGAGAG
1 AAAAAAGA-A-AGAG
486033 AAAAAAGAAAGAG
1 AAAAAAGAAAGAG
486046 AAAAAA
1 AAAAAA
486052 AAAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAG
Found at i:486052 original size:15 final size:15
Alignment explanation
Indices: 486016--486053 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
486006 ACCAGGTTAA
*
486016 AAAAAAAAGAGAGAG
1 AAAAAAAAGAAAGAG
*
486031 AGAAAAAAGAAAGAG
1 AAAAAAAAGAAAGAG
486046 AAAAAAAA
1 AAAAAAAA
486054 AAAAAGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAGAG
Found at i:486706 original size:11 final size:11
Alignment explanation
Indices: 486692--486726 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
486682 CTAAAACATC
486692 AAAAAAAAGAA
1 AAAAAAAAGAA
*
486703 AAAAAAAGGAA
1 AAAAAAAAGAA
*
486714 AAAAAATAGAA
1 AAAAAAAAGAA
486725 AA
1 AA
486727 TCAAGTGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:492441 original size:34 final size:35
Alignment explanation
Indices: 492388--492455 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
492378 AATTTATAAT
*
492388 TTTTTATTTATAAAAAAATAATTAT-TTACAAAAC
1 TTTTTATTTATAAAAAAATAATTATATTAAAAAAC
* *
492422 TTTTTATATTAT-AATAAATATTTATATTAAAAAA
1 TTTTTAT-TTATAAAAAAATAATTATATTAAAAAA
492456 ATCAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (35 bp):
TTTTTATTTATAAAAAAATAATTATATTAAAAAAC
Found at i:492698 original size:17 final size:16
Alignment explanation
Indices: 492662--492720 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 16
492652 TTCTTGAAAC
492662 AAAAATATATATATAT
1 AAAAATATATATATAT
*
492678 -AAAATATATATACTTT
1 AAAAATATATATA-TAT
* *
492694 AAAAAAATCA-ATAAAT
1 AAAAATAT-ATATATAT
492710 AAAAATATATA
1 AAAAATATATA
492721 AAAAATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 13 0.38
16 11 0.32
17 9 0.26
18 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATATATATATAT
Found at i:492734 original size:25 final size:25
Alignment explanation
Indices: 492695--492744 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
492685 ATATACTTTA
* *
492695 AAAAAATCAATAAATAAAAATATAT
1 AAAAAATAAAAAAATAAAAATATAT
**
492720 AAAAAATAAAAAAATGTAAATATAT
1 AAAAAATAAAAAAATAAAAATATAT
492745 TTTTAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAAATAAAAAAATAAAAATATAT
Found at i:499905 original size:17 final size:17
Alignment explanation
Indices: 499883--499929 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
499873 TAAAAATATA
499883 TTTATATTTTTTTATTT
1 TTTATATTTTTTTATTT
*
499900 TTTATATGTTTTTATTT
1 TTTATATTTTTTTATTT
*
499917 ATTA-ATTTTTTTA
1 TTTATATTTTTTTA
499930 AAGTATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTATATTTTTTTATTT
Found at i:499915 original size:25 final size:25
Alignment explanation
Indices: 499878--499927 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
499868 AGTTTTAAAA
* *
499878 ATATATTTATATTTTTTTATTTTTT
1 ATATATTTATATTTATTAATTTTTT
* *
499903 ATATGTTTTTATTTATTAATTTTTT
1 ATATATTTATATTTATTAATTTTTT
499928 TAAAGTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (25 bp):
ATATATTTATATTTATTAATTTTTT
Found at i:502321 original size:18 final size:17
Alignment explanation
Indices: 502294--502327 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
502284 AGCTCTCTAA
502294 ATTTACTTTAATAAAAGC
1 ATTTACTTTAA-AAAAGC
*
502312 ATTTAGTTTAAAAAAG
1 ATTTACTTTAAAAAAG
502328 ATACATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
ATTTACTTTAAAAAAGC
Found at i:505092 original size:16 final size:15
Alignment explanation
Indices: 505073--505127 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 15
505063 ATTATATTGT
505073 TTTTAAATTTAAGTTA
1 TTTTAAATTTAA-TTA
505089 TTTTAAATCTATAATTA
1 TTTTAAAT-T-TAATTA
*
505106 TTTCAAATTTAAATTA
1 TTTTAAATTT-AATTA
505122 TTTTAA
1 TTTTAA
505128 GTTCGGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 1 0.03
16 19 0.56
17 11 0.32
18 3 0.09
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTTAAATTTAATTA
Found at i:507236 original size:32 final size:32
Alignment explanation
Indices: 507177--507237 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
507167 CAAGTTCAAG
* * *
507177 TTTGGATCTTAATGGATTCAAGTCTTTACAGA
1 TTTGGATCTCAATAGATTCAAGCCTTTACAGA
* *
507209 TTTGGATCTCAATAGATTTAGGCCTTTAC
1 TTTGGATCTCAATAGATTCAAGCCTTTAC
507238 GGCTTTTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (32 bp):
TTTGGATCTCAATAGATTCAAGCCTTTACAGA
Found at i:515316 original size:16 final size:16
Alignment explanation
Indices: 515295--515334 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
515285 ATATATAACA
515295 TTGTTTCTGACTCTTC
1 TTGTTTCTGACTCTTC
515311 TTGTTTCTGACTCTTC
1 TTGTTTCTGACTCTTC
515327 TTGTTTCT
1 TTGTTTCT
515335 TCATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.23, G:0.12, T:0.60
Consensus pattern (16 bp):
TTGTTTCTGACTCTTC
Found at i:517541 original size:13 final size:13
Alignment explanation
Indices: 517525--517554 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
517515 ATACGTTGTT
517525 CATTGTATCGATA
1 CATTGTATCGATA
*
517538 CATTGTATTGATA
1 CATTGTATCGATA
517551 CATT
1 CATT
517555 CTGGGTTTTA
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:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:519937 original size:24 final size:25
Alignment explanation
Indices: 519910--519962 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
519900 GAGAGATAAT
* * *
519910 AGAGATAGAAGGGATGATAG-GAGG
1 AGAGATAGAAGAGATAATAGAGAGA
519934 AGAGATAGAAGAGATAATAGAGAGA
1 AGAGATAGAAGAGATAATAGAGAGA
519959 AGAG
1 AGAG
519963 GGATGACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (25 bp):
AGAGATAGAAGAGATAATAGAGAGA
Found at i:519942 original size:30 final size:30
Alignment explanation
Indices: 519872--519932 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
519862 TAGCCCTCAA
* *
519872 AGAGA-AAAAGAGATAGGAGGGATGATAGG
1 AGAGATAATAGAGATAGAAGGGATGATAGG
519901 AGAGATAATAGAGATAGAAGGGATGATAGG
1 AGAGATAATAGAGATAGAAGGGATGATAGG
519931 AG
1 AG
519933 GAGAGATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.48, C:0.00, G:0.39, T:0.13
Consensus pattern (30 bp):
AGAGATAATAGAGATAGAAGGGATGATAGG
Found at i:519965 original size:42 final size:42
Alignment explanation
Indices: 519883--519986 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
519873 GAGAAAAAGA
* *
519883 GATAGGAGG-GATGATAGGAGAGATAATAGAGATAGAAGGGAT
1 GATAGGAGGAGA-GATAGAAGAGATAATAGAGAAAGAAGGGAT
519925 GATAGGAGGAGAGATAGAAGAGATAATAGAGAGAAG-AGGGAT
1 GATAGGAGGAGAGATAGAAGAGATAATAGAGA-AAGAAGGGAT
* * *
519967 GACAAGAGGAG-GAGAGAAGA
1 GATAGGAGGAGAGATAGAAGA
519987 AGATGGAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 8 0.15
42 43 0.78
43 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.41, T:0.12
Consensus pattern (42 bp):
GATAGGAGGAGAGATAGAAGAGATAATAGAGAAAGAAGGGAT
Found at i:520004 original size:23 final size:24
Alignment explanation
Indices: 519952--520014 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
519942 AAGAGATAAT
*
519952 AGAGAGAAGAGGGATGACAAGAGG
1 AGAGAGAAGAGAGATGACAAGAGG
*
519976 AGGAGAGAAGA-AGATG-GAAGAGTG
1 A-GAGAGAAGAGAGATGACAAGAG-G
*
520000 AGAGAAAATGAGAGA
1 AGAGAGAA-GAGAGA
520015 ATCGGTGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 11 0.34
24 9 0.28
25 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.43, T:0.06
Consensus pattern (24 bp):
AGAGAGAAGAGAGATGACAAGAGG
Found at i:526713 original size:79 final size:78
Alignment explanation
Indices: 526615--526797 Score: 267
Period size: 79 Copynumber: 2.3 Consensus size: 78
526605 CATTCATGTT
*
526615 TTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCATAATCGGGG
1 TTATTTCCGA-GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
526680 ATACTCCAACCCCA
65 ATACTCCAACCCCA
** * *
526694 TTATTTTTGAGAGGATACTCAAACCCCGATTTTATTTTTAAAACACCAATTTTTCACAATCGGGG
1 TTATTTCCGAG-GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGG
* * *
526759 ATACTCTAGCCCCG
65 ATACTCCAACCCCA
526773 TTATTTCCGAGGAGATACTCCAACC
1 TTATTTCCGAGG-GATACTCCAACC
526798 TCGTTATTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 2 0.02
79 89 0.98
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
TTATTTCCGAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGA
TACTCCAACCCCA
Found at i:526802 original size:28 final size:28
Alignment explanation
Indices: 526771--526825 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
526761 ACTCTAGCCC
*
526771 CGTTATTTCCGAGGAGATACTCCAACCT
1 CGTTATTTCCAAGGAGATACTCCAACCT
* * *
526799 CGTTATTTTCAAGGGGATACTCTAACC
1 CGTTATTTCCAAGGAGATACTCCAACC
526826 CTGATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (28 bp):
CGTTATTTCCAAGGAGATACTCCAACCT
Found at i:526870 original size:107 final size:107
Alignment explanation
Indices: 526679--526886 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 107
526669 CATAATCGGG
** **
526679 GATACTCCAACCCCATTATTTTTGAGAGGATACTCAAACCCCGATTTTATTTTTAAAACACCAAT
1 GATACTCCAACCCCATTATTTTCAAGAGGATACTCAAACCCCGATTTTATTTCCAAAACACCAAT
* * *
526744 TTTTCACAATCGGGGATACTCTAGCCCCGTTATTTCCGAGGA
66 TTTTCACAATCGGGAATACTCCAACCCCGTTATTTCCGAGGA
* * * * * *
526786 GATACTCCAACCTCGTTATTTTCAAGGGGATACTCTAACCCTGATTTTATTTCCAAAACATCAAT
1 GATACTCCAACCCCATTATTTTCAAGAGGATACTCAAACCCCGATTTTATTTCCAAAACACCAAT
* *
526851 TTTTCATAATCGGGAATACTCCAACCCTGTTATTTC
66 TTTTCACAATCGGGAATACTCCAACCCCGTTATTTC
526887 TAAAGGGATA
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (107 bp):
GATACTCCAACCCCATTATTTTCAAGAGGATACTCAAACCCCGATTTTATTTCCAAAACACCAAT
TTTTCACAATCGGGAATACTCCAACCCCGTTATTTCCGAGGA
Found at i:528804 original size:32 final size:32
Alignment explanation
Indices: 528745--528806 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
528735 CAAGTTCAGG
* * *
528745 TTTGGATCTTAATGTATTCAAGTCTTTACAGA
1 TTTGGATCTCAATGGATTCAAGCCTTTACAGA
* *
528777 TTTGGATCTCAATGGATTTAGGCCTTTACA
1 TTTGGATCTCAATGGATTCAAGCCTTTACA
528807 TGTTTCAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (32 bp):
TTTGGATCTCAATGGATTCAAGCCTTTACAGA
Found at i:529131 original size:18 final size:19
Alignment explanation
Indices: 529103--529138 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
529093 AATTTGTAAT
529103 ACATAAAATAAAAAAAATC
1 ACATAAAATAAAAAAAATC
*
529122 ACAT-AAATAAACAAAAT
1 ACATAAAATAAAAAAAAT
529139 TAAGAATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (19 bp):
ACATAAAATAAAAAAAATC
Found at i:533467 original size:2 final size:2
Alignment explanation
Indices: 533460--533505 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
533450 GGATATAAGA
533460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
533502 AT AT
1 AT AT
533506 GCGCGTAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:534414 original size:17 final size:18
Alignment explanation
Indices: 534392--534430 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
534382 TATTTTTTTG
534392 TTTATTTTT-TAAAAATT
1 TTTATTTTTGTAAAAATT
*
534409 TTTATTTTTGTTAAAATT
1 TTTATTTTTGTAAAAATT
534427 TTTA
1 TTTA
534431 AGATGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTATTTTTGTAAAAATT
Found at i:534527 original size:13 final size:13
Alignment explanation
Indices: 534511--534539 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
534501 TAATATCAAA
534511 AAATAATTAAACT
1 AAATAATTAAACT
534524 AAATAATTAAACT
1 AAATAATTAAACT
534537 AAA
1 AAA
534540 AATCAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATTAAACT
Found at i:535139 original size:18 final size:19
Alignment explanation
Indices: 535105--535149 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
535095 TTGATCATTT
535105 TTATATTTTTATCATAT-A
1 TTATATTTTTATCATATAA
*
535123 TTATTATTTTT-TGATATAA
1 TTA-TATTTTTATCATATAA
535142 TTATATTT
1 TTATATTT
535150 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATATTTTTATCATATAA
Found at i:535277 original size:12 final size:12
Alignment explanation
Indices: 535234--535280 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 12
535224 TCATATAATA
535234 TTTATATTATA-
1 TTTATATTATAT
535245 TTT-T-TTATAT
1 TTTATATTATAT
535255 TTTA-ATT-TAT
1 TTTATATTATAT
535265 TTTATATTATAT
1 TTTATATTATAT
535277 TTTA
1 TTTA
535281 ATTTTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
9 5 0.16
10 11 0.35
11 8 0.26
12 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:535817 original size:25 final size:24
Alignment explanation
Indices: 535758--535817 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
535748 TATAATTTTT
* * *
535758 ATATTATATATTTATAAATTTTAAT
1 ATATT-TATATTTATAAAATTCAAC
* *
535783 ACATTAATATTATATAAAATTCAAC
1 ATATTTATATT-TATAAAATTCAAC
535808 ATATTTATAT
1 ATATTTATAT
535818 ATTAATTCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTATATTTATAAAATTCAAC
Found at i:543507 original size:15 final size:15
Alignment explanation
Indices: 543487--543518 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
543477 TATTGTTGAA
*
543487 AATAATTAAAAAGAT
1 AATAATTAAAAAAAT
543502 AATAATTAAAAAAAT
1 AATAATTAAAAAAAT
543517 AA
1 AA
543519 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATTAAAAAAAT
Found at i:543813 original size:107 final size:109
Alignment explanation
Indices: 543692--543901 Score: 352
Period size: 107 Copynumber: 1.9 Consensus size: 109
543682 ATTAAAACTA
*
543692 TAATAGAAATATATAATATTCAATATTTATAATTAGAAAAGAACAATTGAACGAGTTCTGATGAA
1 TAATAGAAATATATAATACTCAATATTTATAATTAGAAAAGAACAATTGAACGAGTTCTGATGAA
* *
543757 TTCGAGTCAAGTTACATCGGACTCATATTTTATTAGATATAATG
66 TTCGAGTCAAGTTACATCAGACTCATATTATATTAGATATAATG
* * *
543801 TAATA-AAA-ATATAATACTCAATATTTATAATTAGAAAAGGACAATTGAATGAGTTTTGATGAA
1 TAATAGAAATATATAATACTCAATATTTATAATTAGAAAAGAACAATTGAACGAGTTCTGATGAA
543864 TTCGAGTCAAGTTACATCAGACTCATATTATATTAGAT
66 TTCGAGTCAAGTTACATCAGACTCATATTATATTAGAT
543902 TTAGATTTAT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 87 0.92
108 3 0.03
109 5 0.05
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (109 bp):
TAATAGAAATATATAATACTCAATATTTATAATTAGAAAAGAACAATTGAACGAGTTCTGATGAA
TTCGAGTCAAGTTACATCAGACTCATATTATATTAGATATAATG
Found at i:544026 original size:3 final size:3
Alignment explanation
Indices: 544018--544053 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
544008 AAATGAATTG
544018 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
544054 GTTTTTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:544457 original size:11 final size:11
Alignment explanation
Indices: 544441--544476 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
544431 AATATGTTTA
544441 TATATTTATAT
1 TATATTTATAT
*
544452 TATATTTGTAT
1 TATATTTATAT
*
544463 TATTTTTATAT
1 TATATTTATAT
544474 TAT
1 TAT
544477 GTAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:544471 original size:17 final size:18
Alignment explanation
Indices: 544451--544486 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
544441 TATATTTATA
*
544451 TTATATT-TGTATTATTT
1 TTATATTATGTAATATTT
544468 TTATATTATGTAATATTT
1 TTATATTATGTAATATTT
544486 T
1 T
544487 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATATTATGTAATATTT
Found at i:544646 original size:15 final size:14
Alignment explanation
Indices: 544626--544673 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
544616 TAGCTTTTGT
544626 ATTATTTAATTAAAA
1 ATTATTT-ATTAAAA
544641 ATTATTGTATTAATAA
1 ATTATT-TATTAA-AA
544657 ATTA-TTATTAAAA
1 ATTATTTATTAAAA
544670 ATTA
1 ATTA
544674 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 12 0.39
16 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTATTTATTAAAA
Found at i:544660 original size:16 final size:13
Alignment explanation
Indices: 544634--544673 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
544624 GTATTATTTA
544634 ATTAAAAATTATTGT
1 ATTAAAAATTA-T-T
544649 ATTAATAAATTATT
1 ATTAA-AAATTATT
544663 ATTAAAAATTA
1 ATTAAAAATTA
544674 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTAAAAATTATT
Found at i:545583 original size:15 final size:16
Alignment explanation
Indices: 545553--545585 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
545543 ATATGAATAG
545553 ATTTTTTGTTAGATTA
1 ATTTTTTGTTAGATTA
*
545569 ATTTTTT-TTATATTA
1 ATTTTTTGTTAGATTA
545584 AT
1 AT
545586 AGATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTTTTTGTTAGATTA
Found at i:545694 original size:26 final size:27
Alignment explanation
Indices: 545652--545703 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
545642 ATATTTTTAA
*
545652 TTTAATTTTTAATAA-TTAAA-TATAT
1 TTTAATTTTTAAAAATTTAAAGTATAT
*
545677 TTTATTTTTTAAAAAATTTAAAGTATA
1 TTTAATTTTT-AAAAATTTAAAGTATA
545704 ACTTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 5 0.23
28 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAATTTTTAAAAATTTAAAGTATAT
Found at i:545787 original size:20 final size:21
Alignment explanation
Indices: 545749--545801 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
545739 ATAATAAAAT
* * *
545749 AAAATTATAATTATTATTATA
1 AAAAATATAATTATCATTACA
545770 AAAAATATAATTA-CATTACA
1 AAAAATATAATTATCATTACA
* *
545790 AAATATAAAATT
1 AAAAATATAATT
545802 TATAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATATAATTATCATTACA
Found at i:545948 original size:16 final size:17
Alignment explanation
Indices: 545910--545949 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
545900 TATTTATCAA
545910 ATTAAA-ATTTTTAAAT
1 ATTAAATATTTTTAAAT
*
545926 ATCAAATATTTTTAAAT
1 ATTAAATATTTTTAAAT
545943 -TTAAATA
1 ATTAAATA
545950 AATAATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAATATTTTTAAAT
Found at i:546036 original size:40 final size:41
Alignment explanation
Indices: 545960--546038 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 41
545950 AATAATTCAA
*
545960 TTTAAATGTATTAATAATAAATAATATATATTTTATATAAT
1 TTTAAATGTATTAATAATAAATAATATATATATTATATAAT
* ** *
546001 TTTAAAT-TATTAATAATATATTTTATTTATATTATATA
1 TTTAAATGTATTAATAATAAATAATATATATATTATATA
546039 TAAATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (41 bp):
TTTAAATGTATTAATAATAAATAATATATATATTATATAAT
Found at i:550820 original size:48 final size:48
Alignment explanation
Indices: 550761--550856 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
550751 TTGATTTGCA
550761 AGATGCTACTTTTTGTGTGGTTGTAGTTAAGTGCTGTTGATGGGCTTG
1 AGATGCTACTTTTTGTGTGGTTGTAGTTAAGTGCTGTTGATGGGCTTG
550809 AGATGCTACTTTTTGTGTGGTTGTAGTTAAGTGCTGTTGATGGGCTTG
1 AGATGCTACTTTTTGTGTGGTTGTAGTTAAGTGCTGTTGATGGGCTTG
550857 TCATGGATAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.15, C:0.08, G:0.33, T:0.44
Consensus pattern (48 bp):
AGATGCTACTTTTTGTGTGGTTGTAGTTAAGTGCTGTTGATGGGCTTG
Found at i:550857 original size:25 final size:25
Alignment explanation
Indices: 550781--550857 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 25
550771 TTTTGTGTGG
550781 TTGTAGTTAAGTGCTGTTGATGGGC
1 TTGTAGTTAAGTGCTGTTGATGGGC
* * *
550806 TTG-AG--ATGCTACTTTTTG-TGTGG-
1 TTGTAGTTAAG-TGC-TGTTGATG-GGC
550829 TTGTAGTTAAGTGCTGTTGATGGGC
1 TTGTAGTTAAGTGCTGTTGATGGGC
550854 TTGT
1 TTGT
550858 CATGGATACC
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 16 0.42
25 11 0.29
26 2 0.05
ACGTcount: A:0.14, C:0.08, G:0.34, T:0.44
Consensus pattern (25 bp):
TTGTAGTTAAGTGCTGTTGATGGGC
Found at i:555020 original size:22 final size:22
Alignment explanation
Indices: 554992--555038 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
554982 ATGCTAAGAA
554992 TGATTATGATTTTGAACAGCTT
1 TGATTATGATTTTGAACAGCTT
555014 TGATTATGATTTTGAACAGCTT
1 TGATTATGATTTTGAACAGCTT
555036 TGA
1 TGA
555039 GAGGAACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (22 bp):
TGATTATGATTTTGAACAGCTT
Found at i:571103 original size:15 final size:15
Alignment explanation
Indices: 571085--571123 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
571075 AATCAAAAGT
*
571085 AAACACAAAAAAACA
1 AAACAAAAAAAAACA
571100 AAACAAAAAAAAAC-
1 AAACAAAAAAAAACA
*
571114 ACACAAAAAA
1 AAACAAAAAA
571124 GTGTAAAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAAACA
Found at i:571106 original size:25 final size:27
Alignment explanation
Indices: 571073--571123 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
571063 AAAATGATAA
**
571073 AAAATCAAAAGTAAACACA-AAAAAAC
1 AAAATCAAAAAAAAACACACAAAAAAC
571099 AAAA-CAAAAAAAAACACACAAAAAA
1 AAAATCAAAAAAAAACACACAAAAAA
571124 GTGTAAAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.78, C:0.16, G:0.02, T:0.04
Consensus pattern (27 bp):
AAAATCAAAAAAAAACACACAAAAAAC
Found at i:571107 original size:12 final size:12
Alignment explanation
Indices: 571085--571123 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
571075 AATCAAAAGT
571085 AAACACAAAAAA
1 AAACACAAAAAA
*
571097 ACAAAACAAAAAA
1 A-AACACAAAAAA
571110 AAACACACAAAAA
1 AAACACA-AAAAA
571123 A
1 A
571124 GTGTAAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACACAAAAAA
Found at i:572295 original size:16 final size:17
Alignment explanation
Indices: 572270--572307 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
572260 TTGTGCTGTA
*
572270 ATCATGACATC-ATAAC
1 ATCATAACATCAATAAC
*
572286 ATCATAACATCAATAAT
1 ATCATAACATCAATAAC
572303 ATCAT
1 ATCAT
572308 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:572455 original size:31 final size:30
Alignment explanation
Indices: 572407--572796 Score: 424
Period size: 31 Copynumber: 12.5 Consensus size: 30
572397 TTCAAATACC
*
572407 TTCTTAAAGTCCACGACTCAGTGGCAATCTT
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
*
572438 TTCTCAAAGCCCACGACTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATC-TT
*
572469 CCTTCTTAAAGTCCACGACTCAGTGGCAATCTT
1 --TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
** *
572502 TTCTCAAAACCCATGACTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATC-TT
*
572533 CCTTCTTAAAGTCCACGACTCAGTGGCAATCTT
1 --TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
* * *
572566 TTCTCAAAGCCCATGACTCAGTGGCATC-C
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
* *
572595 TTCTTAAAGTCCACGACTCAGTGGCATC-C
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
* * *
572624 TTCTTAAAGTCCACGACTTAGTGACAATCTT
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
* *
572655 TTCTCAAAGCCCATGACTCAGTGGCATCTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
*
572685 TCTTTCAAAGTCCACGACTCAGTGGCATCTATT
1 T-TCTCAAAGTCCACGACTCAGTGGCATC--TT
572718 TTCTTCAAAGTCCACGACTCAGTGGCATCTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTT
*
572749 TTCCTTCTTAAAGTCCACGACTTAGTGGCATCTT
1 TT-C-TC--AAAGTCCACGACTCAGTGGCATCTT
*
572783 GTCTCAAAGTCCAC
1 TTCTCAAAGTCCAC
572797 ACCTCCGTGG
Statistics
Matches: 309, Mismatches: 33, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
29 49 0.16
30 27 0.09
31 118 0.38
32 7 0.02
33 77 0.25
34 31 0.10
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (30 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:572506 original size:64 final size:63
Alignment explanation
Indices: 572405--572782 Score: 452
Period size: 64 Copynumber: 6.0 Consensus size: 63
572395 TCTTCAAATA
572405 CCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTCTCAAAGCCCACGACTCAGTGGCATCTTT
1 CCTTCTTAAAGTCCACGACTCAGTGGC-ATCTTTTCTCAAAGCCCACGACTCAGTGGCATCTTT
* *
572469 CCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTCTCAAAACCCATGACTCAGTGGCATCTTT
1 CCTTCTTAAAGTCCACGACTCAGTGGC-ATCTTTTCTCAAAGCCCACGACTCAGTGGCATCTTT
*
572533 CCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTCTCAAAGCCCATGACTCAGTGGCA----T
1 CCTTCTTAAAGTCCACGACTCAGTGGC-ATCTTTTCTCAAAGCCCACGACTCAGTGGCATCTTT
* * * * *
572593 CCTTCTTAAAGTCCACGACTCAGTGGCATC-CTTCTTAAAGTCCACGACTTAGTGACAATC-TT
1 CCTTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGCCCACGACTCAGTGGC-ATCTTT
* * * * *
572655 --TTCTCAAAGCCCATGACTCAGTGGCATCTTTCTTTCAAAGTCCACGACTCAGTGGCATCTATT
1 CCTTCTTAAAGTCCACGACTCAGTGGCATCTTT-TCTCAAAGCCCACGACTCAGTGGCATCT-TT
* *
572718 --TTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCTTCTTAAAGTCCACGACTTAGTGGCATC
1 CCTTCTT-AAAGTCCACGACTCAGTGGCATCTTTT-C-TC--AAAGCCCACGACTCAGTGGCATC
572781 TT
61 TT
572783 GTCTCAAAGT
Statistics
Matches: 279, Mismatches: 22, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
58 20 0.07
59 4 0.01
60 53 0.19
61 4 0.01
62 21 0.08
63 7 0.03
64 144 0.52
65 2 0.01
66 1 0.00
67 23 0.08
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (63 bp):
CCTTCTTAAAGTCCACGACTCAGTGGCATCTTTTCTCAAAGCCCACGACTCAGTGGCATCTTT
Found at i:572790 original size:64 final size:62
Alignment explanation
Indices: 572407--572846 Score: 401
Period size: 64 Copynumber: 7.0 Consensus size: 62
572397 TTCAAATACC
*
572407 TTCTT-AAAGTCCACGACTCAGTGGCAATCTTTTC-TC-AAAGCCCACGACTCAGTGGCATCT
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTTTTCTTCTAAAGTCCACGACTCAGTGGCATCT
** *
572467 TTCCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTC-TC-AAAACCCATGACTCAGTGGCATC
1 TT-CTTC--AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCTAAAGTCCACGACTCAGTGGCATC
572530 T
62 T
* *
572531 TTCCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTC-TC-AAAGCCCATGACTCAGTGGCATC
1 TT-CTTC--AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCTAAAGTCCACGACTCAGTGGCATC
*
572594 C
62 T
* * *
572595 TTCTT-AAAGTCCACGACTCAGTGGCATC-CTTC-T-TAAAGTCCACGACTTAGTGACAATCT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCTAAAGTCCACGACTCAGTGGC-ATCT
* *
572654 TT-TCTCAAAGCCCATGACTCAGTGGCATC-TTTCTT-TCAAAGTCCACGACTCAGTGGCATCTA
1 TTCT-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCT-AAAGTCCACGACTCAGTGGCATC--
572716 TT
62 -T
*
572718 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCTTCTTAAAGTCCACGACTTAGTGGCATCT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT-CTTC-TAAAGTCCACGACTCAGTGGCATCT
* * * * * *
572782 TGTC-TCAAAGTCCAC-ACCTCCGTGGCACCTTGTTCCTT-TTAAGTCCACAATTCTGTGGCATC
1 T-TCTTCAAAGTCCACGA-CTCAGTGGCATCTT-TT-CTTCTAAAGTCCACGACTCAGTGGCATC
572844 T
62 T
572845 TT
1 TT
572847 TTCCTTTTAA
Statistics
Matches: 334, Mismatches: 25, Indels: 40
0.84 0.06 0.10
Matches are distributed among these distances:
58 21 0.06
59 9 0.03
60 46 0.14
61 8 0.02
62 19 0.06
63 25 0.07
64 168 0.50
65 12 0.04
66 3 0.01
67 22 0.07
68 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.32
Consensus pattern (62 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCTAAAGTCCACGACTCAGTGGCATCT
Found at i:572874 original size:97 final size:93
Alignment explanation
Indices: 572458--572971 Score: 317
Period size: 97 Copynumber: 5.4 Consensus size: 93
572448 CCACGACTCA
* ** *
572458 GTGGCATC--TTTCCTTCTTAAAGTCCACGACTCAGTGGCAATCTTTTCTCAAAACCCATGACTC
1 GTGGCATCTTTTTCCTT-TTAAAGTCCACAACTCAGTGGC-ATC-TTTCTCAAAGTCCA-CACTC
* * *
572521 AGTGGCATC-TTTCCTTCTTAAAGTCCACGACTC
62 AGTGGCACCTTTTCCTT-TT-AAGTCCACAATTC
* * ** * *
572554 AGTGGCAATC-TTTT-C--TCAAAGCCCATGACTCAGTGGCATCCTTCTTAAAGTCCACGACTCA
1 -GTGGC-ATCTTTTTCCTTTTAAAGTCCACAACTCAGTGGCATCTTTCTCAAAGTCCAC-ACTCA
* * *
572615 GTGGCATCC--TT-C-TTAAAGTCCACGACTTA
63 GTGGCA-CCTTTTCCTTTTAAGTCCAC-AATTC
* * * **
572644 GTGACAATC-TTTT-C--TCAAAGCCCATGACTCAGTGGCATCTTTCTTTCAAAGTCCACGACTC
1 GTGGC-ATCTTTTTCCTTTTAAAGTCCACAACTCAGTGGCATCTTTC--TCAAAGTCCAC-ACTC
* * ** * *
572705 AGTGGCATCTATTTTCTTCAAAGTCCACGACTC
62 AGTGGCACCT-TTTCCTTTTAAGTCCACAATTC
* *
572738 AGTGGCATC-TTTTCCTTCTTAAAGTCCACGACTTAGTGGCATCTTGTCTCAAAGTCCACACCTC
1 -GTGGCATCTTTTTCCTT-TTAAAGTCCACAACTCAGTGGCATCTT-TCTCAAAGTCCACA-CTC
*
572802 CGTGGCACCTTGTTCCTTTTAAGTCCACAATTC
62 AGTGGCACCTT-TTCCTTTTAAGTCCACAATTC
* * * * *
572835 TGTGGCATCTTTTTCCTTTTAAAGTCCATAACTCCGTGGCACCTTT-T-TAAGTCCACAACTCTG
1 -GTGGCATCTTTTTCCTTTTAAAGTCCACAACTCAGTGGCATCTTTCTCAAAGTCCAC-ACTCAG
*
572898 TGGCACCTTTTTCCTTTTAAAGCCCACAACTTC
64 TGGCACC-TTTTCCTTTT-AAGTCCACAA-TTC
* *
572931 GTGGCATTCTTTTTTCTTTTAAAGTCCACAACTCCGTGGCA
1 GTGGCA-TCTTTTTCCTTTTAAAGTCCACAACTCAGTGGCA
572972 CCCTTGTTCC
Statistics
Matches: 345, Mismatches: 46, Indels: 53
0.78 0.10 0.12
Matches are distributed among these distances:
89 49 0.14
90 3 0.01
91 23 0.07
92 1 0.00
93 25 0.07
94 40 0.12
95 53 0.15
96 38 0.11
97 73 0.21
98 35 0.10
99 5 0.01
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (93 bp):
GTGGCATCTTTTTCCTTTTAAAGTCCACAACTCAGTGGCATCTTTCTCAAAGTCCACACTCAGTG
GCACCTTTTCCTTTTAAGTCCACAATTC
Found at i:572887 original size:27 final size:27
Alignment explanation
Indices: 572849--572909 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
572839 GCATCTTTTT
* *
572849 CCTTTTAAAGTCCATAACTCCGTGGCA
1 CCTTTTTAAGTCCACAACTCCGTGGCA
*
572876 CCTTTTTAAGTCCACAACTCTGTGGCA
1 CCTTTTTAAGTCCACAACTCCGTGGCA
572903 CCTTTTT
1 CCTTTTT
572910 CCTTTTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (27 bp):
CCTTTTTAAGTCCACAACTCCGTGGCA
Found at i:572892 original size:61 final size:61
Alignment explanation
Indices: 572818--573010 Score: 199
Period size: 61 Copynumber: 3.0 Consensus size: 61
572808 ACCTTGTTCC
* * * *
572818 TTTTAAGTCCACAATTCTGTGGCATCTTTTTCCTTTTAAAGTCCATAACTCCGTGGCACCT
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCT
*
572879 TTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGCCCACAACTTCGTGGCATTCTTTT
1 TTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCA--C----
572944 TTCT
60 --CT
* * * * * *
572948 TTTAAAGTCCACAACTCCGTGGCACCCTTGTTCCTTTT-AAGTCCACAACTCTGTGGCATCT
1 TTTTAAGTCCACAACTCTGTGGCA-CCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCT
573009 TT
1 TT
573011 CTCCTGTTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
61 57 0.51
63 1 0.01
69 41 0.37
70 12 0.11
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCT
Found at i:572957 original size:69 final size:68
Alignment explanation
Indices: 572877--573010 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 68
572867 TCCGTGGCAC
* * *
572877 CTTTTTAAGTCCACAACTCTGTGGCA-CCTTTTTCCTTTTAAAGCCCACAACT-TCGTGGCATTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTGTTCCTTTT-AAGCCCACAACTCT-GTGGCA-TC
572940 TTTTTT
63 TTTTTT
*
572946 CTTTTAAAGTCCACAACTCCGTGGCACCCTTGTTCCTTTTAAGTCCACAACTCTGTGGCATCTTT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTGTTCCTTTTAAGCCCACAACTCTGTGGCATCTTT
573011 CTCCTGTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
68 5 0.08
69 41 0.69
70 13 0.22
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (68 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTGTTCCTTTTAAGCCCACAACTCTGTGGCATCTTT
TTT
Found at i:572995 original size:34 final size:34
Alignment explanation
Indices: 572686--573046 Score: 252
Period size: 33 Copynumber: 11.0 Consensus size: 34
572676 TGGCATCTTT
* * * *
572686 CTTTCAAAGTCCACGACTCAGTGGCATCTATTTT-
1 CTTTTAAAGTCCACAACTCCGTGGCACCT-TTTTC
* * * *
572720 C-TTCAAAGTCCACGACTCAGTGGCATC-TTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
* ** * *
572752 CTTCTTAAAGTCCACGACTTAGTGGCATC-TTGT-
1 CTT-TTAAAGTCCACAACTCCGTGGCACCTTTTTC
* * *
572785 C--TCAAAGTCCACACCTCCGTGGCACCTTGTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
* * *
572817 CTTTT-AAGTCCACAATTCTGTGGCATCTTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
*
572850 CTTTTAAAGTCCATAACTCCGTGGCACC----T-
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
*
572879 -TTTT-AAGTCCACAACTCTGTGGCACCTTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
* * * *
572911 CTTTTAAAGCCCACAACTTCGTGGCATTCTTTTTT
1 CTTTTAAAGTCCACAACTCCGTGGCA-CCTTTTTC
*
572946 CTTTTAAAGTCCACAACTCCGTGGCACCCTTGTTC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CCTTTTTC
* * *
572981 CTTTT-AAGTCCACAACTCTGTGGCATCTTTCTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
* * * ** *
573014 CTGTT-AAGCCCACAAGTTAGTGGCACCCTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
573047 TAAAGCCCAC
Statistics
Matches: 265, Mismatches: 46, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
27 20 0.08
28 4 0.02
30 20 0.08
31 7 0.03
32 2 0.01
33 90 0.34
34 82 0.31
35 40 0.15
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.35
Consensus pattern (34 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
Found at i:573086 original size:33 final size:33
Alignment explanation
Indices: 573045--573249 Score: 292
Period size: 33 Copynumber: 6.3 Consensus size: 33
573035 GGCACCCTTT
* *
573045 TCTAAAGCCCACACAAGTTGGTGGTAACCACTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
* *
573078 TCTAAAG-CCACACAAGTCGGTGTCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
* *
573110 TCTAAAGCCCACACAAGTCGGTGGCAACCATTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
573143 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
* * *
573176 TCTAAAGGCCACACAAGTTGGTGGCAACTACTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
*
573209 TCTAAAGCCCACACAAGTTGGTGGCAACC-CT-
1 TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
573240 TCT-AAGCCCA
1 TCTAAAGCCCA
573250 ATATCGCTGG
Statistics
Matches: 158, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.04
31 3 0.02
32 30 0.19
33 118 0.75
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCACTC
Found at i:573237 original size:99 final size:98
Alignment explanation
Indices: 573024--573237 Score: 331
Period size: 99 Copynumber: 2.2 Consensus size: 98
573014 CTGTTAAGCC
* * * *
573024 CACAAGTTAGTGGC-ACCCTTTTCTAAAGCCCACACAAGTTGGTGGTAACCACTCTCTAAAGCCA
1 CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCA
* *
573088 CACAAGTCGGTGTCAACCATTCTCTAAAGCCCA
66 CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
*
573121 CACAAGTCGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGGCC
1 CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAA-GCC
* *
573186 ACACAAGTTGGTGGCAACTACTCTCTAAAGCCCA
65 ACACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
573220 CACAAGTTGGTGGCAACC
1 CACAAGTTGGTGGCAACC
573238 CTTCTAAGCC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
97 12 0.11
98 43 0.41
99 50 0.48
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (98 bp):
CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCA
CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
Found at i:573308 original size:49 final size:49
Alignment explanation
Indices: 573255--573873 Score: 718
Period size: 49 Copynumber: 12.6 Consensus size: 49
573245 GCCCAATATC
573255 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * * *
573304 GCTGGCCTTAAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * *
573353 GCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * *
573401 GCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
573444 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * * *
573493 GCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
573541 GTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * * *
573590 GCTGGACTTGAATCAGCACATTGGCACC-TTACCTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
573638 GCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * * * * *
573687 GTTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * ** *
573736 GCTGGCCTTGAATCAGCATATTGGCGCCTTCATCATTTTTAAAACCCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTT-AAGTCCAATGTA
* * * * * * *
573789 GTTGGCCTTGAATCAGCAAATTAGCATTCTTCTCATCTTCAAGTCTAACTGTT
1 GCTGGCCTTGAATCAGCATATTGGCA-CCTT-T-ATCTTTAAGTCCAA-TGTA
* *
573842 GCT-GACTGTGAATCAGCATATTGACATCCTTT
1 GCTGGCCT-TGAATCAGCATATTGGCA-CCTTT
573874 TTGTCATCTT
Statistics
Matches: 485, Mismatches: 70, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
43 39 0.08
44 1 0.00
47 1 0.00
48 126 0.26
49 240 0.49
52 14 0.03
53 61 0.13
54 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
Found at i:573423 original size:97 final size:97
Alignment explanation
Indices: 573237--573806 Score: 837
Period size: 97 Copynumber: 5.9 Consensus size: 97
573227 TGGTGGCAAC
* *
573237 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
* *
573302 TAGCTGGCCTTAAATCAGCACATTGGCACCTTTA
65 TAGCTGGCCTTGAATCAGCACATTGGCACC-TCA
* *
573336 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
*
573400 CGCTGGCCTTGAATCAGCACATTGG-----CA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTCA
*
573427 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
573492 AGCTGGCCTTGAATCAGCACATTGGCACCTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTCA
*
573524 CCTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
573589 AGCTGGACTTGAATCAGCACATTGGCACCTTA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTCA
*
573621 CCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
573686 AGTTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACC-TCA
* * * * **
573719 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCATTTTTAAAACCCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTT-AAGTCCA
* *
573784 ATGTCGTTGGCCTTGAATCAGCA
62 ATGTAGCTGGCCTTGAATCAGCA
573807 AATTAGCATT
Statistics
Matches: 430, Mismatches: 30, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
91 45 0.10
92 41 0.10
97 224 0.52
98 84 0.20
99 4 0.01
100 1 0.00
101 5 0.01
102 26 0.06
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (97 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTCA
Found at i:573675 original size:146 final size:146
Alignment explanation
Indices: 573242--573765 Score: 738
Period size: 146 Copynumber: 3.6 Consensus size: 146
573232 GCAACCCTTC
* * * *
573242 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATAGCT
*
573307 GGCCTTAAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
*
573372 ATTGGCACCTTGTCTT
131 ATTGGCACCTTATCTT
* * * *
573388 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATAGCT
* * * *
573447 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
* *
573512 ATTGGCACCTCACCTT
131 ATTGGCACCTTATCTT
* * *
573528 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATAGCT
* *
573593 GGACTTGAATCAGCACATTGGCACC-TTACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
573657 ATTGGCACCTTTATCTT
131 ATTGGCACC-TTATCTT
* * * * *
573674 TAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATAGCT
* *
573739 GGCCTTGAATCAGCATATTGGCGCCTT
66 GGCCTTGAATCAGCACATTGGCACCTT
573766 CATCATTTTT
Statistics
Matches: 333, Mismatches: 37, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
140 124 0.37
141 1 0.00
145 45 0.14
146 162 0.49
147 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (146 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATAGCT
GGCCTTGAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
ATTGGCACCTTATCTT
Found at i:576327 original size:24 final size:26
Alignment explanation
Indices: 576300--576350 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
576290 TATCAAAATT
576300 TATTCAT-C-GGGGACACTCCAACCC
1 TATTCATCCAGGGGACACTCCAACCC
*
576324 TATTCCTCCGAGGGGACACTCCAACCC
1 TATTCATCC-AGGGGACACTCCAACCC
576351 CGTTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.20
Consensus pattern (26 bp):
TATTCATCCAGGGGACACTCCAACCC
Found at i:580457 original size:66 final size:66
Alignment explanation
Indices: 580353--580503 Score: 166
Period size: 66 Copynumber: 2.3 Consensus size: 66
580343 TTCCACGTCC
* * * * *
580353 ATGACTCAGTAGCA-TCTTTTTTTTCAAGTCCATGACTTAATGGTAT-CTTTTTTCTTCT-AAGT
1 ATGACTTAGTAGCATTCTTTTCTTCCAAGTCCACGACTTAATGGCATCCTTTTTT-TTCTCAAGT
580415 CT
65 CT
* *
580417 ATGACTTAGTAGCATTCTTTTCCTTCCAAGTCCACGACTTATTGGCATCCTTTTTTTTTTCAAGT
1 ATGACTTAGTAGCATTCTTTT-CTTCCAAGTCCACGACTTAATGGCATCCTTTTTTTTCTCAAGT
580482 CT
65 CT
* *
580484 ACGA-TTAGTGGCATCTCTTT
1 ATGACTTAGTAGCAT-TCTTT
580504 ACCAGGACTC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 13 0.18
65 6 0.08
66 33 0.45
67 21 0.29
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (66 bp):
ATGACTTAGTAGCATTCTTTTCTTCCAAGTCCACGACTTAATGGCATCCTTTTTTTTCTCAAGTC
T
Found at i:580470 original size:33 final size:32
Alignment explanation
Indices: 580322--580470 Score: 129
Period size: 33 Copynumber: 4.6 Consensus size: 32
580312 AAAAGTTCAC
* *
580322 GACTCAGTGGCATCTATTTCCTTCCACGTCCAT
1 GACTTAGTGGCATCT-TTTCCTTCCAAGTCCAT
* * * *
580355 GACTCAGTAGCATCTTTT-TTTTCAAGTCCAT
1 GACTTAGTGGCATCTTTTCCTTCCAAGTCCAT
* * * * *
580386 GACTTAATGGTATCTTTTTTCTTCTAAGTCTAT
1 GACTTAGTGGCATC-TTTTCCTTCCAAGTCCAT
* *
580419 GACTTAGTAGCATTCTTTTCCTTCCAAGTCCAC
1 GACTTAGTGGCA-TCTTTTCCTTCCAAGTCCAT
*
580452 GACTTATTGGCATCCTTTT
1 GACTTAGTGGCAT-CTTTT
580471 TTTTTTCAAG
Statistics
Matches: 91, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
31 20 0.22
32 8 0.09
33 61 0.67
34 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (32 bp):
GACTTAGTGGCATCTTTTCCTTCCAAGTCCAT
Found at i:580496 original size:33 final size:33
Alignment explanation
Indices: 580369--580503 Score: 112
Period size: 33 Copynumber: 4.1 Consensus size: 33
580359 CAGTAGCATC
* * *
580369 TTTTTTTTCAAGTCCATGACTTAATGGTAT-CT
1 TTTTTTTTCAAGTCCACGACTTAGTGGCATCCT
* * * * *
580401 TTTTTCTTCTAAGTCTATGACTTAGTAGCATTCT
1 TTTTTTTTC-AAGTCCACGACTTAGTGGCATCCT
** * *
580435 TTTCCTTCCAAGTCCACGACTTATTGGCATCCTT
1 TTTTTTTTCAAGTCCACGACTTAGTGGCATCC-T
*
580469 TTTTTTTTCAAGTCTACGA-TTAGTGGCATCTCT
1 TTTTTTTTCAAGTCCACGACTTAGTGGCATC-CT
580502 TT
1 TT
580504 ACCAGGACTC
Statistics
Matches: 80, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
32 8 0.10
33 48 0.60
34 24 0.30
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (33 bp):
TTTTTTTTCAAGTCCACGACTTAGTGGCATCCT
Found at i:580650 original size:33 final size:33
Alignment explanation
Indices: 580613--580695 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
580603 CATAACTCTG
* *
580613 TGGCACCTTTTTCCTTTTAAGTCGACAACTCCA
1 TGGCACCTTTTTCCTTTTAAGTCCAAAACTCCA
* * *
580646 TGGCACCTTATTCCTTTTAAGTCCAAAACTTCG
1 TGGCACCTTTTTCCTTTTAAGTCCAAAACTCCA
580679 TGGCACCTTTTT-CTTTT
1 TGGCACCTTTTTCCTTTT
580696 CAAAGCCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 5 0.11
33 39 0.89
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (33 bp):
TGGCACCTTTTTCCTTTTAAGTCCAAAACTCCA
Found at i:580844 original size:27 final size:27
Alignment explanation
Indices: 580785--580843 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
580775 GCACCTTGCT
* *
580785 CCTTTTAAGTCAACAACTCCGTGGTAT
1 CCTTTTAAGTCAACAACTCCATGGTAA
* *
580812 CCTTTTAAGTCTACAACTCTATGG-AA
1 CCTTTTAAGTCAACAACTCCATGGTAA
580838 CCTTTT
1 CCTTTT
580844 TCTTTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.37
Consensus pattern (27 bp):
CCTTTTAAGTCAACAACTCCATGGTAA
Found at i:580898 original size:96 final size:94
Alignment explanation
Indices: 580766--580950 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 94
580756 TTAAGTTCAT
* * * *
580766 AACTCCGTGGCACCTTGCTCCTTTTAAGTCAACAACTCCGTGGTATCCTTTTAAGTCTACAACTC
1 AACTCCGTGACACCTTGCTCCTTTAAAGTCAACAACTCCGTGGCATCCTTTTAAGTCCACAACTC
580831 TATGGAACCTTTTTCTTTTCAAAGCCTAC
66 TATGGAACCTTTTTCTTTTCAAAGCCTAC
** * *
580860 AACTCCGTGACACCCTTTTTCCTTTAAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAAC
1 AACTCCGTGACA-CCTTGCTCCTTT-AAAGTCAACAACTCCGTGGCATCCTTTTAAGTCCACAAC
* * *
580925 TCTGTGGCACCTTTTTCTTTTTAAAG
64 TCTATGGAACCTTTTTCTTTTCAAAG
580951 TCCACATAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 11 0.14
95 10 0.13
96 57 0.73
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (94 bp):
AACTCCGTGACACCTTGCTCCTTTAAAGTCAACAACTCCGTGGCATCCTTTTAAGTCCACAACTC
TATGGAACCTTTTTCTTTTCAAAGCCTAC
Found at i:580940 original size:27 final size:27
Alignment explanation
Indices: 580887--580939 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
580877 TTTCCTTTAA
*
580887 AAGTCCACAACTCCGTGGCATTCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT
*
580914 AAGTCCACAACTCTGTGGCAC-CTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT
580940 TCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACTCTTTT
Found at i:580947 original size:156 final size:156
Alignment explanation
Indices: 580606--580948 Score: 386
Period size: 156 Copynumber: 2.2 Consensus size: 156
580596 CAAAGCCCAT
*
580606 AACTCTGTGGCACCTTTTTCCTTTTAAGTCGACAACTCCATGGCACCTTATTCCTTTTAAGTCCA
1 AACTCTGTGGCACCTTTTTCCTTTTAAGTCAACAACTCCATGG---C-TATTCCTTTTAAGTCCA
* * * * * *
580671 AAACTTCGTGGCACCTTTTTCTTTTCAAAGCCCATAACTCTTGGCCCTTTTTTCCTCCAAAAGTC
62 AAACTTCATGGAACCTTTTTCTTTTCAAAGCCCACAACTCGTGACCCCTTTTTCCTCCAAAAGTC
* * *
580736 CACAACTTCATGGCACCCTATTAAGTTCAT
127 CACAACTCCATGGCACCCTATTAAGTCCAC
* ** * * *
580766 AACTCCGTGGCACCTTGCTCCTTTTAAGTCAACAACTCCGTGG-TA-TCCTTTTAAGTCTACAAC
1 AACTCTGTGGCACCTTTTTCCTTTTAAGTCAACAACTCCATGGCTATTCCTTTTAAGTCCAAAAC
* **
580829 -TCTATGGAACCTTTTTCTTTTCAAAGCCTACAACTCCGTGACACCCTTTTTCCTTTAAAAGTCC
66 TTC-ATGGAACCTTTTTCTTTTCAAAGCCCACAACT-CGTGAC-CCCTTTTTCCTCCAAAAGTCC
* ** *
580893 ACAACTCCGTGGCATTCTTTTAAGTCCAC
128 ACAACTCCATGGCACCCTATTAAGTCCAC
*
580922 AACTCTGTGGCACCTTTTTCTTTTTAA
1 AACTCTGTGGCACCTTTTTCCTTTTAA
580949 AGTCCACATA
Statistics
Matches: 153, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
153 2 0.01
154 44 0.29
155 6 0.04
156 63 0.41
160 38 0.25
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (156 bp):
AACTCTGTGGCACCTTTTTCCTTTTAAGTCAACAACTCCATGGCTATTCCTTTTAAGTCCAAAAC
TTCATGGAACCTTTTTCTTTTCAAAGCCCACAACTCGTGACCCCTTTTTCCTCCAAAAGTCCACA
ACTCCATGGCACCCTATTAAGTCCAC
Found at i:580954 original size:34 final size:34
Alignment explanation
Indices: 580814--580956 Score: 124
Period size: 35 Copynumber: 4.4 Consensus size: 34
580804 CGTGGTATCC
* ** *
580814 TTTT-AAGTCTACAACTCTATGGAACCTTTTTCT
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTTCT
* * *
580847 TTTCAAAG-CCTACAACTCCGTGACACCCTTTTTCC
1 TTTTAAAGTCC-ACAACTCCGTGGCA-CCTTTTTCT
*
580882 TTTAAAAGTCCACAACTCCGTGGCA-----TTC-
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTTCT
*
580910 TTTT-AAGTCCACAACTCTGTGGCACCTTTTTCT
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTTCT
580943 TTTTAAAGTCCACA
1 TTTTAAAGTCCACA
580957 TAAGTCGGTG
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
27 19 0.22
28 3 0.03
29 3 0.03
32 3 0.03
33 8 0.09
34 22 0.25
35 28 0.32
36 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.37
Consensus pattern (34 bp):
TTTTAAAGTCCACAACTCCGTGGCACCTTTTTCT
Found at i:581220 original size:49 final size:49
Alignment explanation
Indices: 581006--582038 Score: 1034
Period size: 49 Copynumber: 20.9 Consensus size: 49
580996 CAGTGGCAAC
* *
581006 TCTTCTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCA----C-
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
581051 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTCTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CT-TCA
* *** * *
581102 TCTTTAAGTCCAATGTCACTGATTTTAAATCAGTACATTGGCACCACACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG-----CACCTTCA
* * *
581156 TCTTCAAGTCTAACGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
581205 TCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
581254 TCTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
581303 TCTTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATCGGCA----C-
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
581347 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTCTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CT-TCA
* * ** * *
581398 TCTTTAAGTCCAACGTCACTAACCTTAAATCAGTACATTGGCACCACACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG-----CACCTTCA
* **
581452 TCTTCAAGTCCAACATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
581501 TCTTTAAGTCTAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
581550 TC-TTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
581598 TCTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
581647 TCTTCAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
581696 TCTTTAAGTCCAATATC-CTTGGTCTTGAATCAGCATATTGGAACATTTA
1 TCTTTAAGTCCAATGTCGC-TGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
581745 TCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCACATTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
581794 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
581843 TCTTCAAGTCCAATGTCACTGACCTTGAATTAGCACCTTGGCATCC-TCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCA
** * * * * *
581892 TCTTTAAGTCTGATATCACTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
581941 ACATTCCTCAGCCCAATGTCGCTAGCCTTGAATCAGCAAATTGGCATTCTTTTCA
1 TC-TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--C-CTTCA
* ** *
581996 TGTTTAAGTATAATGTCGCTGGCCGTGAATCAGCACATTGGCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
582039 TTTTTCTTAT
Statistics
Matches: 818, Mismatches: 131, Indels: 71
0.80 0.13 0.07
Matches are distributed among these distances:
43 71 0.09
44 3 0.00
45 1 0.00
48 43 0.05
49 479 0.59
50 7 0.01
51 2 0.00
52 125 0.15
54 74 0.09
55 7 0.01
56 2 0.00
57 4 0.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (49 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:581445 original size:296 final size:296
Alignment explanation
Indices: 581006--581926 Score: 1288
Period size: 296 Copynumber: 3.1 Consensus size: 296
580996 CAGTGGCAAC
581006 TCTTCTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACTTTTAAGTCCAATATCGCTG
1 TCTT-TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACTTTTAAGTCCAATATCGCTG
*
581071 GCCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAATGTCACTGATTTTAAATCAGT
65 GCCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAATGTCACTGATCTTAAATCAGT
*
581136 ACATTGGCACCACACCTTCATCTTCAAGTCTAACGTCGCTGGCCTTGAATCAGCACATTGGCACC
130 ACATTGGCACCACACCTTCATCTTCAAGTCCAACGTCGCTGGCCTTGAATCAGCACATTGGCACC
581201 TTCATCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATCTTTAAGTCCA
195 TTCATCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATCTTTAAGTCCA
* *
581266 ATGTCGCTGGCATTGAATCAGCACATTGGCACCTTTA
260 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
581303 TCTTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATCGGCACTTTTAAGTCCAATATCGCTGG
1 TCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACTTTTAAGTCCAATATCGCTGG
* * *
581368 CCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAACGTCACTAACCTTAAATCAGTA
66 CCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAATGTCACTGATCTTAAATCAGTA
*
581433 CATTGGCACCACACCTTCATCTTCAAGTCCAACATCGCTGGCCTTGAATCAGCACATTGGCACCT
131 CATTGGCACCACACCTTCATCTTCAAGTCCAACGTCGCTGGCCTTGAATCAGCACATTGGCACCT
*
581498 TCATCTTTAAGTCTAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATC-TTAAGTCCAA
196 TCATCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATCTTTAAGTCCAA
*
581562 TGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCA
261 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
581598 TCTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTTATCTTCAAGCCCAATGT
1 TCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCA-C--T-T-TT-AAGTCCAATAT
* * * * * *
581663 CGTTGGCCTTGAATCAGCACATTGGCA-C-CT-TTATCTTTAAGTCCAATATC-CTTGGTCTTGA
60 CGCTGGCCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAATGTCAC-TGATCTTAA
* * * * * * *
581724 ATCAGCATATTGG-A--ACA--TTTATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATT
124 ATCAGTACATTGGCACCACACCTTCATCTTCAAGTCCAACGTCGCTGGCCTTGAATCAGCACATT
* * * * * *
581784 GGCACATTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTACCTTTATCTTCA
189 GGCACCTTCATCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATCTTTA
* * * *
581849 AGTCCAATGTCACTGACCTTGAATTAGCACCTTGGCATCC-TCA
254 AGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCA
* ** * *
581892 TCTTTAAGTCTGATATCACTGGCCTTGAATCAGCA
1 TCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCA
581927 TATTGGCATC
Statistics
Matches: 564, Mismatches: 51, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
293 92 0.16
294 67 0.12
295 87 0.15
296 238 0.42
297 6 0.01
298 34 0.06
299 3 0.01
300 3 0.01
301 34 0.06
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (296 bp):
TCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACTTTTAAGTCCAATATCGCTGG
CCTTGAATCAGCATATTGGCATCTCTGTCATCTTTAAGTCCAATGTCACTGATCTTAAATCAGTA
CATTGGCACCACACCTTCATCTTCAAGTCCAACGTCGCTGGCCTTGAATCAGCACATTGGCACCT
TCATCTTTAAGTCCAACGTCGTTGGCCTTGAATCAACACATTGGCACCTTTATCTTTAAGTCCAA
TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:591156 original size:17 final size:15
Alignment explanation
Indices: 591133--591201 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 15
591123 TTTTAAAATT
591133 AATTAATATATTATTA
1 AATTAATATATT-TTA
591149 ATATTAATA-ATTTTA
1 A-ATTAATATATTTTA
*
591164 AATTAA-ATA--TAA
1 AATTAATATATTTTA
591176 AATTAATA-A-TTTA
1 AATTAATATATTTTA
*
591189 AATTTAT-TATTTT
1 AATTAATATATTTT
591202 TGAGTTTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
12 9 0.20
13 11 0.25
14 9 0.20
15 4 0.09
16 4 0.09
17 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATATATTTTA
Found at i:591172 original size:15 final size:16
Alignment explanation
Indices: 591133--591173 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
591123 TTTTAAAATT
591133 AATTAATATATTATTA
1 AATTAATATATTATTA
591149 ATATTAATA-ATT-TTA
1 A-ATTAATATATTATTA
591164 AATTAA-ATAT
1 AATTAATATAT
591174 AAAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 7 0.30
15 4 0.17
16 4 0.17
17 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATATATTATTA
Found at i:591710 original size:20 final size:20
Alignment explanation
Indices: 591685--591746 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 20
591675 TTGTATGAGC
591685 TAAAAATATTATTTTAATAA
1 TAAAAATATTATTTTAATAA
591705 TAAAAATATTATTTAAATTTAATAA
1 TAAAAATATTA--T---TTTAATAA
591730 TAAAAATATTATTTTAA
1 TAAAAATATTATTTTAA
591747 ATTATTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 16 0.43
22 1 0.03
23 1 0.03
25 19 0.51
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAATATTATTTTAATAA
Found at i:591725 original size:25 final size:26
Alignment explanation
Indices: 591697--591749 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
591687 AAAATATTAT
591697 TTTAATAATAAAAATATTA-TTTAAA
1 TTTAATAATAAAAATATTATTTTAAA
591722 TTTAATAATAAAAATATTATTTTAAA
1 TTTAATAATAAAAATATTATTTTAAA
591748 TT
1 TT
591750 ATTATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTAATAATAAAAATATTATTTTAAA
Found at i:592387 original size:27 final size:27
Alignment explanation
Indices: 592357--592410 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
592347 ATAATAATAA
* *
592357 AATTAAAT-TAAATTAATTTTATAATTT
1 AATTAAATCTAAA-TAATCTTAAAATTT
*
592384 AATTTAATCTAAATAATCTTAAAATTT
1 AATTAAATCTAAATAATCTTAAAATTT
592411 TATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTAAATCTAAATAATCTTAAAATTT
Found at i:592443 original size:70 final size:67
Alignment explanation
Indices: 592327--592457 Score: 181
Period size: 70 Copynumber: 1.9 Consensus size: 67
592317 TCACTTATCC
* * *
592327 AAATAATCTTAAAAATAATAATAATAATAAAATTAAATTAAATTAATTTTATAATTTAATTTAAT
1 AAATAATCTTAAAAATAATAAAAATAATAAAAATAAATTAAATTAATTTAATAATTTAATTTAAT
592392 CT
66 CT
* * *
592394 AAATAATCTTAAAATTTTATAAAAATTAACTAAAAATAAATTAACTTAATTTAATAATTTAATT
1 AAATAATCTTAAAA-ATAATAAAAA-TAA-TAAAAATAAATTAAATTAATTTAATAATTTAATT
592458 ATAAAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 14 0.25
68 7 0.13
69 3 0.05
70 31 0.56
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (67 bp):
AAATAATCTTAAAAATAATAAAAATAATAAAAATAAATTAAATTAATTTAATAATTTAATTTAAT
CT
Found at i:593125 original size:16 final size:16
Alignment explanation
Indices: 593088--593123 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
593078 TAAATTTTTA
593088 TTTTTAAATTTAGATT
1 TTTTTAAATTTAGATT
*
593104 ATTTTAAATTTA-ATT
1 TTTTTAAATTTAGATT
593119 TTTTT
1 TTTTT
593124 TATTTTGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTTAAATTTAGATT
Found at i:593630 original size:20 final size:21
Alignment explanation
Indices: 593586--593631 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
593576 TTTTACAATT
*
593586 TGTATGGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* *
593607 TGTATCGATACATA-AGTGAA
1 TGTATCGATACAAACAGTAAA
593627 TGTAT
1 TGTAT
593632 GAATACATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:593637 original size:20 final size:20
Alignment explanation
Indices: 593586--593639 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
593576 TTTTACAATT
*
593586 TGTATGGATACAAACAGTAAA
1 TGTAT-GATACATACAGTAAA
*
593607 TGTATCGATACATA-AGTGAA
1 TGTAT-GATACATACAGTAAA
593627 TGTATGAATACAT
1 TGTATG-ATACAT
593640 TCCTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 12 0.41
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATGATACATACAGTAAA
Found at i:593707 original size:20 final size:20
Alignment explanation
Indices: 593679--593719 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
593669 TACATACTGC
593679 TAAGGAAATATATCGACACA
1 TAAGGAAATATATCGACACA
* * *
593699 TAAGTAAATGTATCGATACA
1 TAAGGAAATATATCGACACA
593719 T
1 T
593720 GTTTTCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (20 bp):
TAAGGAAATATATCGACACA
Found at i:593750 original size:20 final size:21
Alignment explanation
Indices: 593707--593762 Score: 96
Period size: 20 Copynumber: 2.7 Consensus size: 21
593697 CATAAGTAAA
593707 TGTATCGATACATGTTTTCAAT
1 TGTATCGATACAT-TTTTCAAT
593729 TGTATCGATACATTTTTC-AT
1 TGTATCGATACATTTTTCAAT
593749 TGTATCGATACATT
1 TGTATCGATACATT
593763 CTAGGTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.47
21 5 0.15
22 13 0.38
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATTTTTCAAT
Found at i:596260 original size:79 final size:77
Alignment explanation
Indices: 596128--596588 Score: 390
Period size: 79 Copynumber: 5.9 Consensus size: 77
596118 TCATCTCGGT
* ** ** * * *
596128 GATACTCCAACTCTGGTTTTATTTCTAAAACATTAATTTTTTACCATCGGGGATACTCCAACCTC
1 GATACTCCAACCCCAGTTTTATTTCTAAAACA-CCATTTTTCACCATAGGGGATACTCCAACCCC
596193 GTTATTTCTGAGGG
65 GTTATTT-TGAGGG
* * * *
596207 GATACTCCAACCCCAGTTTTATTTCTAAAACACCACTTTTTTACCATAAGGGATACTCCTATCCC
1 GATACTCCAACCCCAGTTTTATTTCTAAAACACCA-TTTTTCACCATAGGGGATACTCCAACCCC
*
596272 GTTATTTTTGAGGA
65 GTTA-TTTTGAGGG
* * * * * * * * *
596286 GATACTCTAACTCC-GATTTTATTTTTAAAGCATCGATTTTTCACCATTGGGGATATTCTAACCT
1 GATACTCCAACCCCAG-TTTTATTTCTAAAACA-CCATTTTTCACCATAGGGGATACTCCAACCC
*
596350 CGTTATTTTTGAGAG
64 CGTTA-TTTTGAGGG
* * * * *
596365 AATACTCCAACCCGA-TTTTATTTCTAAAACATCGA-TTTCCACCATTGGGGATACTCCAACCCC
1 GATACTCCAACCCCAGTTTTATTTCTAAAACA-CCATTTTTCACCATAGGGGATACTCCAACCCC
* * *
596428 ATTATTTTCAAAGG
65 GTTATTTT-GAGGG
* * * * * *
596442 GATACTCTAACCCTAATTTTATTTCCAAAACACCGATTTTCCACCATCA-AGGATACTCCAACCC
1 GATACTCCAACCCCAGTTTTATTTCTAAAACACC-ATTTTTCACCAT-AGGGGATACTCCAACCC
*
596506 CGTTATTTTCGAAGG
64 CGTTATTTT-GAGGG
* * * * *
596521 GATACTCTAACCCCAGTTTTATTTCTAAAACATCAATTTTTTATCATCGGGGATACTCCAACCCC
1 GATACTCCAACCCCAGTTTTATTTCTAAAACA-CCATTTTTCACCATAGGGGATACTCCAACCCC
596586 GTT
65 GTT
596589 TTCACTTTCA
Statistics
Matches: 312, Mismatches: 58, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
76 4 0.01
77 42 0.13
78 36 0.12
79 224 0.72
80 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (77 bp):
GATACTCCAACCCCAGTTTTATTTCTAAAACACCATTTTTCACCATAGGGGATACTCCAACCCCG
TTATTTTGAGGG
Found at i:596633 original size:53 final size:51
Alignment explanation
Indices: 596519--596637 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 51
596509 TATTTTCGAA
*
596519 GGGATACTCTAACCCCAGTTTTATTTCTAAAACATCAATTTTTTATCATCG
1 GGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTTATCATCG
* *
596570 GGGATACTCCAACCCC-GTTTTCACTTTC-AAAACATTAAGTTTTTTTTATC-TTG
1 GGGATACTCCAACCCCAGTTTT-A-TTTCTAAAACATCAA---TTTTTTATCATCG
596623 GGGATACTCCAACCC
1 GGGATACTCCAACCC
596638 TTTTATTCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
50 5 0.08
51 25 0.42
52 4 0.07
53 17 0.28
54 9 0.15
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (51 bp):
GGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTTATCATCG
Found at i:598190 original size:15 final size:16
Alignment explanation
Indices: 598170--598199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
598160 TAAAAGGTCT
598170 AAATTT-CTAAAATTA
1 AAATTTACTAAAATTA
598185 AAATTTACTAAAATT
1 AAATTTACTAAAATT
598200 TTTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTACTAAAATTA
Found at i:599355 original size:60 final size:60
Alignment explanation
Indices: 599249--599362 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
599239 AGATATAAAC
* * *
599249 ATTTAATTTAATAAATTAATTTAATTCATGTATGAAGAGAAAAGATGTATATATGAATAT
1 ATTTAATTTAATAAATAAATTTAATTCATGTACGAAGAGAAAAGATGAATATATGAATAT
* * *
599309 ATTTGATTTAATAAATAAATTTGATTCATGTACGAAGA-AAGGAGATGAATATAT
1 ATTTAATTTAATAAATAAATTTAATTCATGTACGAAGAGAA-AAGATGAATATAT
599363 TCAATAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.38
Consensus pattern (60 bp):
ATTTAATTTAATAAATAAATTTAATTCATGTACGAAGAGAAAAGATGAATATATGAATAT
Done.