Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:430846 original size:60 final size:60
Alignment explanation
Indices: 430778--430897 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
430768 ATTCTCTATG
* * *
430778 TGTATTTTTATTGATAATATGTTTTCATCTCTTATAATTTTATAAATTTGCTCCCCTCTA
1 TGTATTTTTATTGATAATATGTTTCCATCTCCTAGAATTTTATAAATTTGCTCCCCTCTA
*
430838 TGTATTTTTATTGATAATATGTTTCCATCTCCTAGAATTTTATAAATTTGCTCCCTTCTA
1 TGTATTTTTATTGATAATATGTTTCCATCTCCTAGAATTTTATAAATTTGCTCCCCTCTA
430898 AGATTTTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (60 bp):
TGTATTTTTATTGATAATATGTTTCCATCTCCTAGAATTTTATAAATTTGCTCCCCTCTA
Found at i:434520 original size:2 final size:2
Alignment explanation
Indices: 434513--434544 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
434503 ATAATATCAA
434513 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
434545 TTCGTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439759 original size:2 final size:2
Alignment explanation
Indices: 439752--439778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
439742 TTTTCCCTCT
439752 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 T
439779 TATGCATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:440464 original size:31 final size:29
Alignment explanation
Indices: 440399--440464 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
440389 TCATTCTATC
* *
440399 ATTAAATTTATAAAAATTATAAAATAGTT
1 ATTAAATTTATAAAAACTATAAAATAATT
* *
440428 CTTAAATTTATTAAACAACTATAAAGTAATT
1 ATTAAATTTA-TAAA-AACTATAAAATAATT
440459 ATTAAA
1 ATTAAA
440465 ATCATAATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 9 0.30
30 4 0.13
31 17 0.57
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTAAATTTATAAAAACTATAAAATAATT
Found at i:445894 original size:18 final size:16
Alignment explanation
Indices: 445871--445919 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
445861 TGTTTCCGAG
445871 GGAATTAGAATCTGTTAA
1 GGAATT-GAATCTG-TAA
*
445889 GGAATTGAAATCTGTCA
1 GGAATTG-AATCTGTAA
445906 GGAATTGGAATCTG
1 GGAATT-GAATCTG
445920 AATCTGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (16 bp):
GGAATTGAATCTGTAA
Found at i:446537 original size:14 final size:14
Alignment explanation
Indices: 446486--446670 Score: 91
Period size: 15 Copynumber: 13.1 Consensus size: 14
446476 AAAAGTAATG
*
446486 AAGATAAATAAACTA
1 AAGA-AAATAAAATA
446501 AAGAAAAATAAAATA
1 AAG-AAAATAAAATA
*
446516 AAGGAAATGAAAAT-
1 AAGAAAAT-AAAATA
*
446530 AAGAAAATAAGATA
1 AAGAAAATAAAATA
* * *
446544 AACAAAAGACAAAAA
1 AAGAAAATA-AAATA
*
446559 AATAAAGATAAAA-A
1 AAGAAA-ATAAAATA
**
446573 AACTAAATAAAATA
1 AAGAAAATAAAATA
*
446587 AAGAACATAAAA-A
1 AAGAAAATAAAATA
* *
446600 ATGAAGA-AAAATA
1 AAGAAAATAAAATA
446613 AAGATAACAAGTAAAATA
1 AAG--AA-AA-TAAAATA
*
446631 AA-ATAA-AAAAT-
1 AAGAAAATAAAATA
446642 AAG--AATAAAATA
1 AAGAAAATAAAATA
446654 AAGGAAAATACAAATA
1 AA-GAAAATA-AAATA
446670 A
1 A
446671 TTGTATATAC
Statistics
Matches: 131, Mismatches: 20, Indels: 37
0.70 0.11 0.20
Matches are distributed among these distances:
10 2 0.02
11 7 0.05
12 11 0.08
13 20 0.15
14 35 0.27
15 38 0.29
16 10 0.08
18 8 0.06
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (14 bp):
AAGAAAATAAAATA
Found at i:446574 original size:24 final size:24
Alignment explanation
Indices: 446533--446619 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 24
446523 TGAAAATAAG
446533 AAAAT-AAGATAAACAAAAGACAAA
1 AAAATAAAGATAAA-AAAAGACAAA
446557 AAAATAAAGAT-AAAAAA-ACTAAA
1 AAAATAAAGATAAAAAAAGAC-AAA
* *
446580 TAAAATAAAGAACATAAAAAATGA-AGA
1 -AAAATAAAG---ATAAAAAAAGACAAA
446607 AAAATAAAGATAA
1 AAAATAAAGATAA
446620 CAAGTAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
22 2 0.04
23 11 0.21
24 16 0.30
25 5 0.09
26 9 0.17
27 4 0.08
28 5 0.09
29 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.13
Consensus pattern (24 bp):
AAAATAAAGATAAAAAAAGACAAA
Found at i:446598 original size:26 final size:25
Alignment explanation
Indices: 446556--446616 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
446546 CAAAAGACAA
*
446556 AAAAATAAAGATA-AAAAAACT-AA-
1 AAAAATAAAGA-ACAAAAAAATGAAG
446579 ATAAAATAAAGAACATAAAAAATGAAG
1 A-AAAATAAAGAACA-AAAAAATGAAG
446606 AAAAATAAAGA
1 AAAAATAAAGA
446617 TAACAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 2 0.06
24 11 0.34
25 6 0.19
26 12 0.38
27 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.13
Consensus pattern (25 bp):
AAAAATAAAGAACAAAAAAATGAAG
Found at i:446630 original size:18 final size:17
Alignment explanation
Indices: 446607--446655 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
446597 AAAATGAAGA
* *
446607 AAAATAAAGATAACAAGT
1 AAAATAAA-ATAAAAAAT
446625 AAAATAAAATAAAAAAT
1 AAAATAAAATAAAAAAT
446642 AAGAATAAAATAAA
1 AA-AATAAAATAAA
446656 GGAAAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAAAAT
Found at i:446633 original size:23 final size:23
Alignment explanation
Indices: 446533--446655 Score: 64
Period size: 23 Copynumber: 5.3 Consensus size: 23
446523 TGAAAATAAG
* *
446533 AAAATAAGATAAACAAA-AGACAAA
1 AAAATAAAATAAA-AAATA-ACAAT
446557 AAAATAAAGAT-AAAAA-AAC--T
1 AAAATAAA-ATAAAAAATAACAAT
*
446577 -AAATAAAATAAAGAACATAAAAAAT
1 AAAATAAAATAAA-AA-AT-AACAAT
* *
446602 GAAGA-AAAAT-AAAGATAACAAGT
1 -AAAATAAAATAAAAAATAACAA-T
*
446625 AAAATAAAATAAAAAATAAGAAT
1 AAAATAAAATAAAAAATAACAAT
446648 AAAATAAA
1 AAAATAAA
446656 GGAAAATACA
Statistics
Matches: 77, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
18 2 0.03
19 9 0.12
20 2 0.03
21 1 0.01
22 9 0.12
23 23 0.30
24 19 0.25
25 5 0.06
26 5 0.06
27 2 0.03
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAATAAAATAAAAAATAACAAT
Found at i:446650 original size:13 final size:12
Alignment explanation
Indices: 446504--446655 Score: 59
Period size: 13 Copynumber: 12.2 Consensus size: 12
446494 TAAACTAAAG
446504 AAAAATAAAATA
1 AAAAATAAAATA
446516 AAGGAAATGAAAATA
1 AA--AAAT-AAAATA
*
446531 AGAAAATAAGATA
1 A-AAAATAAAATA
*
446544 AACAAA-AGACA-A
1 AA-AAATA-AAATA
446556 AAAAATAAAGATA
1 AAAAATAAA-ATA
446569 AAAAA-ACTAAATA
1 AAAAATA--AAATA
446582 AAATAA-AGAACATA
1 AAA-AATA-AA-ATA
* *
446596 AAAAAT-GAA-G
1 AAAAATAAAATA
446606 AAAAATAAAGATA
1 AAAAATAAA-ATA
* *
446619 ACAAGTAAAATA
1 AAAAATAAAATA
446631 AAATAA-AAAAT-
1 AAA-AATAAAATA
*
446642 AAGAATAAAATA
1 AAAAATAAAATA
446654 AA
1 AA
446656 GGAAAATACA
Statistics
Matches: 107, Mismatches: 13, Indels: 40
0.67 0.08 0.25
Matches are distributed among these distances:
10 8 0.07
11 13 0.12
12 24 0.22
13 35 0.33
14 19 0.18
15 7 0.07
16 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:446772 original size:14 final size:14
Alignment explanation
Indices: 446754--446823 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
446744 ACTAATATTA
446754 AAAAATTAAAAAAAG
1 AAAAA-TAAAAAAAG
*
446769 AAAAGA-AAAAAAAT
1 AAAA-ATAAAAAAAG
* *
446783 AAAAGTAAAGAAAAC
1 AAAAATAAA-AAAAG
*
446798 AACAAATAAAATAAG
1 AA-AAATAAAAAAAG
446813 AAAAATAAAAA
1 AAAAATAAAAA
446824 GTAAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
14 22 0.50
15 15 0.34
16 7 0.16
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAAAAG
Found at i:463563 original size:17 final size:17
Alignment explanation
Indices: 463541--463574 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
463531 ATCCTTATAC
463541 TTAAATAAAATAATAAT
1 TTAAATAAAATAATAAT
* *
463558 TTAAATTAAATATTAAT
1 TTAAATAAAATAATAAT
463575 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAAAATAATAAT
Found at i:467033 original size:15 final size:16
Alignment explanation
Indices: 467013--467045 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
467003 TGAGAAGCTT
*
467013 ATGGAAAGA-AAAAAA
1 ATGGAAACAGAAAAAA
467028 ATGGAAACAGAAAAAA
1 ATGGAAACAGAAAAAA
467044 AT
1 AT
467046 TAAAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.09
Consensus pattern (16 bp):
ATGGAAACAGAAAAAA
Found at i:470811 original size:63 final size:63
Alignment explanation
Indices: 470708--470828 Score: 197
Period size: 63 Copynumber: 1.9 Consensus size: 63
470698 CGAAGCATCT
*
470708 CTTTTCTTCAACATTTACGTTAGGCAATAGGCTTTGCCTAGCTAAGCTGTCTCTAATCTGTTC
1 CTTTTCTTCAACATTTACGTTAGGCAATAGGCTTTGCCTAGCTAAGCTATCTCTAATCTGTTC
** * *
470771 CTTTTCTTCAACATTTTTGTTAGGCAATAGGCTTTTCCTAGGTAAGCTATCTCTAATC
1 CTTTTCTTCAACATTTACGTTAGGCAATAGGCTTTGCCTAGCTAAGCTATCTCTAATC
470829 ACTTCCCTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (63 bp):
CTTTTCTTCAACATTTACGTTAGGCAATAGGCTTTGCCTAGCTAAGCTATCTCTAATCTGTTC
Found at i:473016 original size:22 final size:22
Alignment explanation
Indices: 472973--473016 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
472963 TTTTTTTAAT
* **
472973 TTTTTATTAAATGTTTTTAATA
1 TTTTTATTAAATATTTAAAATA
*
472995 TTTTTATTTAATATTTAAAATA
1 TTTTTATTAAATATTTAAAATA
473017 ATTATGACAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTATTAAATATTTAAAATA
Found at i:474594 original size:19 final size:19
Alignment explanation
Indices: 474570--474815 Score: 80
Period size: 19 Copynumber: 12.9 Consensus size: 19
474560 TCCAAGTTCG
*
474570 CGTTGCGATTTTCTAAATT
1 CGTTGCGATTTTCCAAATT
474589 CGTTGCGATTTTCCAAA-T
1 CGTTGCGATTTTCCAAATT
* *
474607 --TTACG-TTAGTCCAAATT
1 CGTTGCGATT-TTCCAAATT
** * *
474624 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
*
474643 CGCGTTACGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
** *
474664 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
** *
474683 CACGTT-CGAAGTT-C----G
1 --CGTTGCGATTTTCCAAATT
474698 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
474717 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
** * *
474736 CACGTTGCGATAGTCGAAGTTT
1 --CGTTGCGATTTTCCAA-ATT
* *
474758 GTGTTGCGATTTTCAAAATT
1 -CGTTGCGATTTTCCAAATT
** * *
474778 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
474797 CGCGTTGCGATTTTCCAAA
1 --CGTTGCGATTTTCCAAA
474816 ATCGCAACGA
Statistics
Matches: 164, Mismatches: 43, Indels: 38
0.67 0.18 0.16
Matches are distributed among these distances:
13 4 0.02
14 5 0.03
15 3 0.02
16 10 0.06
17 1 0.01
18 1 0.01
19 73 0.45
20 7 0.04
21 58 0.35
22 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:474662 original size:40 final size:40
Alignment explanation
Indices: 474551--474815 Score: 205
Period size: 40 Copynumber: 6.9 Consensus size: 40
474541 CAACGCGATT
*
474551 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCTAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
** * ** *
474591 TTGCGATTTTCCAAATTTACGTT---A--GTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* *
474626 TTGCGATAGTCGAAGTTCGCGTTACGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
* ** *
474666 TTGCGATAGTCCAAGTTCACGTT-CGAAGTT-C----GCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
** * ** *
474700 TTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CG
* * * *
474740 TTGCGATAGTCGAAGTTTGTGTTGCGATTTTCAAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
474780 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA
474816 ATCGCAACGA
Statistics
Matches: 172, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
32 4 0.02
33 4 0.02
34 17 0.10
35 26 0.15
37 1 0.01
38 2 0.01
39 5 0.03
40 99 0.58
42 14 0.08
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:474701 original size:53 final size:53
Alignment explanation
Indices: 474635--474741 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
474625 GTTGCGATAG
474635 TCGAAGTTCGCGTTACGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
1 TCGAAGTTCGCGTTACGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
*
474688 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
1 TCGAAGTTCGCGTTACGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
474741 T
1 T
474742 GCGATAGTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (53 bp):
TCGAAGTTCGCGTTACGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
Found at i:474743 original size:21 final size:21
Alignment explanation
Indices: 474691--474807 Score: 98
Period size: 21 Copynumber: 5.8 Consensus size: 21
474681 TTCACGTTCG
**
474691 AAGTTCGCGTTGCGATTTTCC
1 AAGTTCGCGTTGCGATAGTCC
*
474712 AAATT--CGTTGCGATAGTCC
1 AAGTTCGCGTTGCGATAGTCC
* *
474731 AAGTTCACGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATAGTCC
* * ** *
474752 AAGTTTGTGTTGCGATTTTCA
1 AAGTTCGCGTTGCGATAGTCC
* *
474773 AAATT--CGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATAGTCC
474792 AAGTTCGCGTTGCGAT
1 AAGTTCGCGTTGCGAT
474808 TTTCCAAAAT
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
19 30 0.40
21 45 0.60
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
AAGTTCGCGTTGCGATAGTCC
Found at i:474783 original size:61 final size:61
Alignment explanation
Indices: 474688--474807 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
474678 AAGTTCACGT
*
474688 TCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAG
1 TCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAG
* * * *
474749 TCGAAGTTTGTGTTGCGATTTTCAAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1 TCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGAT
474808 TTTCCAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (61 bp):
TCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAG
Found at i:474820 original size:21 final size:21
Alignment explanation
Indices: 474760--474820 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
474750 CGAAGTTTGT
*
474760 GTTGCGATTTT-CAAAAT-TC
1 GTTGCGATTTTCCAAAATCGC
** * **
474779 GTTGCGATAGTCGAAGTTCGC
1 GTTGCGATTTTCCAAAATCGC
474800 GTTGCGATTTTCCAAAATCGC
1 GTTGCGATTTTCCAAAATCGC
474821 AACGACTGGT
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 17 0.59
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (21 bp):
GTTGCGATTTTCCAAAATCGC
Found at i:475243 original size:19 final size:20
Alignment explanation
Indices: 475218--475308 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
475208 CTTATTTTGG
475218 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
475238 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
475258 ACGTTTTTCAAACTTTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
475282 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
475301 ATTTTTCA
1 ATTTTTCA
475309 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:475280 original size:44 final size:41
Alignment explanation
Indices: 475229--475310 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
475219 TTTTTCACTA
* *
475229 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTT
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTT
475273 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
475311 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTT
Found at i:476136 original size:11 final size:11
Alignment explanation
Indices: 476107--476139 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
476097 AAAATTTTTG
476107 ATTTATAATTA
1 ATTTATAATTA
476118 ATTT-TAATTA
1 ATTTATAATTA
*
476128 TTTTATAATTA
1 ATTTATAATTA
476139 A
1 A
476140 AAAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTATAATTA
Found at i:479731 original size:25 final size:26
Alignment explanation
Indices: 479683--479732 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
479673 ATATAATTAC
*
479683 ATATATCAAAGTTCATTTATTATATT
1 ATATATCAAAGTTAATTTATTATATT
* *
479709 ATATATTAAA-TTAATTTTTTATAT
1 ATATATCAAAGTTAATTTATTATAT
479733 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
ATATATCAAAGTTAATTTATTATATT
Found at i:509366 original size:16 final size:16
Alignment explanation
Indices: 509345--509377 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
509335 TTATGGAGTT
509345 AGTCACTTGAAAACTC
1 AGTCACTTGAAAACTC
509361 AGTCACTTGAAAACTC
1 AGTCACTTGAAAACTC
509377 A
1 A
509378 CTCTTTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
AGTCACTTGAAAACTC
Found at i:510769 original size:21 final size:21
Alignment explanation
Indices: 510744--510783 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
510734 ATACCTTGTC
510744 TTTTTATTAATAAAA-ATATAT
1 TTTTTATTAA-AAAACATATAT
*
510765 TTTTTGTTAAAAAACATAT
1 TTTTTATTAAAAAACATAT
510784 CTTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTTATTAAAAAACATATAT
Found at i:512889 original size:21 final size:21
Alignment explanation
Indices: 512865--513040 Score: 81
Period size: 21 Copynumber: 8.6 Consensus size: 21
512855 ACTTCGACTA
*
512865 TCGCATTACGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
512886 TCGCGTTGCGA-TTTACATAT
1 TCGCATTGCGATTTTCCAAAT
** *
512906 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTTCCAAAT
* ** ** *
512927 TCGCGTTGCGATAGTCGGAGT
1 TCGCATTGCGATTTTCCAAAT
*
512948 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
** *
512969 TCG--TTGCGATAGTCCAAGT
1 TCGCATTGCGATTTTCCAAAT
* * ** * *
512988 TCACGTTGCGATAGTCGAAGT
1 TCGCATTGCGATTTTCCAAAT
* * * *
513009 TCACGTTGCGA-TTTACATAT
1 TCGCATTGCGATTTTCCAAAT
513029 TCGCATTGCGAT
1 TCGCATTGCGAT
513041 AGTCGAAGTT
Statistics
Matches: 117, Mismatches: 34, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
19 14 0.12
20 29 0.25
21 74 0.63
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:512985 original size:61 final size:61
Alignment explanation
Indices: 512885--513061 Score: 248
Period size: 61 Copynumber: 2.9 Consensus size: 61
512875 ATTTTCCAAA
*
512885 TTCGCGTTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGGAG
1 TTCGCGTTGCGATTTACATATTCG-ATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
* * * *
512947 TTCGCATTGCGATTTTTCAAATTCG-TTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTTACATATTCGATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
* * *
513008 TTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGCTGCGAT
1 TTCGCGTTGCGATTTACATATTCG-ATTGCGATAGTCCAAGTTCGCGTTGCGAT
513062 TTTTCAAATT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 10 0.10
61 44 0.44
62 36 0.36
63 10 0.10
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (61 bp):
TTCGCGTTGCGATTTACATATTCGATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
Found at i:513059 original size:21 final size:21
Alignment explanation
Indices: 512905--513061 Score: 128
Period size: 21 Copynumber: 7.6 Consensus size: 21
512895 GATTTACATA
* *
512905 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCGAAG
*
512926 TTCGCGTTGCGATAGTCGGAG
1 TTCGCGTTGCGATAGTCGAAG
* ** *
512947 TTCGCATTGCGATTTTTC-AAA
1 TTCGCGTTGCGA-TAGTCGAAG
*
512968 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCGAAG
*
512987 TTCACGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
513008 TTCACGTTGCGAT-TTAC-ATA-
1 TTCGCGTTGCGATAGT-CGA-AG
*
513028 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
513049 TTCGCGCTGCGAT
1 TTCGCGTTGCGAT
513062 TTTTCAAATT
Statistics
Matches: 108, Mismatches: 19, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
18 3 0.03
19 11 0.10
20 15 0.14
21 76 0.70
22 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:514048 original size:21 final size:21
Alignment explanation
Indices: 514018--514058 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
514008 GCGATTTTGA
*
514018 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTAGACTATCG
*
514039 CAACGTGAACTTAGACTATC
1 CAACGCGAACTTAGACTATC
514059 TTGGAAACAC
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:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (21 bp):
CAACGCGAACTTAGACTATCG
Found at i:514311 original size:21 final size:21
Alignment explanation
Indices: 514281--514373 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
514271 CGATTTTTGA
514281 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
* *
514302 CAACGTGAACTTAGACTATCG
1 CAACGCGAACTTCGACTATCG
*
514323 CAACGCGAACTCCGACTATCG
1 CAACGCGAACTTCGACTATCG
* * * *
514344 CAAAGTGAACTTGGACTATTG
1 CAACGCGAACTTCGACTATCG
*
514365 CAATGCGAA
1 CAACGCGAA
514374 TAAGTAAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:514340 original size:42 final size:42
Alignment explanation
Indices: 514281--514373 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
514271 CGATTTTTGA
* *
514281 CAACGCGAACTTCGACTATCGCAACGTGAACTTAGACTATCG
1 CAACGCGAACTCCGACTATCGCAAAGTGAACTTAGACTATCG
* *
514323 CAACGCGAACTCCGACTATCGCAAAGTGAACTTGGACTATTG
1 CAACGCGAACTCCGACTATCGCAAAGTGAACTTAGACTATCG
*
514365 CAATGCGAA
1 CAACGCGAA
514374 TAAGTAAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (42 bp):
CAACGCGAACTCCGACTATCGCAAAGTGAACTTAGACTATCG
Found at i:518083 original size:14 final size:15
Alignment explanation
Indices: 518064--518093 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
518054 GTTTTTAATT
518064 TATTTAA-TTATTGA
1 TATTTAATTTATTGA
518078 TATTTAATTTATTGA
1 TATTTAATTTATTGA
518093 T
1 T
518094 TAACTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATTTAATTTATTGA
Found at i:527672 original size:11 final size:11
Alignment explanation
Indices: 527656--527682 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
527646 AGTTAAATAT
527656 ATAAACAAACA
1 ATAAACAAACA
527667 ATAAACAAACA
1 ATAAACAAACA
527678 ATAAA
1 ATAAA
527683 TAAAATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (11 bp):
ATAAACAAACA
Found at i:532724 original size:2 final size:2
Alignment explanation
Indices: 532717--532760 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
532707 AGTACCTACA
532717 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
532759 AT
1 AT
532761 TATTTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533262 original size:26 final size:27
Alignment explanation
Indices: 533214--533267 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
533204 CAAACGTCCC
**
533214 ATTAATTAAGAACCAAGACCCCTACCA
1 ATTAATTAAGAAAAAAGACCCCTACCA
533241 ATTAATTAA-AAAAAAGACCCCTACCA
1 ATTAATTAAGAAAAAAGACCCCTACCA
533267 A
1 A
533268 CCTCTCCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.50, C:0.26, G:0.06, T:0.19
Consensus pattern (27 bp):
ATTAATTAAGAAAAAAGACCCCTACCA
Found at i:543275 original size:31 final size:30
Alignment explanation
Indices: 543196--543281 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
543186 ACTCTTAAAT
* *
543196 TTTAGATAAAATAATAATTTGACCCTGTAT
1 TTTAGATAAAATATTAATTTGACCCTGTAC
* * **
543226 TTTA-AAAAAAAATTAATTTGATCTTTGTAC
1 TTTAGATAAAATATTAATTTGA-CCCTGTAC
*
543256 TTTAGATAAAATATTAATTTAACCCT
1 TTTAGATAAAATATTAATTTGACCCT
543282 TGAATATTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
29 14 0.33
30 15 0.35
31 14 0.33
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTAGATAAAATATTAATTTGACCCTGTAC
Found at i:547606 original size:2 final size:2
Alignment explanation
Indices: 547599--547627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
547589 ACCATCTCTT
547599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
547628 TAATTAGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:552167 original size:2 final size:2
Alignment explanation
Indices: 552160--552188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
552150 TATTTTAATT
552160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
552189 CGGGTTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:552380 original size:39 final size:39
Alignment explanation
Indices: 552320--552396 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
552310 TGTTTGTTAA
* *
552320 AAATATAGTGTGACTTTATCCATAATCATTCTTATATAC
1 AAATATAGTGTGACATGATCCATAATCATTCTTATATAC
*
552359 AAATATAGTGTGACATGATCCATAGTCATTCTTATATA
1 AAATATAGTGTGACATGATCCATAATCATTCTTATATA
552397 TAAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (39 bp):
AAATATAGTGTGACATGATCCATAATCATTCTTATATAC
Found at i:561093 original size:39 final size:40
Alignment explanation
Indices: 561045--561125 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 40
561035 ACCGTAAACT
561045 AAAACACATAATAATAACATTTTTCTATATTTATTAATAAA
1 AAAACA-ATAATAATAACATTTTTCTATATTTATTAATAAA
561086 AAAACATAATAATAATAACATTTTTCTATATTTATTAATA
1 AAAAC--AATAATAATAACATTTTTCTATATTTATTAATA
561126 CGAAAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 5 0.13
42 32 0.84
43 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.41
Consensus pattern (40 bp):
AAAACAATAATAATAACATTTTTCTATATTTATTAATAAA
Found at i:563437 original size:25 final size:25
Alignment explanation
Indices: 563403--563450 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
563393 TGCATTAATT
563403 AACTTTATCCCTCTTGTATATAAAG
1 AACTTTATCCCTCTTGTATATAAAG
*
563428 AACTTTATCCCTCTTGTTTATAA
1 AACTTTATCCCTCTTGTATATAA
563451 GTTTGCATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (25 bp):
AACTTTATCCCTCTTGTATATAAAG
Found at i:568404 original size:22 final size:23
Alignment explanation
Indices: 568360--568404 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
568350 TTCGGTTTAA
*
568360 ATTGATTAATTAATAAATTAAAT
1 ATTGATTAATTAATAAATAAAAT
568383 ATTGA-TAATTAA-AATATAAAAT
1 ATTGATTAATTAATAA-ATAAAAT
568405 TAATAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 13 0.65
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTGATTAATTAATAAATAAAAT
Found at i:568410 original size:20 final size:20
Alignment explanation
Indices: 568374--568411 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
568364 ATTAATTAAT
*
568374 AAATTAAATATTGATAATTA
1 AAATTAAATATTAATAATTA
568394 AAATATAAA-ATTAATAAT
1 AAAT-TAAATATTAATAAT
568412 ACTTAAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTAAATATTAATAATTA
Found at i:568694 original size:15 final size:15
Alignment explanation
Indices: 568628--568695 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
568618 TGCATAATGA
*
568628 AAAATATAAAATTTG
1 AAAATATAAAATTTT
*
568643 AAATTATAAAA--TT
1 AAAATATAAAATTTT
568656 AAAGTATTGATAAAAATATTT
1 AAA--A-T-AT-AAAAT-TTT
568677 AAAATATAAAATTTT
1 AAAATATAAAATTTT
568692 AAAA
1 AAAA
568696 ATAGTACCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
13 4 0.10
15 17 0.40
16 6 0.14
17 4 0.10
18 5 0.12
19 1 0.02
21 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
AAAATATAAAATTTT
Found at i:572872 original size:31 final size:31
Alignment explanation
Indices: 572837--572904 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
572827 TCAATAAAGT
* **
572837 TTAAAAAATTATAAAATTCTTATTAAATTTA
1 TTAAAAAATTATAAAATTATTAACAAATTTA
*
572868 TTAAAAGATTATAAAATTATTAACAAATTTA
1 TTAAAAAATTATAAAATTATTAACAAATTTA
572899 TCTAAA
1 T-TAAA
572905 TACTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAACAAATTTA
Found at i:572912 original size:31 final size:31
Alignment explanation
Indices: 572837--572920 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
572827 TCAATAAAGT
* * * **
572837 TTAAAAAATTATAAAATTCTTATTAAATTTA
1 TTAAAAGACTATAAAATTATTAACAAATTTA
*
572868 TTAAAAGATTATAAAATTATTAACAAATTTA
1 TTAAAAGACTATAAAATTATTAACAAATTTA
* *
572899 TCT-AAATACTATAAAATAATTA
1 T-TAAAAGACTATAAAATTATTA
572921 TTATATTATC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAGACTATAAAATTATTAACAAATTTA
Found at i:577933 original size:37 final size:37
Alignment explanation
Indices: 577860--577934 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
577850 GTTGAAAAAT
* *
577860 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
577897 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
577934 A
1 A
577935 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:578536 original size:29 final size:29
Alignment explanation
Indices: 578482--578569 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
578472 CTTCCCAGCA
* * *
578482 TAGGTCGCCATGC-CCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACGT-TGGGAGACCTTG
578511 TAGGTCGCCATGCACGTTGGGAGACCTT-
1 TAGGTCGCCATGCACGTTGGGAGACCTTG
*** * *
578539 TTCCTGCGCCTTGCACGCTGGGAGACCTTG
1 TAGGT-CGCCATGCACGTTGGGAGACCTTG
578569 T
1 T
578570 CCTGCGCCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.04
29 43 0.90
30 3 0.06
ACGTcount: A:0.12, C:0.32, G:0.31, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACGTTGGGAGACCTTG
Found at i:578572 original size:29 final size:29
Alignment explanation
Indices: 578516--578581 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
578506 CCTTGTAGGT
* * *
578516 CGCCATGCACGTTGGGAGACCTTTTCCTG
1 CGCCTTGCACGCTGGGAGACCTTGTCCTG
578545 CGCCTTGCACGCTGGGAGACCTTGTCCTG
1 CGCCTTGCACGCTGGGAGACCTTGTCCTG
578574 CGCCTTGC
1 CGCCTTGC
578582 TTCCCGCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.11, C:0.35, G:0.29, T:0.26
Consensus pattern (29 bp):
CGCCTTGCACGCTGGGAGACCTTGTCCTG
Found at i:578974 original size:30 final size:29
Alignment explanation
Indices: 578927--578985 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
578917 CCATTTGAAC
* *
578927 AATTATTTTTTGGACAGCATTATCACGTG
1 AATTATTTTTTGCACAGCAATATCACGTG
* *
578956 AATTATTTTTTTTCACAGCAATATCTCGTG
1 AATTA-TTTTTTGCACAGCAATATCACGTG
578986 CGTTTTGCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (29 bp):
AATTATTTTTTGCACAGCAATATCACGTG
Found at i:585917 original size:15 final size:15
Alignment explanation
Indices: 585899--585986 Score: 140
Period size: 15 Copynumber: 5.9 Consensus size: 15
585889 ATAAGGTTAT
* *
585899 TTATTTTAAAATAAT
1 TTATTATAAAATAAA
*
585914 TTATTATAAAATAAT
1 TTATTATAAAATAAA
585929 TTATTATAAAATAAA
1 TTATTATAAAATAAA
585944 TTATTATAAAATAAA
1 TTATTATAAAATAAA
*
585959 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
585974 TTATTATAAAATA
1 TTATTATAAAATA
585987 TGGATTGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 69 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:585933 original size:30 final size:30
Alignment explanation
Indices: 585897--586048 Score: 144
Period size: 30 Copynumber: 4.8 Consensus size: 30
585887 TAATAAGGTT
585897 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
585927 ATTTATTATAAAATAAATTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
585957 AATTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A
* * *
585991 TTGATTTATTTTAAAATAATTTATTAGTATGTATTG
1 ---ATTTATTTTAAAATAATTTATTA-TA--AAATA
586027 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
586049 GTATGGATTG
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
30 50 0.49
31 3 0.03
32 15 0.15
33 9 0.09
34 1 0.01
37 22 0.21
38 2 0.02
39 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:586045 original size:32 final size:32
Alignment explanation
Indices: 585985--586542 Score: 218
Period size: 32 Copynumber: 17.5 Consensus size: 32
585975 TATTATAAAA
585985 TATGGATTGATTTATTTTAAAATAATTTATTAG
1 TATGGATTGATTTATTTT-AAATAATTTATTAG
*
586018 TATGTATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
586050 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
586072 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* **
586104 CATGGATTGATTTATTTTAAA-ATATGGATT-G
1 TATGGATTGATTTATTTTAAATA-ATTTATTAG
** * * *
586135 -ATTTATT-ATTGTAGTTGTATGGATTGATTTATT--
1 TATGGATTGATT-TA-TT-T-T-AAATAATTTATTAG
* * * * *
586168 T-T-AAATAATTTATTAGTATGAATTGATTTATT--
1 TATGGATTGATTTATT--T-T-AAATAATTTATTAG
* * * * * *
586200 T-T-AAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATT--T-T-AAATAATTTA--TT--AG
586238 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
586270 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
586302 TATGGATTGATTTATTTTAAAATATGGATTTATTTAT
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAG
* ** * * *
586339 TATTGTAGTTGTATGGATTGA-TTTATTTTAAATAATTTAT
1 TA-TGGA-TTG-AT---TT-ATTTTA-AATAATTTA-TTAG
* * * * *
586379 TA-GTATGGATTGA-TTT--AT--TTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
586404 TATTGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
586436 TATGGAATGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
586468 TATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAATAATTTA-TTAG
586494 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
586526 TATGAATTGATTTATTT
1 TATGGATTGATTTATTT
586543 CAAAATATGG
Statistics
Matches: 422, Mismatches: 47, Indels: 113
0.73 0.08 0.19
Matches are distributed among these distances:
22 14 0.03
23 4 0.01
25 4 0.01
26 28 0.07
27 7 0.02
28 7 0.02
29 7 0.02
30 11 0.03
31 16 0.04
32 221 0.52
33 28 0.07
34 10 0.02
36 15 0.04
37 8 0.02
38 8 0.02
39 4 0.01
40 21 0.05
42 1 0.00
43 7 0.02
44 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:586066 original size:22 final size:22
Alignment explanation
Indices: 586050--586092 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
586040 AATTTATTAG
586050 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
586072 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
586093 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:586081 original size:54 final size:54
Alignment explanation
Indices: 586018--586456 Score: 458
Period size: 54 Copynumber: 8.0 Consensus size: 54
586008 AATTTATTAG
*
586018 TATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
586072 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
586126 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA
*
586176 TTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 --TA-T-G---G-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
586238 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT---TAA---A--A
** * ***
586301 GTATGGATTGATTTATTTTAAA-ATATGGATT--TAT---TT-A-TTATTGTAGTTG
1 -TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTA-AAA
586350 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
586404 TATTGATTGATTTATTTTAAATAATTTATTAGTATGGAATGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
586457 TAATTTATTT
Statistics
Matches: 326, Mismatches: 21, Indels: 76
0.77 0.05 0.18
Matches are distributed among these distances:
48 47 0.14
49 5 0.02
50 7 0.02
52 4 0.01
53 5 0.02
54 159 0.49
55 11 0.03
56 2 0.01
57 4 0.01
58 14 0.04
59 3 0.01
60 4 0.01
61 1 0.00
62 7 0.02
63 6 0.02
64 47 0.14
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:586180 original size:14 final size:14
Alignment explanation
Indices: 586161--586213 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
586151 GTATGGATTG
586161 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
586175 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
586193 ATTTATTTTAAATA
1 ATTTATTTTAAATA
586207 ATTTATT
1 ATTTATT
586214 AGTATGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:586195 original size:166 final size:166
Alignment explanation
Indices: 585985--586542 Score: 763
Period size: 166 Copynumber: 3.3 Consensus size: 166
585975 TATTATAAAA
*
585985 TATGGATTGATTTATTTTAAAATAATTTATTAGTATGTATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAG
*
586050 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGAT
65 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
586115 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
130 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
586152 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
*
586217 ATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
66 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
** ** *
586282 TATTTT-AAATAATTTATTAGTATGGATTGATT-TA-TTT
131 TATTTTAAAAT-ATGGATT-G-ATTTATT-ATTGTAGTTG
** * *
586319 TA-AAATATGGATTTA-TTT--ATTATTGTAGTT-GTATGGATTGATTTATTTTAAATAATTTAT
1 TATGGAT-T-GATTTATTTTAAATAATT-TA-TTAGTATGAATTGATTTATTTTAAATAATTTAT
* *
586379 TAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTTTAAATAATTTATTAGTATGGAAT
62 TAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATT
586444 GATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTATTGTAGTTG
127 GATTTATTTT--A-AA---A----TATGGATTGATTTATTATTGTAGTTG
586494 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
586543 CAAAATATGG
Statistics
Matches: 341, Mismatches: 24, Indels: 43
0.84 0.06 0.11
Matches are distributed among these distances:
165 9 0.03
166 225 0.66
167 29 0.09
168 13 0.04
169 3 0.01
170 2 0.01
173 4 0.01
174 13 0.04
175 11 0.03
176 26 0.08
177 6 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (166 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
ATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
TATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:586208 original size:198 final size:197
Alignment explanation
Indices: 585985--586456 Score: 680
Period size: 198 Copynumber: 2.4 Consensus size: 197
585975 TATTATAAAA
585985 TATGGATTGATTTATTTTAAAATAATTTATTAGTATGTATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTT-AAATAATTTATTAGTATG-ATTGATTTATTTTAAATAATTTATTAG
586050 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGAT
64 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGAT
586115 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTA
129 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTA
586180 TTAG
194 TTAG
* **
586184 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA-ATATGGATT-G
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAATA-ATTTATTAG
** * ** * * * *
586247 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
64 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTG
*
586311 ATTTATTTTAAAATATGGATTTATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATT
127 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATT
586376 TATTAG
192 TATTAG
586382 TATGGATTGATTTATTTT--A-AA---A-TA-T-TGATTGATTTATTTTAAATAATTTATTAGTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATAATTTATTAGTA
*
586438 TGGAATGATTTATTTTAAA
66 TGGATTGATTTATTTTAAA
586457 TAATTTATTT
Statistics
Matches: 242, Mismatches: 25, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
188 22 0.09
189 12 0.05
190 4 0.02
191 2 0.01
192 1 0.00
195 2 0.01
196 4 0.02
197 11 0.05
198 167 0.69
199 17 0.07
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (197 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTT
ATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATT
AG
Found at i:586241 original size:22 final size:22
Alignment explanation
Indices: 586216--586258 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
586206 AATTTATTAG
586216 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
586238 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
586259 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:586263 original size:86 final size:86
Alignment explanation
Indices: 586152--586542 Score: 582
Period size: 86 Copynumber: 4.6 Consensus size: 86
586142 ATTGTAGTTG
586152 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
*
586217 ATGAATTGATTTATTTTAAAA
66 ATGGATTGATTTATTTTAAAA
*
586238 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
586303 ATGGATTGATTTATTTTAAAA
66 ATGGATTGATTTATTTTAAAA
* * *
586324 TATGGATTTATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAATAATTTATTAG
586382 TATGGATTGATTTATTTTAAAA
65 TATGGATTGATTTATTTTAAAA
* *
586404 TATTGATTGATTTATTTTAAATAATTTATTAGTATGGAA-TGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAATAATTTATTAG
***
586468 TATGGATTGATTTATTATTGTAGTTG
65 TATGGATTGATTTA-T-TT-TA-AAA
586494 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
586543 CAAAATATGG
Statistics
Matches: 278, Mismatches: 13, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
80 70 0.25
81 2 0.01
82 4 0.01
84 4 0.01
85 2 0.01
86 142 0.51
87 3 0.01
88 2 0.01
89 5 0.02
90 44 0.16
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (86 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
ATGGATTGATTTATTTTAAAA
Found at i:586432 original size:14 final size:14
Alignment explanation
Indices: 586413--586466 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
586403 ATATTGATTG
586413 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
586427 ATTTATTAGTATGGAATG
1 ATTTATT--T-T-AAATA
586445 ATTTATTTTAAATA
1 ATTTATTTTAAATA
586459 ATTTATTT
1 ATTTATTT
586467 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:586565 original size:54 final size:58
Alignment explanation
Indices: 586436--586578 Score: 195
Period size: 58 Copynumber: 2.5 Consensus size: 58
586426 AATTTATTAG
* * * * ***
586436 TATGGAATGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTATTGCAGAAA
586494 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-T-TT-CA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTATTGCAGAAA
586548 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
586579 TTGTAGTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
54 31 0.40
55 1 0.01
56 2 0.03
57 1 0.01
58 43 0.55
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (58 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTATTGCAGAAA
Found at i:586628 original size:31 final size:31
Alignment explanation
Indices: 586593--586651 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
586583 AGTTGTATGG
* *
586593 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
586624 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
586652 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:587531 original size:43 final size:43
Alignment explanation
Indices: 587483--587603 Score: 172
Period size: 43 Copynumber: 2.8 Consensus size: 43
587473 TATAGCGGCG
* *
587483 AACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTGGCAGAA-A
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCA-AACA
* * *
587526 AACGCCTCAATAGGTGTTGATATTTAACGGCATTTGGCAAACA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAAACA
*
587569 AACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTT
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
587604 TCTTCACAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 2 0.03
43 66 0.97
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (43 bp):
AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAAACA
Found at i:587613 original size:43 final size:43
Alignment explanation
Indices: 587483--587703 Score: 155
Period size: 43 Copynumber: 5.1 Consensus size: 43
587473 TATAGCGGCG
* * * * *
587483 AACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTGGC-AGAAA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCTACACA
* * * * *
587526 AACGCCTCAATAGGTGTTGATATTTAACGGCATTTGGC-AAACA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCTACACA
* *
587569 AACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCTTCACA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCTACACA
* * * * * * *
587612 AACGTCGCAAGAGATGTTGATTTTTA-CTGACGTTTT-TCCTACT
1 AACGCCGCAATAGGTGTTGATATTTAGC-GGCGTTTTCTAC-ACA
* * * *
587655 AACGCCGCAATATGTGTTGAGATTTAGCGGTGTTTT-TATCAAA
1 AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCTA-CACA
587698 AACGCC
1 AACGCC
587704 ACTAAATGTA
Statistics
Matches: 141, Mismatches: 32, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
42 4 0.03
43 135 0.96
44 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (43 bp):
AACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCTACACA
Found at i:588087 original size:21 final size:21
Alignment explanation
Indices: 588046--588111 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
588036 TTATATATTA
*
588046 CTTCTCTCT-AGCTGCCACTG
1 CTTCTCTCTGTGCTGCCACTG
**
588066 CTTCTCTCTGTGCTGCTGCTG
1 CTTCTCTCTGTGCTGCCACTG
* **
588087 CCTCTCTCTGTATTGCCACTG
1 CTTCTCTCTGTGCTGCCACTG
588108 CTTC
1 CTTC
588112 CGCTGCTGCT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.06, C:0.38, G:0.17, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTGTGCTGCCACTG
Found at i:595001 original size:82 final size:83
Alignment explanation
Indices: 594909--595072 Score: 190
Period size: 83 Copynumber: 2.0 Consensus size: 83
594899 TACAATAATA
* * * *
594909 TTACGGCGTTT-ATCAAAAAACGCCGTACCATTAAT-ACTCAATAGCGGCGTTTG-TACAAAAAC
1 TTACGGCGTTTGATCAAAAAACACC--ACAATAAATAACTCAATACCGGCGTTTGTTACAAAAAC
*
594971 GTCGCTAAATGACTACTCTT
64 GCCGCTAAATGACTACTCTT
* * * * *
594991 TTACGGCGTTTGTTGATAAAACACCACAATAAATAACTCTATACCGGCGTTTGTTCCAAAAACGC
1 TTACGGCGTTTGATCAAAAAACACCACAATAAATAACTCAATACCGGCGTTTGTTACAAAAACGC
*
595056 CGCTAAATTACTACTCT
66 CGCTAAATGACTACTCT
595073 ATTGCGGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 7 0.10
82 27 0.40
83 34 0.50
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (83 bp):
TTACGGCGTTTGATCAAAAAACACCACAATAAATAACTCAATACCGGCGTTTGTTACAAAAACGC
CGCTAAATGACTACTCTT
Found at i:595280 original size:41 final size:42
Alignment explanation
Indices: 595218--595456 Score: 217
Period size: 41 Copynumber: 5.8 Consensus size: 42
595208 TTGTAGTGAT
*
595218 TATTGCGGCGTTTGTT-AAAAAACGCCACTATTGATTAAAAC
1 TATTGCGGCGTTTGTTGTAAAAACGCCACTATTGATTAAAAC
*
595259 TATTGCGGCGTTT-TTGTAAAAACGCCACTATTGATTAACAC
1 TATTGCGGCGTTTGTTGTAAAAACGCCACTATTGATTAAAAC
* * *
595300 TATTGCGGCGTTTG-TATAAAAACGCCACTATTTATTATAAC
1 TATTGCGGCGTTTGTTGTAAAAACGCCACTATTGATTAAAAC
* * * *
595341 TATTGCGACGTTT-TAAG-AATAAATGCCACTATATG-TGT-AATC
1 TATTGCGGCGTTTGT-TGTAA-AAACGCCACTAT-TGAT-TAAAAC
* * * * * *
595383 TATTGCGGCGTTTGTGGTATAAATGCCGCTAAT--TTACAGATC
1 TATTGCGGCGTTTGTTGTAAAAACGCCACTATTGATTA-A-AAC
*
595425 TATTGCGGCGTTTGTTGTAAAAACGCCGCTAT
1 TATTGCGGCGTTTGTTGTAAAAACGCCACTAT
595457 ATGTCAACTC
Statistics
Matches: 164, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 88 0.54
42 68 0.41
43 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (42 bp):
TATTGCGGCGTTTGTTGTAAAAACGCCACTATTGATTAAAAC
Found at i:595457 original size:84 final size:82
Alignment explanation
Indices: 595218--595493 Score: 265
Period size: 84 Copynumber: 3.3 Consensus size: 82
595208 TTGTAGTGAT
* * *
595218 TATTGCGGCGTTTGT-TAAAAAACGCCACTATTGATTAAAACTATTGCGGCGTTTTTGTAAAAAC
1 TATTGCGGCGTTTGTAT-AAAAACGCCACTATTTATCAGAACTATTGCGGCGTTTTTGTAAAAAC
*
595282 GCCACTAT-TGATTAACAC
65 GCCACTATATG-TTAACTC
* * * *
595300 TATTGCGGCGTTTGTATAAAAACGCCACTATTTATTATAACTATTGCGACGTTTTAAG-AATAAA
1 TATTGCGGCGTTTGTATAAAAACGCCACTATTTATCAGAACTATTGCGGCGTTTT-TGTAA-AAA
*
595364 TGCCACTATATGTGTAA-TC
64 CGCCACTATATGT-TAACTC
* * * * *
595383 TATTGCGGCGTTTGTGGTATAAATGCCGCTAATTTA-CAGATCTATTGCGGCGTTTGTTGTAAAA
1 TATTGCGGCGTTTGT-ATAAAAACGCCACT-ATTTATCAGAACTATTGCGGCGTTT-TTGTAAAA
* *
595447 ACGCCGCTATATGTCAACTC
63 ACGCCACTATATGTTAACTC
* * *
595467 TATTGCAGCGTTTTTACAACAAACGCC
1 TATTGCGGCGTTTGTATAA-AAACGCC
595494 GCTAAAGTAT
Statistics
Matches: 159, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
82 52 0.33
83 33 0.21
84 66 0.42
85 8 0.05
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (82 bp):
TATTGCGGCGTTTGTATAAAAACGCCACTATTTATCAGAACTATTGCGGCGTTTTTGTAAAAACG
CCACTATATGTTAACTC
Found at i:596112 original size:119 final size:119
Alignment explanation
Indices: 595901--596139 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 119
595891 CTTTTGTTAG
595901 ATCTAGGATTAACATCTAAGCCTAGATAAAAACAGGTGTTTACATGGAAATCTTTTATGAATTTG
1 ATCTAGGATTAACATCTAAGCCTAGATAAAAACAGGTGTTTACATGGAAATCTTTTATGAATTTG
*
595966 ATTTTTTTTTTTATATTTTGATGATGTGACACTATGAGATTATGTTATGGGTCA
66 ATTTTTTTTTATATATTTTGATGATGTGACACTATGAGATTATGTTATGGGTCA
596020 ATCTAGGATTAACATCTAAGCCTAGATAAAAACAGGTGTTTACATGGAAATCTTTTATGAATTTG
1 ATCTAGGATTAACATCTAAGCCTAGATAAAAACAGGTGTTTACATGGAAATCTTTTATGAATTTG
596085 ATTTTTTTTTATATATTTTGATGATGTGACACTATGAGATTATGTTATGGGTCA
66 ATTTTTTTTTATATATTTTGATGATGTGACACTATGAGATTATGTTATGGGTCA
596139 A
1 A
596140 AATATCATAG
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (119 bp):
ATCTAGGATTAACATCTAAGCCTAGATAAAAACAGGTGTTTACATGGAAATCTTTTATGAATTTG
ATTTTTTTTTATATATTTTGATGATGTGACACTATGAGATTATGTTATGGGTCA
Found at i:597933 original size:26 final size:25
Alignment explanation
Indices: 597891--597940 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
597881 TGTTTGTATA
597891 TAATTATTGAAATTTAATTTATTATT
1 TAATTATTGAAATTTAATTT-TTATT
*
597917 TAATTATTTTAAA-TTAATTTTTAT
1 TAATTA-TTGAAATTTAATTTTTAT
597941 AAATATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 13 0.59
27 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATTATTGAAATTTAATTTTTATT
Found at i:598895 original size:34 final size:31
Alignment explanation
Indices: 598852--598926 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 31
598842 CTAAACCCGG
598852 CCCGACCCGACCCGAACAGTACATTTTAAAAAAA
1 CCCGACCCGACCCGAA-A-T-CATTTTAAAAAAA
**
598886 CCCGACCCGACCCGAAATTTTTTTAAAAAAA
1 CCCGACCCGACCCGAAATCATTTTAAAAAAA
*
598917 TCCGACCCGA
1 CCCGACCCGA
598927 TCAGGTCGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.53
32 1 0.03
33 1 0.03
34 16 0.42
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.17
Consensus pattern (31 bp):
CCCGACCCGACCCGAAATCATTTTAAAAAAA
Found at i:600341 original size:226 final size:227
Alignment explanation
Indices: 599909--600370 Score: 574
Period size: 226 Copynumber: 2.0 Consensus size: 227
599899 ACATAACCAG
* * * * * *
599909 TTAATTACTATAAATATTATTAACCATAATAACATAACAGGTAGCGTTTATGTAACGTAATAGGT
1 TTAATTACTAGAAACATTATAAACCATAATAACATAACAAGCAGCGCTTATGTAACGTAATAGGT
* * * *
599974 AGCACATTTTTAAAGTTGATGCGGACTTTAGAAATCCGACGATAACAAAATAAGTTAATTACTTG
66 AGCACATTTTTAAAGCTGATGCGGACATTAGAAATCCGACAATAACAAAATAAGTTAATTACTTA
* * * *
600039 ATTTGTTATCAATATTATCAACATATTAGGTAGCGCTTAAAATGTTACTAAAGTCTAAGCTGATA
131 ATTTGTTATCAATATTATCAACATATTAGATAGAGCCTAAAATGTTACTAAAGTCTAAGCTAATA
* *
600104 GATCCTTAGAAATCCGACGATAAAAAAATAAA
196 GAGCATTAGAAATCCGACGATAAAAAAATAAA
* * * * *
600136 TTAATTACTGGAAACATTATAAACCATAATAACATAGCAAGCATCGCTTATTTAATGTAATAGGT
1 TTAATTACTAGAAACATTATAAACCATAATAACATAACAAGCAGCGCTTATGTAACGTAATAGGT
* * * *
600201 AGCATC-TTTTTAAAGCTGAT--GGAGCATTAGAAATCTGACAATAATAAAATAGGTTAATTATT
66 AGCA-CATTTTTAAAGCTGATGCGGA-CATTAGAAATCCGACAATAACAAAATAAGTTAATTACT
*
600263 TAATTTGTTATCAATATTATCAACATATTAGATAGAGCCTAAAATAG-TA-TCAAAGTTTAAGCT
129 TAATTTGTTATCAATATTATCAACATATTAGATAGAGCCTAAAAT-GTTACT-AAAGTCTAAGCT
* * * **
600326 AATAGGGCATTAGAAATCTGACGATAACAAAATATG
192 AATAGAGCATTAGAAATCCGACGATAAAAAAATAAA
600362 TTAATTACT
1 TTAATTACT
600371 TATTTTGTTA
Statistics
Matches: 200, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
225 4 0.02
226 123 0.62
227 72 0.36
228 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (227 bp):
TTAATTACTAGAAACATTATAAACCATAATAACATAACAAGCAGCGCTTATGTAACGTAATAGGT
AGCACATTTTTAAAGCTGATGCGGACATTAGAAATCCGACAATAACAAAATAAGTTAATTACTTA
ATTTGTTATCAATATTATCAACATATTAGATAGAGCCTAAAATGTTACTAAAGTCTAAGCTAATA
GAGCATTAGAAATCCGACGATAAAAAAATAAA
Found at i:600343 original size:108 final size:108
Alignment explanation
Indices: 600224--600489 Score: 329
Period size: 108 Copynumber: 2.5 Consensus size: 108
600214 AGCTGATGGA
* * * *
600224 GCATTAGAAATCTGACAATAATAAAATAGGTTAATTATTTAATTTGTTATCA-ATATTATCAACA
1 GCATTAGAAATCTGACGATAACAAAATAAGTTAATTACTTAATTTGTTATCAGA-ATTATCAACA
* *
600288 TATT-AGATAGAGCCTAAAATAGTATCAAAGTTTAAGCTAATAGG
65 TATTAAG-TAGAGCCTAAAATAGTAGCAAAATTTAAGCTAATAGG
* * *
600332 GCATTAGAAATCTGACGATAACAAAATATGTTAATTACTTATTTTGTTATTAGAATTATCAACAT
1 GCATTAGAAATCTGACGATAACAAAATAAGTTAATTACTTAATTTGTTATCAGAATTATCAACAT
* * * *
600397 ATTAAGTAGCGCCTAAAATATTAGCAAAATTTAAGCTGATGGG
66 ATTAAGTAGAGCCTAAAATAGTAGCAAAATTTAAGCTAATAGG
* * * * * *
600440 GCATTCGAAATCTCACGACAACAAAATAAGTTAATTTCTTATTTTATTAT
1 GCATTAGAAATCTGACGATAACAAAATAAGTTAATTACTTAATTTGTTAT
600490 AAATAAATAT
Statistics
Matches: 138, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
108 135 0.98
109 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (108 bp):
GCATTAGAAATCTGACGATAACAAAATAAGTTAATTACTTAATTTGTTATCAGAATTATCAACAT
ATTAAGTAGAGCCTAAAATAGTAGCAAAATTTAAGCTAATAGG
Found at i:601165 original size:76 final size:76
Alignment explanation
Indices: 601085--601226 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 76
601075 TAGGTATCAC
* * *
601085 CTATTTTATTTTACCGTTTACATTACTAGTAACCATTAAACAAACCGGTAGGTATTTTAACATAA
1 CTATTTTATTTTACCATTTACATTACTAGTAACCATTAAACAAACCAGTAGCTATTTTAACATAA
601150 TTAGGTAGCGT
66 TTAGGTAGCGT
* * * * * *
601161 CTATTTTCTTTTACCATTTACATTATTATTAACCTTTAAATAAACCAGTAGCTATTTTAACGTAA
1 CTATTTTATTTTACCATTTACATTACTAGTAACCATTAAACAAACCAGTAGCTATTTTAACATAA
601226 T
66 T
601227 AGTTAACGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 57 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (76 bp):
CTATTTTATTTTACCATTTACATTACTAGTAACCATTAAACAAACCAGTAGCTATTTTAACATAA
TTAGGTAGCGT
Found at i:601243 original size:23 final size:22
Alignment explanation
Indices: 601216--601279 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
601206 CAGTAGCTAT
601216 TTTAACGTAATAGTTAACGCTTA
1 TTTAACGTAATAG-TAACGCTTA
* *
601239 TTTAACGTAATAAGTAGCTCTTA
1 TTTAACGTAAT-AGTAACGCTTA
*
601262 TTTAACATAATAAGTAAC
1 TTTAACGTAAT-AGTAAC
601280 ACCTATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTAACGTAATAGTAACGCTTA
Found at i:601286 original size:23 final size:23
Alignment explanation
Indices: 601237--601287 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
601227 AGTTAACGCT
* * * *
601237 TATTTAACGTAATAAGTAGCTCT
1 TATTTAACATAATAAGTAACACC
601260 TATTTAACATAATAAGTAACACC
1 TATTTAACATAATAAGTAACACC
601283 TATTT
1 TATTT
601288 TATTTTACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (23 bp):
TATTTAACATAATAAGTAACACC
Found at i:601323 original size:197 final size:195
Alignment explanation
Indices: 600970--601403 Score: 490
Period size: 197 Copynumber: 2.2 Consensus size: 195
600960 AAGTTGTATA
* * * * * *
600970 TATTTTATCGTTTACATTATTATTAATCTTTAAACAAATCCGTAACTAGTTTAATGTTATAGATA
1 TATTTTACCATTTACATTATTATTAACCTTTAAATAAA-CCGTAACTAGTTTAACGTAATAGATA
* * * ** ** * *
601035 TCGCTTATTTCACGTTATCGGTAGCACCTATTTAATTTAATAGGTATCACCTATTTTATTTTACC
65 ACGCTTATTTAACGTAATAAGTAGCACCTATTTAACATAATAAGTAACACCTATTTTATTTTACC
* ** * **
601100 GTTTACATTACTAGTAACCATTAAACAAACCGGTAGGTATTTTAACATAATTAGGTAGCGTCTAT
130 GTTTACATTACTAGTAACCATTAAACAAACAGGTAAATATTTTAACATAA-TAAGTAGCACCTAT
601165 TT
194 TT
* * * *
601167 TCTTTTACCATTTACATTATTATTAACCTTTAAATAAACCAGTAGCTATTTTAACGTAATAGTTA
1 TATTTTACCATTTACATTATTATTAACCTTTAAATAAACC-GTAACTAGTTTAACGTAATAGATA
* *
601232 ACGCTTATTTAACGTAATAAGTAGCTCTTATTTAACATAATAAGTAACACCTATTTTATTTTACC
65 ACGCTTATTTAACGTAATAAGTAGCACCTATTTAACATAATAAGTAACACCTATTTTATTTTACC
* * ** * *
601297 GTTTACATTATTATTAACTTTTAAACAAACATGTAAATATTTTAACGTAATAAGTAGCACCTATT
130 GTTTACATTACTAGTAACCATTAAACAAACAGGTAAATATTTTAACATAATAAGTAGCACCTATT
601362 T
195 T
*** * * *
601363 TATTTTACTGCTTACATTATTAGTAACATTCAAATAAACCG
1 TATTTTACCATTTACATTATTATTAACCTTTAAATAAACCG
601404 ATAGGTAGTT
Statistics
Matches: 196, Mismatches: 40, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
195 1 0.01
196 48 0.24
197 147 0.75
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (195 bp):
TATTTTACCATTTACATTATTATTAACCTTTAAATAAACCGTAACTAGTTTAACGTAATAGATAA
CGCTTATTTAACGTAATAAGTAGCACCTATTTAACATAATAAGTAACACCTATTTTATTTTACCG
TTTACATTACTAGTAACCATTAAACAAACAGGTAAATATTTTAACATAATAAGTAGCACCTATTT
Found at i:601416 original size:75 final size:75
Alignment explanation
Indices: 601262--601444 Score: 215
Period size: 75 Copynumber: 2.4 Consensus size: 75
601252 GTAGCTCTTA
* * * * *
601262 TTTAACATAATAAGTAACACCTATTTTATTTTACCGTTTACATTATTATTAACTTTTAAACAAAC
1 TTTAACATAATAAGTAGCACCTATTTTATTTTACCGCTTACATTATTAGTAACATTCAAACAAAC
* *
601327 ATGTAAATAT
66 ACGTAAATAG
* * *
601337 TTTAACGTAATAAGTAGCACCTATTTTATTTTACTGCTTACATTATTAGTAACATTCAAATAAAC
1 TTTAACATAATAAGTAGCACCTATTTTATTTTACCGCTTACATTATTAGTAACATTCAAACAAAC
**
601402 -CGATAGGTAG
66 ACG-TAAATAG
* **
601412 TTTAATATAATAAGTAGTGCCTATTTTATTTTA
1 TTTAACATAATAAGTAGCACCTATTTTATTTTA
601445 ACCGATTAAG
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 1 0.01
75 90 0.99
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (75 bp):
TTTAACATAATAAGTAGCACCTATTTTATTTTACCGCTTACATTATTAGTAACATTCAAACAAAC
ACGTAAATAG
Found at i:611596 original size:12 final size:12
Alignment explanation
Indices: 611564--611597 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
611554 AGAATAAACA
611564 AGTTTATAAATG
1 AGTTTATAAATG
**
611576 AGTCGATAAATG
1 AGTTTATAAATG
611588 AGTTTATAAA
1 AGTTTATAAA
611598 CATGCAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (12 bp):
AGTTTATAAATG
Found at i:614860 original size:22 final size:22
Alignment explanation
Indices: 614834--614878 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
614824 GATGTTAATA
614834 TTAA-TCAAAATATTTAATTTTT
1 TTAATTCAAAA-ATTTAATTTTT
* *
614856 TTAATTCAAGAGTTTAATTTTT
1 TTAATTCAAAAATTTAATTTTT
614878 T
1 T
614879 ATTTGAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (22 bp):
TTAATTCAAAAATTTAATTTTT
Found at i:626189 original size:17 final size:17
Alignment explanation
Indices: 626167--626229 Score: 126
Period size: 17 Copynumber: 3.7 Consensus size: 17
626157 GATCGAATAG
626167 ACTCGACTCGAGCTCGA
1 ACTCGACTCGAGCTCGA
626184 ACTCGACTCGAGCTCGA
1 ACTCGACTCGAGCTCGA
626201 ACTCGACTCGAGCTCGA
1 ACTCGACTCGAGCTCGA
626218 ACTCGACTCGAG
1 ACTCGACTCGAG
626230 TTCTTAACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (17 bp):
ACTCGACTCGAGCTCGA
Found at i:626193 original size:11 final size:11
Alignment explanation
Indices: 626166--626228 Score: 76
Period size: 11 Copynumber: 5.6 Consensus size: 11
626156 GGATCGAATA
626166 GACTCG-ACTC
1 GACTCGAACTC
626176 GAGCTCGAACTC
1 GA-CTCGAACTC
*
626188 GACTCGAGCTC
1 GACTCGAACTC
626199 GAACTCG-ACTC
1 G-ACTCGAACTC
626210 GAGCTCGAACTC
1 GA-CTCGAACTC
626222 GACTCGA
1 GACTCGA
626229 GTTCTTAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
10 3 0.07
11 26 0.57
12 17 0.37
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (11 bp):
GACTCGAACTC
Found at i:626885 original size:20 final size:20
Alignment explanation
Indices: 626791--627119 Score: 387
Period size: 20 Copynumber: 16.4 Consensus size: 20
626781 GATTTTCCAT
* ** *
626791 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
626811 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
626831 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
626851 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
626871 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
626891 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
626911 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
626931 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
626951 AATCGCAATACGTATCCGTA
1 AATCGCAACGCGTATCCGTA
626971 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
626991 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
627011 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
627031 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
627051 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
627071 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
627091 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
627111 AATCACAAC
1 AATCGCAAC
627120 ACTTAAATTT
Statistics
Matches: 267, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 261 0.98
21 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:627841 original size:24 final size:24
Alignment explanation
Indices: 627802--627848 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
627792 AAATTTGGTC
627802 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
627826 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
627849 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:628040 original size:12 final size:12
Alignment explanation
Indices: 628023--628047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
628013 ATATAATCCT
628023 GAAGAAGAAAAA
1 GAAGAAGAAAAA
628035 GAAGAAGAAAAA
1 GAAGAAGAAAAA
628047 G
1 G
628048 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:630353 original size:19 final size:19
Alignment explanation
Indices: 630331--630585 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
630321 CGGAAAATAC
*
630331 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
630350 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
630364 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
630384 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
630398 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630417 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
630436 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
630450 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
630469 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630488 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630507 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630526 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
630540 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630559 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
630578 AATCGCAA
1 AATCGCAA
630586 CGAGATAATC
Statistics
Matches: 207, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
14 38 0.18
15 1 0.00
16 14 0.07
17 12 0.06
18 2 0.01
19 127 0.61
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:630418 original size:33 final size:34
Alignment explanation
Indices: 630331--630585 Score: 240
Period size: 33 Copynumber: 7.2 Consensus size: 34
630321 CGGAAAATAC
* *
630331 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
630364 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
630398 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
630436 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
630469 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
630507 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
630539 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
630578 AATCGCAA
1 AATCGCAA
630586 CGAGATAATC
Statistics
Matches: 195, Mismatches: 8, Indels: 33
0.83 0.03 0.14
Matches are distributed among these distances:
32 2 0.01
33 79 0.41
34 30 0.15
35 10 0.05
36 7 0.04
37 2 0.01
38 63 0.32
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:630446 original size:52 final size:55
Alignment explanation
Indices: 630359--630585 Score: 298
Period size: 52 Copynumber: 4.2 Consensus size: 55
630349 AAATCCCAAC
*
630359 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
630412 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
630464 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
630521 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
630573 ATGAAAATCGCAA
1 ATGAAAATCGCAA
630586 CGAGATAATC
Statistics
Matches: 164, Mismatches: 2, Indels: 17
0.90 0.01 0.09
Matches are distributed among these distances:
52 109 0.66
53 16 0.10
54 6 0.04
55 7 0.04
57 26 0.16
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:630482 original size:71 final size:71
Alignment explanation
Indices: 630398--630623 Score: 311
Period size: 71 Copynumber: 3.2 Consensus size: 71
630388 GCAACGAGAG
*
630398 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
630463 AATTAA
66 AATTAA
630469 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAA
*
630534 --CG-AA--AG
61 TGCGAAATTAA
* *
630540 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
630605 AATTATA
66 AATTA-A
*
630612 AA-CGCATTGCGA
1 AATCGCAATGCGA
630624 TTTTCATTTC
Statistics
Matches: 138, Mismatches: 6, Indels: 22
0.83 0.04 0.13
Matches are distributed among these distances:
66 8 0.06
68 2 0.01
69 6 0.04
71 103 0.75
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.06
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATTAA
Found at i:630513 original size:90 final size:89
Alignment explanation
Indices: 630331--630607 Score: 387
Period size: 90 Copynumber: 3.2 Consensus size: 89
630321 CGGAAAATAC
* *
630331 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAGAATCGCAATGC-GAAATGAAAATCGCAATGC
*
630393 G--A-GAGAATCGCAATGCGAAATGAA
63 GAAATGAAAATCGCAATGCGAAATGAA
*
630417 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-AGAATCGCAATGCGAAATGAAAATCGCAATGCGA
630482 AATGAAAATCGCAATGCGAAATGAA
65 AATGAAAATCGCAATGCGAAATGAA
630507 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACG-AAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
*
630572 AATGAAAATCGCAA--CG--A-GAT
65 AATGAAAATCGCAATGCGAAATGAA
630592 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
630608 TATAAACGCA
Statistics
Matches: 177, Mismatches: 6, Indels: 17
0.88 0.03 0.09
Matches are distributed among these distances:
84 2 0.01
85 34 0.19
86 38 0.21
87 2 0.01
88 2 0.01
89 1 0.01
90 97 0.55
91 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (89 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
ATGAAAATCGCAATGCGAAATGAA
Found at i:630581 original size:142 final size:139
Alignment explanation
Indices: 630331--630623 Score: 466
Period size: 142 Copynumber: 2.1 Consensus size: 139
630321 CGGAAAATAC
* *
630331 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
630396 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
630461 GAAATTA-A
131 GAAATTATA
*
630469 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
630533 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
630598 AATGCGAAATTATA
126 AATGCGAAATTATA
*
630612 AA-CGCATTGCGA
1 AATCGCAATGCGA
630624 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
138 25 0.17
140 1 0.01
142 98 0.69
143 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (139 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATA
Found at i:630586 original size:52 final size:55
Alignment explanation
Indices: 630331--630607 Score: 290
Period size: 52 Copynumber: 5.3 Consensus size: 55
630321 CGGAAAATAC
* *
630331 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
630384 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
630436 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
630488 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
630540 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
630592 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
630608 TATAAACGCA
Statistics
Matches: 205, Mismatches: 6, Indels: 27
0.86 0.03 0.11
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 129 0.63
53 24 0.12
54 7 0.03
55 6 0.03
57 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:630723 original size:19 final size:19
Alignment explanation
Indices: 630614--630715 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
630604 AAATTATAAA
630614 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
630633 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
630653 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
630669 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
630686 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
630705 CGCATTGCGAT
1 CGCATTGCGAT
630716 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:630841 original size:14 final size:14
Alignment explanation
Indices: 630822--630858 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
630812 CATCAATTAC
630822 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
630836 ACAAATCATCTTTT
1 ACAAATCAACTTTT
630850 ACAAATCAA
1 ACAAATCAA
630859 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:632834 original size:14 final size:14
Alignment explanation
Indices: 632815--632871 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
632805 GCGAAATGAA
*
632815 AATCGCAACGACAG
1 AATCGCAACGAAAG
632829 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
632846 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
632862 AATCGCAACG
1 AATCGCAACG
632872 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:632842 original size:33 final size:33
Alignment explanation
Indices: 632796--632888 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
632786 GCGAAACCAA
*
632796 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
632829 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
632862 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
632889 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:632853 original size:19 final size:19
Alignment explanation
Indices: 632759--632893 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
632749 TAGTTTACTT
* *
632759 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
632779 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
632798 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
632817 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
632831 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
632850 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
632864 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
632883 TCGCAATGCGA
1 TCGCAACGCGA
632894 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:632911 original size:19 final size:19
Alignment explanation
Indices: 632889--633017 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
632879 AAAATCGCAA
632889 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
632908 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
632922 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
632941 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
632955 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
632974 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
632993 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
633013 TGCGA
1 TGCGA
633018 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:632931 original size:33 final size:33
Alignment explanation
Indices: 632889--632980 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
632879 AAAATCGCAA
632889 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
632922 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
632955 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
632981 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:633352 original size:93 final size:93
Alignment explanation
Indices: 633061--633532 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
633051 TTGAATGGAT
633061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633126 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
633154 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633218 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
633246 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633311 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
633339 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633403 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
633431 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
633496 AGTTTAGTAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
633524 AAATTTACT
1 AAATTTACT
633533 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 190 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:633373 original size:185 final size:185
Alignment explanation
Indices: 633061--633532 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
633051 TTGAATGGAT
633061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633126 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
633191 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
633246 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
633311 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
633376 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
633431 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
633496 AGTTTAGTAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
633533 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 284 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:635258 original size:14 final size:14
Alignment explanation
Indices: 635239--635328 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
635229 TTGAAATGAA
635239 AATCGCAACGAGAG
1 AATCGCAACGAGAG
635253 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
635270 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
635286 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
635305 AATCGCAACGAGAG
1 AATCGCAACGAGAG
635319 AATCGCAACG
1 AATCGCAACG
635329 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:635276 original size:33 final size:33
Alignment explanation
Indices: 635231--635345 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
635221 TCTTTTGGTT
635231 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
635264 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
635297 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
635330 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
635346 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:635277 original size:19 final size:18
Alignment explanation
Indices: 635238--635350 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
635228 GTTGAAATGA
635238 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
635253 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
635270 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
635286 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
635303 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
635319 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
635336 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
635351 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:635394 original size:33 final size:35
Alignment explanation
Indices: 635346--635431 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 35
635336 AAAATCGCAA
**
635346 TGCGATTTTGGTTTCGCGTTGC-G-ATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCTGCATTCTCTCGT
635379 TGCGATTTTCATTTCGCGTTGCGATTGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGC---TG-CATTCTCTCGT
635418 TGCGATTTTCATTT
1 TGCGATTTTCATTT
635432 ATCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 20 0.44
37 1 0.02
39 24 0.53
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (35 bp):
TGCGATTTTCATTTCGCGTTGCTGCATTCTCTCGT
Found at i:635420 original size:20 final size:20
Alignment explanation
Indices: 635369--635443 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
635359 TCGCGTTGCG
635369 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
635389 ATT-TCGCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTTTC
635408 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
635428 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
635444 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.35
20 18 0.38
21 13 0.27
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:635565 original size:33 final size:33
Alignment explanation
Indices: 635523--635593 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
635513 AATACTAACT
*
635523 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
635556 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
635589 TGAAA
1 TGAAA
635594 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:635827 original size:22 final size:22
Alignment explanation
Indices: 635775--635829 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
635765 TGGTTATGAG
**
635775 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
635797 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
635819 GGATTTCTTCG
1 GGATTTCTTCG
635830 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:636000 original size:20 final size:20
Alignment explanation
Indices: 635975--636167 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
635965 CTTTAAATAT
635975 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
635995 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
636017 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
636036 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
636056 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
636076 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
636096 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
636116 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
636136 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
636156 CGCGTTGCGATT
1 CGCGTTGCGATT
636168 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:636162 original size:60 final size:60
Alignment explanation
Indices: 635975--636167 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
635965 CTTTAAATAT
**
635975 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
636036 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
636096 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
636156 CGCGTTGCGATT
1 CGCGTTGCGATT
636168 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:636248 original size:20 final size:20
Alignment explanation
Indices: 636223--636274 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
636213 AAGAATCGCG
*
636223 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
636243 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
636263 TTGCGATTCTGG
1 TTGCGATTCTGG
636275 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:636564 original size:22 final size:22
Alignment explanation
Indices: 636531--636587 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
636521 ATACTCTCTA
636531 TCCTTTCACTAAGCCATCACAT
1 TCCTTTCACTAAGCCATCACAT
* *
636553 TTCTTTCGCTAAGCCATCACAT
1 TCCTTTCACTAAGCCATCACAT
636575 TCCTTTCACTAAG
1 TCCTTTCACTAAG
636588 ACATATATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.33, G:0.07, T:0.35
Consensus pattern (22 bp):
TCCTTTCACTAAGCCATCACAT
Found at i:637259 original size:7 final size:7
Alignment explanation
Indices: 637247--637491 Score: 79
Period size: 7 Copynumber: 35.6 Consensus size: 7
637237 TCATTTTCAT
637247 TAAACCC
1 TAAACCC
637254 TAAACCC
1 TAAACCC
637261 TAAACCC
1 TAAACCC
*
637268 TAAACCT
1 TAAACCC
*
637275 TAAACCA
1 TAAACCC
*
637282 T-AACCT
1 TAAACCC
637288 TAAACCC
1 TAAACCC
**
637295 TAAAATC
1 TAAACCC
**
637302 TAAGGCC
1 TAAACCC
***
637309 TAAAATA
1 TAAACCC
* *
637316 TGAACCT
1 TAAACCC
637323 TAAA-CC
1 TAAACCC
**
637329 TAAA-TG
1 TAAACCC
*
637335 TAAA-CT
1 TAAACCC
637341 TAAAACCC
1 T-AAACCC
637349 TAAACCC
1 TAAACCC
**
637356 TAAACAT
1 TAAACCC
637363 TAAACCC
1 TAAACCC
*
637370 TAGACCC
1 TAAACCC
***
637377 TAAATAA
1 TAAACCC
**
637384 TAAACTA
1 TAAACCC
637391 TAAACCC
1 TAAACCC
637398 TAAACCC
1 TAAACCC
**
637405 T-AACTAA
1 TAAAC-CC
**
637412 TAAACTA
1 TAAACCC
*
637419 TAAATCC
1 TAAACCC
637426 TAAACCC
1 TAAACCC
* *
637433 TGAA-CA
1 TAAACCC
* **
637439 TGAACTT
1 TAAACCC
*
637446 TAAATCC
1 TAAACCC
*
637453 TAAATCC
1 TAAACCC
637460 TAAACCC
1 TAAACCC
**
637467 TAAACTA
1 TAAACCC
**
637474 TAAATAC
1 TAAACCC
637481 TAAACCC
1 TAAACCC
637488 TAAA
1 TAAA
637492 TAATGATTAA
Statistics
Matches: 172, Mismatches: 60, Indels: 12
0.70 0.25 0.05
Matches are distributed among these distances:
6 23 0.13
7 144 0.84
8 5 0.03
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:637278 original size:28 final size:28
Alignment explanation
Indices: 637254--637491 Score: 125
Period size: 28 Copynumber: 8.6 Consensus size: 28
637244 CATTAAACCC
* *
637254 TAAACCCTAAACCCTAAACCTTAAACCA
1 TAAACCCTAAACCCTAAACCCTAAACTA
* ** *
637282 T-AACCTTAAACCCTAAAATCTAAGGCCTA
1 TAAACCCTAAACCCTAAACCCTAA--ACTA
** * * *
637311 -AAA-TATGAACCTTAAA-CCTAAA-TG
1 TAAACCCTAAACCCTAAACCCTAAACTA
*
637335 TAAA-CTTAAAACCCTAAACCCTAAAC-A
1 TAAACCCT-AAACCCTAAACCCTAAACTA
* ***
637362 TTAAACCCTAGACCCTAAATAATAAACTA
1 -TAAACCCTAAACCCTAAACCCTAAACTA
**
637391 TAAACCCTAAACCCT-AACTAATAAACTA
1 TAAACCCTAAACCCTAAAC-CCTAAACTA
* * * * *
637419 TAAATCCTAAACCCTGAA-CATGAACTT
1 TAAACCCTAAACCCTAAACCCTAAACTA
* *
637446 TAAATCCTAAATCCTAAACCCTAAACTA
1 TAAACCCTAAACCCTAAACCCTAAACTA
**
637474 TAAATACTAAACCCTAAA
1 TAAACCCTAAACCCTAAA
637492 TAATGATTAA
Statistics
Matches: 161, Mismatches: 36, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
24 1 0.01
25 4 0.02
26 8 0.05
27 52 0.32
28 87 0.54
29 9 0.06
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAACCCTAAACTA
Found at i:638234 original size:3 final size:3
Alignment explanation
Indices: 638226--638255 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
638216 TGTATTTTCC
638226 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
638256 CAAAATGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:639569 original size:17 final size:17
Alignment explanation
Indices: 639547--639602 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
639537 AAATTTGAGT
639547 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
639564 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
639581 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
639598 TCGAG
1 TCGAG
639603 CTCAAATTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Done.