Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007717.1 Hibiscus syriacus cultivar Beakdansim tig00109948_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: 900945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:465166 original size:30 final size:29
Alignment explanation
Indices: 465093--465168 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
465083 TACTAAACCC
*
465093 TTCCCGTCCCCGTTTAACATAAACTATTT
1 TTCCCGTCCCCGTTTAACATAAACAATTT
* *
465122 TTCCC-TATCCCGTTTAGCATAAACAATTT
1 TTCCCGT-CCCCGTTTAACATAAACAATTT
465151 TTCTCCGTCCCCGTTTAA
1 TTC-CCGTCCCCGTTTAA
465169 TTCGGTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 27 0.69
30 10 0.26
31 1 0.03
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.38
Consensus pattern (29 bp):
TTCCCGTCCCCGTTTAACATAAACAATTT
Found at i:466080 original size:14 final size:14
Alignment explanation
Indices: 466058--466104 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
466048 TGCAAAGGAA
*
466058 AATTAATATAGTTT
1 AATTTATATAGTTT
466072 AATTTATATA----
1 AATTTATATAGTTT
466082 AA-TTATATAGTTT
1 AATTTATATAGTTT
466095 AATTTATATA
1 AATTTATATA
466105 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:466091 original size:23 final size:24
Alignment explanation
Indices: 466057--466106 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
466047 ATGCAAAGGA
466057 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
466081 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
466104 AAA
1 AAA
466107 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:466371 original size:11 final size:11
Alignment explanation
Indices: 466355--466393 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
466345 TGATAATGAT
466355 AATTTAAATAA
1 AATTTAAATAA
466366 AATTTAATATAA
1 AATTTAA-ATAA
*
466378 AATTTGAATAA
1 AATTTAAATAA
*
466389 CATTT
1 AATTT
466394 GAGTCAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
AATTTAAATAA
Found at i:466379 original size:12 final size:12
Alignment explanation
Indices: 466355--466387 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
466345 TGATAATGAT
466355 AATTTAA-ATAA
1 AATTTAATATAA
466366 AATTTAATATAA
1 AATTTAATATAA
466378 AATTTGAATA
1 AATTT-AATA
466388 ACATTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 9 0.45
13 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AATTTAATATAA
Found at i:469746 original size:6 final size:6
Alignment explanation
Indices: 469735--469848 Score: 111
Period size: 6 Copynumber: 18.7 Consensus size: 6
469725 TTCAATTTTA
* * * * *
469735 GGTTTG GGTTTG GATTTA GTTTTG GGTTTG GCTTTG GGTTAG GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* * * * *
469783 GGTATG GGTTTG GGTTTG GGTTCG GGTTCG GGTTTG GGTTTG AGTTTAA
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTT-G
*
469832 GGTTTA GGTTTAG GGTT
1 GGTTTG GGTTT-G GGTT
469849 CAAGTTAGGG
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
6 81 0.91
7 8 0.09
ACGTcount: A:0.08, C:0.03, G:0.43, T:0.46
Consensus pattern (6 bp):
GGTTTG
Found at i:470581 original size:14 final size:14
Alignment explanation
Indices: 470552--470667 Score: 54
Period size: 16 Copynumber: 7.4 Consensus size: 14
470542 CATCCCTATA
*
470552 TAATTTTTATTAAT
1 TAATATTTATTAAT
470566 TAACTATTTA-TAAT
1 TAA-TATTTATTAAT
* *
470580 TAATATTAAAATAAT
1 TAATATT-TATTAAT
*
470595 TATATATATAATTAATAT
1 TA-ATAT-TTATT-A-AT
*
470613 TAATATTAATATAAT
1 TAATATTTAT-TAAT
470628 TAATATTAATATTAATAT
1 TAATATT--TATT-A-AT
*
470646 TAATATTAACTTATAT
1 TAATATTTA-TTA-AT
470662 TAATAT
1 TAATAT
470668 AATATAGTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 24
0.74 0.04 0.21
Matches are distributed among these distances:
13 4 0.05
14 11 0.13
15 20 0.24
16 24 0.29
17 12 0.14
18 13 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTTATTAAT
Found at i:470606 original size:27 final size:23
Alignment explanation
Indices: 470574--470645 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 23
470564 ATTAACTATT
470574 TATAATTAATATTAAAATAATTATATA
1 TATAATTAATATTAAAAT-A-T-TA-A
470601 TATAATTAATATT--AATATTAA
1 TATAATTAATATTAAAATATTAA
470622 TATAATTAATATT--AATATTAA
1 TATAATTAATATTAAAATATTAA
470643 TAT
1 TAT
470646 TAATATTAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 25 0.56
22 2 0.04
23 1 0.02
24 1 0.02
25 3 0.07
27 13 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAATTAATATTAAAATATTAA
Found at i:470608 original size:21 final size:21
Alignment explanation
Indices: 470584--470670 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
470574 TATAATTAAT
470584 ATTAA-AATAAT-TATATATATA
1 ATTAATAATAATAT-TA-ATATA
*
470605 ATTAATATTAATATTAATATA
1 ATTAATAATAATATTAATATA
*
470626 ATTAATATTAATATTAATATTA
1 ATTAATAATAATATTAATA-TA
* *
470648 A-TATTAACTTATATTAATATA
1 ATTAATAA-TAATATTAATATA
470669 AT
1 AT
470671 ATAGTTTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
21 36 0.63
22 20 0.35
23 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAATAATAATATTAATATA
Found at i:470614 original size:6 final size:6
Alignment explanation
Indices: 470605--470672 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
470595 TATATATATA
470605 ATTAAT ATTAAT ATTAAT A-T-A- ATTAAT ATTAAT ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
*
470650 ATTAA- CTT-AT ATTAAT A-TAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT AT
470673 AGTTTATTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 1 0.02
4 3 0.06
5 11 0.20
6 39 0.72
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:470616 original size:33 final size:33
Alignment explanation
Indices: 470564--470672 Score: 116
Period size: 33 Copynumber: 3.2 Consensus size: 33
470554 ATTTTTATTA
*
470564 ATTAACTATTTATAATTAATATTAAAATAATT-AT
1 ATTAA-TATTAAT-ATTAATATTAAAATAATTAAT
*
470598 A-TATATAATTAATATTAATATTAATATAATTAAT
1 ATTA-AT-ATTAATATTAATATTAAAATAATTAAT
**
470632 ATTAATATTAATATTAATATTAACTTATATTAAT
1 ATTAATATTAATATTAATATTAAAATA-ATTAAT
470666 A-TAATAT
1 ATTAATAT
470673 AGTTTATTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
33 45 0.68
34 19 0.29
35 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTAATATTAATATTAATATTAAAATAATTAAT
Found at i:470646 original size:27 final size:28
Alignment explanation
Indices: 470605--470672 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
470595 TATATATATA
470605 ATTAATATTAATATTAATA-TAA-TTAAT
1 ATTAATATTAATATTAATATTAACTT-AT
470632 ATTAATATTAATATTAATATTAACTTAT
1 ATTAATATTAATATTAATATTAACTTAT
470660 ATTAATA-TAATAT
1 ATTAATATTAATAT
470673 AGTTTATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 25 0.64
28 12 0.31
29 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTAATATTAATATTAATATTAACTTAT
Found at i:470720 original size:31 final size:30
Alignment explanation
Indices: 470684--470749 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
470674 GTTTATTTGT
470684 AATTAATATTAATATAAAATATA-GTCTATA
1 AATTAATATTAATATAAAATATATGT-TATA
*
470714 ACATTAATATTAATATAAACTATATGTTATA
1 A-ATTAATATTAATATAAAATATATGTTATA
470745 AATTA
1 AATTA
470750 TATAGTATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 5 0.15
31 26 0.79
32 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATATGTTATA
Found at i:470736 original size:24 final size:25
Alignment explanation
Indices: 470691--470737 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
470681 TGTAATTAAT
**
470691 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
470716 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
470738 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:470758 original size:21 final size:21
Alignment explanation
Indices: 470727--470794 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
470717 TTAATATTAA
*
470727 TATAAACTATATGTTATAAAT
1 TATATACTATATGTTATAAAT
* *
470748 TATATAGTATA-GTTTATAAAC
1 TATATACTATATG-TTATAAAT
470769 TATATACTATAT-TAATATAAAT
1 TATATACTATATGT--TATAAAT
470791 TATA
1 TATA
470795 GTTAAGATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.05
21 26 0.68
22 10 0.26
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATACTATATGTTATAAAT
Found at i:470795 original size:88 final size:89
Alignment explanation
Indices: 470689--470868 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 89
470679 TTTGTAATTA
* * *
470689 ATATTAATATAAAATATAGTCTATA-A-CATTAATATTAATATAAACTATAT-GT-TATAAATTA
1 ATATTAATATAAAATATAGT-TA-AGATAATTAACATTAATATAAACTATATAGTACATAAA-TA
*
470750 TATAGTATAGTTTATAAACTATATACT
63 TAAAGTATAGTTTATAAACTATATACT
* * *
470777 ATATTAATATAAATTATAGTTAAGATAATTAACATTAATATAAACTGTATAGTACATTAATATAA
1 ATATTAATATAAAATATAGTTAAGATAATTAACATTAATATAAACTATATAGTACATAAATATAA
* *
470842 ATTATAGTTTATAAATTATATACT
66 AGTATAGTTTATAAACTATATACT
470866 ATA
1 ATA
470869 GGTTATAAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 40 0.51
89 31 0.39
90 4 0.05
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (89 bp):
ATATTAATATAAAATATAGTTAAGATAATTAACATTAATATAAACTATATAGTACATAAATATAA
AGTATAGTTTATAAACTATATACT
Found at i:470849 original size:20 final size:22
Alignment explanation
Indices: 470808--470849 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
470798 AAGATAATTA
470808 ACATTAATATAAACTGTATAGT
1 ACATTAATATAAACTGTATAGT
470830 ACATTAATATAAA-T-TATAGT
1 ACATTAATATAAACTGTATAGT
470850 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (22 bp):
ACATTAATATAAACTGTATAGT
Found at i:470868 original size:21 final size:21
Alignment explanation
Indices: 470837--470889 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
470827 AGTACATTAA
* * *
470837 TATAAATTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
470858 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
470879 TATAAACTATA
1 TATAAACTATA
470890 TAGTACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:470959 original size:20 final size:22
Alignment explanation
Indices: 470936--471033 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 22
470926 GGTTACATAT
470936 ATAGTTTATATA-ACATATA-A
1 ATAGTTTATATATACATATACA
*
470956 ATAGATTGTATATATACATATACT
1 ATAG-TT-TATATATACATATACA
*
470980 ATAGGTTATATAT--ATAT---
1 ATAGTTTATATATACATATACA
* *
470997 ATTGTTTATATATA-TTATAC-
1 ATAGTTTATATATACATATACA
*
471017 ATAGTTTATACATACAT
1 ATAGTTTATATATACAT
471034 GTACTATAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.18
18 3 0.05
20 20 0.32
21 3 0.05
22 13 0.21
23 8 0.13
24 4 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (22 bp):
ATAGTTTATATATACATATACA
Found at i:470971 original size:24 final size:25
Alignment explanation
Indices: 470942--470995 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
470932 ATATATAGTT
*
470942 TATATAACATATA-AATAGATTGTA
1 TATATAACATATACAATAGATTATA
* *
470966 TATAT-ACATATACTATAGGTTATA
1 TATATAACATATACAATAGATTATA
470990 TATATA
1 TATATA
470996 TATTGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATAACATATACAATAGATTATA
Found at i:471001 original size:37 final size:37
Alignment explanation
Indices: 470950--471026 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
470940 TTTATATAAC
470950 ATATAAATAGATTGTATATATACA-TATACTATAGGTT
1 ATATAAATAGATTGTATATATACATTATAC-ATAGGTT
* * * * *
470987 ATATATATATATTGTTTATATATATTATACATAGTTT
1 ATATAAATAGATTGTATATATACATTATACATAGGTT
471024 ATA
1 ATA
471027 CATACATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 29 0.85
38 5 0.15
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (37 bp):
ATATAAATAGATTGTATATATACATTATACATAGGTT
Found at i:471039 original size:59 final size:62
Alignment explanation
Indices: 470932--471059 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 62
470922 TATAGGTTAC
* *
470932 ATATATAGTTTATATAACATATAAATAGATTGTATATATACATATACTATAGGTT-ATATAT
1 ATATATAGTTTATATAACATATAAATAGATTGTATACATACATATACTATAAGTTCATATAT
* * * *
470993 ATATATTGTTTATATATA-TTATACATAG-TT-TATACATACATGTACTATAAGTTGCATATAT
1 ATATATAGTTTATATA-ACATATAAATAGATTGTATACATACATATACTATAAGTT-CATATAT
471054 AGTATA
1 A-TATA
471060 CATGTATACA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
59 20 0.35
60 2 0.04
61 30 0.53
62 5 0.09
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (62 bp):
ATATATAGTTTATATAACATATAAATAGATTGTATACATACATATACTATAAGTTCATATAT
Found at i:471236 original size:20 final size:20
Alignment explanation
Indices: 471208--471247 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
471198 ATATGTTTTA
* *
471208 TATATATAGTTTATATATAC
1 TATACATAGTTTATACATAC
471228 TATACATAGTTTATACATAC
1 TATACATAGTTTATACATAC
471248 ATGTACTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
TATACATAGTTTATACATAC
Found at i:474506 original size:2 final size:2
Alignment explanation
Indices: 474499--474841 Score: 109
Period size: 2 Copynumber: 174.0 Consensus size: 2
474489 TTCTTCAACA
474499 AT AT AT AT AT AT AT AT AT AT AT AT -T AGT -T AT AT -T AGT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
* * *
474539 AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
474578 AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT AT AT AGT TT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
* *
474620 AT AT AT AT AT AT AT AT AT AC ACT AT AT -T A- AT AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * * * *
474660 -T TT TT AT AA ACT AT AT ACT TT TT AT AGT TT AT AC AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
* * * * * *
474702 -T TT AT AT AC AT AGT TT AT AT AT AT AGT -T CAC AT AA AC AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT -AT AT AT AT AT AT
* * * *
474742 AT TT AT AT AT AT AG CT CAT A- AT A- AT -T AT AT AGT TT AT A- AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
474782 AT AA AT AT AGT TT AT AT AT AA ACT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
474825 AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
474842 TTTTCAATTT
Statistics
Matches: 250, Mismatches: 52, Indels: 78
0.66 0.14 0.21
Matches are distributed among these distances:
1 22 0.09
2 212 0.85
3 16 0.06
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:474585 original size:29 final size:29
Alignment explanation
Indices: 474545--474675 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
474535 TTATACATAC
*
474545 ATATATATACTATATTAATATAAATTATA
1 ATATATAAACTATATTAATATAAATTATA
* **
474574 ATATATAAACTATATATTTTATATAGTTTATA
1 ATATATAAAC--TATA-TTAATATAAATTATA
*** *
474606 CATATATAGTTTATA-T-ATATATA-TAT-
1 -ATATATAAACTATATTAATATAAATTATA
* *
474632 ATATATACACTATATTAATATAAATTATT
1 ATATATAAACTATATTAATATAAATTATA
* *
474661 TTTTATAAACTATAT
1 ATATATAAACTATAT
474676 ACTTTTTATA
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
25 11 0.14
26 1 0.01
27 9 0.12
28 8 0.10
29 22 0.28
31 8 0.10
32 12 0.15
33 7 0.09
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (29 bp):
ATATATAAACTATATTAATATAAATTATA
Found at i:474597 original size:47 final size:46
Alignment explanation
Indices: 474546--474685 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 46
474536 TATACATACA
474546 TATATATACTATATTAATATAAATTATAATATATAAACTATATATTT
1 TATATATACTATATTAATATAAATTAT-ATATATAAACTATATATTT
* *
474593 TATATAGT--T-TA-TACATATATAGTT-TATATAT--A-TATATA-TA
1 TATATA-TACTATATTA-ATATA-AATTATATATATAAACTATATATTT
* * *
474633 TATATACACTATATTAATATAAATTATTTTTTATAAACTATATACTTT
1 TATATATACTATATTAATATAAATTA-TATATATAAACTATATA-TTT
474681 T-TATA
1 TATATA
474686 GTTTATACAT
Statistics
Matches: 72, Mismatches: 7, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
40 7 0.10
41 10 0.14
42 8 0.11
43 7 0.10
44 8 0.11
45 9 0.12
46 10 0.14
47 10 0.14
48 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (46 bp):
TATATATACTATATTAATATAAATTATATATATAAACTATATATTT
Found at i:474613 original size:15 final size:15
Alignment explanation
Indices: 474593--474628 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
474583 CTATATATTT
474593 TATATAGTTTATACA
1 TATATAGTTTATACA
*
474608 TATATAGTTTATATA
1 TATATAGTTTATACA
474623 TATATA
1 TATATA
474629 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:474625 original size:66 final size:69
Alignment explanation
Indices: 474502--474634 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 69
474492 TTCAACAATA
*
474502 TATATATATATATATATATATTAGTTATATTAGTTATACATACATATATATACTATAT-TA-ATA
1 TATATATATATAAATATATATTA-TTATATTAGTTATACATACATATATATACTATATATATATA
474565 TAAAT
65 TAAAT
* *
474570 TATA-ATATATAAACTATATATT-TTATA-TAGTTTATACATATATAGTTTATA-TATATATATA
1 TATATATATATAAA-TATATATTATTATATTAG-TTATACATACATA-TATATACTATATATATA
474631 TATA
63 TATA
474635 TATACACTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
65 3 0.05
66 22 0.39
67 15 0.26
68 17 0.30
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (69 bp):
TATATATATATAAATATATATTATTATATTAGTTATACATACATATATATACTATATATATATAT
AAAT
Found at i:474652 original size:87 final size:87
Alignment explanation
Indices: 474536--474726 Score: 276
Period size: 87 Copynumber: 2.2 Consensus size: 87
474526 TTATATTAGT
* * *
474536 TATACATACATATATATACTATATTAATATAAATTATAATATATAAACTATATA-TTTTATATAG
1 TATATATATATATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTT-TATAG
474600 TTTATACATATATAGTTTATATA
65 TTTATACATATATAGTTTATATA
** *
474623 TATATATATATATATACACTATATTAATATAAATTATTTTTTATAAACTATATACTTTTTATAGT
1 TATATATATATATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTTTATAGT
*
474688 TTATACATATATATTTTATATA
66 TTATACATATATAGTTTATATA
* *
474710 CATAGTTTATATATATA
1 TATA-TATATATATATA
474727 GTTCACATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
87 78 0.84
88 15 0.16
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (87 bp):
TATATATATATATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTTTATAGT
TTATACATATATAGTTTATATA
Found at i:474720 original size:13 final size:13
Alignment explanation
Indices: 474682--474829 Score: 65
Period size: 13 Copynumber: 11.3 Consensus size: 13
474672 ATATACTTTT
474682 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
474697 TATATTTTATATA
1 TATAGTTTATATA
*
474710 CATAGTTTATATA
1 TATAGTTTATATA
* *
474723 TATAGTTCACATAAA
1 TATAGTT--TATATA
* *
474738 CATAATTTATATA
1 TATAGTTTATATA
* *
474751 TATAGCTCATA-A
1 TATAGTTTATATA
474763 TA-A--TTATATA
1 TATAGTTTATATA
* * *
474773 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
474787 TATAGTTTATATA
1 TATAGTTTATATA
* *
474800 TAAACTTATATATA
1 TATAGTT-TATATA
*
474814 TATA-TATATATA
1 TATAGTTTATATA
474826 TATA
1 TATA
474830 TATATATTAT
Statistics
Matches: 99, Mismatches: 25, Indels: 21
0.68 0.17 0.14
Matches are distributed among these distances:
9 4 0.04
10 1 0.01
11 2 0.02
12 14 0.14
13 45 0.45
14 15 0.15
15 18 0.18
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:478474 original size:45 final size:45
Alignment explanation
Indices: 478296--478720 Score: 527
Period size: 45 Copynumber: 9.4 Consensus size: 45
478286 ATTCATATTT
* *
478296 ATAATGCA-CCATTATGCACTTTCAACTATAGCATACTTTTCTGTTG
1 ATAATGCACCCA-TATACA-TTTCAACTATAGTATACTTTTCTGTTG
*
478342 ATAATGCACCCATATGA-ATTTC-ACTATAGTATACTTTTCTATTG
1 ATAATGCACCCATAT-ACATTTCAACTATAGTATACTTTTCTGTTG
*
478386 ATAATGCACCCATATGCATTTCAA-TATAGTATACTTTTCTGTTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* *
478430 ATAATGTACCCATATACATTTCAACTATAGCATACTTTTCTGTTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* *
478475 ATAATGCACCCTTATGCATTTCAACTATAGTATACTTTTCTGTTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* * *
478520 ATAACGCACCCATATTCATTTCAACTATAGTATACTTTTCTATTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* * * *
478565 ATAATGCACTCATATGCATTTCAACTATAGTACAATTTTCTGTTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* * *
478610 ATAATGTACCCATATACATTTCAACTATTGTATACTTTTCTCTTG
1 ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
* * * * * * **
478655 ATAATGTACCCTTTATACATTTCACCTATGGCAT-CCTTTCATGCAG
1 ATAATGCACCC-ATATACATTTCAACTATAGTATACTTTTC-TGTTG
*
478701 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATACATT
478721 ATTATTTTCA
Statistics
Matches: 332, Mismatches: 40, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
44 81 0.24
45 206 0.62
46 42 0.13
47 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
ATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTG
Found at i:497437 original size:45 final size:45
Alignment explanation
Indices: 497313--497548 Score: 334
Period size: 45 Copynumber: 5.2 Consensus size: 45
497303 ATTCATATTT
* *
497313 ATAATGCA-CCATTATGCACTTTCAACTATAGCATACTTTTATGTTG
1 ATAATGCACCCA-TATGCA-TTTCAACTATAGTATACTTTTCTGTTG
* * *
497359 ATAATGCACCC-TATACATTTCAGCTATAGTATATTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
* *
497403 ATAATGCACCCATATGCATTTCAACTATAATATATTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
* *
497448 ATAATGTACCCATATACATTTCAACTATA-TCATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGT-ATACTTTTCTGTTG
497493 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
*
497538 ATAATGTACCC
1 ATAATGCACCC
497549 TAATATCTCG
Statistics
Matches: 172, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.20
45 126 0.73
46 9 0.05
47 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
Found at i:497998 original size:27 final size:28
Alignment explanation
Indices: 497968--498021 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
497958 AGTTCCATCT
* *
497968 TGATGTTT-TCTCAAGTGAGATTGAAAA
1 TGATGTTTATCTCAAGGGAGATGGAAAA
497995 TGATGTTTATCTCAAGGGAGATGGAAA
1 TGATGTTTATCTCAAGGGAGATGGAAA
498022 TTTGTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (28 bp):
TGATGTTTATCTCAAGGGAGATGGAAAA
Found at i:498190 original size:65 final size:63
Alignment explanation
Indices: 498072--498241 Score: 159
Period size: 65 Copynumber: 2.6 Consensus size: 63
498062 GAAAGATTAT
* * *
498072 CTCAAGTGAGACAAAATTTGTTTTATGAAAAATAATTTCAAGGTTTAAGTTTCAAAAGAAA-TAA
1 CTCAAGTGA-A-AAAATTTGTTTTAAGAAAAACAATTTCAAAGTTTAAGTTTCAAAAGAAACTAA
* *
498136 CCTCAAGTGACAAGAAATTTGTTTTAAG-AAAACCATTCTCAAAGTTTGAA-TTTCATAAGAAAC
1 -CTCAAGTGA-AA-AAATTTGTTTTAAGAAAAACAATT-TCAAAGTTT-AAGTTTCAAAAGAAAC
*
498199 TGA
61 TAA
* *
498202 CTCAAGTGAGACAAATTTGTTTTAA-AAACAACAATCTCAA
1 CTCAAGTGA-AAAAATTTGTTTTAAGAAA-AACAATTTCAA
498242 GTGAGATGAA
Statistics
Matches: 88, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
64 27 0.31
65 57 0.65
66 4 0.05
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (63 bp):
CTCAAGTGAAAAAATTTGTTTTAAGAAAAACAATTTCAAAGTTTAAGTTTCAAAAGAAACTAA
Found at i:498241 original size:35 final size:36
Alignment explanation
Indices: 498202--498277 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
498192 AAGAAACTGA
*
498202 CTCAAGTGAGA-CAAA-TTTGTTTTAAAAACAACAAT
1 CTCAAGTGAGATCAAATTTTATTTTAAAAA-AACAAT
* *
498237 CTCAAGTGAGATGAAATTTTATTTTAAGAAAACAAT
1 CTCAAGTGAGATCAAATTTTATTTTAAAAAAACAAT
498273 CTCAA
1 CTCAA
498278 AGTTTGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 11 0.31
36 14 0.39
37 11 0.31
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (36 bp):
CTCAAGTGAGATCAAATTTTATTTTAAAAAAACAAT
Found at i:498276 original size:100 final size:100
Alignment explanation
Indices: 498137--498454 Score: 340
Period size: 100 Copynumber: 3.2 Consensus size: 100
498127 AAGAAATAAC
* * * * *
498137 CTCAAGTGACAAGAAA-TTTGTTTTAAGAAAACCATTCTCAAAGTTTGAATTTCATAAGAAACTG
1 CTCAAGTGAGATGAAATTTTATTTTAAGAAAA-CAATCTCAAAGTTTGAGTTTCATAAGAAACTG
* *
498201 ACTCAAGTGAGACAAATTTGTTTTAAAAACAACAAT
65 TCTCAAGCGAGACAAATTTGTTTTAAAAACAACAAT
*
498237 CTCAAGTGAGATGAAATTTTATTTTAAGAAAACAATCTCAAAGTTTGAGTTTCA-AGAGAAATTG
1 CTCAAGTGAGATGAAATTTTATTTTAAGAAAACAATCTCAAAGTTTGAGTTTCATA-AGAAACTG
* * * *
498301 TCTCAAACGAGAAGAAATTTGTTTTAAGACCAACAAT
65 TCTCAAGCGAG-ACAAATTTGTTTTAAAAACAACAAT
* * * * * * *
498338 CTTAAGTGATATG--ATTTTTTTTTAAGAAAAATAATCTCAAAGTTTGAGTTTCGTGAGAAACTT
1 CTCAAGTGAGATGAAATTTTATTTTAAG-AAAACAATCTCAAAGTTTGAGTTTCATAAGAAACTG
* *
498401 TCTAAAGCGAGACGAAATTTGTTTTAAGAAA-AATAAT
65 TCTCAAGCGAGAC-AAATTTGTTTTAA-AAACAACAAT
* *
498438 CTCAAGAGAGATAAAAT
1 CTCAAGTGAGATGAAAT
498455 CTTAAGTGAA
Statistics
Matches: 179, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
99 14 0.08
100 115 0.64
101 48 0.27
102 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (100 bp):
CTCAAGTGAGATGAAATTTTATTTTAAGAAAACAATCTCAAAGTTTGAGTTTCATAAGAAACTGT
CTCAAGCGAGACAAATTTGTTTTAAAAACAACAAT
Found at i:498737 original size:72 final size:71
Alignment explanation
Indices: 498616--499025 Score: 412
Period size: 73 Copynumber: 5.6 Consensus size: 71
498606 ATATAAAAAA
* * * *
498616 TTTCAACGGGAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCGAGTGATA
1 TTTCAA-GGAAAATATCTCAAGTGAGAT-AAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGA
498681 ATAAAAGT
64 ATAAAAGT
* * * *
498689 TTTCAAGGAAAAATATCTCAAGGGAGATAAAAATTTGTTTCGAGAGAAACTGTCTCAAGTGA-TA
1 TTTCAAGG-AAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGAA
498753 TGGAAAA-T
65 T--AAAAGT
* * *
498761 TTTCAAAGGGAAATATCTCAAGTGAGAGGAAAAATTTGTTTCAAGAGAAACTGTCTCAAGTGAGA
1 TTTC-AAGGAAAATATCTCAAGTGAGA-TAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGA
**
498826 CGAAAAGT
64 ATAAAAGT
* * *
498834 TTTCAAGGGAAAATATCTCAAGAGAGATAAAATTTTGTTTCAAGAGAAACTATCTCAAGTGAGAC
1 TTTCAA-GGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGAA
* *
498899 GAAAAAT
65 TAAAAGT
* * * ** *
498906 TTTCAAAGGGAAAATAACTCAAGTTAGATGAAATTTATGTTTCAAGAGAATTTGTCTCGAGTGAG
1 TTTC-AA-GGAAAATATCTCAAGTGAGATAAAATTT-TGTTTCAAGAGAAACTGTCTCAAGTGAG
* ***
498971 ATGTATTTTGT
63 A-ATA-AAAGT
*
498982 TTT-AAGAAAAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGA
1 TTTCAAGGAAAAT-ATCTCAAGTGAGATAAAATTTTGTTTCAAGA
499026 TAAAATTTAT
Statistics
Matches: 286, Mismatches: 38, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
71 2 0.01
72 104 0.36
73 130 0.45
74 45 0.16
75 1 0.00
76 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (71 bp):
TTTCAAGGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGAAT
AAAAGT
Found at i:498799 original size:145 final size:145
Alignment explanation
Indices: 498602--499025 Score: 541
Period size: 145 Copynumber: 2.9 Consensus size: 145
498592 TTTTGTTTCG
* * *
498602 AGTGATAT-AAAAAATTTCAACGGGAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAA
1 AGTGATATGAAAAATTTTCAAAGGGAAATATCTCAAGTGAGATGAAAATTTTGTTTCAAGAGAAA
* * * *
498666 CTGTCTCGAGTGATAATAAAAGTTTTCAAGGAAAAATATCTCAAGGGAGATAAAAATTTGTTTCG
66 CTGTCTCGAGTGAGAATAAAAGTTTTCAAGGAAAAATATCTCAAGAGAGATAAAATTTTGTTTCA
*
498731 AGAGAAACTGTCTCA
131 AGAGAAACTATCTCA
* * *
498746 AGTGATATGGAAAATTTTCAAAGGGAAATATCTCAAGTGAGAGGAAAAATTTGTTTCAAGAGAAA
1 AGTGATATGAAAAATTTTCAAAGGGAAATATCTCAAGTGAGATGAAAATTTTGTTTCAAGAGAAA
* ** *
498811 CTGTCTCAAGTGAGACGAAAAGTTTTCAAGGGAAAATATCTCAAGAGAGATAAAATTTTGTTTCA
66 CTGTCTCGAGTGAGAATAAAAGTTTTCAAGGAAAAATATCTCAAGAGAGATAAAATTTTGTTTCA
498876 AGAGAAACTATCTCA
131 AGAGAAACTATCTCA
* * * *
498891 AGTGAGACGAAAAATTTTCAAAGGGAAAATAACTCAAGTTAGATG-AAATTTATGTTTCAAGAGA
1 AGTGATATGAAAAATTTTCAAAGGG-AAATATCTCAAGTGAGATGAAAATTT-TGTTTCAAGAGA
** * *** *
498955 ATTTGTCTCGAGTGAGATGTATTTTGTTTT-AA-GAAAAATGATCTCAAGTGAGATAAAATTTTG
64 AACTGTCTCGAGTGAGA-ATA-AAAGTTTTCAAGGAAAAAT-ATCTCAAGAGAGATAAAATTTTG
499018 TTTCAAGA
126 TTTCAAGA
499026 TAAAATTTAT
Statistics
Matches: 242, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
144 8 0.03
145 148 0.61
146 48 0.20
147 33 0.14
148 5 0.02
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (145 bp):
AGTGATATGAAAAATTTTCAAAGGGAAATATCTCAAGTGAGATGAAAATTTTGTTTCAAGAGAAA
CTGTCTCGAGTGAGAATAAAAGTTTTCAAGGAAAAATATCTCAAGAGAGATAAAATTTTGTTTCA
AGAGAAACTATCTCA
Found at i:499005 original size:36 final size:38
Alignment explanation
Indices: 498626--499031 Score: 173
Period size: 35 Copynumber: 11.1 Consensus size: 38
498616 TTTCAACGGG
* *
498626 AAAT-ATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGA
1 AAATGATCTCAAGTGAGAT-AAAATTTTGTTTCAAGATA
* * * *
498664 AACTG-TCTCGAGTGATAATAAAA--GT-TTTCAAGGA-A
1 AAATGATCTCAAGTGA-GATAAAATTTTGTTTCAA-GATA
* * * *
498699 AAAT-ATCTCAAGGGAGATAAAAATTTGTTTCGAGAGA
1 AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
* * **
498736 AACTG-TCTCAAGTGATATGGAAAA---T-TTTCAA-AGGG
1 AAATGATCTCAAGTGAGAT--AAAATTTTGTTTCAAGA-TA
* * *
498771 AAAT-ATCTCAAGTGAGAGGAAAAATTTGTTTCAAGAGA
1 AAATGATCTCAAGTGAGA-TAAAATTTTGTTTCAAGATA
* * * **
498809 AACTG-TCTCAAGTGAGACGAAAA--GT-TTTCAAGGGA
1 AAATGATCTCAAGTGAGA-TAAAATTTTGTTTCAAGATA
* *
498844 AAAT-ATCTCAAGAGAGATAAAATTTTGTTTCAAGAGA
1 AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
* * * **
498881 AACT-ATCTCAAGTGAGACGAAAA--AT-TTTCAAAGGGA
1 AAATGATCTCAAGTGAGA-TAAAATTTTGTTTC-AAGATA
* * * *
498917 AAAT-AACTCAAGTTAGATGAAATTTATGTTTCAAGAGA
1 AAATGATCTCAAGTGAGATAAAATTT-TGTTTCAAGATA
** * ** *
498955 ATTTG-TCTCGAGTGAGAT-GTATTTTGTTTTAAGA-A
1 AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
498990 AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
1 AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
499028 AAAT
1 AAAT
499032 TTATTTTTAA
Statistics
Matches: 279, Mismatches: 55, Indels: 68
0.69 0.14 0.17
Matches are distributed among these distances:
34 15 0.05
35 72 0.26
36 50 0.18
37 62 0.22
38 69 0.25
39 11 0.04
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (38 bp):
AAATGATCTCAAGTGAGATAAAATTTTGTTTCAAGATA
Found at i:499698 original size:25 final size:26
Alignment explanation
Indices: 499664--499731 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
499654 ATGATTAATG
*
499664 AAGAAGTTTTGAAAAATAATTGATAA
1 AAGAATTTTTGAAAAATAATTGATAA
* * *
499690 AATAATTTTTGAAAAATATTTGATGA
1 AAGAATTTTTGAAAAATAATTGATAA
*
499716 AAGAA-TTTCGAAAAAT
1 AAGAATTTTTGAAAAAT
499732 GTTACCCCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 10 0.28
26 26 0.72
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.34
Consensus pattern (26 bp):
AAGAATTTTTGAAAAATAATTGATAA
Found at i:500737 original size:38 final size:39
Alignment explanation
Indices: 500669--500759 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 39
500659 CGAGTCAAAT
*
500669 ATATGCACCGTAGTGCTTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACC
* *
500708 ATATGCACCAAAGTGC-TACACATAAGGTCGTGCCCACT
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACC
500746 ATATGCACCGAAGT
1 ATATGCACCGAAGT
500760 AATTAATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
38 34 0.71
39 14 0.29
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACC
Found at i:501765 original size:37 final size:32
Alignment explanation
Indices: 501700--501764 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
501690 GCATCACAAA
501700 TCACATAACATTTTAGGAGTAACTCCTTACCT
1 TCACATAACATTTTAGGAGTAACTCCTTACCT
*
501732 TCACATAACATTTTAGGAGTCACTCCTTACCT
1 TCACATAACATTTTAGGAGTAACTCCTTACCT
501764 T
1 T
501765 AGTAACTCCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (32 bp):
TCACATAACATTTTAGGAGTAACTCCTTACCT
Found at i:507375 original size:85 final size:84
Alignment explanation
Indices: 507150--507412 Score: 273
Period size: 85 Copynumber: 3.1 Consensus size: 84
507140 GATGCGCAAC
* * *
507150 TGTGTGTCATAAATCTATGACACGCAT-TAATGACGTT-CATTGAGTGTCATGGAAGACCCCGTC
1 TGTGTGTCATAAATTTATGACACGCATGT-ATGAC-TTACATTGAGTGTCATTGAAGCCCCCGTC
*
507213 ATAAATTAAGATGCCACACATT
64 ATAAATT-AGATGACACACATT
* * *
507235 TGTGCGTCATAAATTTATGACACGCATGTATGAATTACATTGCA-CGTCATTGAAGCCCCCGTCA
1 TGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTG-AGTGTCATTGAAGCCCCCGTCA
* *
507299 TAAATCT-GCTTGACATACATT
65 TAAAT-TAG-ATGACACACATT
* * * *
507320 TGTGTGTCATAAATTTATGACACACATGTATGACTTACATTGTGTGTCATTGAAGCACACGTCAT
1 TGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCA-
** * * *
507385 TAAAAAAGATGAAAAACGTT
65 TAAATTAGATGACACACATT
507405 TGTGTGTC
1 TGTGTGTC
507413 GTGATTGTAT
Statistics
Matches: 148, Mismatches: 22, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
84 3 0.02
85 137 0.93
86 8 0.05
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (84 bp):
TGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCAT
AAATTAGATGACACACATT
Found at i:507439 original size:2 final size:2
Alignment explanation
Indices: 507432--507491 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
507422 TTTCATAAAT
* *
507432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
507474 TA -A AA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
507492 TGTAGATTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:509883 original size:37 final size:37
Alignment explanation
Indices: 509842--509928 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 37
509832 CCTTTTTTTT
*
509842 TTTTTCCTCTTTGGTGTCCCTTCTCCTTT-CTCTCTCC
1 TTTTTCCTCTTTGGCGTCCCTTCTCCTTTACTCT-TCC
509879 TTTTTCCT-TTGTGGCGTCCCTTCTCCTTTACTCTTCC
1 TTTTTCCTCTT-TGGCGTCCCTTCTCCTTTACTCTTCC
*
509916 TTTCTTTCTCTTT
1 TTT-TTCCTCTTT
509929 TTCCATCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
36 2 0.05
37 31 0.70
38 9 0.20
39 2 0.05
ACGTcount: A:0.01, C:0.34, G:0.08, T:0.56
Consensus pattern (37 bp):
TTTTTCCTCTTTGGCGTCCCTTCTCCTTTACTCTTCC
Found at i:513795 original size:15 final size:15
Alignment explanation
Indices: 513770--513825 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
513760 GATGCTTTCT
*
513770 TTTTCCTTCTTTGACA
1 TTTT-CTTCTTTGACG
513786 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
513801 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
513816 TTGTCTTCTT
1 TTTTCTTCTT
513826 ACCCCATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.21, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:519118 original size:21 final size:22
Alignment explanation
Indices: 519056--519111 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
519046 TCATTCATCA
*
519056 TTTTTTCTATTTTTTCC-TTTCT
1 TTTTTTCT-TTATTTCCTTTTCT
519078 TTTTTTCTTTATTTCCTTTTCT
1 TTTTTTCTTTATTTCCTTTTCT
519100 TTTTTT-TTTATT
1 TTTTTTCTTTATT
519112 CATTTTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTCTTTATTTCCTTTTCT
Found at i:521299 original size:20 final size:20
Alignment explanation
Indices: 521271--521309 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
521261 TTCATATTCT
*
521271 AATGATTGAATACATGCAAA
1 AATGATTGAATAAATGCAAA
* *
521291 AATGCTTGACTAAATGCAA
1 AATGATTGAATAAATGCAA
521310 TGCAAAATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGATTGAATAAATGCAAA
Found at i:523650 original size:30 final size:30
Alignment explanation
Indices: 523614--523673 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
523604 CCTTACAATA
*
523614 TAAACGTATTATAAATAATTAGAAAACATT
1 TAAACGTATAATAAATAATTAGAAAACATT
523644 TAAACGTATAATAAATAATTAGAAAACATT
1 TAAACGTATAATAAATAATTAGAAAACATT
523674 CGTAAACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAACGTATAATAAATAATTAGAAAACATT
Found at i:524990 original size:3 final size:3
Alignment explanation
Indices: 524984--525012 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
524974 ATAAAATAAT
524984 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
525013 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:527189 original size:30 final size:31
Alignment explanation
Indices: 527139--527214 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
527129 AGTTTCAAAA
*
527139 GTAATAAATTGATCACTAATATTATCTATTT
1 GTAATAAATTGATCACTAATATTATCAATTT
* *
527170 GTAATAAA-TGGTTACTAATATTATCAATTT
1 GTAATAAATTGATCACTAATATTATCAATTT
* *
527200 GTAACAAAATGATCA
1 GTAATAAATTGATCA
527215 ATCCACCGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (31 bp):
GTAATAAATTGATCACTAATATTATCAATTT
Found at i:528238 original size:51 final size:51
Alignment explanation
Indices: 528178--528279 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
528168 AAAATCGAAC
528178 AAATTCTATCCAGATTGTATGTCTTATTAAAAATCTTCCTAATCCTAAATA
1 AAATTCTATCCAGATTGTATGTCTTATTAAAAATCTTCCTAATCCTAAATA
528229 AAATTCTATCCAGATTGTATGTCTTATTAAAAATCTTCCTAATCCTAAATA
1 AAATTCTATCCAGATTGTATGTCTTATTAAAAATCTTCCTAATCCTAAATA
528280 GAAGGAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (51 bp):
AAATTCTATCCAGATTGTATGTCTTATTAAAAATCTTCCTAATCCTAAATA
Found at i:536693 original size:31 final size:31
Alignment explanation
Indices: 536658--536736 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
536648 ATGACGATGG
* * * *
536658 AGTGACCATTTTGTTATAAACCGGTAATGTT
1 AGTGACTATTTTGTTATAAACAGATAATATT
* *
536689 AGTGACTATTTTGTTAGAAATAGATAATATT
1 AGTGACTATTTTGTTATAAACAGATAATATT
*
536720 AGTGACTAATTTGTTAT
1 AGTGACTATTTTGTTAT
536737 TTTGTAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (31 bp):
AGTGACTATTTTGTTATAAACAGATAATATT
Found at i:538212 original size:22 final size:22
Alignment explanation
Indices: 538187--538232 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
538177 ATTGGTTTAA
538187 TTATAAATTTAGTCCTTCAACT
1 TTATAAATTTAGTCCTTCAACT
538209 TTATAAATTTAGTCCTTCAACT
1 TTATAAATTTAGTCCTTCAACT
538231 TT
1 TT
538233 GAAGTATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (22 bp):
TTATAAATTTAGTCCTTCAACT
Found at i:540254 original size:3 final size:3
Alignment explanation
Indices: 540205--540235 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
540195 CATCAAGTTA
540205 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
540236 GAAAGGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:542337 original size:24 final size:23
Alignment explanation
Indices: 542297--542342 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
542287 ACTAGAAAGG
542297 TAAAATATATATTATTA-AAAAC
1 TAAAATATATATTATTATAAAAC
542319 TAAAATATATCATTAATTATAAAA
1 TAAAATATAT-ATT-ATTATAAAA
542343 TTATAGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 4 0.19
25 4 0.19
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAATATATATTATTATAAAAC
Found at i:542400 original size:2 final size:2
Alignment explanation
Indices: 542383--542423 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
542373 ATTAAAACAC
542383 AT AT ACT AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
542424 GTAACATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.89
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:542414 original size:17 final size:17
Alignment explanation
Indices: 542383--542423 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
542373 ATTAAAACAC
542383 ATATACTATAATATATAT
1 ATATA-TATAATATATAT
*
542401 ATATATATATTATATAT
1 ATATATATAATATATAT
542418 ATATAT
1 ATATAT
542424 GTAACATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATAATATATAT
Found at i:544207 original size:13 final size:13
Alignment explanation
Indices: 544169--544200 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
544159 ACTTTGGAAG
544169 TTGGGAGATGAGA
1 TTGGGAGATGAGA
544182 TTGGGAGATGAGA
1 TTGGGAGATGAGA
544195 TTGGGA
1 TTGGGA
544201 TTTGAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (13 bp):
TTGGGAGATGAGA
Found at i:544840 original size:193 final size:192
Alignment explanation
Indices: 544475--544854 Score: 645
Period size: 193 Copynumber: 2.0 Consensus size: 192
544465 ACATTTATTT
* *
544475 TAATTCAATTTAATTTAGTCATTTTGTGTTCTTTAAATTTATTCAAATTTCATTCAACATTTCAA
1 TAATTCAATTAAATTTAGTCATTTTGTGTTCTTTAAATTTATTCAAATTCCATTCAACATTTCAA
* *
544540 CCTTCATTTTCTTATTTCTATACATTTTTATTACCATTACTTTTAATTTCAACATAATTTTTATC
66 CCTTCATTTTCTTATTTCTATACATTTTTATTACCAATACATTTAATTTCAACATAATTTTTATC
* *
544605 TTATCATATTACCAAGTTTTTAATGTTTTCTATTTGGTTAAACTAAATTATATGTGTTTGTG
131 TTATCATATTACCAAGTTTTTAATATTTCCTATTTGGTTAAACTAAATTATATGTGTTTGTG
544667 TAATTCAATTAAATTTAGTCATTTTGTGTTCTTTAAATTTATTCAAATTCCATTCAACATTTCAA
1 TAATTCAATTAAATTTAGTCATTTTGTGTTCTTTAAATTTATTCAAATTCCATTCAACATTTCAA
* * *
544732 CCTTCATTTTTTGTATTTC-AGTACATTTTTATTATCAATACATTTAATTTCAACCTAATTTTTA
66 CCTTCATTTTCT-TATTTCTA-TACATTTTTATTACCAATACATTTAATTTCAACATAATTTTTA
*
544796 TCTTATCCTATTACCAAGTTTTTAATATTTCCTATTTGGTTAAACTAAATTATATGTGT
129 TCTTATCATATTACCAAGTTTTTAATATTTCCTATTTGGTTAAACTAAATTATATGTGT
544855 GTTCGTCCAT
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
192 75 0.43
193 101 0.57
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (192 bp):
TAATTCAATTAAATTTAGTCATTTTGTGTTCTTTAAATTTATTCAAATTCCATTCAACATTTCAA
CCTTCATTTTCTTATTTCTATACATTTTTATTACCAATACATTTAATTTCAACATAATTTTTATC
TTATCATATTACCAAGTTTTTAATATTTCCTATTTGGTTAAACTAAATTATATGTGTTTGTG
Found at i:547011 original size:30 final size:30
Alignment explanation
Indices: 546975--547039 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
546965 GCCAGCTCTA
546975 GAGGACTCATCCGAAAAGGGCACATCACTG
1 GAGGACTCATCCGAAAAGGGCACATCACTG
*
547005 GAGGACTCATCCGAAAAGGGCACATCGCTG
1 GAGGACTCATCCGAAAAGGGCACATCACTG
547035 GAGGA
1 GAGGA
547040 TTAACTCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.25, G:0.31, T:0.12
Consensus pattern (30 bp):
GAGGACTCATCCGAAAAGGGCACATCACTG
Found at i:559923 original size:6 final size:7
Alignment explanation
Indices: 559892--559921 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
559882 TAGTAAAATG
559892 TTTAATT
1 TTTAATT
559899 TTTAATT
1 TTTAATT
559906 TTTAATT
1 TTTAATT
559913 TTTAATT
1 TTTAATT
559920 TT
1 TT
559922 AAATAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTAATT
Found at i:561772 original size:21 final size:21
Alignment explanation
Indices: 561748--561951 Score: 154
Period size: 21 Copynumber: 9.9 Consensus size: 21
561738 CGCATTGTGG
561748 TAGTCCAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
*
561769 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
** *
561790 TTTTCCAAATT--CGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
*
561809 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
** * *
561830 TTTTTCAAATT--CGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
*
561849 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
* * *
561870 TTTATTCCAAATT--CGTTGTGA
1 --TAGTCCAAGTTCGCGTTGCGA
*
561891 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
* * *
561912 TTTATTCTAAATT--CGTTGCGA
1 --TAGTCCAAGTTCGCGTTGCGA
*
561933 TAGTCCAAGTTCGCTTTGC
1 TAGTCCAAGTTCGCGTTGC
561952 TATTTATTTC
Statistics
Matches: 137, Mismatches: 34, Indels: 24
0.70 0.17 0.12
Matches are distributed among these distances:
19 45 0.33
21 76 0.55
23 16 0.12
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
TAGTCCAAGTTCGCGTTGCGA
Found at i:561810 original size:40 final size:42
Alignment explanation
Indices: 561761--561979 Score: 347
Period size: 42 Copynumber: 5.3 Consensus size: 42
561751 TCCAAGTTCG
561761 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
561801 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TT-CAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
561841 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
561883 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * * *
561925 CGTTGCGATAGTCCAAGTTCGCTTTGCTATTTATTTCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
561967 CGTTGCTATAGTC
1 CGTTGCGATAGTC
561980 CAAAATCGCA
Statistics
Matches: 167, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 67 0.40
41 6 0.04
42 94 0.56
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:562619 original size:6 final size:6
Alignment explanation
Indices: 562597--562646 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
562587 TCTCGTCTCA
* * * *
562597 GGTCGT -GTCGT GATCGT GGTCGT GGTCGT GGTTGT GGTAGT GGTAGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
562644 GGT
1 GGT
562647 AATACGTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.06, C:0.10, G:0.48, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:562796 original size:21 final size:21
Alignment explanation
Indices: 562729--562816 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
562719 CACCAGTCGT
*
562729 TGCGATTTTGGACT-ATCGCAA
1 TGCGAATTTGGA-TAATCGCAA
*
562750 --CGAATTTGGAATAAATCGCAG
1 TGCGAATTTGG-AT-AATCGCAA
* *
562771 CGCGAATTTGGATTATCGCAA
1 TGCGAATTTGGATAATCGCAA
* *
562792 TGCGAATATGTA-AATCGCAA
1 TGCGAATTTGGATAATCGCAA
562812 TGCGA
1 TGCGA
562817 TAGTCGAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.17
20 13 0.24
21 21 0.39
22 2 0.04
23 9 0.17
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCGAATTTGGATAATCGCAA
Found at i:563143 original size:16 final size:16
Alignment explanation
Indices: 563122--563160 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
563112 ATTATTTTAT
563122 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
563138 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
*
563154 AATGTTT
1 TATGTTT
563161 TTTTTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (16 bp):
TATGTTTCTTAATGGA
Found at i:563482 original size:21 final size:21
Alignment explanation
Indices: 563456--563503 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
563446 AGTGTCCAAC
563456 AATAATAAAACTT-ATAGAAAA
1 AATAATAAAA-TTGATAGAAAA
* *
563477 AATAATAAAATTGGTAGAAAT
1 AATAATAAAATTGATAGAAAA
563498 AATAAT
1 AATAAT
563504 GTTTCCGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (21 bp):
AATAATAAAATTGATAGAAAA
Found at i:566398 original size:36 final size:35
Alignment explanation
Indices: 566320--566551 Score: 234
Period size: 36 Copynumber: 6.2 Consensus size: 35
566310 TGAAAATACG
* *
566320 TATATAATATATATGGTTTTTAAAACACTTTTAAAAA
1 TATATAATATATA--ATTTTTAAAACATTTTTAAAAA
* *
566357 CTATATATTATATATATTTTCAAAACATTTTTAAAAA
1 -TATATAATATATA-ATTTTTAAAACATTTTTAAAAA
566394 TATATAATATATAATTTTTGAAAAACA-TTTTAAAAA
1 TATATAATATATAATTTTT--AAAACATTTTTAAAAA
*
566430 TATATAATATATAATTTTTGAAAAACA-TTTTGAAAA
1 TATATAATATATAATTTTT--AAAACATTTTTAAAAA
* * *
566466 CATATAATATATAATTTTTAGAGCATTTTTGAAAACTTA
1 TATATAATATATAATTTTTAAAACATTTTT-AAAA---A
566505 TATATAATATATAATTTTTTTAAAACATTTTTAAAAAA
1 TATATAATATATAA--TTTTTAAAACATTTTT-AAAAA
566543 TTATATAAT
1 -TATATAAT
566552 TTTTTTAAAA
Statistics
Matches: 168, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
34 4 0.02
35 9 0.05
36 77 0.46
37 25 0.15
38 13 0.08
39 22 0.13
41 18 0.11
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATAATATATAATTTTTAAAACATTTTTAAAAA
Found at i:566573 original size:19 final size:20
Alignment explanation
Indices: 566532--566581 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
566522 TTTTAAAACA
566532 TTTTTAAAAAATTATATAAT
1 TTTTTAAAAAATTATATAAT
* *
566552 TTTTTTAAAAATTAT-TAGT
1 TTTTTAAAAAATTATATAAT
566571 TTTTTGAAAAA
1 TTTTT-AAAAA
566582 CATTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTTAAAAAATTATATAAT
Found at i:566670 original size:13 final size:13
Alignment explanation
Indices: 566652--566677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
566642 ATATTATATA
566652 GTTTTTATTTATT
1 GTTTTTATTTATT
566665 GTTTTTATTTATT
1 GTTTTTATTTATT
566678 ATTATTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:568002 original size:13 final size:14
Alignment explanation
Indices: 567986--568015 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
567976 TTTCATCTAT
567986 TTTTATTATT-TTA
1 TTTTATTATTATTA
567999 TTTTATTATTATTA
1 TTTTATTATTATTA
568013 TTT
1 TTT
568016 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:570075 original size:18 final size:19
Alignment explanation
Indices: 570054--570098 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
570044 ATTTAGACAT
570054 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
570072 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
*
570091 TCTGCATT
1 TTTGCATT
570099 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:573633 original size:84 final size:84
Alignment explanation
Indices: 573487--574005 Score: 600
Period size: 84 Copynumber: 6.2 Consensus size: 84
573477 ATTTTTTAAA
*
573487 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
573552 ACTACGCTCAGCTCCAAGG
66 ACTACGCTCAGCTCCAAGG
** * * * * *
573571 CATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
*
573636 ACTACGCTTAGCT-CAACGG
66 ACTACGCTCAGCTCCAA-GG
* * * *
573655 CACATCATTTGCAGCATAAATTAAGCCGAGAAGGGTTATCTGCCAACCAAAGTCCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
573720 ACTACGCTCAGCTCCAAGG
66 ACTACGCTCAGCTCCAAGG
* * * * * *
573739 CATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
573804 ACTACGCTCAGCT-CAACGG
66 ACTACGCTCAGCTCCAA-GG
* * * * **
573823 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CTAAAGACCCCCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
* * * *
573884 ATTACACTCAGCTTCGAGGG
66 ACTACGCTCAGC-TCCAAGG
* * * * * *** * *
573904 CACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
*
573969 ACTACGCTCAACTCCAAGG
66 ACTACGCTCAGCTCCAAGG
*
573988 CACATCATTTACAGCATA
1 CACATCATTTGCAGCATA
574006 GCTCAAGGCA
Statistics
Matches: 361, Mismatches: 65, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
80 25 0.07
81 36 0.10
82 1 0.00
83 6 0.02
84 266 0.74
85 27 0.07
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
ACTACGCTCAGCTCCAAGG
Found at i:573765 original size:168 final size:168
Alignment explanation
Indices: 573487--574005 Score: 715
Period size: 168 Copynumber: 3.1 Consensus size: 168
573477 ATTTTTTAAA
573487 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
*
573552 ACTACGCTCAGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
66 ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
* *
573617 CAAAAGACCTTTGAGTTTGACTACGCTTAGCTCAACGG
131 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGG
* * *
573655 CACATCATTTGCAGCATAAATTAAGCCGAGAAGGGTTATCTGCCAACCAAAGTCCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
*
573720 ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAA
66 ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
573785 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGG
131 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGG
* * * * **
573823 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CTAAAGACCCCCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
* * * * * * * * * * * ***
573884 ATTACACTCAGCTTCGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTATGA
66 ACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCA
* *
573949 CCAAAAGACCTTTGAGTTCGACTACGCTCAACTCCAA-GG
130 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGG
*
573988 CACATCATTTACAGCATA
1 CACATCATTTGCAGCATA
574006 GCTCAAGGCA
Statistics
Matches: 315, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
164 25 0.08
165 89 0.28
166 3 0.01
168 198 0.63
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (168 bp):
CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGG
Found at i:574712 original size:36 final size:35
Alignment explanation
Indices: 574634--574865 Score: 207
Period size: 36 Copynumber: 6.2 Consensus size: 35
574624 TGAAAATACG
* * *
574634 TATATAATATATATGGTTTTTAAAACACTTTTAAAAA
1 TATATAATATATA--ATTTTAAAAACATTTTTAAAAA
* *
574671 CTATATATTATATATATTTTCAAAACATTTTTAAAAA
1 -TATATAATATATA-ATTTTAAAAACATTTTTAAAAA
*
574708 TATATAATATATAATTTTTGAAAATCA-TTTTAAAAA
1 TATATAATATATAA-TTTT-AAAAACATTTTTAAAAA
*
574744 TATATAATATATAATTTTTGAAAAACA-TTTTGAAAA
1 TATATAATATATAA-TTTT-AAAAACATTTTTAAAAA
* * * *
574780 CATATAATATATAATTTTTAGAGCATTTTTGAAAACTTA
1 TATATAATATATAATTTTAAAAACATTTTT-AAAA---A
574819 TATATAATATATAATTTTTTAAAAACATTTTTAAAAAA
1 TATATAATATATAA--TTTTAAAAACATTTTT-AAAAA
574857 TTATATAAT
1 -TATATAAT
574866 TTTTTAAAAA
Statistics
Matches: 164, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
34 4 0.02
35 9 0.05
36 75 0.46
37 24 0.15
38 13 0.08
39 22 0.13
41 17 0.10
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATAATATATAATTTTAAAAACATTTTTAAAAA
Found at i:574718 original size:72 final size:71
Alignment explanation
Indices: 574634--574865 Score: 236
Period size: 72 Copynumber: 3.1 Consensus size: 71
574624 TGAAAATACG
* *
574634 TATATAATATATATGGTTTTTAAAACACTTTTAAAAACTATATATTATATATATTTTCAAAACAT
1 TATATAATATATA--ATTTTTAAAACA-TTTTAAAAACTATATATTATATATATTTTAAAAACAT
574699 TTTTAAAAA
63 TTTTAAAAA
*
574708 TATATAATATATAATTTTTGAAAATCATTTTAAAAA-TATATAATATATA-ATTTTTGAAAAACA
1 TATATAATATATAATTTTT-AAAA-CATTTTAAAAACTATATATTATATATA-TTTT-AAAAACA
*
574771 -TTTTGAAAA
62 TTTTTAAAAA
* * * * *
574780 CATATAATATATAATTTTTAGAGCATTTTTGAAAACTTATATATAATATATAATTTTTTAAAAAC
1 TATATAATATATAATTTTTAAAACA-TTTTAAAAAC-TATATAT--TATAT-ATATTTTAAAAAC
574845 ATTTTTAAAAAA
61 ATTTTT-AAAAA
574857 TTATATAAT
1 -TATATAAT
574866 TTTTTAAAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
70 2 0.02
71 11 0.08
72 47 0.36
73 25 0.19
74 15 0.11
75 12 0.09
76 9 0.07
77 4 0.03
78 7 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (71 bp):
TATATAATATATAATTTTTAAAACATTTTAAAAACTATATATTATATATATTTTAAAAACATTTT
TAAAAA
Found at i:574887 original size:19 final size:20
Alignment explanation
Indices: 574846--574895 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
574836 TTTAAAAACA
574846 TTTTTAAAAAATTATATAAT
1 TTTTTAAAAAATTATATAAT
*
574866 TTTTTAAAAAATTAT-TAGT
1 TTTTTAAAAAATTATATAAT
574885 TTTTTGAAAAA
1 TTTTT-AAAAA
574896 CATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTTAAAAAATTATATAAT
Found at i:574987 original size:13 final size:13
Alignment explanation
Indices: 574969--574994 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
574959 ATATTATATA
574969 GTTTTTATTTATT
1 GTTTTTATTTATT
574982 GTTTTTATTTATT
1 GTTTTTATTTATT
574995 ATTATTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:576319 original size:13 final size:14
Alignment explanation
Indices: 576303--576332 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
576293 TTTCATCTAT
576303 TTTTATTATT-TTA
1 TTTTATTATTATTA
576316 TTTTATTATTATTA
1 TTTTATTATTATTA
576330 TTT
1 TTT
576333 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:580587 original size:22 final size:23
Alignment explanation
Indices: 580559--580615 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
580549 CGATACTGAT
580559 AAGGTATCGATACTATCAAA-GG
1 AAGGTATCGATACTATCAAAGGG
580581 AAGGTATCGATACTATCAAAGGG
1 AAGGTATCGATACTATCAAAGGG
580604 AA-GTATCGATAC
1 AAGGTATCGATAC
580616 CATAGATCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (23 bp):
AAGGTATCGATACTATCAAAGGG
Found at i:581261 original size:45 final size:45
Alignment explanation
Indices: 581206--581430 Score: 258
Period size: 45 Copynumber: 5.0 Consensus size: 45
581196 AATGAATGAA
*
581206 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGAATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* *
581251 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
*
581296 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATAC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
** * * * *
581341 CATAGTTGA-AATGCATATGGGTGCATTATCAACATAAAAGTATGC
1 CA-AAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* * ** *
581386 TATAATTGAA-AATGCATAAT-GGTGCATTATAAACATGAATGGATG
1 CA-AAAT-AATAATGCAT-ATGGGTGCATTATCGACATGAAAGGATG
581431 TTATTAATGA
Statistics
Matches: 157, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 123 0.78
46 32 0.20
47 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
Found at i:583684 original size:22 final size:22
Alignment explanation
Indices: 583659--583714 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
583649 TGAAATGAAC
583659 AAAAAAATAAAATGAAA-TAGTT
1 AAAAAAATAAAATGAAAGTA-TT
* * *
583681 AAAAGACTAAAATTAAAGTATT
1 AAAAAAATAAAATGAAAGTATT
583703 AAAAAATATAAA
1 AAAAAA-ATAAA
583715 GAAAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (22 bp):
AAAAAAATAAAATGAAAGTATT
Found at i:583763 original size:14 final size:13
Alignment explanation
Indices: 583719--583770 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
583709 TATAAAGAAA
583719 AAATAA-AAAATT
1 AAATAATAAAATT
*
583731 AAATTAATGAAATT
1 AAA-TAATAAAATT
583745 AAATAACTAAAATT
1 AAATAA-TAAAATT
583759 AAATAAATAAAA
1 AAAT-AATAAAA
583771 ACTAATTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 23 0.68
15 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AAATAATAAAATT
Found at i:583836 original size:33 final size:34
Alignment explanation
Indices: 583783--583865 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 34
583773 TAATTGGCAT
*
583783 AAATTTTAAAA-ATAAAGTAAA-AGACTAAAAT-A
1 AAATATTAAAATATAAAGTAAAGA-ACTAAAATAA
583815 AAATATTAAAATATAAAGTAAAGAACTAAAATAA
1 AAATATTAAAATATAAAGTAAAGAACTAAAATAA
*
583849 AAGATATCAAAATATAA
1 AA-ATATTAAAATATAA
583866 TGCCCAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
32 10 0.22
33 18 0.40
34 4 0.09
35 13 0.29
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (34 bp):
AAATATTAAAATATAAAGTAAAGAACTAAAATAA
Found at i:586020 original size:43 final size:42
Alignment explanation
Indices: 585921--586488 Score: 538
Period size: 43 Copynumber: 13.1 Consensus size: 42
585911 CTCATTTGTA
* ** * *
585921 AACATCCTGCACTGAAGGTCTTATGGATGACTCGAAGGCTTT
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
*
585963 AACATCTTGCACTGAAAGG-CTTACAGATGACCTGAAGGATTT
1 AACATCTTGCACTG-AAGGTCTTACAGATGACCCGAAGGATTT
586005 CAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
1 -AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
*
586048 CAACATCTTGCACTAAAGGTCTTACAGATGACCCGAAGGATTT
1 -AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
*
586091 CAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTT
1 -AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
*
586134 AACATCTTGCACTGAAGGTCTTACAGATGACCTGAAGGATTT
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
* * * * ** ** *** **
586176 ATAGAT-TAAGAAACCCCCGAA-GAATT--AG-TTTCTAAAATATCATTT
1 A-ACATCT-TG----CACTGAAGGTCTTACAGATGAC-CCGA-AGGATTT
* **
586221 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTATTT
1 ---AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGG--ATTT
* * ** * * *
586268 GGAAACATCCTACACTGAAGGTCTTATGGATGATCCAAAGGCTTT
1 ---AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
* *
586313 AACATATTGCACTGAAGGGCTTACA-ACTGACCCGAAGGATTT
1 AACATCTTGCACTGAAGGTCTTACAGA-TGACCCGAAGGATTT
*
586355 CAACATCTTGCACTGAAGGTCTTACAGACGACCCGAAGGATTT
1 -AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
586398 CAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTTT
1 -AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGA-TTT
* *
586442 GACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGCTTT
1 AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
586484 AACAT
1 AACAT
586489 TAAGAAACCC
Statistics
Matches: 440, Mismatches: 61, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.00
42 115 0.26
43 247 0.56
44 10 0.02
45 9 0.02
46 5 0.01
47 52 0.12
48 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
AACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTT
Found at i:586170 original size:20 final size:20
Alignment explanation
Indices: 586103--586171 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
586093 ACATCTTGCA
586103 CTGAAGGTCTTACAGATGAC
1 CTGAAGGTCTTACAGATGAC
* **
586123 CCGAAGG-CTTTAACATCTTG-C
1 CTGAAGGTC-TT-ACA-GATGAC
586144 ACTGAAGGTCTTACAGATGAC
1 -CTGAAGGTCTTACAGATGAC
586165 CTGAAGG
1 CTGAAGG
586172 ATTTATAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 1 0.03
20 17 0.46
21 8 0.22
22 10 0.27
23 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (20 bp):
CTGAAGGTCTTACAGATGAC
Found at i:587049 original size:25 final size:25
Alignment explanation
Indices: 587015--587069 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
587005 GTGTCTTCTT
587015 TGTTTCATTAAAGACTCAGAAAAAA
1 TGTTTCATTAAAGACTCAGAAAAAA
** *
587040 TGTTTCATTAAAGTTTCATAAAAAA
1 TGTTTCATTAAAGACTCAGAAAAAA
587065 TGTTT
1 TGTTT
587070 AATTTATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (25 bp):
TGTTTCATTAAAGACTCAGAAAAAA
Found at i:589198 original size:17 final size:19
Alignment explanation
Indices: 589161--589198 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
589151 CCTTTTTTTC
*
589161 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCGCTTT
589180 TTTCGAACAGT-T-GCTTT
1 TTTCGAACAGTCTCGCTTT
589197 TT
1 TT
589199 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 1 0.06
19 11 0.61
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTCGAACAGTCTCGCTTT
Found at i:591775 original size:19 final size:19
Alignment explanation
Indices: 591751--591790 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
591741 TCTTTTTTTC
591751 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCTCTTT
591770 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCTCTTT
591789 TT
1 TT
591791 GAACAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.25, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTCGAACAGTCTCTCTTT
Found at i:591789 original size:17 final size:18
Alignment explanation
Indices: 591751--591796 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
591741 TCTTTTTTTC
591751 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCTC-TT
591770 TTTCGAACAGTCTCTCTT
1 TTTCGAACAGTCTCTCTT
591788 TTT-GAACAG
1 TTTCGAACAG
591797 CTTTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.22
18 5 0.19
19 16 0.59
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (18 bp):
TTTCGAACAGTCTCTCTT
Found at i:592683 original size:13 final size:12
Alignment explanation
Indices: 592664--592697 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
592654 GCTTAATCGG
592664 AAAAAAAATAAA
1 AAAAAAAATAAA
*
592676 AGAAAAAATAAA
1 AAAAAAAATAAA
*
592688 AATAAAAATA
1 AAAAAAAATA
592698 TAACGGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:597120 original size:54 final size:54
Alignment explanation
Indices: 597013--597125 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
597003 CATAATTACT
* * * **
597013 GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTTTCCAGA
1 GGTTCATAAAACAGTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGA
*
597067 GGTTCATAAAGCAGTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGA
1 GGTTCATAAAACAGTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGA
*
597121 TGTTC
1 GGTTC
597126 TCAATCATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (54 bp):
GGTTCATAAAACAGTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGA
Found at i:598203 original size:24 final size:24
Alignment explanation
Indices: 598169--598215 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
598159 AATGCCCCAT
*
598169 ATGGATTTGTCTGAAGTGGCCTTC
1 ATGGATCTGTCTGAAGTGGCCTTC
598193 ATGGATCTGTCTGAAGTGGCCTT
1 ATGGATCTGTCTGAAGTGGCCTT
598216 TAAAATGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.36
Consensus pattern (24 bp):
ATGGATCTGTCTGAAGTGGCCTTC
Found at i:600201 original size:72 final size:71
Alignment explanation
Indices: 600084--600222 Score: 210
Period size: 72 Copynumber: 1.9 Consensus size: 71
600074 TCACCTTTAT
* *
600084 CAGGCTAGTTGAAACTTATCCATAAAGCCGGGGTAATTAACCAATTGCTTTAGGGGGACAACTCA
1 CAGGCTAGCTGAAACTTATCCATAAAGCCGGGCTAATTAACCAATTGCTTTA-GGGGACAACTCA
600149 AGCATAA
65 AGCATAA
*
600156 CAGGCTAGCTGAATA-TTATCCATAAAGCCTGGGCT-ATTAACCAATTGCTTTAGGGGATAACTC
1 CAGGCTAGCTGAA-ACTTATCCATAAAGCC-GGGCTAATTAACCAATTGCTTTAGGGGACAACTC
600219 AAGC
64 AAGC
600223 TTTATTGTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 14 0.23
72 43 0.69
73 5 0.08
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (71 bp):
CAGGCTAGCTGAAACTTATCCATAAAGCCGGGCTAATTAACCAATTGCTTTAGGGGACAACTCAA
GCATAA
Found at i:602194 original size:12 final size:12
Alignment explanation
Indices: 602170--602203 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
602160 GCAAAGATGC
602170 AAATATAAAATGA
1 AAATAT-AAATGA
*
602183 AAATGTAAATGA
1 AAATATAAATGA
602195 AAATATAAA
1 AAATATAAA
602204 AATGCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AAATATAAATGA
Found at i:602207 original size:20 final size:21
Alignment explanation
Indices: 602182--602234 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
602172 ATATAAAATG
* *
602182 AAAATGTAAATG-AAAATATA
1 AAAATGCAAATGCAAAATAAA
*
602202 AAAATGCAAATGCAAACTAAA
1 AAAATGCAAATGCAAAATAAA
602223 AAAATGCAAATG
1 AAAATGCAAATG
602235 TAATGGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (21 bp):
AAAATGCAAATGCAAAATAAA
Found at i:605629 original size:14 final size:14
Alignment explanation
Indices: 605609--605654 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
605599 GCAAAAATAA
605609 AAAATTAAAGTAA-T
1 AAAATTAAA-TAACT
*
605623 GAAATTAAATAACT
1 AAAATTAAATAACT
*
605637 AAAATTAAATAAAT
1 AAAATTAAATAACT
605651 AAAA
1 AAAA
605655 AGTAAATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAATTAAATAACT
Found at i:605708 original size:33 final size:33
Alignment explanation
Indices: 605671--605734 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
605661 TGGCATAAAT
605671 TTAAAATATAAAGTAAA-AGACTAAAATAAAAGA
1 TTAAAATATAAAGTAAAGA-ACTAAAATAAAAGA
605704 TTAAAATATAAAGTAAAGAACTAAAATAAAA
1 TTAAAATATAAAGTAAAGAACTAAAATAAAA
605735 AATATCAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (33 bp):
TTAAAATATAAAGTAAAGAACTAAAATAAAAGA
Found at i:605715 original size:20 final size:21
Alignment explanation
Indices: 605692--605738 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
605682 AGTAAAAGAC
*
605692 TAAAATAAAAG-ATTAAAATA
1 TAAAATAAAAGAACTAAAATA
*
605712 TAAAGT-AAAGAACTAAAATA
1 TAAAATAAAAGAACTAAAATA
*
605732 AAAAATA
1 TAAAATA
605739 TCAGAATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (21 bp):
TAAAATAAAAGAACTAAAATA
Found at i:608346 original size:23 final size:23
Alignment explanation
Indices: 608315--608360 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
608305 AGTGACAATT
608315 ATTTATGTCATCAAATAATTTATA
1 ATTTATGTCA-CAAATAATTTATA
* *
608339 ATTT-TGTCACTAATTATTTATA
1 ATTTATGTCACAAATAATTTATA
608361 TCATCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTTATGTCACAAATAATTTATA
Found at i:608558 original size:28 final size:26
Alignment explanation
Indices: 608492--608594 Score: 71
Period size: 28 Copynumber: 3.7 Consensus size: 26
608482 TAAATTAAAA
608492 AAATTATATTAAAGGACAACATTTTAT
1 AAATTATA-TAAAGGACAACATTTTAT
* * * *
608519 AAATAAAAATAAAGGACACCTTTTTTAT
1 AAAT-TATATAAAGGACAAC-ATTTTAT
* *
608547 AAATTATGATAAAGGAAAAAACTTTTTAT
1 AAATTAT-ATAAAGG--ACAACATTTTAT
* *
608576 AAATATTTATAAATGACAA
1 AAAT-TATATAAAGGACAA
608595 AACTTCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
27 18 0.31
28 19 0.32
29 17 0.29
30 5 0.08
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (26 bp):
AAATTATATAAAGGACAACATTTTAT
Found at i:608587 original size:29 final size:29
Alignment explanation
Indices: 608540--608610 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
608530 AAGGACACCT
608540 TTTTTATAAATTATGATAAAGGAAAAAAC
1 TTTTTATAAATTATGATAAAGGAAAAAAC
* * *
608569 TTTTTATAAA-TATTTATAAATGACAAAAC
1 TTTTTATAAATTA-TGATAAAGGAAAAAAC
* *
608598 TTCTAATAAATTA
1 TTTTTATAAATTA
608611 CAATACTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 31 0.89
30 2 0.06
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTTTATAAATTATGATAAAGGAAAAAAC
Found at i:609630 original size:2 final size:2
Alignment explanation
Indices: 609623--609665 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
609613 AGTTGCTACA
609623 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
609665 A
1 A
609666 GATTTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:634236 original size:28 final size:28
Alignment explanation
Indices: 634186--634257 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
634176 GTGTAGGAAT
*
634186 TATAGAG--ATGA-TTTGTTATCATTCC
1 TATAGAGATATGATTTTGTTACCATTCC
634211 TATAGAGATATGATTTTGTTACCATTCC
1 TATAGAGATATGATTTTGTTACCATTCC
634239 TATAGAGATATGATTTTGT
1 TATAGAGATATGATTTTGT
634258 AAATAGATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
25 7 0.16
27 4 0.09
28 32 0.74
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (28 bp):
TATAGAGATATGATTTTGTTACCATTCC
Found at i:637997 original size:27 final size:26
Alignment explanation
Indices: 637955--638022 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 26
637945 GTGTAGGAAT
637955 TATAGAG-ATGATTTGTTACCATTCC
1 TATAGAGAATGATTTGTTACCATTCC
*
637980 TATAGAGATATGATTTGTTACCATTTC
1 TATAGAGA-ATGATTTGTTACCATTCC
638007 TATAGAGAAATGATTT
1 TATAGAG-AATGATTT
638023 TGTAAATAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 7 0.18
27 31 0.79
28 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (26 bp):
TATAGAGAATGATTTGTTACCATTCC
Found at i:643802 original size:3 final size:3
Alignment explanation
Indices: 643794--643855 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
643784 ATTTTAAAAT
* * *
643794 TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
643840 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
643856 CAAAACCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:651585 original size:19 final size:19
Alignment explanation
Indices: 651561--651599 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
651551 GAATTTCTTA
651561 TTGATTTCTTTCCCATTAT
1 TTGATTTCTTTCCCATTAT
651580 TTGATTTCTTTCCCATTAT
1 TTGATTTCTTTCCCATTAT
651599 T
1 T
651600 CAAGTTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.05, T:0.59
Consensus pattern (19 bp):
TTGATTTCTTTCCCATTAT
Found at i:656452 original size:34 final size:34
Alignment explanation
Indices: 656408--656479 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
656398 TTGGGGTGCA
* *
656408 TATTTCTATTTTTGATGATAGCACCTGGAATGCT
1 TATTTATATTTATGATGATAGCACCTGGAATGCT
* *
656442 TATTTATATTTATGATGATAGCACTTGGAGTGCT
1 TATTTATATTTATGATGATAGCACCTGGAATGCT
656476 TATT
1 TATT
656480 GTGAACACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (34 bp):
TATTTATATTTATGATGATAGCACCTGGAATGCT
Found at i:656584 original size:19 final size:19
Alignment explanation
Indices: 656559--656630 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
656549 AAATATGATA
*
656559 TATGAATCTCAAAATGAGC
1 TATGAATCTGAAAATGAGC
* * *
656578 TAAGAATATGGAAATGAGC
1 TATGAATCTGAAAATGAGC
*
656597 TATGAATCTGAAAATGAGT
1 TATGAATCTGAAAATGAGC
656616 TATGAATCTGAAAAT
1 TATGAATCTGAAAAT
656631 AAAGAAAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (19 bp):
TATGAATCTGAAAATGAGC
Found at i:656586 original size:38 final size:37
Alignment explanation
Indices: 656540--656614 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
656530 GGATACGAAT
*
656540 CTAAAATAT-AAATATGATATATGAATCTCAAAATGAG
1 CTAAAATATGAAA-ATGAGATATGAATCTCAAAATGAG
* * *
656577 CTAAGAATATGGAAATGAGCTATGAATCTGAAAATGAG
1 CTAA-AATATGAAAATGAGATATGAATCTCAAAATGAG
656615 TTATGAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 4 0.12
38 26 0.81
39 2 0.06
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (37 bp):
CTAAAATATGAAAATGAGATATGAATCTCAAAATGAG
Found at i:659222 original size:24 final size:24
Alignment explanation
Indices: 659195--659266 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
659185 ATAAATACTA
*
659195 GACAATCAATAATCACAAATCAAT
1 GACAATCAACAATCACAAATCAAT
659219 GACAATCAACAATCACAAATCAAT
1 GACAATCAACAATCACAAATCAAT
659243 GACAATCAACAATCACAAATCAAT
1 GACAATCAACAATCACAAATCAAT
659267 CATACTCTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.54, C:0.24, G:0.04, T:0.18
Consensus pattern (24 bp):
GACAATCAACAATCACAAATCAAT
Found at i:659231 original size:13 final size:13
Alignment explanation
Indices: 659196--659265 Score: 58
Period size: 13 Copynumber: 5.6 Consensus size: 13
659186 TAAATACTAG
*
659196 ACAATCAATAATC
1 ACAATCAACAATC
* *
659209 ACAA--ATCAATG
1 ACAATCAACAATC
659220 ACAATCAACAATC
1 ACAATCAACAATC
* *
659233 ACAA--ATCAATG
1 ACAATCAACAATC
659244 ACAATCAACAATC
1 ACAATCAACAATC
659257 ACAAATCAA
1 AC-AATCAA
659266 TCATACTCTC
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
11 17 0.40
13 20 0.47
14 6 0.14
ACGTcount: A:0.56, C:0.24, G:0.03, T:0.17
Consensus pattern (13 bp):
ACAATCAACAATC
Found at i:659921 original size:16 final size:16
Alignment explanation
Indices: 659900--659932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
659890 TTCGTCGATT
659900 CTGGCT-GCCTCCATCG
1 CTGGCTCGCCT-CATCG
659916 CTGGCTCGCCTCATCG
1 CTGGCTCGCCTCATCG
659932 C
1 C
659933 CACCCTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.06, C:0.45, G:0.24, T:0.24
Consensus pattern (16 bp):
CTGGCTCGCCTCATCG
Found at i:660266 original size:19 final size:19
Alignment explanation
Indices: 660239--660307 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
660229 AACTGGTCTG
*
660239 ACCCGTTGACTTTAACCCA
1 ACCCATTGACTTTAACCCA
* * * *
660258 ACCCATTGAATTGAA-TCT
1 ACCCATTGACTTTAACCCA
*
660276 ACCCATTGACTTTAACCCG
1 ACCCATTGACTTTAACCCA
*
660295 ACCCGTTGACTTT
1 ACCCATTGACTTT
660308 GACCAAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (19 bp):
ACCCATTGACTTTAACCCA
Found at i:660798 original size:8 final size:8
Alignment explanation
Indices: 660777--660815 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
660767 GTTCATTGAA
660777 ATTTA-TG
1 ATTTACTG
660784 ATTTACTG
1 ATTTACTG
*
660792 TTTTACTG
1 ATTTACTG
660800 ATTTACTG
1 ATTTACTG
660808 ATTTACTG
1 ATTTACTG
660816 GTTGATGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (8 bp):
ATTTACTG
Found at i:666462 original size:2 final size:2
Alignment explanation
Indices: 666455--666496 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
666445 TAATTTTCCA
666455 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
666497 TTTAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:666638 original size:20 final size:20
Alignment explanation
Indices: 666613--666652 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
666603 GATATAAATC
*
666613 ATTGTTCAATGACCTATTTG
1 ATTGTTCAATGACCAATTTG
* *
666633 ATTGTTTAGTGACCAATTTG
1 ATTGTTCAATGACCAATTTG
666653 TTATTTTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTGTTCAATGACCAATTTG
Found at i:671899 original size:158 final size:158
Alignment explanation
Indices: 671611--671926 Score: 632
Period size: 158 Copynumber: 2.0 Consensus size: 158
671601 ACCATATTTC
671611 CAAGGTGTATCTCAGAATGTGTTAAGTACACCTCCTCGACAAGATGATGACGATGACGACGACAA
1 CAAGGTGTATCTCAGAATGTGTTAAGTACACCTCCTCGACAAGATGATGACGATGACGACGACAA
671676 CGAAAACAATCAAGGCATACGACCCCATCGTACTCAACGAGCCCAACGCCATTATCATTCGACAA
66 CGAAAACAATCAAGGCATACGACCCCATCGTACTCAACGAGCCCAACGCCATTATCATTCGACAA
671741 CTTCTCGACATTGTCAAGAACTTAGAAA
131 CTTCTCGACATTGTCAAGAACTTAGAAA
671769 CAAGGTGTATCTCAGAATGTGTTAAGTACACCTCCTCGACAAGATGATGACGATGACGACGACAA
1 CAAGGTGTATCTCAGAATGTGTTAAGTACACCTCCTCGACAAGATGATGACGATGACGACGACAA
671834 CGAAAACAATCAAGGCATACGACCCCATCGTACTCAACGAGCCCAACGCCATTATCATTCGACAA
66 CGAAAACAATCAAGGCATACGACCCCATCGTACTCAACGAGCCCAACGCCATTATCATTCGACAA
671899 CTTCTCGACATTGTCAAGAACTTAGAAA
131 CTTCTCGACATTGTCAAGAACTTAGAAA
671927 ATATAGATAA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (158 bp):
CAAGGTGTATCTCAGAATGTGTTAAGTACACCTCCTCGACAAGATGATGACGATGACGACGACAA
CGAAAACAATCAAGGCATACGACCCCATCGTACTCAACGAGCCCAACGCCATTATCATTCGACAA
CTTCTCGACATTGTCAAGAACTTAGAAA
Found at i:675788 original size:23 final size:23
Alignment explanation
Indices: 675762--675817 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
675752 GTGCTCAATG
675762 TAATGGTCCAGATCCAGCAGACA
1 TAATGGTCCAGATCCAGCAGACA
675785 TAATGGTCCAGATCCAGCAGACA
1 TAATGGTCCAGATCCAGCAGACA
675808 TAATGGTCCA
1 TAATGGTCCA
675818 AACTTTCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (23 bp):
TAATGGTCCAGATCCAGCAGACA
Done.