Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:475551 original size:2 final size:2
Alignment explanation
Indices: 475512--475788 Score: 95
Period size: 2 Copynumber: 145.5 Consensus size: 2
475502 AATAATGATA
* * *
475512 AT AT AT A- AT AT AA AT AT ACT AT AGT AT AT A- AT AA AT AT AT GCT
1 AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT -AT
* * * *
475555 AT A- AT AT AT A- AT AC AT AC AC AT A- AT AT AT ACT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
475595 AT -T AT ACT AC A- AT A- AT A- AT AT AT A- AT AT AT A- AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
475632 A- AT A- AT ACT ACC AC A- AA AT AT AT CAT AT CAT AT AC AT A- AT
1 AT AT AT AT A-T A-T AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT
*
475672 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T A- AT CT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
475711 AA AT AT AT A- AT AT TT AT A- AT AT A- AT AT AT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
475749 A- AT AT A- AT AT GT AT ACT AT AT ACT -T AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT
475788 A
1 A
475789 CACTATCTCA
Statistics
Matches: 210, Mismatches: 26, Indels: 78
0.67 0.08 0.25
Matches are distributed among these distances:
1 27 0.13
2 159 0.76
3 24 0.11
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:475652 original size:37 final size:38
Alignment explanation
Indices: 475575--475744 Score: 101
Period size: 37 Copynumber: 4.6 Consensus size: 38
475565 ATACATACAC
* *
475575 ATAATATATACTATATATAAATTATACTACAATAATAATAT
1 ATAATATATA--ATATAT-AATAATACTACAACAATAATAT
*
475616 ATAATATATAATATATAATAATACTACCACAA-AATAT
1 ATAATATATAATATATAATAATACTACAACAATAATAT
* * * *
475653 ATCATATCAT-ATACATAAT-ATA-TA-TA-TAT-ATAT
1 ATAATAT-ATAATATATAATAATACTACAACAATAATAT
* *
475686 AT-ATATATAATAT-TAAT-CTACTATAA-AATATATAAT
1 ATAATATATAATATATAATAATACTACAACAATA-AT-AT
*
475722 ATTTATAATATAATATATAATAA
1 A-TAAT-ATATAATATATAATAA
475745 ATATAATATA
Statistics
Matches: 104, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
31 8 0.08
32 9 0.09
33 10 0.10
34 1 0.01
35 4 0.04
36 6 0.06
37 20 0.19
38 17 0.16
39 15 0.14
40 4 0.04
41 10 0.10
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (38 bp):
ATAATATATAATATATAATAATACTACAACAATAATAT
Found at i:475714 original size:64 final size:61
Alignment explanation
Indices: 475587--475766 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 61
475577 AATATATACT
* *
475587 ATATATAAATTATACTACAATAATAATATATAATATATA-ATAT-ATAATAATACTACCACAAA
1 ATATAT-AA-TATA-TATAATAATAATATATAATATATATATATAATATTAATACTACCACAAA
* * *
475649 ATATATCATATCATATACATAATATATATATATATATATATATATAATATTAAT-CTACTATAAA
1 ATATATAATAT-ATATA-ATAATA-ATATATA-ATATATATATATAATATTAATACTACCACAAA
* *
475713 ATATATAATATTTATAAT-ATAATATATAATAAATATAATATAATATGT-ATACTA
1 ATATATAATATATATAATAATAATATATAATATATAT-ATATAATAT-TAATACTA
475767 TATACTTATA
Statistics
Matches: 101, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
59 7 0.07
60 24 0.24
61 15 0.15
62 15 0.15
63 11 0.11
64 22 0.22
65 7 0.07
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (61 bp):
ATATATAATATATATAATAATAATATATAATATATATATATAATATTAATACTACCACAAA
Found at i:476560 original size:50 final size:51
Alignment explanation
Indices: 476466--476587 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 51
476456 CGTGGGTAAC
* * **
476466 TCCTTCGTTGTGAAGTTG-ATTTCAAATTGAACATTATTCTGAGTTGGATA
1 TCCTTCGTTGTGAAGTTGAAATCCAAATTGAACATTATTCTGAGTTCAATA
* * ** *
476516 TCCTTCATTGTGAAGTTGAAATCCAACTTGAATGTTCTTC-GAGTTCAATA
1 TCCTTCGTTGTGAAGTTGAAATCCAAATTGAACATTATTCTGAGTTCAATA
* *
476566 TCCTTCGCTGTGAAGATGAAAT
1 TCCTTCGTTGTGAAGTTGAAAT
476588 TGACTCTGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 44 0.75
51 15 0.25
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (51 bp):
TCCTTCGTTGTGAAGTTGAAATCCAAATTGAACATTATTCTGAGTTCAATA
Found at i:477417 original size:11 final size:11
Alignment explanation
Indices: 477395--477437 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
477385 TTGGACCCAC
477395 CTTTTATTTTTT
1 CTTTT-TTTTTT
*
477407 ATTTTTTTTTT
1 CTTTTTTTTTT
477418 CTTTTTTTTTT
1 CTTTTTTTTTT
477429 CTTTTTTTT
1 CTTTTTTTT
477438 CAGCCCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:477976 original size:29 final size:29
Alignment explanation
Indices: 477942--477998 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
477932 AAATTTTAGA
477942 TAGTGACAAAAATACAAATTTTAAAAAAT
1 TAGTGACAAAAATACAAATTTTAAAAAAT
* * * *
477971 TAGTGACCAAAGTATAAATTTTGAAAAA
1 TAGTGACAAAAATACAAATTTTAAAAAA
477999 GTTTAAGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (29 bp):
TAGTGACAAAAATACAAATTTTAAAAAAT
Found at i:479734 original size:24 final size:24
Alignment explanation
Indices: 479707--479755 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
479697 TGCATAACAT
* *
479707 TGTATATATATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
479731 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
479755 T
1 T
479756 TACGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:485525 original size:29 final size:30
Alignment explanation
Indices: 485491--485561 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
485481 TTTTAAATAA
485491 TGACCAAAATGCAAACTTTG-AAAATTTAG
1 TGACCAAAATGCAAACTTTGAAAAATTTAG
* **
485520 TGACCAAAGTATAAACTTTGAAAAAATTTAG
1 TGACCAAAATGCAAACTTTG-AAAAATTTAG
*
485551 GGACCAAAATG
1 TGACCAAAATG
485562 GTAATTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (30 bp):
TGACCAAAATGCAAACTTTGAAAAATTTAG
Found at i:487279 original size:24 final size:25
Alignment explanation
Indices: 487247--487298 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
487237 ACATGCATAA
487247 CATTGTACATAGATGTTTTATACAT
1 CATTGTACATAGATGTTTTATACAT
* *
487272 CATT-TACATAGATTTTTTATTCAT
1 CATTGTACATAGATGTTTTATACAT
487296 CAT
1 CAT
487299 CAGGAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (25 bp):
CATTGTACATAGATGTTTTATACAT
Found at i:497844 original size:25 final size:24
Alignment explanation
Indices: 497798--497844 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
497788 CTAAAAATTC
*
497798 AAATTAATATCAAATAACAAAATA
1 AAATTAATATCAAATAAAAAAATA
497822 AAATATAATAT-AAATTAAAAAAA
1 AAAT-TAATATCAAA-TAAAAAAA
497845 ATTAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATTAATATCAAATAAAAAAATA
Found at i:497856 original size:14 final size:14
Alignment explanation
Indices: 497817--497864 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
497807 TCAAATAACA
*
497817 AAATAAAATATAATAT
1 AAATAAAA-AAAAT-T
497833 AAATTAAAAAAAATT
1 AAA-TAAAAAAAATT
497848 AAATAAAAAAAATT
1 AAATAAAAAAAATT
497862 AAA
1 AAA
497865 GATGGATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 14 0.47
15 4 0.13
16 7 0.23
17 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAAAAAAATT
Found at i:499532 original size:25 final size:26
Alignment explanation
Indices: 499489--499539 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
499479 AGCTTTTTCT
*
499489 TTTTACTTTTCAAGTTTTTATTTTTA
1 TTTTACTTTTCAAGCTTTTATTTTTA
*
499515 TTTTA-TTTTTAAGCTTTTATTTTTA
1 TTTTACTTTTCAAGCTTTTATTTTTA
499540 ATATGCTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTACTTTTCAAGCTTTTATTTTTA
Found at i:499538 original size:14 final size:13
Alignment explanation
Indices: 499489--499540 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
499479 AGCTTTTTCT
*
499489 TTTTACTTTTCAAG
1 TTTTA-TTTTTAAG
499503 TTTTTATTTTT-A-
1 -TTTTATTTTTAAG
499515 TTTTATTTTTAAG
1 TTTTATTTTTAAG
499528 CTTTTATTTTTAA
1 -TTTTATTTTTAA
499541 TATGCTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 10 0.30
12 1 0.03
13 1 0.03
14 16 0.48
15 5 0.15
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:506806 original size:7 final size:7
Alignment explanation
Indices: 506738--506927 Score: 109
Period size: 7 Copynumber: 27.7 Consensus size: 7
506728 GTATGAATCC
506738 TATAATA
1 TATAATA
506745 T-TAATA
1 TATAATA
506751 -ATAATACAA
1 TATAAT---A
506760 TATAATA
1 TATAATA
*
506767 AATAAT-
1 TATAATA
*
506773 GATAATA
1 TATAATA
*
506780 TTTAATA
1 TATAATA
*
506787 TAAATATA
1 TATA-ATA
506795 CTATAATA
1 -TATAATA
506803 TATAATA
1 TATAATA
*
506810 TATACTA
1 TATAATA
506817 TATAA-A
1 TATAATA
506823 T-T-ATA
1 TATAATA
*
506828 CTACAATA
1 -TATAATA
506836 -ATAATA
1 TATAATA
*
506842 TATACTA
1 TATAATA
506849 TATAATA
1 TATAATA
506856 TATAAT-
1 TATAATA
*
506862 TACT-A-C
1 TA-TAATA
*
506868 TATAACA
1 TATAATA
*
506875 TATAACA
1 TATAATA
506882 TATAATA
1 TATAATA
506889 TTTATAATA
1 --TATAATA
506898 TAT-AT-
1 TATAATA
506903 TAT-ATA
1 TATAATA
506909 TATAATA
1 TATAATA
*
506916 TATACTA
1 TATAATA
506923 TATAA
1 TATAA
506928 AATAATACTA
Statistics
Matches: 145, Mismatches: 17, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
4 1 0.01
5 8 0.06
6 33 0.23
7 78 0.54
8 9 0.06
9 11 0.08
10 5 0.03
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (7 bp):
TATAATA
Found at i:506818 original size:14 final size:14
Alignment explanation
Indices: 506748--507005 Score: 110
Period size: 14 Copynumber: 18.0 Consensus size: 14
506738 TATAATATTA
*
506748 ATAATA-ATACAAT
1 ATAATATATACTAT
*
506761 ATAATAAATA--AT
1 ATAATATATACTAT
* *
506773 GATAATATTTAATAT
1 -ATAATATATACTAT
* *
506788 AAATATACTATAATAT
1 ATA-ATA-TATACTAT
506804 ATAATATATACTAT
1 ATAATATATACTAT
*
506818 ATAAATTATACTACAAT
1 AT-AA-TATA-TACTAT
506835 AATAATATATACTAT
1 -ATAATATATACTAT
506850 ATAATATATAATTACTACT
1 AT-A-ATAT-A-TACTA-T
*
506869 ATAACATATAAC-AT
1 ATAATATAT-ACTAT
*
506883 ATAATATTTA-TA-
1 ATAATATATACTAT
506895 ATATATATTATA-TAT
1 ATA-ATA-TATACTAT
506910 ATAATATATACTAT
1 ATAATATATACTAT
* *
506924 ATAAAATAATACTACC
1 ATAATAT-ATACTA-T
506940 ATAA-A-ATA-TAT
1 ATAATATATACTAT
* *
506951 CAT-ATACATAGTAT
1 -ATAATATATACTAT
*
506965 -TATGTATATACTAT
1 ATA-ATATATACTAT
*
506979 ATACT-TATACTAT
1 ATAATATATACTAT
*
506992 GTAATATATACTAT
1 ATAATATATACTAT
507006 CCCAGACGAA
Statistics
Matches: 193, Mismatches: 21, Indels: 61
0.70 0.08 0.22
Matches are distributed among these distances:
11 1 0.01
12 11 0.06
13 40 0.21
14 61 0.32
15 30 0.16
16 28 0.15
17 11 0.06
18 8 0.04
19 3 0.02
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (14 bp):
ATAATATATACTAT
Found at i:506856 original size:53 final size:54
Alignment explanation
Indices: 506796--506990 Score: 162
Period size: 53 Copynumber: 3.7 Consensus size: 54
506786 ATAAATATAC
506796 TATA-ATATATAATATATACTATATAAATTATACTACAATAATAATATATACTA
1 TATACATATATAATATATACTATATAAATTATACTACAATAATAATATATACTA
* *
506849 TATA-ATATATAAT-TACTACTATA-ACA-TATA--ACATATAATATTTATAATA-TA
1 TATACATATATAATATA-TACTATATAAATTATACTACA-ATAATA-ATAT-ATACTA
* * *
506900 TATTATATATATAATATATACTATATAAAATAATACTACCATAA-AATATAT-C-A
1 TA-TACATATATAATATATACTATAT-AAATTATACTACAATAATAATATATACTA
* *
506953 TATACATAGTATTATGTATATACTATAT-ACTTATACTA
1 TATACATA-TA-TA-ATATATACTATATAAATTATACTA
506991 TGTAATATAT
Statistics
Matches: 116, Mismatches: 10, Indels: 32
0.73 0.06 0.20
Matches are distributed among these distances:
49 3 0.03
50 6 0.05
51 11 0.09
52 14 0.12
53 49 0.42
54 6 0.05
55 17 0.15
56 4 0.03
57 4 0.03
58 2 0.02
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.41
Consensus pattern (54 bp):
TATACATATATAATATATACTATATAAATTATACTACAATAATAATATATACTA
Found at i:506973 original size:25 final size:26
Alignment explanation
Indices: 506944--507005 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
506934 ACTACCATAA
*
506944 AATATATC-ATATACATAGTATTATGT
1 AATATATCTATATACATA-TACTATGT
*
506970 -ATATA-CTATATACTTATACTATGT
1 AATATATCTATATACATATACTATGT
506994 AATATATACTAT
1 AATATAT-CTAT
507006 CCCAGACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 8 0.27
25 18 0.60
27 4 0.13
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (26 bp):
AATATATCTATATACATATACTATGT
Found at i:513683 original size:29 final size:30
Alignment explanation
Indices: 513632--513702 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
513622 AAAATTTAGA
*
513632 TAGTGACCAAAATGAAAA-TTTTG-AAAGTT
1 TAGTGACC-AAATGAAAACTTTGGAAAAGTT
*
513661 TAGTGACCAAATTATAAACTTTGGAAAAGTT
1 TAGTGACCAAATGA-AAACTTTGGAAAAGTT
513692 TAG-GAACCAAA
1 TAGTG-ACCAAA
513703 CGGTAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 11 0.31
30 5 0.14
31 15 0.42
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (30 bp):
TAGTGACCAAATGAAAACTTTGGAAAAGTT
Found at i:514112 original size:30 final size:30
Alignment explanation
Indices: 514072--514129 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
514062 TGACTTAAGG
*
514072 AAGATGATAAGGGTTAGGT-TCTTGGTTTGA
1 AAGAAGATAA-GGTTAGGTGTCTTGGTTTGA
514102 AAGAAGATAAGGTTAGGTGTCTTGGTTT
1 AAGAAGATAAGGTTAGGTGTCTTGGTTT
514130 AATGGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.36
Consensus pattern (30 bp):
AAGAAGATAAGGTTAGGTGTCTTGGTTTGA
Found at i:516725 original size:17 final size:17
Alignment explanation
Indices: 516703--516740 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
516693 GTCATTATCT
*
516703 TTCATATTTATCACATA-
1 TTCATATCTAT-ACATAG
516720 TTCATATCTATACATAG
1 TTCATATCTATACATAG
516737 TTCA
1 TTCA
516741 CTTACATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (17 bp):
TTCATATCTATACATAG
Found at i:516907 original size:14 final size:14
Alignment explanation
Indices: 516888--516921 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
516878 CCATGTAATG
516888 ATATAAATCGTATC
1 ATATAAATCGTATC
516902 ATATAAATCGTATC
1 ATATAAATCGTATC
516916 ATATAA
1 ATATAA
516922 CTTATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (14 bp):
ATATAAATCGTATC
Found at i:523969 original size:29 final size:32
Alignment explanation
Indices: 523922--524003 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 32
523912 AAAATTTAGA
523922 TAGTGACCAAAATGA-AAATTTT-GA-AAGTT
1 TAGTGACCAAAATGATAAATTTTGGAGAAGTT
523951 TAGTGACCAAAAT-ATAAATTTTGGAGAAGTT
1 TAGTGACCAAAATGATAAATTTTGGAGAAGTT
523982 TAG-GTACCAAAATGATAAATTT
1 TAGTG-ACCAAAATGATAAATTT
524004 AAAAAGTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.02
29 20 0.42
30 3 0.06
31 16 0.33
32 8 0.17
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (32 bp):
TAGTGACCAAAATGATAAATTTTGGAGAAGTT
Found at i:524418 original size:30 final size:30
Alignment explanation
Indices: 524363--524420 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
524353 TGACTTAAGT
* *
524363 AAGATGATAAGGGTTAGTTTTTTGGTTTGA
1 AAGATGATAAGGGTTAGTGTCTTGGTTTGA
524393 AAGATGATAA-GGTTAGGTGTCTTGGTTT
1 AAGATGATAAGGGTTA-GTGTCTTGGTTT
524421 AATGGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.41
Consensus pattern (30 bp):
AAGATGATAAGGGTTAGTGTCTTGGTTTGA
Found at i:525147 original size:30 final size:31
Alignment explanation
Indices: 525113--525178 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
525103 ATAAGCCTTA
* *
525113 GAAAAATTTGGAGACC-ATTATG-TAATTTTT
1 GAAAAATTAGGAGACCAATT-CGATAATTTTT
* *
525143 GAAAAGTTAGGGGACCAATTCGATAATTTTT
1 GAAAAATTAGGAGACCAATTCGATAATTTTT
525174 GAAAA
1 GAAAA
525179 GTTGTGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (31 bp):
GAAAAATTAGGAGACCAATTCGATAATTTTT
Found at i:535768 original size:54 final size:54
Alignment explanation
Indices: 535708--536097 Score: 485
Period size: 54 Copynumber: 7.2 Consensus size: 54
535698 TTTCGTACTT
* ** * * *
535708 TGCACACATAGTGTTGAAACGGTTATTTATTCACATAGGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * ** * *
535762 TTCACACTTAGTACCGAAATTGTTATTCATCCGCATAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
535816 AGCACACTTAGTGCCGAAACAGTTATTCATCCTCATATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
535870 TGAACACTTAGTGTCGAAACGGTTATTCATCCGCATAGGATTAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** * * *
535924 TGCACACTTAGTGCCAAAAATGTTATTAATCCACTTAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
535978 TGTACACTTAGT-CTCGAAACGGTTATTCATCCACATAGGATGAATTACGTGAAA
1 TGCACACTTAGTGC-CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
536032 TGCACATTTAGTGCCGAAACGGTTATTCATCCACATATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
536086 TGCACACTTAGT
1 TGCACACTTAGT
536098 ACCTATTATA
Statistics
Matches: 283, Mismatches: 51, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 1 0.00
54 281 0.99
55 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:535896 original size:162 final size:162
Alignment explanation
Indices: 535711--536100 Score: 539
Period size: 162 Copynumber: 2.4 Consensus size: 162
535701 CGTACTTTGC
* * * * * *
535711 ACACATAGTGTTGAAACGGTTATTTATTCACATAGGATGAATTCTGTGAAATTCACACTTAGTAC
1 ACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTAC
* * * *
535776 CGAAATTGTTATTCATCCGCATAGGATGAATTTCGTGAAAAGCACACTTAGTGC-CGAAACAGTT
66 CAAAAATGTTATTAATCCACATAGGATGAATTTCGTGAAAAGCACACTTAGT-CTCGAAACAGTT
* * *
535840 ATTCATCCTCATATGATGAATTCCGTGAAATGA
130 ATTCATCCACATAGGATGAATTACGTGAAATGA
* * * *
535873 ACACTTAGTGTCGAAACGGTTATTCATCCGCATAGGATTAATTCCATGAAATGCACACTTAGTGC
1 ACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTAC
* * * *
535938 CAAAAATGTTATTAATCCACTTAGGATGAATTTCGTGAAATGTACACTTAGTCTCGAAACGGTTA
66 CAAAAATGTTATTAATCCACATAGGATGAATTTCGTGAAAAGCACACTTAGTCTCGAAACAGTTA
*
536003 TTCATCCACATAGGATGAATTACGTGAAATGC
131 TTCATCCACATAGGATGAATTACGTGAAATGA
* * *
536035 ACATTTAGTGCCGAAACGGTTATTCATCCACATATGATGAATTCCGTGAAATGCACACTTAGTAC
1 ACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTAC
536100 C
66 C
536101 TATTATACTC
Statistics
Matches: 198, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
161 1 0.01
162 197 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (162 bp):
ACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTAC
CAAAAATGTTATTAATCCACATAGGATGAATTTCGTGAAAAGCACACTTAGTCTCGAAACAGTTA
TTCATCCACATAGGATGAATTACGTGAAATGA
Found at i:541604 original size:3 final size:3
Alignment explanation
Indices: 541596--541622 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
541586 AGTTAGCAAG
541596 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
541623 GTGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:543837 original size:9 final size:9
Alignment explanation
Indices: 543823--543848 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
543813 TTTTGGACCT
543823 AAAAAATAA
1 AAAAAATAA
543832 AAAAAATAA
1 AAAAAATAA
543841 AAAAAATA
1 AAAAAATA
543849 TAAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:543954 original size:24 final size:26
Alignment explanation
Indices: 543905--543970 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
543895 TTCAAAAACA
* *
543905 ATATGTTTTCAAAAATTATATATTAT
1 ATATGCTTTCAAAAATAATATATTAT
543931 ATATG-TTTCAAAAA-AATCAT-TTAT
1 ATATGCTTTCAAAAATAAT-ATATTAT
* *
543955 TTATGCTTTCAGAAAT
1 ATATGCTTTCAAAAAT
543971 TATTTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
25 19 0.56
26 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (26 bp):
ATATGCTTTCAAAAATAATATATTAT
Found at i:544145 original size:36 final size:37
Alignment explanation
Indices: 544040--544208 Score: 145
Period size: 36 Copynumber: 4.7 Consensus size: 37
544030 ATATATATAA
* * * *
544040 ATAT-ATATATGTTTTTAAAA-ATTGTTTTTGAAATT
1 ATATAATATATGTTTTAAAAACATTATTTTTAAAACT
* * *
544075 ATACAATATATGTTTTCAAAA-ATTGTTTTTAAAACT
1 ATATAATATATGTTTTAAAAACATTATTTTTAAAACT
* * *
544111 ATATAATATATGTTTTTAAAACA-TATTTTCAAAACC
1 ATATAATATATGTTTTAAAAACATTATTTTTAAAACT
* *
544147 ATATTATATAT-TTTTAAAAACCA--ATTTTTAAAATT
1 ATATAATATATGTTTTAAAAA-CATTATTTTTAAAACT
* *
544182 ATATATTATATGATTTAAAAACGATTA
1 ATATAATATATGTTTTAAAAAC-ATTA
544209 AATTATGTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
35 30 0.27
36 78 0.71
37 1 0.01
38 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (37 bp):
ATATAATATATGTTTTAAAAACATTATTTTTAAAACT
Found at i:545850 original size:62 final size:62
Alignment explanation
Indices: 545774--545897 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
545764 TTTCATCAGG
545774 TCCCCAATCTTGATAGCATTGTTCAATTGCTGATCTATATCGTACACTCCTCCGAATTTGAA
1 TCCCCAATCTTGATAGCATTGTTCAATTGCTGATCTATATCGTACACTCCTCCGAATTTGAA
545836 TCCCCAATCTTGATAGCATTGTTCAATTGCTGATCTATATCGTACACTCCTCCGAATTTGAA
1 TCCCCAATCTTGATAGCATTGTTCAATTGCTGATCTATATCGTACACTCCTCCGAATTTGAA
545898 AGAGCTCTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (62 bp):
TCCCCAATCTTGATAGCATTGTTCAATTGCTGATCTATATCGTACACTCCTCCGAATTTGAA
Found at i:553638 original size:72 final size:70
Alignment explanation
Indices: 553521--553798 Score: 272
Period size: 72 Copynumber: 3.9 Consensus size: 70
553511 GTCTCTTGTA
* * * *
553521 AGAAACCAACATAGTCTTTCTTT-ATGCCATTTACCTAGAAACCAACCTAGTCTTCCTTAAGACC
1 AGAAACCAACCTAGT-TTTCTTTAAGGCTATTTCCCTAGAAACCAACCTAGTCTTCCTTAAGA-C
553585 ATTTTCCT
64 -TTTTCCT
* * * * *
553593 AGAAACCAACCTAGTTTTCTTTAAGGTTATTTCCCTAGAAACCAACATTGTCTTCCTTAAAGTCG
1 AGAAACCAACCTAGTTTTCTTTAAGGCTATTTCCCTAGAAACCAACCTAGTCTTCCTT-AAGACT
553658 TTTCCAT
65 TTTCC-T
* * * * * * *
553665 AGAAACCAACCTAGTCTTCCTTAATGCAATTTCCTTATAAACCAACCTAGTCTTCTTTAAGACTG
1 AGAAACCAACCTAGTTTTCTTTAAGGCTATTTCCCTAGAAACCAACCTAGTCTTCCTTAAGACT-
553730 TTTCACT
65 TTTC-CT
* * * ** *
553737 AGAAACCAATCTAGACTTTC-TTAAGACTATTTCATTAGAAACCAACTTAGTCTTCCTTAAGA
1 AGAAACCAACCTAG-TTTTCTTTAAGGCTATTTCCCTAGAAACCAACCTAGTCTTCCTTAAGA
553799 TAGTCTCCCT
Statistics
Matches: 169, Mismatches: 31, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
71 16 0.09
72 146 0.86
73 7 0.04
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (70 bp):
AGAAACCAACCTAGTTTTCTTTAAGGCTATTTCCCTAGAAACCAACCTAGTCTTCCTTAAGACTT
TTCCT
Found at i:553710 original size:108 final size:105
Alignment explanation
Indices: 553521--553798 Score: 301
Period size: 108 Copynumber: 2.6 Consensus size: 105
553511 GTCTCTTGTA
* *
553521 AGAAACCAACATAGTCTTTCTTTATGCCATTTACC-TAGAAACCAACCTAGTCTTCCTTAAGACC
1 AGAAACCAACATAGTCTTTC-TTAAGAC-TTT-CCATAGAAACCAACCTAGTCTTCCTTAAGA-C
* * ** *
553585 ATTTTCCTAGAAACCAACCTAGTTTTCTTTAAGGTTATTTCCCT
62 AATTTCCTAGAAACCAACCTAGTCTTCTTTAAGACTATTTCACT
* * *
553629 AGAAACCAACATTGTCTTCCTTAAAGTCGTTTCCATAGAAACCAACCTAGTCTTCCTTAATG-CA
1 AGAAACCAACATAGTCTTTCTT-AAGAC-TTTCCATAGAAACCAACCTAGTCTTCCTTAA-GACA
* *
553693 ATTTCCTTATAAACCAACCTAGTCTTCTTTAAGACTGTTTCACT
63 ATTTCC-TAGAAACCAACCTAGTCTTCTTTAAGACTATTTCACT
* * *
553737 AGAAACCAATC-TAGACTTTCTTAAGACTATTTCATTAGAAACCAACTTAGTCTTCCTTAAGA
1 AGAAACCAA-CATAGTCTTTCTTAAGACT-TTCCA-TAGAAACCAACCTAGTCTTCCTTAAGA
553799 TAGTCTCCCT
Statistics
Matches: 144, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
106 1 0.01
107 20 0.14
108 121 0.84
109 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (105 bp):
AGAAACCAACATAGTCTTTCTTAAGACTTTCCATAGAAACCAACCTAGTCTTCCTTAAGACAATT
TCCTAGAAACCAACCTAGTCTTCTTTAAGACTATTTCACT
Found at i:553796 original size:36 final size:36
Alignment explanation
Indices: 553521--553798 Score: 237
Period size: 36 Copynumber: 7.7 Consensus size: 36
553511 GTCTCTTGTA
* * * *
553521 AGAAACCAACATAGTCTTTCTTTATG-CCATTT-ACCT
1 AGAAACCAACCTAGTC-TTCCTTAAGACTATTTCA-CT
*
553557 AGAAACCAACCTAGTCTTCCTTAAGACCATTTTC-CT
1 AGAAACCAACCTAGTCTTCCTTAAGACTA-TTTCACT
* * ** *
553593 AGAAACCAACCTAGTTTTCTTTAAGGTTATTTCCCT
1 AGAAACCAACCTAGTCTTCCTTAAGACTATTTCACT
* * * *
553629 AGAAACCAACATTGTCTTCCTTAA-AGTCGTTTC-CAT
1 AGAAACCAACCTAGTCTTCCTTAAGACT-ATTTCAC-T
*
553665 AGAAACCAACCTAGTCTTCCTTAATG-CAATTTC-CTT
1 AGAAACCAACCTAGTCTTCCTTAA-GACTATTTCAC-T
* * *
553701 ATAAACCAACCTAGTCTTCTTTAAGACTGTTTCACT
1 AGAAACCAACCTAGTCTTCCTTAAGACTATTTCACT
* * * *
553737 AGAAACCAATCTAGACTTTCTTAAGACTATTTCATT
1 AGAAACCAACCTAGTCTTCCTTAAGACTATTTCACT
*
553773 AGAAACCAACTTAGTCTTCCTTAAGA
1 AGAAACCAACCTAGTCTTCCTTAAGA
553799 TAGTCTCCCT
Statistics
Matches: 196, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
35 14 0.07
36 178 0.91
37 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (36 bp):
AGAAACCAACCTAGTCTTCCTTAAGACTATTTCACT
Found at i:553880 original size:33 final size:33
Alignment explanation
Indices: 553826--553907 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
553816 CTCAATCTCG
* *
553826 TCTTC-TTTAAGGTTGTTCCTCAAGAAACAAATAT
1 TCTTCATTT-AGGTTATCCCTCAAGAAACAAAT-T
553860 T-TTCATTTAGGTTATCCCTCAAGAAACAAATT
1 TCTTCATTTAGGTTATCCCTCAAGAAACAAATT
553892 TCTTCATTTAGGTTAT
1 TCTTCATTTAGGTTAT
553908 TTTCCTTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 2 0.05
33 38 0.86
34 4 0.09
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (33 bp):
TCTTCATTTAGGTTATCCCTCAAGAAACAAATT
Found at i:554226 original size:71 final size:71
Alignment explanation
Indices: 554107--554258 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 71
554097 GCCATGGAGG
* * * * *
554107 AAGTCGAACGCAACACCGAGCCTCAATCATAGAGGACACCCCACTAGTAGGTGAACCCTTAACCA
1 AAGTCGAACACAACACCAAGCCTCAATCATAGAGAAAACCCCACTAGTAGGTGAACCCTCAACCA
*
554172 TATAGA
66 TAAAGA
* * * * * *
554178 AAGTCGAACACATCCCCAAGCCTCAGTCATTGAGAAAACCCCATTAGTAGGTGAACCCTCATCCA
1 AAGTCGAACACAACACCAAGCCTCAATCATAGAGAAAACCCCACTAGTAGGTGAACCCTCAACCA
554243 TAAAGA
66 TAAAGA
*
554249 AAGACGAACA
1 AAGTCGAACA
554259 TAACCTCGAT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.16
Consensus pattern (71 bp):
AAGTCGAACACAACACCAAGCCTCAATCATAGAGAAAACCCCACTAGTAGGTGAACCCTCAACCA
TAAAGA
Found at i:554273 original size:71 final size:71
Alignment explanation
Indices: 554111--554278 Score: 183
Period size: 71 Copynumber: 2.4 Consensus size: 71
554101 TGGAGGAAGT
* * * * * * * *
554111 CGAACGCAACACCGAGCCTCAATCATAGAGGACACCCCACTAGTAGGTGAACCCTTAACCATATA
1 CGAACACAACCCCAAGCCTCAATCATTGAGAAAACCCCACTAGTAGGTGAACCCTCAACCATAAA
*
554176 GAAAGT
66 GAAAGA
* * * *
554182 CGAACACATCCCCAAGCCTCAGTCATTGAGAAAACCCCATTAGTAGGTGAACCCTCATCCATAAA
1 CGAACACAACCCCAAGCCTCAATCATTGAGAAAACCCCACTAGTAGGTGAACCCTCAACCATAAA
554247 GAAAGA
66 GAAAGA
* * * *
554253 CGAACATAACCTCGATCCTCAATCAT
1 CGAACACAACCCCAAGCCTCAATCAT
554279 GGAAGACACC
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.17
Consensus pattern (71 bp):
CGAACACAACCCCAAGCCTCAATCATTGAGAAAACCCCACTAGTAGGTGAACCCTCAACCATAAA
GAAAGA
Found at i:554296 original size:71 final size:71
Alignment explanation
Indices: 554111--554297 Score: 180
Period size: 71 Copynumber: 2.6 Consensus size: 71
554101 TGGAGGAAGT
* * * * * * * *
554111 CGAACGCAACACCGAGCCTCAATCATAGAGGACACCCCACTAGTAGGTGAACCCTTAACCATATA
1 CGAACACAACCCCAAGCCTCAATCATGGAAGACACCCCATTAGTAGGTGAACCCTCAACCATAAA
*
554176 GAAAGT
66 GAAAGA
* * *
554182 CGAACACATCCCCAAGCCTCAGTCATTGAGAA-A-ACCCCATTAGTAGGTGAACCCTCATCCATA
1 CGAACACAACCCCAAGCCTCAATCA-TG-GAAGACACCCCATTAGTAGGTGAACCCTCAACCATA
554245 AAGAAAGA
64 AAGAAAGA
* * * * * *
554253 CGAACATAACCTCGATCCTCAATCATGGAAGACACCTCGTTAGTA
1 CGAACACAACCCCAAGCCTCAATCATGGAAGACACCCCATTAGTA
554298 AGCGAAACCA
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
69 3 0.03
70 3 0.03
71 82 0.89
72 2 0.02
73 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.18
Consensus pattern (71 bp):
CGAACACAACCCCAAGCCTCAATCATGGAAGACACCCCATTAGTAGGTGAACCCTCAACCATAAA
GAAAGA
Found at i:555126 original size:236 final size:235
Alignment explanation
Indices: 554706--555177 Score: 872
Period size: 236 Copynumber: 2.0 Consensus size: 235
554696 TCATTTAGAG
554706 CCTCAACTATGGAAGACACCTAGATCAACTTCGGACATTCAGATTGGACACCGAACGAAAACTTG
1 CCTCAACTATGGAAGACACCTAGATCAACTTCGGACATTCAGATTGGACACCGAACGAAAACTTG
*
554771 TTTCTTTTTATCTTTGCGCTGTTACCATTGCATGACAATAGGAAAAAAGGGCAATTGTAGACATG
66 TTTCTTTTTATCTTTGCGCTATTACCATTGCATGACAATAGGAAAAAAGGGCAATTGTAGACATG
554836 TTTTTGTCTAAGTTGTTCAAATTAATTAATAACTATTATTAGTATTATAATTAATTACTATTGTA
131 TTTTTGTCTAAGTTGTTCAAATTAATTAATAACTATTATTAGTATTATAATTAATTACTATTGTA
* *
554901 ACTAAATTTTAAATATAAAAAAATTAATTCTAGTTTTATTA
196 ACTAAATATTAAATAT-AAAAAATAAATTCTAGTTTTATTA
* *
554942 CCTCAATTATGGAAGACACCTAGATCAACTTCGGACATTCAGATTGGACACCGAACGGAAACTTG
1 CCTCAACTATGGAAGACACCTAGATCAACTTCGGACATTCAGATTGGACACCGAACGAAAACTTG
*
555007 TTTCTTTTTGTCTTTGCGCTATTACCATTGCATGACAATAGGAAAAAAGGGCAATTGTAGACATG
66 TTTCTTTTTATCTTTGCGCTATTACCATTGCATGACAATAGGAAAAAAGGGCAATTGTAGACATG
555072 TTTTTGTCTAAGTTGTTCAAATTAATTAATAACTATTATTAGTATTATAATTAATTACTATTGTA
131 TTTTTGTCTAAGTTGTTCAAATTAATTAATAACTATTATTAGTATTATAATTAATTACTATTGTA
*
555137 AGTAAATATTAAATATAAAAAATAAATTCTAGTTTTATTA
196 ACTAAATATTAAATATAAAAAATAAATTCTAGTTTTATTA
555177 C
1 C
555178 TTTTGCAGCC
Statistics
Matches: 229, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
235 24 0.10
236 205 0.90
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (235 bp):
CCTCAACTATGGAAGACACCTAGATCAACTTCGGACATTCAGATTGGACACCGAACGAAAACTTG
TTTCTTTTTATCTTTGCGCTATTACCATTGCATGACAATAGGAAAAAAGGGCAATTGTAGACATG
TTTTTGTCTAAGTTGTTCAAATTAATTAATAACTATTATTAGTATTATAATTAATTACTATTGTA
ACTAAATATTAAATATAAAAAATAAATTCTAGTTTTATTA
Found at i:557640 original size:47 final size:46
Alignment explanation
Indices: 557573--557780 Score: 308
Period size: 47 Copynumber: 4.4 Consensus size: 46
557563 AATACACCCT
* * * * *
557573 TTTCAAGCATTTCCAATTATGGCATCAGTTCATCCCTTAATGTATCC
1 TTTCATGCATTTTCAATTATGGCATC-GTTCATGCCTTTATGCATCC
*
557620 TTTCATGCATTTTAAATTATGGCATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGGCAT-CGTTCATGCCTTTATGCATCC
*
557667 TTTCATGCATTTTCAATTATGGCATCTGTTCTTGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGGCATC-GTTCATGCCTTTATGCATCC
*
557714 TTTCATGCATTTTCAATTATGGCCTTCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGG-CATCGTTCATGCCTTTATGCATCC
557761 TTTCATGCATTTTCAATTAT
1 TTTCATGCATTTTCAATTAT
557781 AAAATTGATT
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
46 1 0.01
47 143 0.97
48 4 0.03
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (46 bp):
TTTCATGCATTTTCAATTATGGCATCGTTCATGCCTTTATGCATCC
Found at i:557654 original size:27 final size:26
Alignment explanation
Indices: 557616--557748 Score: 74
Period size: 27 Copynumber: 5.5 Consensus size: 26
557606 CCCTTAATGT
*
557616 ATCCTTTCATGCATTTTAAATTATGGC
1 ATCCGTTCATGCATTTT-AATTATGGC
*
557643 ATCCGTTCATGC---CT--TTAT-GC
1 ATCCGTTCATGCATTTTAATTATGGC
*
557663 ATCCTTTCATGCATTTTCAATTATGGC
1 ATCCGTTCATGCATTTT-AATTATGGC
* * *
557690 ATCTGTTCTTGC---CT--TTAT-GC
1 ATCCGTTCATGCATTTTAATTATGGC
*
557710 ATCCTTTCATGCATTTTCAATTATGGC
1 ATCCGTTCATGCATTTT-AATTATGGC
* *
557737 CTTCGTTCATGC
1 ATCCGTTCATGC
557749 CTTTATGCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 28
0.64 0.12 0.23
Matches are distributed among these distances:
20 24 0.31
21 8 0.10
23 2 0.03
24 2 0.03
26 8 0.10
27 33 0.43
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (26 bp):
ATCCGTTCATGCATTTTAATTATGGC
Found at i:557666 original size:20 final size:21
Alignment explanation
Indices: 557636--557674 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
557626 GCATTTTAAA
557636 TTATGGCATCCGTTCATGCCT
1 TTATGGCATCCGTTCATGCCT
*
557657 TTAT-GCATCCTTTCATGC
1 TTATGGCATCCGTTCATGC
557675 ATTTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.41
Consensus pattern (21 bp):
TTATGGCATCCGTTCATGCCT
Found at i:558223 original size:22 final size:21
Alignment explanation
Indices: 558173--558247 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 21
558163 TTCGACCCTT
*
558173 AGGTATCGATACCCCTGCTTA
1 AGGTATCGATACCCCTGATTA
*
558194 TGGTATCGATACTACCCT-ATTA
1 AGGTATCGATAC--CCCTGATTA
*
558216 AGGTATCGATACCCCT--TTC
1 AGGTATCGATACCCCTGATTA
*
558235 ATGTATCGATACC
1 AGGTATCGATACC
558248 AAAATTAGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 14 0.30
20 4 0.09
21 11 0.23
22 14 0.30
23 4 0.09
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (21 bp):
AGGTATCGATACCCCTGATTA
Found at i:566201 original size:16 final size:16
Alignment explanation
Indices: 566180--566241 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
566170 AATAAATAAA
*
566180 AACATAAACAAACACG
1 AACATAAACGAACACG
*
566196 AACATAAACGAACATG
1 AACATAAACGAACACG
*
566212 AACATAAATGAACACG
1 AACATAAACGAACACG
*
566228 AACATAAATGAACA
1 AACATAAACGAACA
566242 TAAATGTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.11
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:566216 original size:32 final size:32
Alignment explanation
Indices: 566180--566242 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
566170 AATAAATAAA
566180 AACATAAACAAACACGAACATAAACGAACATG
1 AACATAAACAAACACGAACATAAACGAACATG
** *
566212 AACATAAATGAACACGAACATAAATGAACAT
1 AACATAAACAAACACGAACATAAACGAACAT
566243 AAATGTTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.13
Consensus pattern (32 bp):
AACATAAACAAACACGAACATAAACGAACATG
Found at i:566486 original size:12 final size:11
Alignment explanation
Indices: 566464--566522 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
566454 TAAAACTCGA
*
566464 GATTCGAGCTT
1 GATTCGAGCTC
*
566475 GATTCTGAGCTT
1 GATTC-GAGCTC
* *
566487 AATTCAAGCTC
1 GATTCGAGCTC
566498 GATTCTGAGCTC
1 GATTC-GAGCTC
*
566510 GATTCAAGCTC
1 GATTCGAGCTC
566521 GA
1 GA
566523 CATTGCCCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 20 0.50
12 20 0.50
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (11 bp):
GATTCGAGCTC
Found at i:566496 original size:23 final size:23
Alignment explanation
Indices: 566465--566522 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
566455 AAAACTCGAG
* * *
566465 ATTCGAGCTTGATTCTGAGCTTA
1 ATTCAAGCTCGATTCTGAGCTCA
*
566488 ATTCAAGCTCGATTCTGAGCTCG
1 ATTCAAGCTCGATTCTGAGCTCA
566511 ATTCAAGCTCGA
1 ATTCAAGCTCGA
566523 CATTGCCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (23 bp):
ATTCAAGCTCGATTCTGAGCTCA
Found at i:566783 original size:17 final size:18
Alignment explanation
Indices: 566761--566798 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
566751 TTTGGTAAGA
*
566761 AAATAA-TAAAAGCGATT
1 AAATAAGTAAAAGCAATT
566778 AAATAAGTAAAAGCAATT
1 AAATAAGTAAAAGCAATT
566796 AAA
1 AAA
566799 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATAAGTAAAAGCAATT
Found at i:568393 original size:24 final size:24
Alignment explanation
Indices: 568307--568393 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
568297 AGATTGGGTT
** *
568307 AAACATAAATGAATGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
* *
568331 GAACATAACCGAACAAACATAAAC
1 AAACATAACCGAACGAACATAAAC
*
568355 AAACATAACCAAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
568379 AAACATAACCGAACG
1 AAACATAACCGAACG
568394 TTCACGAACG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.60, C:0.22, G:0.08, T:0.10
Consensus pattern (24 bp):
AAACATAACCGAACGAACATAAAC
Found at i:569214 original size:27 final size:27
Alignment explanation
Indices: 569184--569251 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
569174 TGACACTTCG
569184 AGTGATGCACATGAAGCTGGTATTTCA
1 AGTGATGCACATGAAGCTGGTATTTCA
*
569211 AGTGATGCACATGAAGCTGGTATTTCG
1 AGTGATGCACATGAAGCTGGTATTTCA
*
569238 AGTGCTGCACATGA
1 AGTGATGCACATGA
569252 TGATATTGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
AGTGATGCACATGAAGCTGGTATTTCA
Found at i:582339 original size:22 final size:21
Alignment explanation
Indices: 582297--582336 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
582287 GAGTTTATTT
*
582297 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
582318 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
582337 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:589749 original size:27 final size:26
Alignment explanation
Indices: 589662--589749 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
589652 GATCAATATA
*
589662 ATTA-TTAATAAAAGA-CATATTATTT
1 ATTATTTAATAAAA-ATAATATTATTT
** * *
589687 ATTAATTTCTTAAATATAATATTATTGA
1 ATT-ATTTAATAAAAATAATATTATT-T
589715 ATTA-TTAATAATAAATAATATTATTT
1 ATTATTTAATAA-AAATAATATTATTT
589741 ATTATTTAA
1 ATTATTTAA
589750 CATTATATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
25 3 0.06
26 11 0.23
27 31 0.65
28 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
ATTATTTAATAAAAATAATATTATTT
Found at i:589759 original size:27 final size:27
Alignment explanation
Indices: 589700--589760 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
589690 AATTTCTTAA
*
589700 ATATAATATTATTGAATTATTAATAAT
1 ATATAATATTATTGAATTATTAACAAT
* * *
589727 AAATAATATTATT-TATTATTTAACATT
1 ATATAATATTATTGAATTA-TTAACAAT
589754 ATATAAT
1 ATATAAT
589761 GGTCTAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATAATATTATTGAATTATTAACAAT
Found at i:604423 original size:19 final size:19
Alignment explanation
Indices: 604399--604444 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
604389 GAGTTGAATA
604399 TTCTTCAATAAGAAAATCC
1 TTCTTCAATAAGAAAATCC
604418 TTCTTCAATAAGAAAATCC
1 TTCTTCAATAAGAAAATCC
604437 TTCTTCAA
1 TTCTTCAA
604445 ACGTTAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (19 bp):
TTCTTCAATAAGAAAATCC
Found at i:604906 original size:25 final size:24
Alignment explanation
Indices: 604859--604982 Score: 63
Period size: 25 Copynumber: 5.0 Consensus size: 24
604849 AAATCCTAAT
* **
604859 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
*
604883 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACAAAGATAAAC
* * * *
604908 TATAAA-AATAATATCTTAAA-ACTTAAT
1 TA-AAATACTAA-AAC--AAAGA-TAAAC
** **
604935 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
604959 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
604983 ATATAATGTT
Statistics
Matches: 72, Mismatches: 19, Indels: 17
0.67 0.18 0.16
Matches are distributed among these distances:
24 21 0.29
25 30 0.42
26 9 0.12
27 12 0.17
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:604943 original size:76 final size:75
Alignment explanation
Indices: 604773--604988 Score: 307
Period size: 76 Copynumber: 2.9 Consensus size: 75
604763 ACTAAAACAC
*
604773 CTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCT--AA-AAA-ATAATAATA
1 CTTAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAGATAA-AATA
* *
604834 TTAAAATGATAT
64 TAAAAATAATAT
604846 -TCTAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATA
1 CT-TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATA
604910 TAAAAATAATAT
64 TAAAAATAATAT
* *
604922 CTTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAT
1 CTTAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATAT
604987 AA
65 AA
604989 TGTTTAAAAT
Statistics
Matches: 130, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
72 7 0.05
73 37 0.28
75 2 0.02
76 78 0.60
77 6 0.05
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
CTTAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
AAAATAATAT
Found at i:606832 original size:5 final size:5
Alignment explanation
Indices: 606822--606919 Score: 67
Period size: 5 Copynumber: 19.2 Consensus size: 5
606812 TGTTCAGAGA
* * * *
606822 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT AAAAAT AAAGTTT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT
** *
606874 GCTAA- AAAAT AAAAT GAAAAT AAAAC AAAAT AAAAT AAAA- AAAAT A
1 -AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
606920 GAACGAAATG
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
4 10 0.14
5 50 0.70
6 9 0.13
7 1 0.01
8 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:606905 original size:21 final size:19
Alignment explanation
Indices: 606879--606917 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
606869 AGTTTGCTAA
606879 AAAATAAAATGAAAATAAAAC
1 AAAATAAAAT-AAAA-AAAAC
606900 AAAATAAAATAAAAAAAA
1 AAAATAAAATAAAAAAAA
606918 TAGAACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (19 bp):
AAAATAAAATAAAAAAAAC
Found at i:607543 original size:18 final size:18
Alignment explanation
Indices: 607520--607573 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
607510 GAAAAAGAAT
*
607520 AAAAAATAAATAATTATA
1 AAAAAATAAATAATAATA
*
607538 AAAAAAGGAAA-AATAATA
1 AAAAAA-TAAATAATAATA
* *
607556 AAACAATAAATATTAATA
1 AAAAAATAAATAATAATA
607574 GTAATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 3 0.10
18 23 0.79
19 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAAAATAAATAATAATA
Found at i:607634 original size:11 final size:11
Alignment explanation
Indices: 607618--607652 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
607608 AAAGAAGTAT
607618 AATTAAATAAA
1 AATTAAATAAA
607629 AATTAAATAAA
1 AATTAAATAAA
*
607640 CAAATAAATAAA
1 -AATTAAATAAA
607652 A
1 A
607653 TAACTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AATTAAATAAA
Found at i:608372 original size:282 final size:283
Alignment explanation
Indices: 607868--608434 Score: 1118
Period size: 282 Copynumber: 2.0 Consensus size: 283
607858 AAGTGTGTTC
607868 TCGGGAAGTTGAATATGCTTCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAATTTCCGG
1 TCGGGAAGTTGAATATGCTTCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAATTTCCGG
607933 ACCAATATCGAAATCATTTTGATTTGAAAAGTAAGCTCAGAAAACAAAGAGAAAAATCTGAAGCG
66 ACCAATATCGAAATCATTTTGATTTGAAAAGTAAGCTCAGAAAACAAAGAGAAAAATCTGAAGCG
607998 ATTTAAGTACCTTACAATTCTCACATTTGGAATTGAGCCTTCGCTTCAGTCTTCGGCTTAAGAGA
131 ATTTAAGTACCTTACAATTCTCACATTTGGAATTGAGCCTTCGCTTCAGTCTTCGGCTTAAGAGA
608063 AAATTAGCTAAGCATGACCAAAGTCATACTTAGCTTAATTGGAAAGTATGCGAAAAAT-AGAGAA
196 AAATTAGCTAAGCATGACCAAAGTCATACTTAGCTTAATTGGAAAGTATGCGAAAAATAAGAGAA
608127 AACTAGAGATAAAAAGAAGATTT
261 AACTAGAGATAAAAAGAAGATTT
608150 TCGGGAAGTTGAATATGCTTCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAATTTCCGG
1 TCGGGAAGTTGAATATGCTTCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAATTTCCGG
608215 ACCAATATCGAAATCATTTTGATTTGAAAAGTAAGCTCAGAAAACAAAGAGAAAAATCTGAAGCG
66 ACCAATATCGAAATCATTTTGATTTGAAAAGTAAGCTCAGAAAACAAAGAGAAAAATCTGAAGCG
608280 ATTTAAGTACCTTACAATTCTCACATTTGGAATTGAGCCTTCGCTTCAGTCTTCGGCTTAAGAGA
131 ATTTAAGTACCTTACAATTCTCACATTTGGAATTGAGCCTTCGCTTCAGTCTTCGGCTTAAGAGA
608345 AAATTAGCTAAGCATGACCAAAGTCATACTTAGCTTAATTGGAAAGTATGCGAAAAATAGAGAGA
196 AAATTAGCTAAGCATGACCAAAGTCATACTTAGCTTAATTGGAAAGTATGCGAAAAATA-AGAGA
608410 AAACTAGAGATAAAAAGAAGATTT
260 AAACTAGAGATAAAAAGAAGATTT
608434 T
1 T
608435 ATTCTCAGAT
Statistics
Matches: 283, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
282 253 0.89
284 30 0.11
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (283 bp):
TCGGGAAGTTGAATATGCTTCAATAAGCAAATCATTCTTCAAACGTTAACCATAACAATTTCCGG
ACCAATATCGAAATCATTTTGATTTGAAAAGTAAGCTCAGAAAACAAAGAGAAAAATCTGAAGCG
ATTTAAGTACCTTACAATTCTCACATTTGGAATTGAGCCTTCGCTTCAGTCTTCGGCTTAAGAGA
AAATTAGCTAAGCATGACCAAAGTCATACTTAGCTTAATTGGAAAGTATGCGAAAAATAAGAGAA
AACTAGAGATAAAAAGAAGATTT
Found at i:608695 original size:73 final size:71
Alignment explanation
Indices: 608520--608723 Score: 254
Period size: 73 Copynumber: 2.8 Consensus size: 71
608510 TAAAACATCT
* * * *
608520 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAA-AAATATAATATTTAAA
1 TAAA-CCTAATTAAAA-AC-TAAAACCTATTTAAACTAAAATACTAAACAAAGATAAAATATAAA
*
608583 ATAATATTC
63 ATAATATCC
*
608592 TAATCCTAATT-AAAACTAAAACCTATTTAAACTAAAATAACTAAACAAAGATAAAATAT-AAAT
1 TAAACCTAATTAAAAACTAAAACCTATTTAAACTAAAAT-ACTAAACAAAGATAAAATATAAAAT
608655 AATATCC
65 AATATCC
*
608662 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAACAAAGATAAAATAT
1 T-AAACCTAATTAAAA-ACTAAAACCTATTTAAACTAAAATACT-AAACAAAGATAAAATAT
608724 TATGTTTAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
68 5 0.04
69 18 0.15
70 19 0.16
71 25 0.21
72 9 0.08
73 41 0.35
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (71 bp):
TAAACCTAATTAAAAACTAAAACCTATTTAAACTAAAATACTAAACAAAGATAAAATATAAAATA
ATATCC
Found at i:608719 original size:24 final size:24
Alignment explanation
Indices: 608673--608719 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
608663 AAAACTTAAT
** **
608673 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
608697 TAAAATACTAAAACAAAGATAAA
1 TAAAATACTAAAACAAAGATAAA
608720 ATATTATGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:616311 original size:16 final size:17
Alignment explanation
Indices: 616290--616322 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
616280 GTATCTATAC
616290 TTTAAT-TCCATGGCAT
1 TTTAATATCCATGGCAT
*
616306 TTTAATATCGATGGCAT
1 TTTAATATCCATGGCAT
616323 ATGTAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (17 bp):
TTTAATATCCATGGCAT
Found at i:618119 original size:26 final size:27
Alignment explanation
Indices: 618074--618126 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
618064 AAAAAAAATT
*
618074 AAGTTTAATTAATTTATAAATTTTAAA
1 AAGTTTAATTAATTTATAAAATTTAAA
618101 AAGTTTAA-TAATTTATAAAATTTAAA
1 AAGTTTAATTAATTTATAAAATTTAAA
618127 TAGAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
AAGTTTAATTAATTTATAAAATTTAAA
Found at i:620283 original size:18 final size:18
Alignment explanation
Indices: 620260--620294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
620250 ACTGAATATT
*
620260 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
620278 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
620295 GTATATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:621162 original size:18 final size:18
Alignment explanation
Indices: 621139--621182 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
621129 CCCTAACTGA
621139 GGTATATACCATGTCTAT
1 GGTATATACCATGTCTAT
*
621157 GGTATAGATACCCTGTCTAT
1 GGTAT--ATACCATGTCTAT
621177 GGTATA
1 GGTATA
621183 GATAGCCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (18 bp):
GGTATATACCATGTCTAT
Found at i:621173 original size:20 final size:20
Alignment explanation
Indices: 621144--621192 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
621134 ACTGAGGTAT
*
621144 ATACCATGTCTATGGTATAG
1 ATACCCTGTCTATGGTATAG
621164 ATACCCTGTCTATGGTATAG
1 ATACCCTGTCTATGGTATAG
621184 ATAGCCCTG
1 ATA-CCCTG
621193 ATGACATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
ATACCCTGTCTATGGTATAG
Found at i:626060 original size:40 final size:40
Alignment explanation
Indices: 626016--626096 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
626006 ACTTAATATT
* * *
626016 TGTCCCGAAGGATCTCTATGTCCCAAATGACCACTGTATA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGTATA
* *
626056 TGTCCCGAAGGACCACTATGTCTCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGTATA
626096 T
1 T
626097 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGTATA
Found at i:626077 original size:18 final size:18
Alignment explanation
Indices: 626016--626090 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
626006 ACTTAATATT
* *
626016 TGTCCCGAAGGATCTCTA
1 TGTCCCGAAGGACCACTA
* *
626034 TGTCCCAAATGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
626056 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
626074 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
626091 GTATATCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
18 30 0.65
22 16 0.35
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:626958 original size:20 final size:20
Alignment explanation
Indices: 626928--627002 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
626918 CCCTAACAGA
*
626928 GGTATAAATACCCTGTCTAT
1 GGTATAGATACCCTGTCTAT
* * *
626948 AGTGTAGATACCCTATCTAT
1 GGTATAGATACCCTGTCTAT
*
626968 GGTATAGACACCCTGTCTAT
1 GGTATAGATACCCTGTCTAT
626988 GGTATAGATACCCTG
1 GGTATAGATACCCTG
627003 ATGACATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (20 bp):
GGTATAGATACCCTGTCTAT
Found at i:628356 original size:54 final size:53
Alignment explanation
Indices: 628179--628375 Score: 175
Period size: 54 Copynumber: 3.6 Consensus size: 53
628169 AGTGGTGCTT
* * * *
628179 GATTTTAGATTGCAA-CACAAAGGTGCTCAATCATCCTAAATGCACA-ACAGTGCTA
1 GATTTTAGATTG-AAGCACAGAGGTGCTCAATCAT-CTAAA-GCACAGA-GGTACCA
* ** ** *
628234 GGTTTTAGATTGAAGCACAGAGGTGCTCAATCATCCTAAAGCACATTGGTGTCT
1 GATTTTAGATTGAAGCACAGAGGTGCTCAATCAT-CTAAAGCACAGAGGTACCA
** *
628288 GATCCTAGATTGAAGCATAGAGGTGCTCAATCGAT-TAAGAGCACAGAGGTACCA
1 GATTTTAGATTGAAGCACAGAGGTGCTCAATC-ATCTAA-AGCACAGAGGTACCA
* *
628342 GATTTTAGACTGAAGCACAGAGGTGCTCAGTCAT
1 GATTTTAGATTGAAGCACAGAGGTGCTCAATCAT
628376 TTTTAATTGC
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
53 5 0.04
54 75 0.64
55 37 0.32
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (53 bp):
GATTTTAGATTGAAGCACAGAGGTGCTCAATCATCTAAAGCACAGAGGTACCA
Found at i:628423 original size:55 final size:55
Alignment explanation
Indices: 628356--628486 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 55
628346 TTAGACTGAA
* * * **
628356 GCACAGAGGTGCTCAGTCATTTTTAATTGCACAAAGGTGTCAGTTCTCGATTGAG
1 GCACAGAGGTGCTCAATCATTTTTAACTACACAAAGGTGTCAACTCTCGATTGAG
* * * * * *
628411 GTACAGAGGTGCTCAATTAGTTTTAGCTACACATAGGTGTCAACTCTCGATTGAT
1 GCACAGAGGTGCTCAATCATTTTTAACTACACAAAGGTGTCAACTCTCGATTGAG
*
628466 GCACAAAGGTGCTCAATCATT
1 GCACAGAGGTGCTCAATCATT
628487 AATTCAAGCA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (55 bp):
GCACAGAGGTGCTCAATCATTTTTAACTACACAAAGGTGTCAACTCTCGATTGAG
Found at i:630635 original size:35 final size:35
Alignment explanation
Indices: 630596--630668 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
630586 TCCAAGGACT
630596 TTGAGAATGTAATGCCAGATAATTTACAAAAAGAG
1 TTGAGAATGTAATGCCAGATAATTTACAAAAAGAG
* *
630631 TTGAGGATGTAATGCCAGATAATTTACAGAAAGAG
1 TTGAGAATGTAATGCCAGATAATTTACAAAAAGAG
630666 TTG
1 TTG
630669 TCACCTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.27
Consensus pattern (35 bp):
TTGAGAATGTAATGCCAGATAATTTACAAAAAGAG
Found at i:635409 original size:22 final size:21
Alignment explanation
Indices: 635337--635409 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
635327 TTTATCCATC
*
635337 TTTAATTTTGTTTTCTTTTA-A
1 TTTAATTTT-TTTTCATTTATA
635358 TTTAATTCTTTTTTCATTTATA
1 TTTAATT-TTTTTTCATTTATA
* *
635380 TTTTATTTTTTTATTATTTGATA
1 TTTAATTTTTTT-TCATTT-ATA
635403 -TTAATTT
1 TTTAATTT
635410 GACTTTTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 21 0.48
22 20 0.45
23 3 0.07
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTAATTTTTTTTCATTTATA
Found at i:636719 original size:27 final size:27
Alignment explanation
Indices: 636688--636750 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
636678 AATTTCAAGA
636688 AAATATATTAATTTTTATATTTTAAAT
1 AAATATATTAATTTTTATATTTTAAAT
* *
636715 CAATATATTAATTTTTATATTTTTAAT
1 AAATATATTAATTTTTATATTTTAAAT
636742 AAATATATT
1 AAATATATT
636751 TTTTAGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATATTAATTTTTATATTTTAAAT
Found at i:636751 original size:23 final size:25
Alignment explanation
Indices: 636692--636769 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 25
636682 TCAAGAAAAT
*
636692 ATATTAATTTTTATATTTTAAATCAA
1 ATATTAATTTTTATATTTTTAAT-AA
636718 TATATTAATTTTTATATTTTTAATAA
1 -ATATTAATTTTTATATTTTTAATAA
* *
636744 ATA-TATTTTTTAGATTTTT-ATAA
1 ATATTAATTTTTATATTTTTAATAA
636767 ATA
1 ATA
636770 AGATATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
23 7 0.15
24 14 0.29
25 3 0.06
26 2 0.04
27 22 0.46
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTAATTTTTATATTTTTAATAA
Found at i:638303 original size:3 final size:3
Alignment explanation
Indices: 638295--638369 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
638285 GGCCTGTAAT
* *
638295 TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAG TAT TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
638340 TGA -AA TAA -AA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
638370 ACCAAATGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
2 7 0.11
3 53 0.85
4 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:638535 original size:20 final size:21
Alignment explanation
Indices: 638512--638569 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
638502 TTGAACAAGT
638512 TCTTCTTATTATGAACTTA-A
1 TCTTCTTATTATGAACTTAGA
* * * *
638532 TCTTCTTCTTAGGGA-TTAGT
1 TCTTCTTATTATGAACTTAGA
*
638552 TCTTCTCATTATGAACTT
1 TCTTCTTATTATGAACTT
638570 TTCCACCGGG
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.50
Consensus pattern (21 bp):
TCTTCTTATTATGAACTTAGA
Found at i:640310 original size:22 final size:22
Alignment explanation
Indices: 640285--640326 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
640275 TTTATAAAAG
640285 AATAAATTGAATTTCGAAAATA
1 AATAAATTGAATTTCGAAAATA
*
640307 AATAAATTTAATTTCGAAAA
1 AATAAATTGAATTTCGAAAA
640327 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (22 bp):
AATAAATTGAATTTCGAAAATA
Found at i:652533 original size:3 final size:3
Alignment explanation
Indices: 652525--652603 Score: 101
Period size: 3 Copynumber: 26.3 Consensus size: 3
652515 GGTTTGGGCG
*
652525 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A A-A ATA ATA GTA ATA GA-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
652571 ATAA ATAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
652604 AACCAAATGG
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
2 5 0.07
3 57 0.81
4 8 0.11
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:654820 original size:20 final size:22
Alignment explanation
Indices: 654776--654841 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
654766 ATAGAATAAG
* *
654776 AGAAAATAATATAAC-AAAGAAA
1 AGAAAAAAAAATAACAAAAG-AA
654798 AGAAAAGAAAAAATAACAAAAGAA
1 AG-AAA-AAAAAATAACAAAAGAA
654822 AGTAAAAAAAAATAACAAAA
1 AG-AAAAAAAAATAACAAAA
654842 AACAAAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 2 0.05
23 17 0.45
24 15 0.39
25 4 0.11
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (22 bp):
AGAAAAAAAAATAACAAAAGAA
Found at i:654823 original size:29 final size:30
Alignment explanation
Indices: 654768--654848 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
654758 TATAAAAGAT
* * *
654768 AGAATAAGAGAAAATAATATAACAAAG-AAA
1 AGAA-AAGAAAAAATAACAAAACAAAGTAAA
*
654798 AGAAAAGAAAAAATAACAAAAGAAAGTAAA
1 AGAAAAGAAAAAATAACAAAACAAAGTAAA
* *
654828 AAAAAATAACAAAA-AACAAAA
1 AGAAAAGAA-AAAATAACAAAA
654849 ATCAGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 18 0.42
30 21 0.49
31 4 0.09
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.09
Consensus pattern (30 bp):
AGAAAAGAAAAAATAACAAAACAAAGTAAA
Found at i:654842 original size:24 final size:24
Alignment explanation
Indices: 654786--654871 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 24
654776 AGAAAATAAT
*
654786 ATAACAAAGAAAAGAAAAGAAAAA
1 ATAACAAAAAAAAGAAAAGAAAAA
* *
654810 ATAACAAAAGAAAGTAAA-AAAAA
1 ATAACAAAAAAAAGAAAAGAAAAA
654833 ATAACAAAAAACAA-AAATCAG-AAAA
1 ATAACAAAAAA-AAGAAA--AGAAAAA
654858 ATAACAACAAAAAA
1 ATAACAA-AAAAAA
654872 TATAATATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
23 17 0.33
24 17 0.33
25 14 0.27
26 4 0.08
ACGTcount: A:0.78, C:0.08, G:0.07, T:0.07
Consensus pattern (24 bp):
ATAACAAAAAAAAGAAAAGAAAAA
Found at i:657168 original size:37 final size:37
Alignment explanation
Indices: 657118--657191 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
657108 ATTTTAAAGT
657118 GGGCACGTGCCCACCCTTAACAAGCTTTGCATCTACC
1 GGGCACGTGCCCACCCTTAACAAGCTTTGCATCTACC
657155 GGGCACGTGCCCACCCTTAACAAGCTTTGCATCTACC
1 GGGCACGTGCCCACCCTTAACAAGCTTTGCATCTACC
657192 ACTGTTGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (37 bp):
GGGCACGTGCCCACCCTTAACAAGCTTTGCATCTACC
Found at i:660196 original size:27 final size:25
Alignment explanation
Indices: 660157--660207 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
660147 TTAGCAAATT
*
660157 TAAAAACAAAACTTTAAAAATAAAG
1 TAAAAACAAAACTTGAAAAATAAAG
660182 TAAAAATCGAAAACTTGAAAAATAAA
1 TAAAAA-C-AAAACTTGAAAAATAAA
660208 ATGAGAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 1 0.04
27 16 0.70
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.20
Consensus pattern (25 bp):
TAAAAACAAAACTTGAAAAATAAAG
Found at i:667175 original size:21 final size:21
Alignment explanation
Indices: 667150--667194 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
667140 GATTTTGGTA
*
667150 AAAAGATATTTAAA-TGATAAT
1 AAAAGAGATTTAAAGTGA-AAT
*
667171 AAAAGCGATTTAAAGTGAAAT
1 AAAAGAGATTTAAAGTGAAAT
667192 AAA
1 AAA
667195 GAAAAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (21 bp):
AAAAGAGATTTAAAGTGAAAT
Found at i:672828 original size:3 final size:3
Alignment explanation
Indices: 672820--672871 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
672810 TACTTACTCT
672820 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
672868 ATA A
1 ATA A
672872 CTTCTATTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:672944 original size:32 final size:34
Alignment explanation
Indices: 672908--672979 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
672898 TTAGCACGTT
***
672908 TAAAAT-T-AAAAACTTCATTTAAGTGTGTAATA
1 TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
*
672940 TAAAATATGATAAACTTCATTTAAGTCCCTAATA
1 TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
672974 TAAAAT
1 TAAAAT
672980 GTATAGGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 6 0.18
33 1 0.03
34 27 0.79
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (34 bp):
TAAAATATGAAAAACTTCATTTAAGTCCCTAATA
Found at i:688509 original size:35 final size:35
Alignment explanation
Indices: 688463--688585 Score: 142
Period size: 35 Copynumber: 3.5 Consensus size: 35
688453 TCTTAGATCC
688463 ATAAGGAATTACCAGTTC-AGTCGGTCTGAACTTAT
1 ATAAGGAATTACCAGTTCGA-TCGGTCTGAACTTAT
* * * **
688498 ATAAGGAATTACTAGTTTGATCTAGT-TGAACCTTCC
1 ATAAGGAATTACCAGTTCGATC-GGTCTGAA-CTTAT
* *
688534 GTAAGGAATTACCAGTTCGATCGGTCTGAACCTAT
1 ATAAGGAATTACCAGTTCGATCGGTCTGAACTTAT
688569 ATAAGGAATTACCAGTT
1 ATAAGGAATTACCAGTT
688586 TGATTAAGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
35 42 0.59
36 29 0.41
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTCGATCGGTCTGAACTTAT
Found at i:688544 original size:36 final size:35
Alignment explanation
Indices: 688463--688602 Score: 135
Period size: 35 Copynumber: 4.0 Consensus size: 35
688453 TCTTAGATCC
* * *
688463 ATAAGGAATTACCAG-TTCAGTCGGTCTGAACTTAT
1 ATAAGGAATTACCAGTTTGA-TCAGTCTGAACCTAT
*
688498 ATAAGGAATTACTAGTTTGATCTAGT-TGAACCT-T
1 ATAAGGAATTACCAGTTTGATC-AGTCTGAACCTAT
* * *
688532 CCGTAAGGAATTACCAGTTCGATCGGTCTGAACCTAT
1 --ATAAGGAATTACCAGTTTGATCAGTCTGAACCTAT
*
688569 ATAAGGAATTACCAGTTTGATTAAG-CTGAACCTA
1 ATAAGGAATTACCAGTTTGA-TCAGTCTGAACCTA
688603 CAGATACTTC
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
34 1 0.01
35 51 0.59
36 33 0.38
37 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTTGATCAGTCTGAACCTAT
Found at i:688599 original size:71 final size:71
Alignment explanation
Indices: 688464--688601 Score: 217
Period size: 71 Copynumber: 1.9 Consensus size: 71
688454 CTTAGATCCA
* * *
688464 TAAGGAATTACCAGTTCAGTCGGTCTGAACTTATATAAGGAATTACTAGTTTGATCTAGTTGAAC
1 TAAGGAATTACCAGTTCAGTCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCTAGCTGAAC
688529 CTTCCG
66 CTTCCG
688535 TAAGGAATTACCAGTTC-GATCGGTCTGAACCTATATAAGGAATTACCAGTTTGAT-TAAGCTGA
1 TAAGGAATTACCAGTTCAG-TCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCT-AGCTGA
688598 ACCT
64 ACCT
688602 ACAGATACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
70 2 0.03
71 60 0.97
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (71 bp):
TAAGGAATTACCAGTTCAGTCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCTAGCTGAAC
CTTCCG
Found at i:690141 original size:27 final size:27
Alignment explanation
Indices: 690085--690157 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
690075 ACCAAAATTC
* * *
690085 TTTTTAAAATATATTTATTTTACTTTAT
1 TTTTTAAAAAATATTT-TTATACTTAAT
690113 TTTTTAAAAAATATTTTTATA-TTAAAT
1 TTTTTAAAAAATATTTTTATACTT-AAT
* *
690140 TTATAAAAAAATATTTTT
1 TTTTTAAAAAATATTTTT
690158 CAAAAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.05
27 22 0.56
28 15 0.38
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTAAAAAATATTTTTATACTTAAT
Found at i:695015 original size:23 final size:22
Alignment explanation
Indices: 694953--695015 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
694943 ATTTTTTGAA
*
694953 AAAAAAAATTA-AATATTATTT
1 AAAAAAAATTAGAATTTTATTT
*
694974 AAAAAAAATTATGACTTTTATTT
1 AAAAAAAATTA-GAATTTTATTT
*
694997 GAAAAAAATTGAGAATTTT
1 AAAAAAAATT-AGAATTTT
695016 GAATTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.31
23 23 0.66
24 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAAAAAATTAGAATTTTATTT
Found at i:697422 original size:3 final size:3
Alignment explanation
Indices: 697405--697464 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
697395 TGTAAAAAAT
* * *
697405 ATA AT- ATA A-A ATA ATA ATA ATG ATT ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
697451 ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA
697465 TTTTAAGACC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:697860 original size:40 final size:40
Alignment explanation
Indices: 697816--697892 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
697806 ATGATGAGGT
* * *
697816 CTGGTCGATTGATGACACGGTTCTTACGTAATGAGGATGC
1 CTGGTCGATGGATGACACAGTTCCTACGTAATGAGGATGC
* * *
697856 CTGGTCGGTGGATGACACAGTTCCTATGTGATGAGGA
1 CTGGTCGATGGATGACACAGTTCCTACGTAATGAGGA
697893 CGACATGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (40 bp):
CTGGTCGATGGATGACACAGTTCCTACGTAATGAGGATGC
Found at i:698321 original size:35 final size:34
Alignment explanation
Indices: 698271--698399 Score: 150
Period size: 37 Copynumber: 3.6 Consensus size: 34
698261 ATCTCAAAGG
* * *
698271 AAAAATGTCTCAAGCGAGACGAAATTTGTTTTCAT
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTT-AC
*
698306 AAAATTGTCTTAAGCGAGACAAAATTTGTTCTTAGC
1 AAAATTGTCTCAAGCGAGACAAAATTTGTT-TTA-C
698342 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAC
1 -AAAATTGTCTCAAGCGAGACAAAATTTG-TTTT-AC
*
698379 AAAACTTGTCTCAAGAGAGAC
1 AAAA-TTGTCTCAAGCGAGAC
698400 GACCCTTTGT
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
35 28 0.34
36 6 0.07
37 45 0.55
38 3 0.04
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (34 bp):
AAAATTGTCTCAAGCGAGACAAAATTTGTTTTAC
Found at i:698331 original size:20 final size:20
Alignment explanation
Indices: 698306--698368 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
698296 TTGTTTTCAT
698306 AAAATTGTCTTAAGCGAGAC
1 AAAATTGTCTTAAGCGAGAC
698326 AAAATTTGTTCTT-AGC--G--
1 AAAA-TTG-TCTTAAGCGAGAC
*
698343 AAAATTGTCTCAAGCGAGAC
1 AAAATTGTCTTAAGCGAGAC
698363 AAAATT
1 AAAATT
698369 TGTTTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
15 3 0.09
16 6 0.17
17 4 0.11
18 1 0.03
19 1 0.03
20 10 0.29
21 6 0.17
22 4 0.11
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (20 bp):
AAAATTGTCTTAAGCGAGAC
Found at i:699590 original size:13 final size:14
Alignment explanation
Indices: 699574--699657 Score: 77
Period size: 13 Copynumber: 5.9 Consensus size: 14
699564 TTTTATCTTC
699574 TTTTT-TCTTTGC-
1 TTTTTCTCTTTGCT
699586 TTTTTCT-TTTGCT
1 TTTTTCTCTTTGCT
699599 TTTTTCTCTTTG-T
1 TTTTTCTCTTTGCT
699612 TTTTTCTCTTTGCTCTTT
1 TTTTTCTCTTTG--C--T
*
699630 GTTTTTTTCTTTGCT
1 -TTTTTCTCTTTGCT
699645 TCTTTTCTCTTTG
1 T-TTTTCTCTTTG
699658 TTCTGATTGG
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
12 10 0.17
13 21 0.35
14 5 0.08
15 11 0.18
17 1 0.02
18 1 0.02
19 11 0.18
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTCTCTTTGCT
Found at i:699624 original size:27 final size:27
Alignment explanation
Indices: 699574--699659 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 27
699564 TTTTATCTTC
*
699574 TTTTT-TCTTTGCTTTTTCT-TTTGCT
1 TTTTTCTCTTTGTTTTTTCTCTTTGCT
699599 TTTTTCTCTTTGTTTTTTCTCTTTG--
1 TTTTTCTCTTTGTTTTTTCTCTTTGCT
699624 -----CTCTTTGTTTTTT-TCTTTGCT
1 TTTTTCTCTTTGTTTTTTCTCTTTGCT
699645 TCTTTTCTCTTTGTT
1 T-TTTTCTCTTTGTT
699660 CTGATTGGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
19 6 0.12
20 13 0.26
25 5 0.10
26 13 0.26
27 13 0.26
ACGTcount: A:0.00, C:0.17, G:0.08, T:0.74
Consensus pattern (27 bp):
TTTTTCTCTTTGTTTTTTCTCTTTGCT
Found at i:699627 original size:20 final size:19
Alignment explanation
Indices: 699574--699649 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 19
699564 TTTTATCTTC
* *
699574 TTTTTTCTTTGCTTTTTCT
1 TTTTTTCTTTGCTCTTTGT
699593 TTTGCTTT-TTT-CTCTTTGT
1 TTT--TTTCTTTGCTCTTTGT
699612 TTTTTCTCTTTGCTCTTTGT
1 TTTTT-TCTTTGCTCTTTGT
699632 TTTTTTCTTTGCTTCTTT
1 TTTTTTCTTTGC-TCTTT
699650 TCTCTTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.04
18 1 0.02
19 22 0.45
20 21 0.43
21 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.08, T:0.75
Consensus pattern (19 bp):
TTTTTTCTTTGCTCTTTGT
Found at i:699651 original size:34 final size:34
Alignment explanation
Indices: 699593--699657 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
699583 TGCTTTTTCT
699593 TTTGCTTTTTTCTCTTTGTTTTTTCTCTTTGCTC
1 TTTGCTTTTTTCTCTTTGTTTTTTCTCTTTGCTC
699627 TTTG-TTTTTT-TCTTTGCTTCTTTTCTCTTTG
1 TTTGCTTTTTTCTCTTTG-TT-TTTTCTCTTTG
699658 TTCTGATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 6 0.21
33 8 0.28
34 15 0.52
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.72
Consensus pattern (34 bp):
TTTGCTTTTTTCTCTTTGTTTTTTCTCTTTGCTC
Found at i:704879 original size:15 final size:15
Alignment explanation
Indices: 704861--704890 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
704851 AGAATATTTA
704861 AATAATAATAATATT
1 AATAATAATAATATT
704876 AATAATAATAATATT
1 AATAATAATAATATT
704891 TTTTAGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATAATAATATT
Found at i:711457 original size:14 final size:15
Alignment explanation
Indices: 711420--711493 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
711410 ATAACTAAAT
711420 TAATATATTATATAA
1 TAATATATTATATAA
711435 TAATATATT-TATAA
1 TAATATATTATATAA
* * **
711449 TCATTTATTATATTT
1 TAATATATTATATAA
* *
711464 TAAAAAATTA-A-AA
1 TAATATATTATATAA
*
711477 TAATATATTTTATAA
1 TAATATATTATATAA
711492 TA
1 TA
711494 TTTTACTACA
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
13 7 0.16
14 14 0.33
15 22 0.51
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATATTATATAA
Found at i:714587 original size:15 final size:15
Alignment explanation
Indices: 714567--714606 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
714557 AAAAATTATT
714567 AATAATAATATAATA
1 AATAATAATATAATA
*
714582 AATAATAATATATTA
1 AATAATAATATAATA
*
714597 AATATTAATA
1 AATAATAATA
714607 ATAACCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATATAATA
Found at i:714589 original size:18 final size:16
Alignment explanation
Indices: 714563--714609 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
714553 AATAAAAAAT
714563 TATT-AATAATAAT-A
1 TATTAAATAATAATAA
*
714577 TAATAAATAATAAT-A
1 TATTAAATAATAATAA
*
714592 TATTAAATATTAATAA
1 TATTAAATAATAATAA
714608 TA
1 TA
714610 ACCCGGACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTAAATAATAATAA
Found at i:715148 original size:18 final size:18
Alignment explanation
Indices: 715125--715186 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
715115 TTTTATTATT
* *
715125 TGGTCACTGCTGGAGAAA
1 TGGTCACGGCTGGAGACA
715143 TGGTCACGGCTGGAGACA
1 TGGTCACGGCTGGAGACA
*
715161 TGGTCACGGCTAGAGACA
1 TGGTCACGGCTGGAGACA
*
715179 TGGGCACG
1 TGGTCACG
715187 AAGTGGTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.37, T:0.18
Consensus pattern (18 bp):
TGGTCACGGCTGGAGACA
Found at i:721901 original size:237 final size:236
Alignment explanation
Indices: 721483--722054 Score: 842
Period size: 237 Copynumber: 2.4 Consensus size: 236
721473 CCTAACTTTA
* *
721483 CATTTGGCAGAAAGGTGCCAATAATGCAAGTTATATGAAAGGTTAAATGCCTAACTGTGCATTTG
1 CATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAATGCCTAACTGTGCATTTG
* * * **
721548 GTAGAAAGGTGTCAATAAAGCAAGTTAGATGAAAGGTTAAGTGTTTAACTGTGCATTTGGAAGAA
66 ATAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAGAA
721613 AGATGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAATTATGCATTTGGAAAAAAAAGGT
131 AGATGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAATTATGCATTTGG--AAAAAAGGT
* **
721678 TCCAATAATGCAAGTTA-ATGAAAGGTTAAATGTCTAATTGTG
194 ACCAATAATGCAAGTTAGATGAAAGGTTAAATGTCTAACCGTG
721720 CATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAATGCCTAACTGTGCATTTG
1 CATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAATGCCTAACTGTGCATTTG
* *
721785 ATAGAAAGGTGTCAATAATGCAAGGTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGTAGAA
66 ATAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAGAA
* * * * * * *
721850 AGGTTCCAATAATGCGAGTTAGATGAAATGTTAAATGCCTAATTGTGCATTTGGCAGAAAGGTAC
131 AGATGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAATTATGCATTTGGAAAAAAGGTAC
* *
721915 CAATAATGTAAGTTAGATGAATGGTTAAATGTCTAACCGTG
196 CAATAATGCAAGTTAGATGAAAGGTTAAATGTCTAACCGTG
* * * * * *
721956 CATTTGGTATAAAGGTGCCAATAATACAAGTTAGATGAAAATTTAAATGTCTAACTATGCATTT-
1 CATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAATGCCTAACTGTGCATTTG
* *
722020 AGTAGAAAGGTGCCACTAATGCAAGTTAGATGAAA
66 A-TAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
722055 AGTAGTGTAC
Statistics
Matches: 303, Mismatches: 30, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
235 23 0.08
236 110 0.36
237 170 0.56
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (236 bp):
CATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAATGCCTAACTGTGCATTTG
ATAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAGAA
AGATGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTAATTATGCATTTGGAAAAAAGGTAC
CAATAATGCAAGTTAGATGAAAGGTTAAATGTCTAACCGTG
Found at i:722055 original size:59 final size:59
Alignment explanation
Indices: 721472--722054 Score: 772
Period size: 59 Copynumber: 9.9 Consensus size: 59
721462 TAGATGAAAG
* * * *
721472 GCCTAACTTTACATTTGGCAGAAAGGTGCCAATAATGCAAGTTATATGAAAGGTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * *
721531 GCCTAACTGTGCATTTGGTAGAAAGGTGTCAATAAAGCAAGTTAGATGAAAGGTTAAGT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
** * *
721590 GTTTAACTGTGCATTTGGAAGAAAGATGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * * * *
721649 GCCTAATTATGCATTTGGAAAAAAAAGGTTCCAATAATGCAAGTTA-ATGAAAGGTTAAAT
1 GCCTAACTGTGCATTTGG--TAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * * *
721709 GTCTAATTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGTTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * *
721768 GCCTAACTGTGCATTTGATAGAAAGGTGTCAATAATGCAAGGTAGATGAAAGGTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * *
721827 GCCTAACTGTGCATTTGGTAGAAAGGTTCCAATAATGCGAGTTAGATGAAATGTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * * * *
721886 GCCTAATTGTGCATTTGGCAGAAAGGTACCAATAATGTAAGTTAGATGAATGGTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * * * **
721945 GTCTAACCGTGCATTTGGTATAAAGGTGCCAATAATACAAGTTAGATGAAAATTTAAAT
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
* * * *
722004 GTCTAACTATGCATTTAGTAGAAAGGTGCCACTAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
722055 AGTAGTGTAC
Statistics
Matches: 457, Mismatches: 64, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
58 23 0.05
59 381 0.83
60 30 0.07
61 23 0.05
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (59 bp):
GCCTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAAT
Found at i:729797 original size:2 final size:2
Alignment explanation
Indices: 729790--729844 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
729780 AATATTTTAT
* * *
729790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TT TT TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
729830 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
729845 TTTATTCATT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:729839 original size:36 final size:35
Alignment explanation
Indices: 729784--729867 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 35
729774 CTTTTTAATA
*
729784 TTTTATTATATATATATATATATATATATATATATTTT
1 TTTTATTATATATATATATATAT-TATAT-T-CATTTT
*
729822 TTTTATTATATATATATATATATTTTATTCATTTT
1 TTTTATTATATATATATATATATTATATTCATTTT
729857 TTATTATTATA
1 TT-TTATTATA
729868 ACTATTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 7 0.16
36 9 0.21
37 4 0.09
38 23 0.53
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (35 bp):
TTTTATTATATATATATATATATTATATTCATTTT
Found at i:729924 original size:4 final size:4
Alignment explanation
Indices: 729891--729976 Score: 54
Period size: 4 Copynumber: 21.2 Consensus size: 4
729881 TTATTATTCG
* *
729891 TATT TGTT TATT T-TT TGTT TATTCT TATT TATTT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TA-T-T TATT TA-TT TATT TATT TATT TATT
* * *
729941 TCTTT TGATT TAGT T-TT TAGT T-TT TATT T-TT TATT T
1 T-ATT T-ATT TATT TATT TATT TATT TATT TATT TATT T
729977 TCTCCTTATT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
3 10 0.16
4 39 0.61
5 12 0.19
6 3 0.05
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:729976 original size:73 final size:75
Alignment explanation
Indices: 729891--730033 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 75
729881 TTATTATTCG
* **
729891 TATTTGTTTATTTTTTGTTTATTCTTATTTATT-TTATT-TAT-TTATTTATTTC-TTTTGATTT
1 TATTTGTTTATTTTCTCCTTATTCTTA-TTATTATTATTATATATTATTTA-TTCATTTT-ATTT
729952 AGTTTTTAGTTTT
63 AGTTTTTAGTTTT
* *
729965 TATTT-TTTATTTTCTCCTTATTCTTATTATTATTATTATATATTTTTTATTCATTTTATTTATT
1 TATTTGTTTATTTTCTCCTTATTCTTATTATTATTATTATATATTATTTATTCATTTTATTTAGT
730029 TTTTA
66 TTTTA
730034 TCTAACACCT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
72 5 0.08
73 23 0.38
74 22 0.37
75 10 0.17
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (75 bp):
TATTTGTTTATTTTCTCCTTATTCTTATTATTATTATTATATATTATTTATTCATTTTATTTAGT
TTTTAGTTTT
Found at i:730014 original size:20 final size:20
Alignment explanation
Indices: 729991--730034 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
729981 CTTATTCTTA
729991 TTATT-ATTATTATATATTTT
1 TTATTCATT-TTATATATTTT
*
730011 TTATTCATTTTATTTATTTT
1 TTATTCATTTTATATATTTT
730031 TTAT
1 TTAT
730035 CTAACACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTCATTTTATATATTTT
Found at i:730030 original size:9 final size:9
Alignment explanation
Indices: 729903--729941 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
729893 TTTGTTTATT
*
729903 TTTTGTTTA
1 TTTTATTTA
729912 TTCTTATTTA
1 TT-TTATTTA
729922 TTTTATTTA
1 TTTTATTTA
729931 -TTTATTTA
1 TTTTATTTA
729939 TTT
1 TTT
729942 CTTTTGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 8 0.30
9 11 0.41
10 8 0.30
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTATTTA
Found at i:730550 original size:19 final size:19
Alignment explanation
Indices: 730517--730570 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
730507 ATGCCCTAAG
730517 GGTACCGATACCCCCTTTGA
1 GGTACCGATA-CCCCTTTGA
730537 GGTACCGATACCCCTTTGA
1 GGTACCGATACCCCTTTGA
730556 GGTACCGATACCCCT
1 GGTACCGATACCCCT
730571 AGTCATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 24 0.71
20 10 0.29
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.24
Consensus pattern (19 bp):
GGTACCGATACCCCTTTGA
Found at i:735057 original size:64 final size:64
Alignment explanation
Indices: 735004--735167 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 64
734994 CGGTGCACCA
*
735004 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
735068 CTTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
735133 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
735168 CAATTAATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 39 0.47
65 44 0.53
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:735156 original size:17 final size:19
Alignment explanation
Indices: 735118--735164 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
735108 ATATTCAGAG
735118 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
735137 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
735154 TGCATTCGATG
1 TGCA-TCGATG
735165 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:737082 original size:21 final size:21
Alignment explanation
Indices: 737022--737085 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
737012 TCAATAAGCC
* *
737022 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* *
737043 ATTAGGTTGATGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
737064 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
737085 A
1 A
737086 GGACGGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.41, T:0.23
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:739800 original size:12 final size:12
Alignment explanation
Indices: 739765--739812 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
739755 GTTTATTAGC
739765 ATTTATATTTAATT
1 ATTTAT-TTT-ATT
*
739779 ATATAGTTTTATT
1 ATTTA-TTTTATT
*
739792 ATTTATTTTCTT
1 ATTTATTTTATT
739804 ATTTATTTT
1 ATTTATTTT
739813 TTTTCTTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 15 0.50
13 7 0.23
14 7 0.23
15 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
ATTTATTTTATT
Done.