Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007871.1 Hibiscus syriacus cultivar Beakdansim tig00110246_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: 163418
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2311 original size:20 final size:20
Alignment explanation
Indices: 2286--2329 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2276 GTGTCATCTC
2286 TAATTCAAGAAAAATAAATT
1 TAATTCAAGAAAAATAAATT
2306 TAATTCAAGAAAAATAAATT
1 TAATTCAAGAAAAATAAATT
2326 TAAT
1 TAAT
2330 GAAGTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TAATTCAAGAAAAATAAATT
Found at i:7635 original size:5 final size:5
Alignment explanation
Indices: 7622--7895 Score: 134
Period size: 5 Copynumber: 54.6 Consensus size: 5
7612 AATATTATTA
*
7622 ATAAT ATAAC ATAAT ATAAT ATAAT ATAA- AT-AT ATAAT AATAA- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
* * * *
7670 ACT-AT A-AAT A-ATAT ATAAT AT-AT GTACT AT-AT A-AAT ATACT ATACT
1 A-TAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
7716 ATAAT ATAAT AATATAT ATACT AT-AT AT-AT ATACT ATAAT ATAAT A-ACAT
1 ATAAT ATAAT -ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
*
7766 ATAATAT ATAAT ATAAT ATAGTACT ATAAT AT-AT AATAAT ATACTGT ATAAT
1 AT-A-AT ATAAT ATAAT ATA--A-T ATAAT ATAAT -ATAAT ATA--AT ATAAT
* * * *
7818 ATACT AT-AT AT-AT ATGATAT ATAAT ATGA- ATAAT ATAAAT GTTAT
1 ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT AT-AAT ATAAT
*
7863 ATAAT AT-AT ACT-AT ATAAT AATAAC ATAAT ATA
1 ATAAT ATAAT A-TAAT ATAAT -ATAAT ATAAT ATA
7896 TAATACTATA
Statistics
Matches: 212, Mismatches: 25, Indels: 64
0.70 0.08 0.21
Matches are distributed among these distances:
3 1 0.00
4 44 0.21
5 122 0.58
6 25 0.12
7 16 0.08
8 4 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:7690 original size:7 final size:7
Alignment explanation
Indices: 7640--7965 Score: 170
Period size: 7 Copynumber: 43.4 Consensus size: 7
7630 ACATAATATA
7640 ATATAAT
1 ATATAAT
7647 ATA-AAT
1 ATATAAT
7653 ATATAAT
1 ATATAAT
7660 A-ATAA-
1 ATATAAT
7665 ATAATACTAT
1 AT-ATA--AT
*
7675 AAATAAT
1 ATATAAT
7682 ATATAAT
1 ATATAAT
*
7689 ATATGTACT
1 ATA--TAAT
7698 ATATAA-
1 ATATAAT
7704 ATATACTAT
1 ATATA--AT
7713 ACTATAAT
1 A-TATAAT
7721 ATAATAAT
1 AT-ATAAT
7729 ATAT-AT
1 ATATAAT
7735 ACTAT-AT
1 A-TATAAT
7742 ATAT-AT
1 ATATAAT
7748 ACTATAAT
1 A-TATAAT
*
7756 ATAATAAC
1 AT-ATAAT
7764 ATATAAT
1 ATATAAT
7771 ATATAAT
1 ATATAAT
7778 ATAATATAGT
1 AT-ATA-A-T
7788 ACTATAAT
1 A-TATAAT
7796 ATATAAT
1 ATATAAT
*
7803 AATATACT
1 -ATATAAT
*
7811 GTATAAT
1 ATATAAT
7818 ATACTATAT
1 ATA-TA-AT
7827 ATATATGAT
1 ATATA--AT
7836 ATATAAT
1 ATATAAT
7843 ATGAATAAT
1 AT--ATAAT
7852 ATA-AATGTT
1 ATATAA---T
7861 ATATAAT
1 ATATAAT
*
7868 ATATACT
1 ATATAAT
7875 ATATAAT
1 ATATAAT
7882 A-AT-A-
1 ATATAAT
*
7886 ACATAAT
1 ATATAAT
7893 ATATAAT
1 ATATAAT
7900 ACTATATACT
1 A-TATA-A-T
*
7910 ATATACT
1 ATATAAT
*
7917 ATTACAAT
1 A-TATAAT
*
7925 ATATATGTT
1 ATATA--AT
7934 ATATAAT
1 ATATAAT
* *
7941 ACCATACT
1 A-TATAAT
7949 ATATAAT
1 ATATAAT
7956 ATATAAT
1 ATATAAT
7963 ATA
1 ATA
7966 GTATAACAAT
Statistics
Matches: 254, Mismatches: 24, Indels: 82
0.71 0.07 0.23
Matches are distributed among these distances:
4 1 0.00
5 4 0.02
6 29 0.11
7 109 0.43
8 49 0.19
9 47 0.19
10 14 0.06
11 1 0.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:7739 original size:40 final size:40
Alignment explanation
Indices: 7636--7844 Score: 187
Period size: 40 Copynumber: 5.4 Consensus size: 40
7626 TATAACATAA
* *
7636 TATAATATAATATAAATATATAATA-ATAAATAATACTATA-
1 TATAATATAATA-ATATATATACTATATAAAT-ATACTATAC
* *
7676 AATAATAT-ATAATATATGTACTATATAAATATACTATAC
1 TATAATATAATAATATATATACTATATAAATATACTATAC
7715 TATAATATAATAATATATATAC--TAT--ATATA-TATAC
1 TATAATATAATAATATATATACTATATAAATATACTATAC
*
7750 TATAATATAATAACATATA-A-TATATAATATAATA-TAGTAC
1 TATAATATAATAATATATATACTATATAA-AT-ATACTA-TAC
*
7790 TATAATAT-ATAATA-ATATACTGTAT-AATATACTATA-
1 TATAATATAATAATATATATACTATATAAATATACTATAC
7826 TATATATGATATATAATAT
1 TATA-AT-ATA-ATAATAT
7845 GAATAATATA
Statistics
Matches: 142, Mismatches: 9, Indels: 35
0.76 0.05 0.19
Matches are distributed among these distances:
34 1 0.01
35 26 0.18
36 9 0.06
37 7 0.05
38 31 0.22
39 28 0.20
40 40 0.28
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (40 bp):
TATAATATAATAATATATATACTATATAAATATACTATAC
Found at i:7818 original size:12 final size:12
Alignment explanation
Indices: 7632--7958 Score: 136
Period size: 12 Copynumber: 26.7 Consensus size: 12
7622 ATAATATAAC
7632 ATAATATA--AT
1 ATAATATACTAT
*
7642 ATAATATAAATAT
1 ATAATAT-ACTAT
*
7655 ATAATA-A-TAA
1 ATAATATACTAT
*
7665 ATAATACTA-TAA
1 ATAATA-TACTAT
7677 ATAATATA-TA-
1 ATAATATACTAT
*
7687 ATATATGTACTAT
1 ATA-ATATACTAT
7700 ATAAATATACTATACT
1 AT-AATATAC--TA-T
*
7716 ATAATATAATA-
1 ATAATATACTAT
7727 ATATATATACTAT
1 ATA-ATATACTAT
7740 ATATATATACTAT
1 ATA-ATATACTAT
7753 A-ATATAATAAC-AT
1 ATA-AT-AT-ACTAT
7766 ATAATATA-TAAT
1 ATAATATACT-AT
*
7778 ATAATATAGTACT
1 ATAATATACTA-T
7791 ATAATATA-TA-
1 ATAATATACTAT
*
7801 ATAATATACTGT
1 ATAATATACTAT
7813 ATAATATACTAT
1 ATAATATACTAT
7825 ATATATATGA-TAT
1 ATA-ATAT-ACTAT
*
7838 ATAATATGAATAAT
1 ATAATAT-ACT-AT
**
7852 ATAA-ATGTTAT
1 ATAATATACTAT
7863 ATAATATATACTAT
1 AT-A-ATATACTAT
*
7877 ATAATA-A-TAAC
1 ATAATATACT-AT
7888 ATAATATA-TA-
1 ATAATATACTAT
7898 ATACTATATACTAT
1 ATA--ATATACTAT
* *
7912 ATACTATTACAAT
1 ATAATA-TACTAT
**
7925 AT-ATATGTTAT
1 ATAATATACTAT
7936 ATAATACCATACTAT
1 ATAAT---ATACTAT
7951 ATAATATA
1 ATAATATA
7959 TAATATAGTA
Statistics
Matches: 256, Mismatches: 20, Indels: 80
0.72 0.06 0.22
Matches are distributed among these distances:
10 30 0.12
11 33 0.13
12 79 0.31
13 72 0.28
14 21 0.08
15 18 0.07
16 3 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (12 bp):
ATAATATACTAT
Found at i:7863 original size:25 final size:25
Alignment explanation
Indices: 7632--7880 Score: 153
Period size: 25 Copynumber: 9.7 Consensus size: 25
7622 ATAATATAAC
7632 ATAATATAATATAATATAAAT-ATAT
1 ATAATATAATAT-ATATAAATGATAT
*
7657 AATAATA-AATAATACTATAAATAATAT
1 -ATAATATAAT-ATA-TATAAATGATAT
*
7684 ATAATATATGTACTATATAAAT-ATACT
1 ATAATATA-ATA-TATATAAATGATA-T
*
7711 ATACTATAATATA-AT-AAT-ATAT
1 ATAATATAATATATATAAATGATAT
*
7733 ATACTATATATATATACTATAAT-ATA-
1 ATAATATA-ATATATA-TA-AATGATAT
* *
7759 ATAACATATAATATATA-ATATAATAT
1 AT-A-ATATAATATATATAAATGATAT
* *
7785 AGTACTATAATATATAATAATAT-ACTGT
1 A-TAATATAATATAT-ATAA-ATGA-TAT
* *
7813 ATAATATACTATATATATATGATAT
1 ATAATATAATATATATAAATGATAT
*
7838 ATAATATGAATA-ATATAAATGTTAT
1 ATAATAT-AATATATATAAATGATAT
7863 ATAATAT-ATACTATATAA
1 ATAATATAATA-TATATAA
7881 TAATAACATA
Statistics
Matches: 183, Mismatches: 15, Indels: 51
0.73 0.06 0.20
Matches are distributed among these distances:
22 9 0.05
23 14 0.08
24 5 0.03
25 56 0.31
26 38 0.21
27 49 0.27
28 12 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATATAATATATATAAATGATAT
Found at i:7891 original size:25 final size:25
Alignment explanation
Indices: 7632--7978 Score: 143
Period size: 25 Copynumber: 14.1 Consensus size: 25
7622 ATAATATAAC
7632 ATAAT-ATAATATAATATA-A--AT
1 ATAATAATAATATAATATATACTAT
7653 AT-ATAATAATA-AATA-ATACTAT
1 ATAATAATAATATAATATATACTAT
7675 A-AATAAT-ATATAATATATGTACTAT
1 ATAATAATAATATAATATA--TACTAT
* *
7700 ATAA-ATATACTATACTATA-A-TAT
1 ATAATA-ATAATATAATATATACTAT
7723 AATAATATATATACTATATATATATACTAT
1 -ATAATA-ATA-A-TATA-ATATATACTAT
7753 A-ATATAATAACATATAATATATA--AT
1 ATA-ATAAT-A-ATATAATATATACTAT
* *
7778 ATAATATAGTACTATAATATATAATAAT
1 ATAATA-A-TAATATAATATATACT-AT
* * *
7806 ATACTGTATAATATACTATATA-TAT
1 ATAAT-AATAATATAATATATACTAT
* *
7831 ATGATATATAATATGA-ATA-A-TAT
1 ATAATA-ATAATATAATATATACTAT
* *
7854 A-AAT-GTTATATAATATATACTAT
1 ATAATAATAATATAATATATACTAT
* *
7877 ATAATAATAACATAATATATAATACT
1 ATAATAATAATATAATATATACTA-T
* * *
7903 AT-ATACT-ATATACTAT-TACAAT
1 ATAATAATAATATAATATATACTAT
* * *
7925 AT-ATATGTTATATAATACCATACTAT
1 ATAATA-ATAATATAATA-TATACTAT
* *
7951 ATAATATATAATATAGTATA-ACAAT
1 ATAATA-ATAATATAATATATACTAT
7976 ATA
1 ATA
7979 TTGTATAAAA
Statistics
Matches: 249, Mismatches: 37, Indels: 76
0.69 0.10 0.21
Matches are distributed among these distances:
19 1 0.00
20 13 0.05
21 14 0.06
22 21 0.08
23 17 0.07
24 25 0.10
25 67 0.27
26 19 0.08
27 44 0.18
28 18 0.07
29 7 0.03
30 3 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATAATAATATAATATATACTAT
Found at i:13547 original size:2 final size:2
Alignment explanation
Indices: 13540--13585 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13530 GAAAGAGGGA
13540 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
13582 AT AT
1 AT AT
13586 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13624 original size:14 final size:14
Alignment explanation
Indices: 13607--13635 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13597 TGTGTGTGTG
13607 TATATATATGTATA
1 TATATATATGTATA
13621 TATATATATGTATA
1 TATATATATGTATA
13635 T
1 T
13636 GAAAGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:19900 original size:20 final size:21
Alignment explanation
Indices: 19875--19917 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19865 ACTATGCAAT
19875 GTTTCTC-ATTG-TCTTTCTTG
1 GTTTCTCTATTGAT-TTTCTTG
19895 GTTTCTCTATTGATTTTCTTG
1 GTTTCTCTATTGATTTTCTTG
19916 GT
1 GT
19918 ATACTGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.07, C:0.16, G:0.16, T:0.60
Consensus pattern (21 bp):
GTTTCTCTATTGATTTTCTTG
Found at i:20323 original size:5 final size:5
Alignment explanation
Indices: 20313--20584 Score: 301
Period size: 5 Copynumber: 53.6 Consensus size: 5
20303 AAATGCAATA
20313 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
20363 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT
*
20415 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATACTGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT
* * *
20467 ATAAT -T-AT ATACT ATAAT ATACTGT ATAAT -T-AT ATACT AT-AT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
20513 ATTAT ATGATAT ATAAT ATAA- ATAAT ATAAAT GTTAT ATAAT AT-AT
1 ATAAT AT-A-AT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT
20559 ACTATAT AATAAT ATAACT -TAAT ATA
1 A-TA-AT -ATAAT ATAA-T ATAAT ATA
20585 TAATACTATA
Statistics
Matches: 231, Mismatches: 14, Indels: 44
0.80 0.05 0.15
Matches are distributed among these distances:
3 4 0.02
4 17 0.07
5 179 0.77
6 10 0.04
7 20 0.09
8 1 0.00
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:20587 original size:17 final size:16
Alignment explanation
Indices: 20310--20654 Score: 137
Period size: 15 Copynumber: 21.5 Consensus size: 16
20300 TAGAAATGCA
*
20310 ATAATAATATAATATAAT
1 ATAAT-ATATACTAT-AT
20328 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20343 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20358 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20373 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20388 ATAATATAATA-TAATAT
1 ATAATAT-ATACT-ATAT
20405 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20420 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
20435 ATAATATA-A-TATAAT
1 ATAATATATACTAT-AT
*
20450 ATAATATAATA-TACTGT
1 ATAATAT-ATACTA-TAT
20467 ATAATTATATACTATAAT
1 ATAA-TATATACTAT-AT
* * *
20485 ATACTGTATAAT-TAT
1 ATAATATATACTATAT
* *
20500 ATACTATATAAATATTAT
1 ATAATATAT-ACTA-TAT
* * *
20518 ATGATATATAATATAA
1 ATAATATATACTATAT
* *
20534 ATAATATA-AATGTTAT
1 ATAATATATACT-ATAT
20550 ATAATATATACTATAT
1 ATAATATATACTATAT
20566 AATAATATA-ACTTAATAT
1 -ATAATATATAC-T-ATAT
20584 ATAATACTATA-TACTATT
1 ATAATA-TATACTA-TA-T
* *
20602 ACAATATATA-TGCTAT
1 ATAATATATACT-ATAT
*
20618 ATAATACCATA-T-TAT
1 ATAATA-TATACTATAT
*
20633 ATAATATGTA--ATAT
1 ATAATATATACTATAT
20647 ATAATATA
1 ATAATATA
20655 GTATAACGTT
Statistics
Matches: 281, Mismatches: 21, Indels: 54
0.79 0.06 0.15
Matches are distributed among these distances:
14 14 0.05
15 121 0.43
16 39 0.14
17 67 0.24
18 39 0.14
19 1 0.00
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATATATACTATAT
Found at i:20594 original size:10 final size:9
Alignment explanation
Indices: 20310--20612 Score: 217
Period size: 10 Copynumber: 33.2 Consensus size: 9
20300 TAGAAATGCA
20310 ATAATA-AT
1 ATAATATAT
20318 ATAATATAAT
1 ATAATAT-AT
20328 ATAATATAAT
1 ATAATAT-AT
20338 ATAATATAAT
1 ATAATAT-AT
20348 ATAATATAAT
1 ATAATAT-AT
20358 ATAATATAAT
1 ATAATAT-AT
20368 ATAATATAAT
1 ATAATAT-AT
20378 ATAATATAAT
1 ATAATAT-AT
20388 ATAATATA-
1 ATAATATAT
20396 AT-ATAATAT
1 ATAAT-ATAT
20405 ATAATATAAT
1 ATAATAT-AT
20415 ATAATATAAT
1 ATAATAT-AT
20425 ATAATATAAT
1 ATAATAT-AT
20435 ATAATATAAT
1 ATAATAT-AT
20445 ATAATATAAT
1 ATAATAT-AT
20455 ATAATATACTGT
1 ATAATATA---T
20467 ATAAT-TAT
1 ATAATATAT
*
20475 ATACTATA-
1 ATAATATAT
*
20483 AT-ATACTGT
1 ATAATA-TAT
20492 ATAAT-TAT
1 ATAATATAT
*
20500 ATACTATAT
1 ATAATATAT
20509 A-AATAT-T
1 ATAATATAT
20516 AT-ATGATAT
1 ATAAT-ATAT
*
20525 ATAATATAA
1 ATAATATAT
*
20534 ATAATATAA
1 ATAATATAT
*
20543 AT-GT-TAT
1 ATAATATAT
20550 ATAATATAT
1 ATAATATAT
20559 ACT-ATATA-
1 A-TAATATAT
20567 ATAATATA-
1 ATAATATAT
*
20575 ACTTA-ATAT
1 A-TAATATAT
20584 ATAATACTAT
1 ATAATA-TAT
*
20594 ATACTAT-T
1 ATAATATAT
*
20602 ACAATATAT
1 ATAATATAT
20611 AT
1 AT
20613 GCTATATAAT
Statistics
Matches: 252, Mismatches: 16, Indels: 53
0.79 0.05 0.17
Matches are distributed among these distances:
7 13 0.05
8 51 0.20
9 47 0.19
10 133 0.53
11 2 0.01
12 6 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (9 bp):
ATAATATAT
Found at i:24444 original size:63 final size:63
Alignment explanation
Indices: 24335--24460 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
24325 TGTATTGCCG
*** * *
24335 GTAAAAAGACTTTGAAAGGTGTTGATAAACTGCATAGCGAATCTAAAAGTAATGGATCTGATT
1 GTAAAAAGACTACAAAAGGCGTTGATAAACTGCATACCGAATCTAAAAGTAATGGATCTGATT
* * *
24398 GTAAAAAGACTACAAAAGGCGTTGATCAATTGCATGACCGAA-CTAAAAGTAATGGGTCTGATT
1 GTAAAAAGACTACAAAAGGCGTTGATAAACTGCAT-ACCGAATCTAAAAGTAATGGATCTGATT
24461 ATAATGATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 49 0.91
64 5 0.09
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (63 bp):
GTAAAAAGACTACAAAAGGCGTTGATAAACTGCATACCGAATCTAAAAGTAATGGATCTGATT
Found at i:26970 original size:24 final size:23
Alignment explanation
Indices: 26939--26984 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
26929 GAAAGAGCAA
26939 TTCGTGAAG-CTCGTGAAAGGGCC
1 TTCGTGAAGTC-CGTGAAAGGGCC
*
26962 TTCGCTGAAGTCCGTGAGAGGGC
1 TTCG-TGAAGTCCGTGAAAGGGC
26985 TGCCGCTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 15 0.75
25 1 0.05
ACGTcount: A:0.20, C:0.22, G:0.37, T:0.22
Consensus pattern (23 bp):
TTCGTGAAGTCCGTGAAAGGGCC
Found at i:27303 original size:3 final size:3
Alignment explanation
Indices: 27295--27329 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
27285 TTCTGGAACG
27295 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27330 GAATGGCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:30338 original size:20 final size:20
Alignment explanation
Indices: 30313--30352 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30303 ATTAAAACTG
30313 ATAGTTTAGATACGAAATGC
1 ATAGTTTAGATACGAAATGC
* *
30333 ATAGTTTATATACTAAATGC
1 ATAGTTTAGATACGAAATGC
30353 GTAATTTACC
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:0.15, T:0.35
Consensus pattern (20 bp):
ATAGTTTAGATACGAAATGC
Found at i:30360 original size:20 final size:20
Alignment explanation
Indices: 30317--30360 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
30307 AAACTGATAG
*
30317 TTTAGATACGAAATGCATAG
1 TTTAGATACGAAATGCATAA
* * *
30337 TTTATATACTAAATGCGTAA
1 TTTAGATACGAAATGCATAA
30357 TTTA
1 TTTA
30361 CCCTTAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (20 bp):
TTTAGATACGAAATGCATAA
Found at i:31039 original size:20 final size:21
Alignment explanation
Indices: 31014--31057 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
31004 CATTTGACAT
31014 AAGAGATCAATC-TTTTGTGA
1 AAGAGATCAATCATTTTGTGA
*
31034 AAGAGATCTATCATTTTGTGA
1 AAGAGATCAATCATTTTGTGA
31055 AAG
1 AAG
31058 GAATCGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (21 bp):
AAGAGATCAATCATTTTGTGA
Found at i:31067 original size:21 final size:21
Alignment explanation
Indices: 31014--31069 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
31004 CATTTGACAT
*
31014 AAGAGATCAATC-TTTTGTGA
1 AAGAGATCGATCATTTTGTGA
*
31034 AAGAGATCTATCATTTTGTGA
1 AAGAGATCGATCATTTTGTGA
31055 AAG-GAATCGATCATT
1 AAGAG-ATCGATCATT
31070 ATTTAATCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (21 bp):
AAGAGATCGATCATTTTGTGA
Found at i:37884 original size:18 final size:19
Alignment explanation
Indices: 37856--37894 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
37846 TCTATTATTT
37856 TTTACTTTAATAGCTTTTA
1 TTTACTTTAATAGCTTTTA
* *
37875 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATAGCTTTTA
37893 TT
1 TT
37895 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTACTTTAATAGCTTTTA
Found at i:43508 original size:18 final size:19
Alignment explanation
Indices: 43480--43518 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
43470 TTCTCTTATT
43480 TTTATTTTAATAGCTTTTA
1 TTTATTTTAATAGCTTTTA
* *
43499 TTTA-TTTAATCGTTTTTA
1 TTTATTTTAATAGCTTTTA
43517 TT
1 TT
43519 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTATTTTAATAGCTTTTA
Found at i:47899 original size:30 final size:30
Alignment explanation
Indices: 47830--47900 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
47820 AGCAAAATCA
*
47830 AACTTGAATTCTTTAATGATAGTAAACTCG
1 AACTTAAATTCTTTAATGATAGTAAACTCG
* * * * *
47860 AA-TTCAAATTCTTTGATGGTTGTAAAGTTG
1 AACTT-AAATTCTTTAATGATAGTAAACTCG
47890 AACTTAAATTC
1 AACTTAAATTC
47901 ATACCAGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.06
30 29 0.88
31 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (30 bp):
AACTTAAATTCTTTAATGATAGTAAACTCG
Found at i:55959 original size:18 final size:18
Alignment explanation
Indices: 55936--55976 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
55926 AACCACCAAT
55936 TATTAGAGTTTTATGTGA
1 TATTAGAGTTTTATGTGA
55954 TATTAGAGTTTTATGTGA
1 TATTAGAGTTTTATGTGA
55972 TATTA
1 TATTA
55977 AGGGGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (18 bp):
TATTAGAGTTTTATGTGA
Found at i:61042 original size:30 final size:30
Alignment explanation
Indices: 61002--61060 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
60992 CTGATGGAAC
61002 ACACATTGATGGAGCAAATACTGGTGGAGA
1 ACACATTGATGGAGCAAATACTGGTGGAGA
* * *
61032 ACACGTTGATGGAGCAGATGCTGGTGGAG
1 ACACATTGATGGAGCAAATACTGGTGGAG
61061 CATGTGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.20
Consensus pattern (30 bp):
ACACATTGATGGAGCAAATACTGGTGGAGA
Found at i:65270 original size:157 final size:152
Alignment explanation
Indices: 65057--65427 Score: 420
Period size: 152 Copynumber: 2.4 Consensus size: 152
65047 TTTGGTATAT
* * * * *
65057 GAGCATGTGGTTCAAATTTAGTAAAAAACGGACTTAAAATAAATGTCAAATTGAAAAAATAAAGA
1 GAGCATGTGGTTCAAATTTGGTAAAAAA-AGACTTAAAATAAAAGACGAATTGAAAAAATAAAGA
* *
65122 TATTATGAAAAAATGAAAGAATAAATTGAAAAATAAAAAAAATTGTTAT-AAAAAAAGGAATTGA
65 TATTA-CAAAAAATGAAAGAATAAA-T---AAAT-AAAAAAATTGTTATCAAAAAAAGAAATTGA
* **
65186 AAATACACATGTATTATATTATGCTTTAG
124 AAATAAACATGTATTATACAATGCTTTAG
* *
65215 GAGCATGTGGTTCAAATTTGGTAAAAAAATACTTAAAATAAAAGACGAATTGAAAAAATAAGGAT
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAAGACGAATTGAAAAAATAAAGAT
* * * * * *
65280 ATTACAAAAATTGAAAGACTAAATAAATAAACAATTTGTTATCAAAAAGAGAAATTGAAAGTAAA
66 ATTACAAAAAATGAAAGAATAAATAAATAAAAAAATTGTTATCAAAAAAAGAAATTGAAAATAAA
* *
65345 CATGTATTCTACAATGGTTTAG
131 CATGTATTATACAATGCTTTAG
* * * * * * * *
65367 GAGAATATGGTTCAAACTTGGTAAAAATAGACTTAAAATAAAGGAGGAACTGAAGAAATAA
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAAGACGAATTGAAAAAATAA
65428 TGAAATCAGG
Statistics
Matches: 183, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
151 12 0.07
152 92 0.50
155 1 0.01
156 16 0.09
157 35 0.19
158 27 0.15
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (152 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAAGACGAATTGAAAAAATAAAGAT
ATTACAAAAAATGAAAGAATAAATAAATAAAAAAATTGTTATCAAAAAAAGAAATTGAAAATAAA
CATGTATTATACAATGCTTTAG
Found at i:71613 original size:18 final size:15
Alignment explanation
Indices: 71565--71606 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
71555 GGATTTATTT
71565 TTATTTTTTTAAGAA
1 TTATTTTTTTAAGAA
71580 TTATTTTTTTAAGAA
1 TTATTTTTTTAAGAA
71595 TTATTTTTTTAA
1 TTATTTTTTTAA
71607 TTTGAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
TTATTTTTTTAAGAA
Found at i:72775 original size:21 final size:19
Alignment explanation
Indices: 72737--72782 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
72727 AATTAATCCT
72737 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
72757 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
72778 A-TAAT
1 ACTAAT
72783 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:82985 original size:21 final size:19
Alignment explanation
Indices: 82947--82992 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
82937 AATTAATCCT
82947 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
82967 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
82988 A-TAAT
1 ACTAAT
82993 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:89437 original size:14 final size:13
Alignment explanation
Indices: 89412--89450 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
89402 TCTTTTGATT
*
89412 AATTTTCATTTTC
1 AATTTTTATTTTC
*
89425 ATTTTTTAGTTTTC
1 AATTTTTA-TTTTC
89439 AATTTTTATTTT
1 AATTTTTATTTT
89451 TTTATTTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (13 bp):
AATTTTTATTTTC
Found at i:89443 original size:21 final size:20
Alignment explanation
Indices: 89414--89452 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
89404 TTTTGATTAA
89414 TTTTCATTTTCATTTTTTAG
1 TTTTCATTTTCATTTTTTAG
*
89434 TTTTCAATTTTTATTTTTT
1 TTTTC-ATTTTCATTTTTT
89453 TATTTTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTCATTTTCATTTTTTAG
Found at i:89458 original size:21 final size:19
Alignment explanation
Indices: 89413--89459 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
89403 CTTTTGATTA
89413 ATTTTCATTTTCATTTTTT
1 ATTTTCATTTTCATTTTTT
*
89432 AGTTTTCAATTTTTATTTTTTT
1 A-TTTTC-ATTTTCA-TTTTTT
89454 ATTTTC
1 ATTTTC
89460 GTTCCTCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 11 0.46
22 7 0.29
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTTCATTTTCATTTTTT
Found at i:101784 original size:18 final size:18
Alignment explanation
Indices: 101765--101798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101755 TACATCAAAT
101765 TTTAT-ATATTTATATTA
1 TTTATGATATTTATATTA
*
101782 TTTATGATCTTTATATT
1 TTTATGATATTTATATT
101799 TATTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTATGATATTTATATTA
Found at i:107187 original size:7 final size:7
Alignment explanation
Indices: 107175--107215 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
107165 CCAAGCTACT
107175 GAATTCA
1 GAATTCA
107182 GAATTCA
1 GAATTCA
107189 GAATTCA
1 GAATTCA
107196 GAATTCA
1 GAATTCA
*
107203 GAACTCA
1 GAATTCA
107210 GAATTC
1 GAATTC
107216 TTACAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (7 bp):
GAATTCA
Found at i:108206 original size:20 final size:20
Alignment explanation
Indices: 108169--108206 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
108159 AAAATCAAAC
*
108169 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
108189 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
108207 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:108933 original size:24 final size:20
Alignment explanation
Indices: 108880--108937 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
108870 TTCCCATTGA
*
108880 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
108900 AGTGCATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-C-T-AC
108923 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
108938 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 1 0.03
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:109945 original size:2 final size:2
Alignment explanation
Indices: 109938--109973 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
109928 TCAATACTCA
109938 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
109974 CTTTCTTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112328 original size:18 final size:18
Alignment explanation
Indices: 112305--112357 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
112295 CGTAGAAATT
*
112305 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
112323 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
112341 TGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCACT
112358 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:112684 original size:20 final size:20
Alignment explanation
Indices: 112659--112726 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
112649 AACATGTATT
112659 CATAACATTCGTTTCACATA
1 CATAACATTCGTTTCACATA
*
112679 CATAACATTTGTTTCACATA
1 CATAACATTCGTTTCACATA
112699 CATAACATTCGTTTCACATA
1 CATAACATTCGTTTCACATA
*
112719 CAAAACAT
1 CATAACAT
112727 ATCATATAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (20 bp):
CATAACATTCGTTTCACATA
Found at i:113785 original size:11 final size:10
Alignment explanation
Indices: 113751--113794 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
113741 CTTAGTGTTT
113751 TAAGCTTACA
1 TAAGCTTACA
113761 TAAGCTTACA
1 TAAGCTTACA
*
113771 TAAGCTTTACT
1 TAAGC-TTACA
*
113782 TAAGCTTATA
1 TAAGCTTACA
113792 TAA
1 TAA
113795 CACCCAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (10 bp):
TAAGCTTACA
Found at i:113785 original size:21 final size:20
Alignment explanation
Indices: 113751--113794 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
113741 CTTAGTGTTT
113751 TAAGCTTACATAAGCTTACA
1 TAAGCTTACATAAGCTTACA
* *
113771 TAAGCTTTACTTAAGCTTATA
1 TAAGC-TTACATAAGCTTACA
113792 TAA
1 TAA
113795 CACCCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (20 bp):
TAAGCTTACATAAGCTTACA
Found at i:115058 original size:86 final size:85
Alignment explanation
Indices: 114808--115074 Score: 311
Period size: 86 Copynumber: 3.1 Consensus size: 85
114798 TCTCGACTCA
* * * * * * *
114808 AGCTAAGCTGTAAATTTGACATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGAC
1 AGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTAATAGAACTCGAAGGTTTTTGTTGAC
*
114873 AGATAACCCTTCTTGCCTTG
66 AGATAACCCTTCTCGCCTTG
* *
114893 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCA-AACTCGAAGGTCTTTTGTTA
1 AGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTAAT-AGAACTCGAAGGT-TTTTGTTG
* ** * *
114957 ACAGGTAGGCATTCTCACCTTG
64 ACAGATAACCCTTCTCGCCTTG
* * * *
114979 AGCTATGTTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATAGAACTCGAATGTATTTTATTGA
1 AGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTAATAGAACTCGAAGGT-TTTTGTTGA
*
115044 CAGATATCCCTTCTCGCCTTG
65 CAGATAACCCTTCTCGCCTTG
*
115065 AGTTATGCTG
1 AGCTATGCTG
115075 GACTGGTTGG
Statistics
Matches: 152, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
85 51 0.34
86 101 0.66
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
AGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATGTAATAGAACTCGAAGGTTTTTGTTGAC
AGATAACCCTTCTCGCCTTG
Found at i:115348 original size:121 final size:121
Alignment explanation
Indices: 115130--115357 Score: 375
Period size: 121 Copynumber: 1.9 Consensus size: 121
115120 TGATTCGTTA
*
115130 GGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGACCTTT
1 GGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGACCTTT
* *
115195 GAATTGGATATCCTTCGTCGTGAATTTAAAATCCAAGGGTTGCATTGCTGCTTGTG
66 GAATTGGATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTGCATTGCTGCTTGTG
* * *
115251 GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCTTTCATTGTGAAGTTGAGCTTT
1 GGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGACCTTT
* * *
115316 GAATTGTATATCCTTCGTTGTAAAGTTGAAATCCAAGGGTTG
66 GAATTGGATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTG
115358 TTTCACCAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (121 bp):
GGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGACCTTT
GAATTGGATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTGCATTGCTGCTTGTG
Found at i:120397 original size:15 final size:16
Alignment explanation
Indices: 120369--120401 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
120359 CATGAGAAAT
120369 AAATAAAAATTAAGAA
1 AAATAAAAATTAAGAA
120385 AAATAAAAA-TAAGAA
1 AAATAAAAATTAAGAA
120400 AA
1 AA
120402 TATTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATAAAAATTAAGAA
Found at i:123435 original size:23 final size:21
Alignment explanation
Indices: 123397--123439 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
123387 TTAATTATTT
123397 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
123418 AAAAACATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
123439 A
1 A
123440 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:124825 original size:12 final size:12
Alignment explanation
Indices: 124810--124856 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
124800 ATTATATTTA
124810 TTTTTATATAAT
1 TTTTTATATAAT
124822 TTTTTATATAA-
1 TTTTTATATAAT
** *
124833 TCCTTAAATAAT
1 TTTTTATATAAT
*
124845 TTTTAATATAAT
1 TTTTTATATAAT
124857 AAATAATTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:124894 original size:24 final size:24
Alignment explanation
Indices: 124850--124895 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
124840 ATAATTTTTA
*
124850 ATATAATAAATAATTTTTATAATT
1 ATATAATAAATAATTTATATAATT
*
124874 ATATATTAAA-AATTATATATAA
1 ATATAATAAATAATT-TATATAA
124896 ACATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATAATAAATAATTTATATAATT
Found at i:124901 original size:13 final size:14
Alignment explanation
Indices: 124870--124902 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
124860 TAATTTTTAT
124870 AATTATATATTAAA
1 AATTATATATTAAA
124884 AATTATATA-TAAA
1 AATTATATATTAAA
*
124897 CATTAT
1 AATTAT
124903 TAATTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTATATATTAAA
Found at i:125299 original size:25 final size:25
Alignment explanation
Indices: 125263--125316 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
125253 TCTACAGGAA
*
125263 TTGG-AATTCAATTCCATATACTAT
1 TTGGTAATCCAATTCCATATACTAT
* * *
125287 TTGGTAATCCAATTTCATATTCTGT
1 TTGGTAATCCAATTCCATATACTAT
125312 TTGGT
1 TTGGT
125317 TCGCAGACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (25 bp):
TTGGTAATCCAATTCCATATACTAT
Found at i:126036 original size:37 final size:38
Alignment explanation
Indices: 125967--126039 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
125957 ACCCGAACCC
*
125967 GACCCGAATATCACACTTAAAAAACCCCGACCCGACTA
1 GACCCAAATATCACACTTAAAAAACCCCGACCCGACTA
126005 GACCCAAATATCACACTTAAAAAA-CCCGACCCGAC
1 GACCCAAATATCACACTTAAAAAACCCCGACCCGAC
126040 CCGAACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 11 0.32
38 23 0.68
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (38 bp):
GACCCAAATATCACACTTAAAAAACCCCGACCCGACTA
Found at i:126051 original size:37 final size:38
Alignment explanation
Indices: 125973--126051 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
125963 ACCCGACCCG
* * *
125973 AATATCACACTTAAAAAACCCCGACCCGACTAGACCCA
1 AATATCACACTTAAAAAACCCCGACCCGACCAGAACAA
*
126011 AATATCACACTTAAAAAA-CCCGACCCGACCCGAACAA
1 AATATCACACTTAAAAAACCCCGACCCGACCAGAACAA
126048 AATA
1 AATA
126052 AAGTTTCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 19 0.51
38 18 0.49
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.13
Consensus pattern (38 bp):
AATATCACACTTAAAAAACCCCGACCCGACCAGAACAA
Found at i:126903 original size:10 final size:10
Alignment explanation
Indices: 126890--126918 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
126880 AATAAAATAA
126890 AATAAAAATT
1 AATAAAAATT
126900 AATAAAAATT
1 AATAAAAATT
126910 AATAAAAAT
1 AATAAAAAT
126919 ATCTTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAAAATT
Found at i:155188 original size:27 final size:24
Alignment explanation
Indices: 155146--155195 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
155136 CCCCACCTTA
155146 AATTTTTACTCATAGCTGAACTGTAT
1 AATTTTTACTCATAGC--AACTGTAT
155172 AATTTTT-CTCCATTAGCAACTGTA
1 AATTTTTACT-CA-TAGCAACTGTA
155196 ATAGTTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (24 bp):
AATTTTTACTCATAGCAACTGTAT
Found at i:160362 original size:22 final size:21
Alignment explanation
Indices: 160320--160359 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
160310 GAGTTTATTT
*
160320 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
160341 TCATTTTT-ACATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
160360 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:0.12, G:0.03, T:0.50
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:161834 original size:2 final size:2
Alignment explanation
Indices: 161827--161862 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
161817 TACAAATTCC
161827 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
161863 CTAACTCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.