Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1154529 original size:15 final size:15
Alignment explanation
Indices: 1154515--1154928 Score: 155
Period size: 15 Copynumber: 26.7 Consensus size: 15
1154505 TTACTATTAT
*
1154515 TTTTTCTTTTTTTATTA
1 TTTTT-TTTTTCT-TTA
1154532 TTTATTTTTTTCTTTA
1 TTT-TTTTTTTCTTTA
*
1154548 TTTTTTATTTTCTCTA
1 TTTTTT-TTTTCTTTA
*
1154564 TCTTTATTTTT-TTTA
1 T-TTTTTTTTTCTTTA
* * *
1154579 TTTTCTTTATATTTA
1 TTTTTTTTTTCTTTA
1154594 TTTTCTTTATTT-TTTA
1 TTTT-TTT-TTTCTTTA
*
1154610 TTTTTATTTTCTTTA
1 TTTTTTTTTTCTTTA
* * * *
1154625 TCTTTATTGTATTTA
1 TTTTTTTTTTCTTTA
* * *
1154640 TCTTATTTATCTTTA
1 TTTTTTTTTTCTTTA
1154655 TTTATTTTTTTTCTTTA
1 -TT-TTTTTTTTCTTTA
* * ** *
1154672 TCTATAATTTATTTA
1 TTTTTTTTTTCTTTA
* *
1154687 TTTATTTATT-TTTA
1 TTTTTTTTTTCTTTA
*
1154701 TTTTTTTCTTCTTTA
1 TTTTTTTTTTCTTTA
*
1154716 TTTATTTATTTCCTTATA
1 TTT-TTT-TTTTCTT-TA
1154734 TTTATTTTATTTCTTTA
1 TTT-TTTT-TTTCTTTA
*
1154751 -TTTTTTTAT-TTTA
1 TTTTTTTTTTCTTTA
*
1154764 TTCTTGTTTATTTATTTA
1 TT-TT-TTT-TTTCTTTA
* * * *
1154782 TTTATTATAT-TATA
1 TTTTTTTTTTCTTTA
* * *
1154796 TTATTTATTTATTTA
1 TTTTTTTTTTCTTTA
*
1154811 TTTATTTATTATCTTTA
1 TTT-TTT-TTTTCTTTA
*
1154828 TTTTTATTTAT-TTTA
1 TTTTT-TTTTTCTTTA
* * *
1154843 TTTTATTTATCATTA
1 TTTTTTTTTTCTTTA
*
1154858 TTTTATTTATT-TTTA
1 TTTT-TTTTTTCTTTA
**
1154873 TTTACTTTTT-TTTA
1 TTTTTTTTTTCTTTA
* *
1154887 TCTTTACTTTATCTTTA
1 T-TTT-TTTTTTCTTTA
*
1154904 -TTTTTTTCTCTTTA
1 TTTTTTTTTTCTTTA
1154918 TCTTTTTTTTT
1 T-TTTTTTTTT
1154929 ATTTCTTTAT
Statistics
Matches: 306, Mismatches: 61, Indels: 61
0.71 0.14 0.14
Matches are distributed among these distances:
13 4 0.01
14 58 0.19
15 105 0.34
16 66 0.22
17 51 0.17
18 22 0.07
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTTCTTTA
Found at i:1154529 original size:35 final size:34
Alignment explanation
Indices: 1154480--1154910 Score: 149
Period size: 35 Copynumber: 12.4 Consensus size: 34
1154470 TTTATTCTTG
*
1154480 TTTTTATTTATTTATTATATTA-TTTTTACTATTAT
1 TTTTTATTTTTTTATTAT-TTATTTTTTACT-TTAT
* *
1154515 TTTTTCTTTTTTTATTATTTATTTTTTTCTTTAT
1 TTTTTATTTTTTTATTATTTATTTTTTACTTTAT
* *
1154549 TTTTTATTTTCTCTA-TCTTTA-TTTTT--TTTATT
1 TTTTTATTTT-TTTATTATTTATTTTTTACTTTA-T
* * *
1154581 TTCTTTATATTTATT-TTCTTTATTTTTTATTTTTATT
1 TT-TTTAT-TTTTTTATTATTTATTTTTTA-CTTTA-T
1154618 TTCTTTATCTTTATTGTATTTATCTTATTTATCTTTA-TTTAT
1 TT-TTTAT-TTT-TT-TA-TTAT-TTA-TT-T-TTTACTTTAT
*
1154660 TTTTT-TTCTTTATCTATAATTTATTTATTTA-TTTA-
1 TTTTTATT-TTT-T-TATTATTTATTT-TTTACTTTAT
* * *
1154695 TTTTTATTTTTTTCTTCTTTATTTATTTA-TTT-C
1 TTTTTATTTTTTTATTATTTATTT-TTTACTTTAT
* * * *
1154728 CTTATATTTATTTTATTTCTTTATTTTTTTATTTTATT
1 TTTTTATTT-TTTTA-TTATTTA-TTTTTTACTTTA-T
* *
1154766 CTTGTTTATTTATTTATTTATTATATTATATTA-TTTAT
1 -TT-TTTATTTTTTTA-TTATT-TATT-TTTTACTTTAT
*
1154804 TTATTTATTTATTTATTATCTT-TATTTTTA-TTTA-
1 TT-TTTATTTTTTTATTAT-TTAT-TTTTTACTTTAT
*
1154838 -TTTTATTTTATTTATCA-TTA--TTTTA-TTTA-
1 TTTTTATTTT-TTTATTATTTATTTTTTACTTTAT
* *
1154867 TTTTTATTTACTTT-TT-TTTA-TCTTTACTTTA-
1 TTTTTATTT-TTTTATTATTTATTTTTTACTTTAT
*
1154898 TCTTTATTTTTTT
1 TTTTTATTTTTTT
1154911 CTCTTTATCT
Statistics
Matches: 320, Mismatches: 35, Indels: 87
0.72 0.08 0.20
Matches are distributed among these distances:
29 13 0.04
30 18 0.06
31 18 0.06
32 10 0.03
33 48 0.15
34 34 0.11
35 54 0.17
36 23 0.07
37 34 0.11
38 5 0.02
39 22 0.07
40 18 0.06
41 6 0.02
42 6 0.02
43 6 0.02
44 1 0.00
45 4 0.01
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTTTATTTTTTTATTATTTATTTTTTACTTTAT
Found at i:1154570 original size:22 final size:20
Alignment explanation
Indices: 1154525--1154940 Score: 160
Period size: 23 Copynumber: 20.1 Consensus size: 20
1154515 TTTTTCTTTT
*
1154525 TTTATTATTTATTTTTT-TC
1 TTTATTTTTTATTTTTTATC
1154544 TTTATTTTTTATTTTCTCTATC
1 TTTATTTTTTATTTT-T-TATC
*
1154566 TTTATTTTTT-TTATTT-TC
1 TTTATTTTTTATTTTTTATC
*
1154584 TTTATATTTATT-TTCTTTAT-
1 TTTAT-TTT-TTATTTTTTATC
*
1154604 TTTTTATTTTTATTTTCTTTATC
1 TTTAT-TTTTTA-TTT-TTTATC
1154627 TTTATTGTATTTATCTTATTTATC
1 TTTATT-T-TTTAT-TT-TTTATC
*
1154651 TTTATTTATTTTTTTTCTTTATC
1 TTTA-TT-TTTTATTT-TTTATC
* *
1154674 TATAATTTATTTATTTATTTATT
1 T-TTATTT-TTTATTT-TTTATC
1154697 TTTATTTTTT-TCTTCTTTA--
1 TTTATTTTTTAT-TT-TTTATC
*
1154716 TTTATTTATTTCCTTATATTTAT-
1 TTTATTT-TTT-ATT-T-TTTATC
1154739 TTTATTTCTTTATTTTTTTAT-
1 TTTATTT-TTTA-TTTTTTATC
*
1154760 TTTATTCTTGTTTATTTATTTATT
1 TTTA-T-TT-TTTATTT-TTTATC
* * *
1154784 TATTATATTATATTATTTA--
1 T-TTATTTTTTATTTTTTATC
*
1154803 TTTATTTATTTATTTATTATC
1 TTTATTT-TTTATTTTTTATC
1154824 TTTA-TTTTTATTTATTTTAT-
1 TTTATTTTTTA-TT-TTTTATC
* *
1154844 TTTATTTATCATTATTTTA--
1 TTTATTTTTTATT-TTTTATC
1154863 TTTA-TTTTTA---TTTA-C
1 TTTATTTTTTATTTTTTATC
*
1154878 TTT-TTTTTATCTTTACTTTATC
1 TTTATTTTT-TATTT--TTTATC
*
1154900 TTTATTTTTT-TCTCTTTATC
1 TTTATTTTTTAT-TTTTTATC
1154920 TTT-TTTTTTATTTCTTTATC
1 TTTATTTTTTATTT-TTTATC
1154940 T
1 T
1154941 CATTTTCTTT
Statistics
Matches: 315, Mismatches: 35, Indels: 93
0.71 0.08 0.21
Matches are distributed among these distances:
14 4 0.01
15 7 0.02
16 1 0.00
18 16 0.05
19 51 0.16
20 54 0.17
21 48 0.15
22 46 0.15
23 58 0.18
24 24 0.08
25 6 0.02
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTATTTTTTATC
Found at i:1154653 original size:52 final size:49
Alignment explanation
Indices: 1154482--1154887 Score: 254
Period size: 52 Copynumber: 8.0 Consensus size: 49
1154472 TATTCTTGTT
* *
1154482 TTTATTTATTTA-TTAT-ATTATTTTTACTATTATT-TTTTCTTT-TTTTA
1 TTTATTTATTTATTTATCTTTATTTTT--TATTTTTATTTTCTTTATTTTA
* *
1154529 -TTATTTATTT-TTT-TCTTTATTTTTTATTTTCTCTATCTTTATTTTTTTTA
1 TTTATTTATTTATTTATCTTTATTTTTTA-TTT-T-TAT-TTTCTTTATTTTA
*
1154579 TTTTCTTTATATTTATTT-TCTTTATTTTTTATTTTTATTTTCTTTATCTTTA
1 -TTT-ATT-TATTTATTTATCTTTATTTTTTATTTTTATTTTCTTTAT-TTTA
*
1154631 TTGTATTTATCTTATTTATCTTTA---TTTA-TTTT-TTTTCTTTATCTATAA
1 TT-TATTTAT-TTATTTATCTTTATTTTTTATTTTTATTTTCTTTAT-T-TTA
* * * **
1154679 TTTATTTATTTATTTATTTTTATTTTTTTCTTCTTTA-TTTATTTATTTCC
1 TTTATTTATTTATTTATCTTTA-TTTTTTATT-TTTATTTTCTTTATTTTA
*
1154729 TTATATTTATTT-TATT-TCTTTATTTTTT-TATTTTATTCTTGTTTA-TTTA
1 TT-TATTTATTTAT-TTATCTTTATTTTTTAT-TTTTATT-TTCTTTATTTTA
* *
1154778 TTTATTTATTATATTATATTATTTATTTATTTATTTATTTATTATCTTTATTTTTA
1 TTTATTTATT-TATT-TA-TCTTTATTT-TTTA-TT-TTTATTTTCTTTA-TTTTA
* * *
1154834 TTTATTTTATTTTATTTATCATTATTTTATTTATTTTTATTTACTTTTTTTTA
1 TTTA-TTTA-TTTATTTATCTTTA-TTT-TTTATTTTTATTTTCTTTATTTTA
1154887 T
1 T
1154888 CTTTACTTTA
Statistics
Matches: 290, Mismatches: 25, Indels: 82
0.73 0.06 0.21
Matches are distributed among these distances:
44 2 0.01
45 3 0.01
46 33 0.11
47 20 0.07
48 22 0.08
49 24 0.08
50 28 0.10
51 30 0.10
52 35 0.12
53 12 0.04
54 24 0.08
55 29 0.10
56 18 0.06
57 8 0.03
58 2 0.01
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (49 bp):
TTTATTTATTTATTTATCTTTATTTTTTATTTTTATTTTCTTTATTTTA
Found at i:1154800 original size:56 final size:55
Alignment explanation
Indices: 1154482--1154938 Score: 257
Period size: 58 Copynumber: 8.1 Consensus size: 55
1154472 TATTCTTGTT
* *
1154482 TTTATTTATTTATTATATTATTTTTACTATTATTT-TTTCTTTTTTTATTATTTATTTT-
1 TTTATTTATTTATT-TATTA-TATTA-TATTATTTCTTTATTTTTTTA-T-TTTATTTTC
* * * * *
1154540 TTTCTTTATTT-TTTATTTTCTCTATCTTTATTTTTTTTATTTTCTTTATATTTATTTTC
1 TTTATTTATTTATTTATTATAT-TAT-ATTA-TTTCTTTATTTT-TTTAT-TTTATTTTC
* * * *
1154599 TTTATTT-TTTATTT-TTAT-TT-TCTT-TATCTTTATTGTATTTATCTTATTTATC
1 TTTATTTATTTATTTATTATATTATATTATTTCTTTATT-TTTTTATTTTATTT-TC
* * * *
1154651 TTTATTTATTT-TTTTTCTTTATCTATAATTTATTTATTTATTTATTTTTATTTTTTTCTTC
1 TTTATTTATTTATTTAT-TATAT-TAT-A-TTATTTCTTTA-TT-TTTTTATTTTATT-TTC
* * *
1154712 TTTATTTATTTATTTCCTTATATTTATTTTATTTCTTTATTTTTTTATTTTATTCTTG
1 TTTATTTATTTATTT-ATTATA-TTATATTATTTCTTTATTTTTTTATTTTATT-TTC
* * *
1154770 TTTATTTATTTATTTATTATATTATATTATTTATTTATTTATTTA-TTTATTATC
1 TTTATTTATTTATTTATTATATTATATTATTTCTTTATTTTTTTATTTTATTTTC
* * * * *
1154824 TTTA-TT-TTTATTTATTTTATTTTATT-TATCATTATTTTATTTATTTTTATTTAC
1 TTTATTTATTTATTTATTATATTATATTATTTCTTTATTTT-TTTA-TTTTATTTTC
* * *
1154878 TTTTTTTTATCTTTACTTTATCTTTATT-T-TT-TTCTCTTTATCTTTTT-TTTTA-TTTC
1 -TTTATTTA--TTTA-TTTAT-TATATTATATTATT-TCTTTATTTTTTTATTTTATTTTC
1154934 TTTAT
1 TTTAT
1154939 CTCATTTTCT
Statistics
Matches: 319, Mismatches: 46, Indels: 71
0.73 0.11 0.16
Matches are distributed among these distances:
51 14 0.04
52 47 0.15
53 7 0.02
54 16 0.05
55 18 0.06
56 37 0.12
57 17 0.05
58 63 0.20
59 27 0.08
60 30 0.09
61 31 0.10
62 10 0.03
63 2 0.01
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (55 bp):
TTTATTTATTTATTTATTATATTATATTATTTCTTTATTTTTTTATTTTATTTTC
Found at i:1154876 original size:4 final size:4
Alignment explanation
Indices: 1154482--1154869 Score: 180
Period size: 4 Copynumber: 93.8 Consensus size: 4
1154472 TATTCTTGTT
* * *
1154482 TTTA TTTA TTTA TTATA TTATT TTTA CTATTA TTT- TTTC TTTT TTTA
1 TTTA TTTA TTTA TT-TA TT-TA TTTA -T-TTA TTTA TTTA TTTA TTTA
* * * * * * *
1154529 -TTA TTTA TTTT TTTC TTTA TTT- TTTA TTT- TCTC TATC TTTA TTTTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
* * *
1154575 TTTA TTT- TCTT- TATA TTTA TTTTC TTTA TTT- TTTA -TT- TTTA TTTTC
1 TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
* *
1154621 TTTA TCTTTA TTGTA TTTA TCTTA TTTA TCTTTA TTTA TTTTT TTTC TTTA
1 TTTA --TTTA TT-TA TTTA T-TTA TTTA --TTTA TTTA -TTTA TTTA TTTA
* * *
1154672 TCTA -TAA TTTA TTTA TTTA TTTA -TT- TTTA TTT- TTT- TCTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
* * *
1154716 TTTA TTTA TTTCC TTATA TTTA TTTTA TTTC TTTA TTTT TTTA TTTTA
1 TTTA TTTA TTT-A TT-TA TTTA -TTTA TTTA TTTA TTTA TTTA -TTTA
*
1154764 TTCTTG TTTA TTTA TTTA TTTA -TTA TATTA TATTA TTTA TTTA TTTA
1 -T-TTA TTTA TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA TTTA
*
1154811 TTTA TTTA TTATC TTTA -TT- TTTA TTTA TTTTA TTTTA TTTA TCATTA
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA T--TTA
1154858 TTTTA TTTA TTT
1 -TTTA TTTA TTT
1154870 TTATTTACTT
Statistics
Matches: 306, Mismatches: 37, Indels: 82
0.72 0.09 0.19
Matches are distributed among these distances:
3 36 0.12
4 182 0.59
5 70 0.23
6 17 0.06
7 1 0.00
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1154897 original size:11 final size:10
Alignment explanation
Indices: 1154562--1154906 Score: 122
Period size: 9 Copynumber: 37.1 Consensus size: 10
1154552 TTATTTTCTC
1154562 TATCTTTATT
1 TATCTTTATT
*
1154572 T-TTTTTATT
1 TATCTTTATT
1154581 T-TCTTTATATT
1 TATC-TT-TATT
*
1154592 TAT-TTTCTT
1 TATCTTTATT
1154601 TA--TTT-TT
1 TATCTTTATT
*
1154608 TATTTTTATT
1 TATCTTTATT
1154618 T-TCTTTATCTT
1 TATCTTTA--TT
*
1154629 TAT-TGTATT
1 TATCTTTATT
1154638 TATC-TTATT
1 TATCTTTATT
1154647 TATCTTTATT
1 TATCTTTATT
1154657 TAT-TTT-TT
1 TATCTTTATT
*
1154665 T-TCTTTATC
1 TATCTTTATT
*
1154674 TATAATTTATT
1 TAT-CTTTATT
1154685 TA--TTTATT
1 TATCTTTATT
*
1154693 TATTTTTA-T
1 TATCTTTATT
*
1154702 T-T-TTT-TC
1 TATCTTTATT
1154709 T-TCTTTATT
1 TATCTTTATT
1154718 TA--TTTATT
1 TATCTTTATT
*
1154726 T-CCTTATATT
1 TATCTT-TATT
1154736 TAT-TTTA-T
1 TATCTTTATT
1154744 T-TCTTTATT
1 TATCTTTATT
1154753 T-T-TTTATTT
1 TATCTTTA-TT
*
1154762 TAT-TCTTGTT
1 TATCT-TTATT
1154772 TA--TTTATT
1 TATCTTTATT
*
1154780 TATTTATTATAT
1 TATCT-TTAT-T
*
1154792 TAT-ATTATT
1 TATCTTTATT
1154801 TA--TTTATT
1 TATCTTTATT
1154809 TA--TTTATT
1 TATCTTTATT
* *
1154817 TAT-TATCTT
1 TATCTTTATT
*
1154826 TATTTTTATT
1 TATCTTTATT
1154836 TAT-TTTATT
1 TATCTTTATT
*
1154845 T-TATTTATCAT
1 TATCTTTAT--T
1154856 TAT-TTTATT
1 TATCTTTATT
*
1154865 TATTTTTATT
1 TATCTTTATT
*
1154875 TA-CTTTTTTT
1 TATC-TTTATT
1154885 TATCTTTACTT
1 TATCTTTA-TT
1154896 TATCTTTATT
1 TATCTTTATT
1154906 T
1 T
1154907 TTTTCTCTTT
Statistics
Matches: 268, Mismatches: 23, Indels: 88
0.71 0.06 0.23
Matches are distributed among these distances:
7 11 0.04
8 60 0.22
9 81 0.30
10 67 0.25
11 42 0.16
12 7 0.03
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (10 bp):
TATCTTTATT
Found at i:1154904 original size:31 final size:30
Alignment explanation
Indices: 1154566--1154922 Score: 104
Period size: 29 Copynumber: 12.0 Consensus size: 30
1154556 TTTCTCTATC
*
1154566 TTTAT-TTT-TTTTATTT-TCTTTATATTTA
1 TTTATCTTTATTTT-TTTCTCTTTATCTTTA
*
1154594 TTT-TCTTTATTTTTTAT-T-TTTAT-TTTC
1 TTTATCTTTATTTTTT-TCTCTTTATCTTTA
*
1154621 TTTATCTTTATTGTATTTATCTTATTTATCTTTA
1 TTTATCTTTATT-T-TTT-TC-TCTTTATCTTTA
* *
1154655 TTTAT-TTTTTTTCTTTATCTATAATTTAT-TTATTTA
1 TTTATCTTTATTT-TTT-TC--T-CTTTATCTT-T--A
*
1154691 TTTATTTTTATTTTTTTCTTCTTTA--TTTA
1 TTTATCTTTATTTTTTTC-TCTTTATCTTTA
* *
1154720 TTTATTTCCTTATATTTATTT-T-ATT-TCTTTA
1 TTTA--T-CTT-TATTTTTTTCTCTTTATCTTTA
* *
1154751 TTT-T-TTTATTTTATTCT-TGTT-TATTTA
1 TTTATCTTTATTTTTTTCTCT-TTATCTTTA
* * * *
1154778 TTTATTTATTATATTATAT-TATTTA--TTTA
1 TTTATCT-TTAT-TTTTTTCTCTTTATCTTTA
* * *
1154807 TTTA--TTTA-TTTATTATCTTTATTTTTA
1 TTTATCTTTATTTTTTTCTCTTTATCTTTA
* *
1154834 TTTAT-TTTATTTTATTTATCATTAT-TTTA
1 TTTATCTTTATTTT-TTTCTCTTTATCTTTA
*
1154863 TTTATTTTTATTTACTTTT-T-TTTATCTTTA
1 TTTATCTTTATTT--TTTTCTCTTTATCTTTA
1154893 CTTTATCTTTATTTTTTTCTCTTTATCTTT
1 -TTTATCTTTATTTTTTTCTCTTTATCTTT
1154923 TTTTTTATTT
Statistics
Matches: 260, Mismatches: 26, Indels: 83
0.70 0.07 0.22
Matches are distributed among these distances:
24 3 0.01
25 12 0.05
26 6 0.02
27 26 0.10
28 27 0.10
29 41 0.16
30 36 0.14
31 38 0.15
32 13 0.05
33 25 0.10
34 16 0.06
35 2 0.01
36 9 0.03
37 6 0.02
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTATCTTTATTTTTTTCTCTTTATCTTTA
Found at i:1154946 original size:20 final size:19
Alignment explanation
Indices: 1154649--1154946 Score: 69
Period size: 20 Copynumber: 14.8 Consensus size: 19
1154639 ATCTTATTTA
1154649 TCTTTAT-TTATTTTTTT-
1 TCTTTATCTTATTTTTTTC
*
1154666 TCTTTATCTATAATTTATTTATT
1 TCTTTATCT-T-ATTT-TTT-TC
* *
1154689 TATTTATTTTTATTTTTTTC
1 TCTTTA-TCTTATTTTTTTC
*
1154709 TTCTTTAT-TTATTTATTTC
1 -TCTTTATCTTATTTTTTTC
1154728 -CTTATAT-TTATTTTATTTC
1 TCTT-TATCTTATTTT-TTTC
* * * *
1154747 TTTATTTTTTTATTTTATTC
1 TCT-TTATCTTATTTTTTTC
*
1154767 TTGTTTAT-TTATTTATTTAT-
1 -TCTTTATCTTATTT-TTT-TC
* * *
1154787 TATATTATATTATTTATTTATT
1 TCT-TTATCTTATTT-TTT-TC
* * *
1154809 TATTTAT-TTATTATCTTTA
1 TCTTTATCTTATT-TTTTTC
*
1154828 TTTTTAT-TTATTTTATTT-
1 TCTTTATCTTATTTT-TTTC
* *
1154846 TATTTATCATTATTTTATTTA
1 TCTTTATC-TTATTTT-TTTC
*
1154867 TTTTTAT-TTACTTTTTTTTATC
1 TCTTTATCTTA---TTTTTT-TC
1154889 TTTACTTTATCTTTATTTTTTTC
1 --T-CTTTATC-TTATTTTTTTC
* *
1154912 TCTTTATCTTTTTTTTTATT
1 TCTTTATCTTATTTTTT-TC
*
1154932 TCTTTATCTCATTTT
1 TCTTTATCTTATTTT
1154947 CTTTAATTCA
Statistics
Matches: 222, Mismatches: 25, Indels: 65
0.71 0.08 0.21
Matches are distributed among these distances:
17 10 0.05
18 17 0.08
19 49 0.22
20 60 0.27
21 48 0.22
22 13 0.06
23 8 0.04
24 9 0.04
25 5 0.02
27 3 0.01
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TCTTTATCTTATTTTTTTC
Found at i:1155891 original size:60 final size:60
Alignment explanation
Indices: 1155827--1155939 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1155817 GTCCCCTGGT
***
1155827 TATAGGGCATTACTTTATTAAG-TCTCTCGATTGTTAAAAGTTACAAAATGATCCTTCGAC
1 TATAGGGCATTACTTTATTAAGTTCTC-CGACAATTAAAAGTTACAAAATGATCCTTCGAC
* * * *
1155887 TATAGGGCGTTGCTTTATTGAGTTCTCCGACAATTAAAAGTTATAAAATGATC
1 TATAGGGCATTACTTTATTAAGTTCTCCGACAATTAAAAGTTACAAAATGATC
1155940 ATTTGATTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 41 0.91
61 4 0.09
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (60 bp):
TATAGGGCATTACTTTATTAAGTTCTCCGACAATTAAAAGTTACAAAATGATCCTTCGAC
Found at i:1159836 original size:2 final size:2
Alignment explanation
Indices: 1159831--1159860 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1159821 ATCACACATC
1159831 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
1159861 TACATACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1160039 original size:28 final size:28
Alignment explanation
Indices: 1159999--1160077 Score: 149
Period size: 28 Copynumber: 2.8 Consensus size: 28
1159989 GTGTAGAATT
*
1159999 TGTCCCGAAGGACCACATAGAACACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
1160027 TGTCCCGAAGGACCACGTAGAACACATA
1 TGTCCCGAAGGACCACGTAGAACACATA
1160055 TGTCCCGAAGGACCACGTAGAAC
1 TGTCCCGAAGGACCACGTAGAAC
1160078 CCTCGACTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (28 bp):
TGTCCCGAAGGACCACGTAGAACACATA
Found at i:1175250 original size:18 final size:18
Alignment explanation
Indices: 1175227--1175278 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
1175217 GCGTAGAATT
1175227 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1175245 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1175263 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
1175279 ATAGAACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1175335 original size:28 final size:28
Alignment explanation
Indices: 1175261--1175341 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
1175251 GAAGGACCAC
*
1175261 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
* *
1175289 TATGTCCTGAAGGACCACGTATAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
1175317 TATGTCCCGAAGGACCACGCAGAAC
1 TATGTCCCGAAGGACCACGTAGAAC
1175342 CCTCGACTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACGTAGAACACA
Found at i:1177207 original size:23 final size:22
Alignment explanation
Indices: 1177162--1177215 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1177152 ATACATATAC
*
1177162 ATATCTTTTCATTATCATCATT
1 ATATCATTTCATTATCATCATT
1177184 AATATCATTTCATTATCA-CTATT
1 -ATATCATTTCATTATCATC-ATT
1177207 ATATTCATT
1 ATA-TCATT
1177216 CATATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATCATTTCATTATCATCATT
Found at i:1177552 original size:21 final size:21
Alignment explanation
Indices: 1177474--1177552 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
1177464 CATAGAAATA
* *
1177474 TCCCGAAGGACCAAATATATG
1 TCCCGAATGACCACATATATG
1177495 TCCCGAATGACCACACATATATG
1 TCCCGAATGA-C-CACATATATG
* *
1177518 TCCCGAATGGCCACATAGATG
1 TCCCGAATGACCACATATATG
1177539 TCCCGAATGACCAC
1 TCCCGAATGACCAC
1177553 TCCTTAAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 31 0.61
22 2 0.04
23 18 0.35
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (21 bp):
TCCCGAATGACCACATATATG
Found at i:1177652 original size:21 final size:21
Alignment explanation
Indices: 1177558--1177653 Score: 57
Period size: 21 Copynumber: 4.6 Consensus size: 21
1177548 ACCACTCCTT
* **
1177558 AAGGATCACATATATATTTCA
1 AAGGACCACATATATATCCCA
* * * * *
1177579 AAGGACAAAATATGTGTCCCG
1 AAGGACCACATATATATCCCA
* * * *
1177600 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATCCCA
** *
1177621 AAGGATTACATATATATCCCG
1 AAGGACCACATATATATCCCA
1177642 AAGGACCACATA
1 AAGGACCACATA
1177654 GAACCCTCGA
Statistics
Matches: 51, Mismatches: 24, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATATCCCA
Found at i:1184550 original size:10 final size:10
Alignment explanation
Indices: 1184528--1184561 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1184518 TCAAACACAC
*
1184528 CAAATCCTTT
1 CAAATCCTCT
*
1184538 CAAATGCTCT
1 CAAATCCTCT
1184548 CAAATCCTCT
1 CAAATCCTCT
1184558 CAAA
1 CAAA
1184562 CCATATCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:1184841 original size:39 final size:37
Alignment explanation
Indices: 1184771--1184843 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 37
1184761 TTACTGACAC
*
1184771 GGTAATATTTTTAAATTATTTTTTAATTTTAATTATT
1 GGTAATATTTTTAAATTATTTTTTAAGTTTAATTATT
*
1184808 GGTAATATTTTGTTTAATTATTTATTT-AGTTTAATT
1 GGTAATA-TTT-TTAAATTATTT-TTTAAGTTTAATT
1184844 TATATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 7 0.23
38 3 0.10
39 18 0.58
40 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (37 bp):
GGTAATATTTTTAAATTATTTTTTAAGTTTAATTATT
Found at i:1186893 original size:35 final size:35
Alignment explanation
Indices: 1186820--1186894 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1186810 CGTCACTAAC
**
1186820 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1186855 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1186890 AGTAA
1 AGTAA
1186895 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1186999 original size:24 final size:24
Alignment explanation
Indices: 1186972--1187046 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1186962 CATAATTCAA
*
1186972 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
1186996 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
1187020 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
1187043 GTCA
1 GTCA
1187047 GGATCATAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1187052 original size:23 final size:23
Alignment explanation
Indices: 1186976--1187052 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1186966 ATTCAAGTCA
*
1186976 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
1186999 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
1187023 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
1187046 AGGATCA
1 AGTATCA
1187053 TAACATAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:1188227 original size:18 final size:18
Alignment explanation
Indices: 1188206--1188246 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1188196 CTTCCATCCG
*
1188206 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1188224 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
1188242 GTCTT
1 ATCTT
1188247 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1189564 original size:7 final size:7
Alignment explanation
Indices: 1189552--1189590 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1189542 TGGTCAACTC
1189552 CGGTCAA
1 CGGTCAA
1189559 CGGTCAA
1 CGGTCAA
1189566 CGGTCAA
1 CGGTCAA
1189573 CGGGTCAA
1 C-GGTCAA
1189581 CGGTCAA
1 CGGTCAA
1189588 CGG
1 CGG
1189591 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:1189580 original size:15 final size:15
Alignment explanation
Indices: 1189552--1189606 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
1189542 TGGTCAACTC
1189552 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
1189566 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1189581 CGGTCAACGGGTC--
1 CGGTCAACGGGTCAA
*
1189594 GGGTCAACGGGTC
1 CGGTCAACGGGTC
1189607 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 12 0.31
14 8 0.21
15 19 0.49
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.15
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1189611 original size:18 final size:18
Alignment explanation
Indices: 1189588--1189651 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
1189578 CAACGGTCAA
1189588 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1189606 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1189624 CGGGTCGGGTCCACGGGT
1 CGGGTCGGGTCAACGGGT
1189642 CGGGTCGGGT
1 CGGGTCGGGT
1189652 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.08, C:0.23, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1189629 original size:13 final size:13
Alignment explanation
Indices: 1189567--1189611 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1189557 AACGGTCAAC
*
1189567 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1189582 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1189595 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1189608 GGTC
1 GGTC
1189612 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1191750 original size:35 final size:35
Alignment explanation
Indices: 1191677--1191751 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1191667 CGTCACTAAC
**
1191677 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1191712 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1191747 AGTAA
1 AGTAA
1191752 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1191856 original size:24 final size:24
Alignment explanation
Indices: 1191829--1191903 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1191819 CATAATTTAA
*
1191829 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
1191853 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
1191877 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
1191900 GTCA
1 GTCA
1191904 GGATCATAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1191909 original size:23 final size:23
Alignment explanation
Indices: 1191833--1191909 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1191823 ATTTAAGTCA
*
1191833 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
1191856 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
1191880 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
1191903 AGGATCA
1 AGTATCA
1191910 TAACATAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:1193085 original size:18 final size:18
Alignment explanation
Indices: 1193062--1193102 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1193052 CTTCCATCCG
*
1193062 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1193080 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
1193098 GTCTT
1 ATCTT
1193103 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1194419 original size:7 final size:7
Alignment explanation
Indices: 1194407--1194445 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1194397 TGGTCAACTC
1194407 CGGTCAA
1 CGGTCAA
1194414 CGGTCAA
1 CGGTCAA
1194421 CGGTCAA
1 CGGTCAA
1194428 CGGGTCAA
1 C-GGTCAA
1194436 CGGTCAA
1 CGGTCAA
1194443 CGG
1 CGG
1194446 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:1194435 original size:15 final size:15
Alignment explanation
Indices: 1194407--1194461 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
1194397 TGGTCAACTC
1194407 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
1194421 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1194436 CGGTCAACGGGTC--
1 CGGTCAACGGGTCAA
*
1194449 GGGTCAACGGGTC
1 CGGTCAACGGGTC
1194462 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 12 0.31
14 8 0.21
15 19 0.49
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.15
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1194466 original size:18 final size:18
Alignment explanation
Indices: 1194443--1194506 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
1194433 CAACGGTCAA
1194443 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1194461 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1194479 CGGGTCGGGTCCACGGGT
1 CGGGTCGGGTCAACGGGT
1194497 CGGGTCGGGT
1 CGGGTCGGGT
1194507 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.08, C:0.23, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1194484 original size:13 final size:13
Alignment explanation
Indices: 1194422--1194466 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1194412 AACGGTCAAC
*
1194422 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1194437 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1194450 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1194463 GGTC
1 GGTC
1194467 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1195361 original size:3 final size:3
Alignment explanation
Indices: 1195347--1195401 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
1195337 TATCTACTCC
* ** * *
1195347 TGA TGG TGA TGA TGA TGA TGA CAA TGG TGA TGA TAA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1195395 TGA TGA T
1 TGA TGA T
1195402 AAGAGTGAGG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1195375 original size:21 final size:21
Alignment explanation
Indices: 1195349--1195403 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1195339 TCTACTCCTG
*
1195349 ATGGTGATGATGATGATGACA
1 ATGGTGATGATAATGATGACA
**
1195370 ATGGTGATGATAATGATGATG
1 ATGGTGATGATAATGATGACA
*
1195391 ATGATGATGATAA
1 ATGGTGATGATAA
1195404 GAGTGAGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (21 bp):
ATGGTGATGATAATGATGACA
Found at i:1198260 original size:7 final size:7
Alignment explanation
Indices: 1198246--1198280 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
1198236 ACCCCCATTC
1198246 TTCTTCT
1 TTCTTCT
*
1198253 TCCTTCT
1 TTCTTCT
1198260 TTCTTCT
1 TTCTTCT
1198267 TTCTTCT
1 TTCTTCT
1198274 TTCTTCT
1 TTCTTCT
1198281 CTCACACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (7 bp):
TTCTTCT
Found at i:1198310 original size:42 final size:41
Alignment explanation
Indices: 1198261--1198359 Score: 150
Period size: 39 Copynumber: 2.5 Consensus size: 41
1198251 CTTCCTTCTT
*
1198261 TCTTCTTTCTTCTTTCTTCTCTCACACCCCCGTTAACCTCAC
1 TCTTCTTTCTTC-TTCTTCTCTCACACCCCCGTTAACCCCAC
*
1198303 TCTTCTTT-TTCTTC-TCTCTCACACCCCTGTTAACCCCAC
1 TCTTCTTTCTTCTTCTTCTCTCACACCCCCGTTAACCCCAC
1198342 TCTTC-TTCTTCTTCTTCT
1 TCTTCTTTCTTCTTCTTCT
1198360 TCTTCTTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
38 2 0.04
39 34 0.64
40 6 0.11
41 3 0.06
42 8 0.15
ACGTcount: A:0.10, C:0.41, G:0.02, T:0.46
Consensus pattern (41 bp):
TCTTCTTTCTTCTTCTTCTCTCACACCCCCGTTAACCCCAC
Found at i:1198350 original size:3 final size:3
Alignment explanation
Indices: 1198342--1198615 Score: 454
Period size: 3 Copynumber: 92.0 Consensus size: 3
1198332 TTAACCCCAC
1198342 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1198390 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1198438 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1198485 TCT TCT T-T CTCT TCT TCT TCT TCTT TCT TCT TC- TCT TC- TCT TCT
1 TCT TCT TCT -TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT
1198529 TCT TCT TC- TCT TCTT TCT TCT T-T CTCT TCTT TCT TCT TCT TC- TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT -TCT TC-T TCT TCT TCT TCT TCT
1198574 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1198616 ATTCTCCCGC
Statistics
Matches: 259, Mismatches: 0, Indels: 24
0.92 0.00 0.08
Matches are distributed among these distances:
2 12 0.05
3 236 0.91
4 11 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1199455 original size:3 final size:3
Alignment explanation
Indices: 1199441--1199501 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
1199431 GAGAATAGAT
* * * *
1199441 GAA GAT GAA GAA GAA GAA GAA GAA TAT GGA GAA GAAA GAA GGAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA -GAA GAA
*
1199488 TGAA GAA TAA GAA G
1 -GAA GAA GAA GAA G
1199502 TCTGGGGGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
3 36 0.80
4 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (3 bp):
GAA
Found at i:1199494 original size:21 final size:19
Alignment explanation
Indices: 1199441--1199501 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 19
1199431 GAGAATAGAT
1199441 GAAG-ATGAAGAAGAAGAA
1 GAAGAATGAAGAAGAAGAA
*
1199459 GAAGAATATGGAGAAGAAAGAA
1 GAAG-A-ATGAAGAAG-AAGAA
*
1199481 GGAAGAATGAAGAATAAGAA
1 -GAAGAATGAAGAAGAAGAA
1199501 G
1 G
1199502 TCTGGGGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 5 0.14
21 15 0.43
22 6 0.17
23 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (19 bp):
GAAGAATGAAGAAGAAGAA
Found at i:1209328 original size:2 final size:2
Alignment explanation
Indices: 1209321--1209395 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
1209311 TCTTATAAAT
1209321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1209362 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1209396 TAATTAGTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1210423 original size:30 final size:30
Alignment explanation
Indices: 1210360--1210574 Score: 111
Period size: 30 Copynumber: 7.2 Consensus size: 30
1210350 ATTTTACGGA
* *
1210360 TAAAATAGCAAAAATAGAAAGTTAAAGGAC
1 TAAAATAGCAAAAACAGAAACTTAAAGGAC
* * **
1210390 TAAAATAGCACAAACAGAAACTTTAAGTCC
1 TAAAATAGCAAAAACAGAAACTTAAAGGAC
* ** ** **
1210420 TAAAACAATAATTACA-AAATCTTAAAGGTT
1 TAAAATAGCAAAAACAGAAA-CTTAAAGGAC
** *
1210450 TAAAATAATAAAAACA-AATACTTAAGGGAC
1 TAAAATAGCAAAAACAGAA-ACTTAAAGGAC
* * *
1210480 T-AAATAGCAAAAATAGACATTTGAAA-GAC
1 TAAAATAGCAAAAACAGAAACTT-AAAGGAC
* *
1210509 --AAAT-GACAAAAAAACAGAAGCTAAAAGGAC
1 TAAAATAG-C--AAAAACAGAAACTTAAAGGAC
* * *
1210539 TAAAACACCAAAAACAGAAACTTAAAGGGC
1 TAAAATAGCAAAAACAGAAACTTAAAGGAC
1210569 TAAAAT
1 TAAAAT
1210575 GAAAATTACA
Statistics
Matches: 135, Mismatches: 39, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
27 1 0.01
28 5 0.04
29 23 0.17
30 101 0.75
31 1 0.01
32 4 0.03
ACGTcount: A:0.57, C:0.13, G:0.12, T:0.18
Consensus pattern (30 bp):
TAAAATAGCAAAAACAGAAACTTAAAGGAC
Found at i:1212394 original size:120 final size:120
Alignment explanation
Indices: 1212245--1212485 Score: 376
Period size: 120 Copynumber: 2.0 Consensus size: 120
1212235 TGTGAAGTTG
* *
1212245 AAATCCACACTTGTACATTGCATCTCTTTCGAGTTCAATATCTTTCACTGTGAAGTTGAAATTGA
1 AAATCCACACTTGTAAATTGCATCACTTTCGAGTTCAATATCTTTCACTGTGAAGTTGAAATTGA
* * * *
1212310 CTCTGAATGACACTGGTTTTTCATTGTTGTGTCACAGATGGCTCCTTCATCGTGA
66 CTCTGAATGAAACTGGTTTATCATTGTTGTGTCACAGATGACTCATTCATCGTGA
* **
1212365 AAATCCA-ATCTTGTAAATTGTATCACTTTCGAGTTCAATATCTTTCGTTGTGAAGTTGAAATTG
1 AAATCCACA-CTTGTAAATTGCATCACTTTCGAGTTCAATATCTTTCACTGTGAAGTTGAAATTG
*
1212429 ACTCTGAATGAAACTGGTTTATCATTGTTGTGTCACAGATGACTCATTCGTCGTGA
65 ACTCTGAATGAAACTGGTTTATCATTGTTGTGTCACAGATGACTCATTCATCGTGA
1212485 A
1 A
1212486 GTTGGGTCAA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 1 0.01
120 109 0.99
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (120 bp):
AAATCCACACTTGTAAATTGCATCACTTTCGAGTTCAATATCTTTCACTGTGAAGTTGAAATTGA
CTCTGAATGAAACTGGTTTATCATTGTTGTGTCACAGATGACTCATTCATCGTGA
Found at i:1212656 original size:69 final size:63
Alignment explanation
Indices: 1212568--1212741 Score: 199
Period size: 61 Copynumber: 2.7 Consensus size: 63
1212558 GTTGAGCTTC
* * * *
1212568 GAGTTAGATATCCTCTGTTGTGAAGTTGAAATCCAATCTCGAGTTGTAGTACTTTTCCAAATTGG
1 GAGTTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTC---TTGT-G--CTTTACCAAATTAG
1212633 ATTT
60 ATTT
*
1212637 GAGTTGGATATCCTTTGTTGTGAAGTTGAAATCCAA--TCTTGTGCTTTACCAAATTAGCTTT
1 GAGTTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTCTTGTGCTTTACCAAATTAGATTT
* * * *
1212698 GAGTTGAATATCCTTCGTTGTGAAGTTGAAATTCAATCTTTTGT
1 GAGTTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTCTTGT
1212742 AAGTTATGTC
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
61 48 0.51
63 6 0.06
64 4 0.04
67 2 0.02
69 34 0.36
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (63 bp):
GAGTTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTCTTGTGCTTTACCAAATTAGATTT
Found at i:1213945 original size:2 final size:2
Alignment explanation
Indices: 1213938--1213968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1213928 TGTATGTATG
1213938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1213969 TATTTTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1216390 original size:18 final size:17
Alignment explanation
Indices: 1216367--1216409 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1216357 ATATATACAT
1216367 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1216385 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1216402 ATAA-AATA
1 ATAATAATA
1216410 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1216816 original size:37 final size:37
Alignment explanation
Indices: 1216766--1216870 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1216756 GTGCTTGTGG
* * * *
1216766 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
1216803 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
1216840 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1216871 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1217717 original size:105 final size:106
Alignment explanation
Indices: 1217412--1217833 Score: 581
Period size: 105 Copynumber: 4.0 Consensus size: 106
1217402 AGCATTGTTC
* * **
1217412 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTGTTTGTTGAC
*
1217476 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
1217518 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAA-T-TTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACA
* * *
1217577 AGCAGCGGTCCCTTCGTTGTGGAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
1217618 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACA
* * * *
1217682 AGCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* * * * *
1217723 GGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACA
*
1217788 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
1217829 CGAGT
1 CGAGT
1217834 GTCACGATAT
Statistics
Matches: 283, Mismatches: 25, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
100 86 0.30
101 2 0.01
102 5 0.02
104 3 0.01
105 101 0.36
106 86 0.30
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
Found at i:1218080 original size:36 final size:36
Alignment explanation
Indices: 1218033--1218108 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1218023 TGTTTGGAGA
* * *
1218033 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
1218069 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
1218105 GAAA
1 GAAA
1218109 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:1218229 original size:106 final size:104
Alignment explanation
Indices: 1218008--1218327 Score: 488
Period size: 106 Copynumber: 3.1 Consensus size: 104
1217998 TTCGTTAAAT
* ** *
1218008 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
1218070 AAACTATCTCAAGCGAG-ATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAG-GAGAAAAAAATTCATTTCAAGGGAAA
1218109 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
1218174 AAACTATCTCAAGAGAGAAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAG-GAG-AAAAAAATTCATTTCAAGGGAAA
* *
1218215 TGTTTCCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAGAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
1218280 AAACTATCTC-AGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGGAGA-AAAAAATTCATTTCAAGGGAAA
1218319 TGTTTTCAA
1 TGTTTTCAA
1218328 GAGAAACTGT
Statistics
Matches: 201, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
101 46 0.23
103 4 0.02
104 56 0.28
105 2 0.01
106 93 0.46
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGGAGAAAAAAATTCATTTCAAGGGAAA
Found at i:1218303 original size:39 final size:39
Alignment explanation
Indices: 1218230--1218304 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1218220 CCAATGTTTA
* *
1218230 TGTTTCAAGAGAAACTGTCTCAAGGGAGAGAAAATTTTC
1 TGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTTC
* *
1218269 TGTTTCGAGGGAAACTATCTC-AGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGG-GAGAAAAAATT
1218305 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTTC
Found at i:1218495 original size:36 final size:36
Alignment explanation
Indices: 1218455--1218569 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
1218445 AACGGTCTCA
1218455 AGTGAGACAAATCTTGTTTTAAGAAAAACAATCTTG
1 AGTGAGACAAATCTTGTTTTAAGAAAAACAATCTTG
* * * * * **
1218491 AGTGAAATAAATCTTCTTTTGAGAAAAACAGTCTCA
1 AGTGAGACAAATCTTGTTTTAAGAAAAACAATCTTG
* *
1218527 AGTGAGACAAAGT-ATGTTTTAAAAAAAACAAAT-TTG
1 AGTGAGACAAA-TCTTGTTTTAAGAAAAAC-AATCTTG
1218563 AGTGAGA
1 AGTGAGA
1218570 TAATCATCTG
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
36 58 0.95
37 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (36 bp):
AGTGAGACAAATCTTGTTTTAAGAAAAACAATCTTG
Found at i:1218534 original size:72 final size:73
Alignment explanation
Indices: 1218398--1218572 Score: 205
Period size: 72 Copynumber: 2.4 Consensus size: 73
1218388 TAAAATCTTC
** * *
1218398 TTAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGTGAGAC
1 TTAAAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGAC
*
1218463 AAA-TCTTGTT
64 AAAGT-ATGTT
*
1218473 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTTGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAA-AAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGACA
1218536 AAGTATGTT
65 AAGTATGTT
*
1218545 TTAAAAAAAACAAAT-TTGAGTGAGATAA
1 TT-AAAAAAAC-AATCTTGAGTGAAATAA
1218573 TCATCTGCAT
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
72 46 0.52
73 16 0.18
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (73 bp):
TTAAAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGTGAGACAA
AGTATGTT
Found at i:1220022 original size:183 final size:183
Alignment explanation
Indices: 1219714--1220246 Score: 969
Period size: 183 Copynumber: 2.9 Consensus size: 183
1219704 GGTTTAACTA
* * *
1219714 AAGGGTTCATCTCATCACAAAGTCTTTGACTTGACAAAAACAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
1219779 AGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCC
66 AGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCC
1219843 TCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
130 TCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
*
1219897 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
*
1219962 AGTGTCCGAGCAGTGTCATAGTTTAAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
1220027 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
*
1220080 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTACCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1220145 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
1220210 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1220247 CGGATTTAAT
Statistics
Matches: 338, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 337 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:1224251 original size:23 final size:21
Alignment explanation
Indices: 1224209--1224262 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
1224199 TAAAATAAAT
*
1224209 AAAATAAATAAGTAAGATAAGG
1 AAAAAAAATAAGTAAGATAA-G
1224231 AAAAAAAAT-AGTAAGAAATAAG
1 AAAAAAAATAAGTAAG--ATAAG
1224253 ACAAAAAAAT
1 A-AAAAAAAT
1224263 GGGCCCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.21
22 10 0.36
23 12 0.43
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAAAATAAGTAAGATAAG
Found at i:1224632 original size:45 final size:47
Alignment explanation
Indices: 1224540--1224629 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 47
1224530 GATAATTACA
* ** *
1224540 ATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGAAAT
1 ATATATATATAGTAATAATAGAAATATAAGTAAAATAATAAAGAAAT
1224587 ATATATATATA-TAATAATA-AAATAT-AGTAAAA-AATAAATGAAA
1 ATATATATATAGTAATAATAGAAATATAAGTAAAATAATAAA-GAAA
1224630 ATAATTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
43 5 0.13
44 11 0.29
45 4 0.11
46 7 0.18
47 11 0.29
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (47 bp):
ATATATATATAGTAATAATAGAAATATAAGTAAAATAATAAAGAAAT
Found at i:1224697 original size:17 final size:19
Alignment explanation
Indices: 1224662--1224705 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
1224652 ATATATACAT
1224662 ATAATAATAAATAACATGA
1 ATAATAATAAATAACATGA
1224681 ATAATAA-AAATAA-ATGA
1 ATAATAATAAATAACATGA
1224698 ATAA-AATA
1 ATAATAATA
1224706 TCCATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 6 0.25
19 7 0.29
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
ATAATAATAAATAACATGA
Found at i:1225112 original size:37 final size:37
Alignment explanation
Indices: 1225062--1225166 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1225052 GTGCTTGTGG
* * * *
1225062 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
1225099 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
*
1225136 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1225167 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:1229928 original size:2 final size:2
Alignment explanation
Indices: 1229921--1229960 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1229911 AATTAATGTT
*
1229921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1229961 AAATTATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1235038 original size:51 final size:51
Alignment explanation
Indices: 1234972--1235085 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
1234962 CATCTGTAGC
* * * *
1234972 AGTAAAGCGCACCCTCTGCACCGCGTTATACGTTGATTTGGCGCCACGTGG
1 AGTATAGCGCGCCCTCTGCACCGCGATATACGGTGATTTGGCGCCACGTGG
* *
1235023 AGTATAGCGCGCCCTCTGCCCCGCGATATATGGTGATTTGGCGCCACGTGG
1 AGTATAGCGCGCCCTCTGCACCGCGATATACGGTGATTTGGCGCCACGTGG
1235074 -GTATAGCGCGCC
1 AGTATAGCGCGCC
1235086 TCTTGATCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 12 0.21
51 45 0.79
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.23
Consensus pattern (51 bp):
AGTATAGCGCGCCCTCTGCACCGCGATATACGGTGATTTGGCGCCACGTGG
Found at i:1235329 original size:17 final size:17
Alignment explanation
Indices: 1235289--1235332 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1235279 TTTTAATATT
1235289 ATATATTTAATTTATTTA
1 ATAT-TTTAATTTATTTA
*
1235307 AGTATTTTACTTTATTTA
1 A-TATTTTAATTTATTTA
1235325 ATATTTTA
1 ATATTTTA
1235333 GTAATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
ATATTTTAATTTATTTA
Found at i:1235600 original size:111 final size:111
Alignment explanation
Indices: 1235404--1235617 Score: 401
Period size: 111 Copynumber: 1.9 Consensus size: 111
1235394 ATATATATCT
*
1235404 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
1235469 TGATTTATTTAATGCGTGATTATTAAATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAAATTAAGAATTAAATATCTCG
1235515 ACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
1235580 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
1235618 TTTTTGTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (111 bp):
ACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAAATTAAGAATTAAATATCTCG
Found at i:1237732 original size:26 final size:24
Alignment explanation
Indices: 1237660--1237732 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1237650 TTATATTTGT
1237660 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
1237685 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1237708 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1237733 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1241243 original size:12 final size:12
Alignment explanation
Indices: 1241226--1241257 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
1241216 ATTTATAAGT
1241226 TGAGAGGAGAGA
1 TGAGAGGAGAGA
1241238 TGAGA-G-GAGA
1 TGAGAGGAGAGA
1241248 TGAGAGGAGA
1 TGAGAGGAGA
1241258 TGTGAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (12 bp):
TGAGAGGAGAGA
Found at i:1241249 original size:10 final size:10
Alignment explanation
Indices: 1241234--1241259 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1241224 GTTGAGAGGA
1241234 GAGATGAGAG
1 GAGATGAGAG
1241244 GAGATGAGAG
1 GAGATGAGAG
1241254 GAGATG
1 GAGATG
1241260 TGAGAAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (10 bp):
GAGATGAGAG
Found at i:1241263 original size:12 final size:11
Alignment explanation
Indices: 1241226--1241264 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1241216 ATTTATAAGT
1241226 TGAGAGGAGAG
1 TGAGAGGAGAG
1241237 ATGAGAGGAGA-
1 -TGAGAGGAGAG
1241248 TGAGAGGAGATG
1 TGAGAGGAGA-G
1241260 TGAGA
1 TGAGA
1241265 AACGTAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.49, T:0.13
Consensus pattern (11 bp):
TGAGAGGAGAG
Found at i:1242974 original size:41 final size:41
Alignment explanation
Indices: 1242921--1243003 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1242911 GTTTTTGGGA
*
1242921 AATTTTGTGGATATGCTTCAGTACAGTTGGGGATCTATGAT
1 AATTTTGAGGATATGCTTCAGTACAGTTGGGGATCTATGAT
1242962 AATTTTGAGGATATGCTTCAGTACAGTTGGGGATCTATGAT
1 AATTTTGAGGATATGCTTCAGTACAGTTGGGGATCTATGAT
1243003 A
1 A
1243004 TTGGTGTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (41 bp):
AATTTTGAGGATATGCTTCAGTACAGTTGGGGATCTATGAT
Found at i:1252621 original size:23 final size:22
Alignment explanation
Indices: 1252579--1252634 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
1252569 CCCAGAGGGA
1252579 ACCGATT-CCCCCCAAGGAGGT
1 ACCGATTCCCCCCCAAGGAGGT
*
1252600 ACCGATTCCCTCCCCAATGAGGT
1 ACCGATTCCC-CCCCAAGGAGGT
1252623 ACCGATTCCCCC
1 ACCGATTCCCCC
1252635 TGAATAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 7 0.22
22 4 0.12
23 21 0.66
ACGTcount: A:0.21, C:0.43, G:0.18, T:0.18
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGAGGT
Found at i:1253695 original size:18 final size:18
Alignment explanation
Indices: 1253672--1253708 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1253662 ATGCCAGAGT
1253672 TGATGTTAAATACGACTA
1 TGATGTTAAATACGACTA
*
1253690 TGATGTTAAATATGACTA
1 TGATGTTAAATACGACTA
1253708 T
1 T
1253709 TTGTCAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (18 bp):
TGATGTTAAATACGACTA
Found at i:1254225 original size:21 final size:21
Alignment explanation
Indices: 1254187--1254230 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1254177 TCGTTGGGGA
** *
1254187 TTAATGAGTATCGGTACTCCT
1 TTAATGAGTATAAGTACTACT
*
1254208 TTAATGAGTATAATTACTACT
1 TTAATGAGTATAAGTACTACT
1254229 TT
1 TT
1254231 TGTAATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
TTAATGAGTATAAGTACTACT
Found at i:1254662 original size:20 final size:20
Alignment explanation
Indices: 1254634--1254676 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1254624 TTTTCAAGTT
1254634 AAAACACATAAATTATTATA
1 AAAACACATAAATTATTATA
*
1254654 AAAATACATAAATTATTATA
1 AAAACACATAAATTATTATA
1254674 AAA
1 AAA
1254677 TAAAGTCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAACACATAAATTATTATA
Found at i:1257790 original size:18 final size:18
Alignment explanation
Indices: 1257769--1257896 Score: 76
Period size: 18 Copynumber: 7.4 Consensus size: 18
1257759 CCGACTTTAA
1257769 CTTTCTTCTCTTCTTTTT
1 CTTTCTTCTCTTCTTTTT
1257787 CTTTCTT-TC-TCTTTTT
1 CTTTCTTCTCTTCTTTTT
* *
1257803 -TCTTCTTCTTTTCTATTT
1 CT-TTCTTCTCTTCTTTTT
* * * *
1257821 -TATCTTCTTTTATTATTC
1 CTTTCTTCTCTTCTT-TTT
*
1257839 CTTT-TTCTTTTCTTTCTT
1 CTTTCTTCTCTTCTTT-TT
*
1257857 CTTTTTTCT-TTC-TTTT
1 CTTTCTTCTCTTCTTTTT
*
1257873 -TTCCTTCTCATT-TTTTT
1 CTTTCTTCTC-TTCTTTTT
1257890 CTTTCTT
1 CTTTCTT
1257897 ATCCCTGGTG
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
15 7 0.08
16 14 0.16
17 22 0.25
18 38 0.44
19 6 0.07
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (18 bp):
CTTTCTTCTCTTCTTTTT
Found at i:1257794 original size:10 final size:10
Alignment explanation
Indices: 1257769--1257873 Score: 55
Period size: 10 Copynumber: 10.6 Consensus size: 10
1257759 CCGACTTTAA
1257769 CTTTCTTCTCTT
1 CTTT-TTCT-TT
1257781 CTTTTTCTTT
1 CTTTTTCTTT
*
1257791 CTTTCTCTTT
1 CTTTTTCTTT
1257801 -TTTCTTC-TT
1 CTTT-TTCTTT
*
1257810 C-TTTTCTAT
1 CTTTTTCTTT
*
1257819 -TTTATC-TT
1 CTTTTTCTTT
1257827 CTTTTAT-TATT
1 CTTTT-TCT-TT
1257838 CCTTTTTCTTT
1 -CTTTTTCTTT
*
1257849 -TCTTTC-TT
1 CTTTTTCTTT
1257857 CTTTTTTCTTT
1 C-TTTTTCTTT
1257868 CTTTTT
1 CTTTTT
1257874 TCCTTCTCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
8 6 0.08
9 20 0.28
10 24 0.33
11 12 0.17
12 10 0.14
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:1257874 original size:30 final size:29
Alignment explanation
Indices: 1257778--1257880 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 29
1257768 ACTTTCTTCT
1257778 CTTC-TTTTTCTTTCTTTC-TC-TTTTTT
1 CTTCTTTTTTCTTTCTTTCTTCTTTTTTT
*
1257804 CTTCTTCTTTTCTATT-TTATCTTCTTTTATT
1 CTTCTT-TTTTCT-TTCTT-TCTTCTTTTTTT
* *
1257835 ATTCCTTTTTCTTTTCTTTCTTC-TTTTTT
1 CTTCTTTTTTC-TTTCTTTCTTCTTTTTTT
*
1257864 CTTTCTTTTTTCCTTCT
1 C-TTCTTTTTTCTTTCT
1257881 CATTTTTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 8 0.13
29 13 0.21
30 23 0.38
31 12 0.20
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (29 bp):
CTTCTTTTTTCTTTCTTTCTTCTTTTTTT
Found at i:1257890 original size:22 final size:22
Alignment explanation
Indices: 1257840--1257893 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1257830 TTATTATTCC
* *
1257840 TTTTTCTTTTCTTTCTTCTTTT
1 TTTTTCTTTTCTTCCTTCTATT
1257862 TTCTTTCTTTT-TTCCTTCTCATT
1 TT-TTTCTTTTCTTCCTTCT-ATT
1257885 TTTTTCTTT
1 TTTTTCTTT
1257894 CTTATCCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTCTTTTCTTCCTTCTATT
Found at i:1258137 original size:39 final size:40
Alignment explanation
Indices: 1258062--1258174 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
1258052 TGCAAGTATG
*
1258062 GGAGAGACGCATAGAGTGCAATGCGTC-TTCGAGGGG-AGA
1 GGAGAGACGCATAGAGTGCAATGCGTCTTTAG-GGGGAAGA
* * *
1258101 GGAGAGATGCATGGAGTGTAATGCGTCTTTAGGGGGAAGA
1 GGAGAGACGCATAGAGTGCAATGCGTCTTTAGGGGGAAGA
* *
1258141 GGA-ATGACGCATAGACTACAATGCGTCTTTAGGG
1 GGAGA-GACGCATAGAGTGCAATGCGTCTTTAGGG
1258175 TGCACTGTAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
39 29 0.47
40 33 0.53
ACGTcount: A:0.28, C:0.13, G:0.38, T:0.20
Consensus pattern (40 bp):
GGAGAGACGCATAGAGTGCAATGCGTCTTTAGGGGGAAGA
Found at i:1259493 original size:25 final size:25
Alignment explanation
Indices: 1259452--1259507 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1259442 TCAAAGTCTA
*
1259452 TCAACGGATGATCAACGTTCAATTG-
1 TCAACGGATGATCAACGGTCAA-TGC
*
1259477 TCAACGG-TCGATTAACGGTCAATGC
1 TCAACGGAT-GATCAACGGTCAATGC
1259502 TCAACG
1 TCAACG
1259508 ACTGATCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (25 bp):
TCAACGGATGATCAACGGTCAATGC
Found at i:1260301 original size:22 final size:22
Alignment explanation
Indices: 1260275--1260401 Score: 209
Period size: 22 Copynumber: 5.8 Consensus size: 22
1260265 AGTGAATATT
1260275 TGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
*
1260297 CGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
1260319 TGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
* *
1260341 TGTCCCGAATGACCATTGGATA
1 TGTCCCGAAGGACCACTGGATA
**
1260363 CATCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
1260385 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1260402 ATACCCTTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGGATA
Found at i:1261037 original size:65 final size:67
Alignment explanation
Indices: 1260949--1261093 Score: 156
Period size: 65 Copynumber: 2.2 Consensus size: 67
1260939 ACCCTGTCTG
* * *
1260949 GGGTATAGATACCCTGCCAACATTCTAGAAATTTTCATC-TTC-AG-GG-GGTATTGATACCCCC
1 GGGTATCGATACCATGCCAACATTCT-GAAATTTT--TCGTTCAAGAGGAGGTATCGATACCCCC
1261010 T-ATA
63 TCATA
** * *
1261014 GGGTATCGATACCATGCTGACATTCTGTAATTTTTCGTTCAAGAGGAGGTATCGATACCCCTTCA
1 GGGTATCGATACCATGCCAACATTCTGAAATTTTTCGTTCAAGAGGAGGTATCGATACCCCCTCA
1261079 TA
66 TA
*
1261081 TGGTATCGATACC
1 GGGTATCGATACC
1261094 CTATGACCAG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
62 2 0.03
63 3 0.04
64 9 0.13
65 24 0.36
66 14 0.21
67 15 0.22
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (67 bp):
GGGTATCGATACCATGCCAACATTCTGAAATTTTTCGTTCAAGAGGAGGTATCGATACCCCCTCA
TA
Found at i:1266792 original size:45 final size:47
Alignment explanation
Indices: 1266705--1266792 Score: 110
Period size: 45 Copynumber: 1.9 Consensus size: 47
1266695 GGAAAAATAA
** *
1266705 GCTTATGAGCTTATGGTATTAAATGGTAAATATATTGGTAAAAATGG
1 GCTTATGAGCTTATGGTAACAAATGGTAAATATATTGATAAAAATGG
*
1266752 GCTTA-GAGCTTATGG-AACAAATGGTAGAA-ATTTTGATAAAA
1 GCTTATGAGCTTATGGTAACAAATGGTA-AATATATTGATAAAA
1266793 TAAGCTTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 19 0.53
46 12 0.33
47 5 0.14
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (47 bp):
GCTTATGAGCTTATGGTAACAAATGGTAAATATATTGATAAAAATGG
Found at i:1267969 original size:27 final size:27
Alignment explanation
Indices: 1267939--1268000 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1267929 AAAATAGCCT
1267939 GATGCATCGATGCATGGCTTGTGCATC
1 GATGCATCGATGCATGGCTTGTGCATC
1267966 GATGCATCGATGCATGGCTTGTGCATC
1 GATGCATCGATGCATGGCTTGTGCATC
1267993 GATGCATC
1 GATGCATC
1268001 AAATGCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (27 bp):
GATGCATCGATGCATGGCTTGTGCATC
Found at i:1268053 original size:19 final size:19
Alignment explanation
Indices: 1268029--1268079 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1268019 GAAAATATTC
1268029 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1268048 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1268067 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1268080 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1268121 original size:65 final size:63
Alignment explanation
Indices: 1267966--1268130 Score: 160
Period size: 65 Copynumber: 2.6 Consensus size: 63
1267956 CTTGTGCATC
* * * *
1267966 GATGCATCGATGCATGGCTTG-TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA
1 GATGCATCGATGCATGAC-TGATGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCA
* *
1268030 GAGTGCATCGATGCATGGA--GAGTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATT
1 GA-TGCATCGATGCAT-GACTGA-TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATT
1268091 CA
62 CA
1268093 TTGATGCATCGATGCATGTACTGATGCATCGGTGCATG
1 --GATGCATCGATGCATG-ACTGATGCATCGGTGCATG
1268131 CCTTTAAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 19
0.77 0.05 0.17
Matches are distributed among these distances:
62 3 0.04
63 9 0.11
64 16 0.19
65 54 0.64
66 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCATGACTGATGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCA
Found at i:1268321 original size:20 final size:21
Alignment explanation
Indices: 1268298--1268337 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1268288 GAATCGAATA
1268298 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1268318 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1268338 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1275767 original size:19 final size:20
Alignment explanation
Indices: 1275737--1275774 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1275727 TTGAAAAATA
1275737 GCTTGATGCATCGATGCATG
1 GCTTGATGCATCGATGCATG
1275757 GCTTG-TGCATCGATGCAT
1 GCTTGATGCATCGATGCAT
1275775 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (20 bp):
GCTTGATGCATCGATGCATG
Found at i:1275799 original size:64 final size:65
Alignment explanation
Indices: 1275694--1275856 Score: 208
Period size: 65 Copynumber: 2.5 Consensus size: 65
1275684 CGGTGCACCA
1275694 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCTT-GA-TGCATCGATGCAT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATA--TTAGAGTGCATCGATGCAT
1275756 GG
64 GG
** *
1275758 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATT-AGAGTGCATCGATGCATG
1275822 G
65 G
* * * *
1275823 AGAGTGCATCGGTACATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1275857 CAATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.02
64 37 0.44
65 46 0.54
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATTAGAGTGCATCGATGCATGG
Found at i:1275828 original size:19 final size:19
Alignment explanation
Indices: 1275804--1275854 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1275794 GAAAATATTC
1275804 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
1275823 AGAGTGCATCGGTACATGG
1 AGAGTGCATCGATGCATGG
1275842 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1275855 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 18 0.67
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1275830 original size:65 final size:64
Alignment explanation
Indices: 1275673--1275856 Score: 203
Period size: 64 Copynumber: 2.9 Consensus size: 64
1275663 CCGTTGGAAC
* *** *
1275673 ACTTGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAAT
1 ACTTGATGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAT
*** *
1275736 AGCTTGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAAT
1 A-CTTGATGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAT
* * *
1275800 A-TTCAGAGTGCATCGATGCATGGAGAGTGCATCGGTACATGGAATGCATTCGATGTT
1 ACTT--GA-TGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1275857 CAATTAATTC
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 53 0.52
65 46 0.45
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
ACTTGATGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAT
Found at i:1276096 original size:20 final size:21
Alignment explanation
Indices: 1276073--1276112 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1276063 GAATCAAATA
1276073 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1276093 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1276113 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1276214 original size:30 final size:30
Alignment explanation
Indices: 1276180--1276237 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1276170 AAAATTACTG
1276180 TAGCAGTTACTGTAGCGTATCGATGCACTA
1 TAGCAGTTACTGTAGCGTATCGATGCACTA
1276210 TAGCAGTTACTGTAGCGTATCGATGCAC
1 TAGCAGTTACTGTAGCGTATCGATGCAC
1276238 AATATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (30 bp):
TAGCAGTTACTGTAGCGTATCGATGCACTA
Found at i:1279109 original size:22 final size:22
Alignment explanation
Indices: 1279081--1279185 Score: 165
Period size: 22 Copynumber: 4.8 Consensus size: 22
1279071 GAATGACCAC
*
1279081 TACGTCCCAAAGGACCACTGGA
1 TACGTCCCGAAGGACCACTGGA
1279103 TACGTCCCGAAGGACCACTGGA
1 TACGTCCCGAAGGACCACTGGA
* *
1279125 TATGTCCAGAAGGACCACTGGA
1 TACGTCCCGAAGGACCACTGGA
*
1279147 TACATCCCGAAGGACCACTGGA
1 TACGTCCCGAAGGACCACTGGA
*
1279169 TATGTCCCGAAGGACCA
1 TACGTCCCGAAGGACCA
1279186 TTATACCCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (22 bp):
TACGTCCCGAAGGACCACTGGA
Found at i:1281262 original size:19 final size:19
Alignment explanation
Indices: 1281238--1281278 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1281228 TGGGTAGGGT
*
1281238 TTTAATCTTTAAGAGGGAG
1 TTTAATCTTGAAGAGGGAG
1281257 TTTAATCTTGAAGAGGGAG
1 TTTAATCTTGAAGAGGGAG
1281276 TTT
1 TTT
1281279 GAGTGCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (19 bp):
TTTAATCTTGAAGAGGGAG
Found at i:1281670 original size:24 final size:25
Alignment explanation
Indices: 1281643--1281689 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1281633 TTTTATTATG
*
1281643 TATAATTATTAA-TATGATTATATT
1 TATAATGATTAATTATGATTATATT
1281667 TATAATGATTAATTATGATTATA
1 TATAATGATTAATTATGATTATA
1281690 ATATGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TATAATGATTAATTATGATTATATT
Found at i:1283197 original size:19 final size:19
Alignment explanation
Indices: 1283173--1283211 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1283163 TTGATACTTG
1283173 ACTCAAACAGCTCGTGAGC
1 ACTCAAACAGCTCGTGAGC
*
1283192 ACTCAAATAGCTCGTGAGC
1 ACTCAAACAGCTCGTGAGC
1283211 A
1 A
1283212 GCTCGAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (19 bp):
ACTCAAACAGCTCGTGAGC
Found at i:1295227 original size:21 final size:21
Alignment explanation
Indices: 1295190--1295229 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1295180 GTTGATTTGC
*
1295190 AGCAGGTGTATTTTGCTCAAA
1 AGCAGGTGTATTGTGCTCAAA
1295211 AGCAGGTTGTA-TGTGCTCA
1 AGCAGG-TGTATTGTGCTCA
1295230 CTAGGGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
AGCAGGTGTATTGTGCTCAAA
Found at i:1298278 original size:21 final size:21
Alignment explanation
Indices: 1298232--1298278 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1298222 TACTCTGCAG
1298232 AGAAAATATCCCCAAACGACT
1 AGAAAATATCCCCAAACGACT
*
1298253 A-AAAATCATCCCC-AACGGCT
1 AGAAAAT-ATCCCCAAACGACT
1298273 AGAAAA
1 AGAAAA
1298279 CGACCACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.49, C:0.28, G:0.11, T:0.13
Consensus pattern (21 bp):
AGAAAATATCCCCAAACGACT
Found at i:1303413 original size:2 final size:2
Alignment explanation
Indices: 1303408--1303432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1303398 GAGGAAGAGC
1303408 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1303433 GATCGATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1307431 original size:21 final size:22
Alignment explanation
Indices: 1307405--1307447 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1307395 ATAATCTCTT
*
1307405 GCATGTC-TGAACCTACAACAA
1 GCATGTCATCAACCTACAACAA
*
1307426 GCATGTCATCAACGTACAACAA
1 GCATGTCATCAACCTACAACAA
1307448 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (22 bp):
GCATGTCATCAACCTACAACAA
Found at i:1309917 original size:22 final size:21
Alignment explanation
Indices: 1309892--1309935 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1309882 ATTCAAATAG
*
1309892 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
1309914 GGGAATCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
1309935 G
1 G
1309936 TATTGCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:1310692 original size:24 final size:24
Alignment explanation
Indices: 1310665--1310730 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
1310655 AGCTCGTATA
1310665 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* *
1310689 AATTTGCACCGAAGTGCCGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
*
1310713 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
1310731 TATAAGATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:1311919 original size:15 final size:15
Alignment explanation
Indices: 1311895--1311928 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1311885 TAAAATCTTT
*
1311895 TTTTCACGTTCTTGA
1 TTTTCACGTTCTGGA
*
1311910 TTTTCCCGTTCTGGA
1 TTTTCACGTTCTGGA
1311925 TTTT
1 TTTT
1311929 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.21, G:0.15, T:0.56
Consensus pattern (15 bp):
TTTTCACGTTCTGGA
Found at i:1319083 original size:14 final size:14
Alignment explanation
Indices: 1319064--1319091 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1319054 AAGTGAAAGA
1319064 ATAGTTATATAATT
1 ATAGTTATATAATT
1319078 ATAGTTATATAATT
1 ATAGTTATATAATT
1319092 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1319419 original size:17 final size:17
Alignment explanation
Indices: 1319397--1319433 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1319387 GATAGCATGA
1319397 CCGGTTCGCTAACCGAT
1 CCGGTTCGCTAACCGAT
* *
1319414 CCGGTTCTCTAACCGGT
1 CCGGTTCGCTAACCGAT
1319431 CCG
1 CCG
1319434 ATTCTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.38, G:0.24, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGAT
Found at i:1319438 original size:17 final size:17
Alignment explanation
Indices: 1319405--1319438 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1319395 GACCGGTTCG
*
1319405 CTAACCGATCCGGTTCT
1 CTAACCGATCCGATTCT
*
1319422 CTAACCGGTCCGATTCT
1 CTAACCGATCCGATTCT
1319439 GAAAACCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (17 bp):
CTAACCGATCCGATTCT
Found at i:1320547 original size:35 final size:34
Alignment explanation
Indices: 1320470--1320549 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
1320460 ATATATACAT
* *
1320470 TAATAAATCAAGTCGAAAAGGCCATTATATGTTA
1 TAATAAATCAAGACGAAAAGACCATTATATGTTA
* * **
1320504 CAACAAATCAAGACGGGAAGACCATTGATATGTTA
1 TAATAAATCAAGACGAAAAGACCATT-ATATGTTA
1320539 TAATAAATCAA
1 TAATAAATCAA
1320550 ATCAAAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
34 20 0.54
35 17 0.46
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (34 bp):
TAATAAATCAAGACGAAAAGACCATTATATGTTA
Found at i:1321925 original size:40 final size:40
Alignment explanation
Indices: 1321870--1322401 Score: 469
Period size: 40 Copynumber: 13.1 Consensus size: 40
1321860 AAAAAGAAAT
1321870 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
*
1321910 AACTGATCAGAATATGATATAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
** * * ** * * * * ***** **
1321950 AACAAAAAATCGTTTCTCA-AGCATGTTGCTGCTTT-AGAAAGAAA
1 AAC--TGATTAGAATATGATA-TA-GTT--TGATTTCATTCCTATC
* * *
1321994 AACTGATTAAAATATGATATAGTTTGAATCCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
* *
1322034 AACTGATTAGAATATAATATAGTTTGATTTCATTACTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
*
1322074 AACTTATTAGAATATGATATAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
*
1322114 AACTTATTAGAATATGATATAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
* *
1322154 AACTTATTAGAATATGATATAGTTTGATTGCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
* *
1322194 AACTTATTAGAATATGATATAGTTTGATTGCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
* *
1322234 AACTGATCAGAATATTATATAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
** * * ** * * * * * *****
1322274 AACAAAAAATCGTTTCTCA-AGCATGTTGCTGCTTTAGAAAGAAAT-
1 AAC--TGATTAGAATATGATA-TA-GTT--TGATTT-CATTCCTATC
* *
1322319 AACTGATTAAAATATGATGTAGTTTGATTTCATTCCTATC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
*
1322359 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTAGC
1 AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
1322399 AAC
1 AAC
1322402 AAAAAAATTG
Statistics
Matches: 385, Mismatches: 90, Indels: 34
0.76 0.18 0.07
Matches are distributed among these distances:
39 6 0.02
40 319 0.83
41 5 0.01
42 21 0.05
43 13 0.03
44 5 0.01
45 13 0.03
46 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (40 bp):
AACTGATTAGAATATGATATAGTTTGATTTCATTCCTATC
Found at i:1322364 original size:125 final size:126
Alignment explanation
Indices: 1322194--1322440 Score: 406
Period size: 125 Copynumber: 2.0 Consensus size: 126
1322184 CATTCCTATC
* * *
1322194 AACTTATTAGAATATGATATAGTTTGATTGCATTCCTATCAACTGATCAGAATATTATATAGTTT
1 AACTGATTAAAATATGATATAGTTTGATTGCATTCCTATCAACTGATCAGAATATGATATAGTTT
* *
1322259 GATTTCATTCCTATCAAC-AAAAAATCGTTTCTCAAGCATGTTGCTGCTTTAGAAAGAAAT
66 GATTTCATTCCTAGCAACAAAAAAATCGTTTCTCAAGCATGTTGCTGCTTAAGAAAGAAAT
* * *
1322319 AACTGATTAAAATATGATGTAGTTTGATTTCATTCCTATCAACTGATTAGAATATGATATAGTTT
1 AACTGATTAAAATATGATATAGTTTGATTGCATTCCTATCAACTGATCAGAATATGATATAGTTT
*
1322384 GATTTCATTCCTAGCAACAAAAAAATTGTTTCTCAAGCATGTTGCTGCTTAAGAAAG
66 GATTTCATTCCTAGCAACAAAAAAATCGTTTCTCAAGCATGTTGCTGCTTAAGAAAG
1322441 CTTATTCAAA
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
125 76 0.68
126 36 0.32
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (126 bp):
AACTGATTAAAATATGATATAGTTTGATTGCATTCCTATCAACTGATCAGAATATGATATAGTTT
GATTTCATTCCTAGCAACAAAAAAATCGTTTCTCAAGCATGTTGCTGCTTAAGAAAGAAAT
Found at i:1327470 original size:2 final size:2
Alignment explanation
Indices: 1327465--1327523 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1327455 TTCAGTTTAA
1327465 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
1327507 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1327524 GTTGTTATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1332352 original size:2 final size:2
Alignment explanation
Indices: 1332345--1332371 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1332335 ATATGCAAAT
1332345 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1332372 GTAAACATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1334527 original size:20 final size:20
Alignment explanation
Indices: 1334489--1334528 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1334479 TTCCACGACA
**
1334489 TTAATTCTTTACATTTTCTT
1 TTAATTCTTTACACATTCTT
*
1334509 TTAATTCTTTTCACATTCTT
1 TTAATTCTTTACACATTCTT
1334529 GTCTACTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTCTTTACACATTCTT
Found at i:1335561 original size:26 final size:25
Alignment explanation
Indices: 1335523--1335575 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
1335513 ATTAATTTTT
*
1335523 TTTTTTTGAAAAAAACCTCACTTAA
1 TTTTTTTGAAAAAAACCTCACATAA
*
1335548 TTTTTTTGATAAAAAATCTCACATAA
1 TTTTTTTGA-AAAAAACCTCACATAA
1335574 TT
1 TT
1335576 AATAATATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (25 bp):
TTTTTTTGAAAAAAACCTCACATAA
Found at i:1340664 original size:22 final size:22
Alignment explanation
Indices: 1340612--1340664 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1340602 CACTGAGTGG
*
1340612 CATATGAGATTTGTCCCGAAGGA
1 CATATGA-ATATGTCCCGAAGGA
*
1340635 CATGTGAATATGTCCCGAAGGA
1 CATATGAATATGTCCCGAAGGA
*
1340657 CCTATGAA
1 CATATGAA
1340665 ACCCTCGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (22 bp):
CATATGAATATGTCCCGAAGGA
Found at i:1347472 original size:22 final size:22
Alignment explanation
Indices: 1347435--1347485 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1347425 CTGAGTGGCA
*
1347435 TATGAGATTTGTCCCGAAGGACC
1 TATGA-ATATGTCCCGAAGGACC
*
1347458 TGTGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
1347480 TATGAA
1 TATGAA
1347486 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGGACC
Found at i:1352282 original size:17 final size:16
Alignment explanation
Indices: 1352251--1352284 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1352241 AGACTTATAA
1352251 ATAATTTATTAATCAT
1 ATAATTTATTAATCAT
*
1352267 ATAATTATATTCATCAT
1 ATAATT-TATTAATCAT
1352284 A
1 A
1352285 GGAAGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTATTAATCAT
Found at i:1355705 original size:24 final size:24
Alignment explanation
Indices: 1355674--1355728 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1355664 GGGTGCGGAG
1355674 GCGG-CCTTTTATAAAGGGGTGGA
1 GCGGCCCTTTTATAAAGGGGTGGA
1355697 GCGGCCCTTTTATAAAGGGGTGGA
1 GCGGCCCTTTTATAAAGGGGTGGA
1355721 GCGGCCCT
1 GCGGCCCT
1355729 CTATTGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.18, C:0.20, G:0.38, T:0.24
Consensus pattern (24 bp):
GCGGCCCTTTTATAAAGGGGTGGA
Found at i:1357089 original size:40 final size:40
Alignment explanation
Indices: 1357045--1357129 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
1357035 TATTTTAGGG
* *
1357045 ACCAAAGATGAA-ATTCCCATGTGTACAAGTTTGGCCACCT
1 ACCAAAGATGAATATTCCAATGTGTACAAG-TTGGCCACCA
* *
1357085 ACCAAAGATGAATTTTTCAATGTGTACAAGTTGGCCACCA
1 ACCAAAGATGAATATTCCAATGTGTACAAGTTGGCCACCA
1357125 ACCAA
1 ACCAA
1357130 CTTGTCAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 26 0.65
41 14 0.35
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (40 bp):
ACCAAAGATGAATATTCCAATGTGTACAAGTTGGCCACCA
Found at i:1368105 original size:22 final size:21
Alignment explanation
Indices: 1368063--1368102 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1368053 GAGTTTGTTT
*
1368063 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1368084 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1368103 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:1370978 original size:20 final size:20
Alignment explanation
Indices: 1370953--1371103 Score: 109
Period size: 21 Copynumber: 7.8 Consensus size: 20
1370943 TCGAAATGGA
1370953 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCATG
* *
1370973 GTGCATCGATGCACTGTATG
1 GTGCATGGATGCACTGCATG
* **
1370993 GTGCATCGATGCA-TTAAT-
1 GTGCATGGATGCACTGCATG
** * * *
1371011 -TGCAT-TCT-AAATGGA--
1 GTGCATGGATGCACTGCATG
*
1371026 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCA-TG
*
1371047 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCATG
*
1371067 GCTGTATGGATGCACTGCAATG
1 G-TGCATGGATGCACTGC-ATG
1371089 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1371104 TTGACACCCT
Statistics
Matches: 105, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.01
16 8 0.08
17 6 0.06
18 4 0.04
19 3 0.03
20 34 0.32
21 46 0.44
22 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (20 bp):
GTGCATGGATGCACTGCATG
Done.