Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002809.1 Hibiscus syriacus cultivar Beakdansim tig00005778_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: 98300
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2956 original size:5 final size:5
Alignment explanation
Indices: 2946--3009 Score: 51
Period size: 5 Copynumber: 11.8 Consensus size: 5
2936 TAAATTGAAA
2946 AAAAG AAAAG AAAAAAG AAAAG AAAAAG AAAACAGG AAAAG AAAA- AAGAA-
1 AAAAG AAAAG --AAAAG AAAAG -AAAAG -AAA-A-G AAAAG AAAAG AA-AAG
2996 AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA
3010 TAAGGTGGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.08
5 28 0.54
6 10 0.19
7 9 0.17
8 1 0.02
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2961 original size:7 final size:7
Alignment explanation
Indices: 2942--3004 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
2932 ACCCTAAATT
2942 GAAAAAA
1 GAAAAAA
*
2949 -AGAAAA
1 GAAAAAA
2955 GAAAAAA
1 GAAAAAA
2962 G--AAAA
1 GAAAAAA
2967 G-AAAAA
1 GAAAAAA
*
2973 GAAAACA
1 GAAAAAA
*
2980 G-GAAAA
1 GAAAAAA
2986 GAAAAAA
1 GAAAAAA
2993 GAAAAAA
1 GAAAAAA
3000 GAAAA
1 GAAAA
3005 GAAAATAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 5 0.11
6 14 0.30
7 27 0.59
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:2961 original size:12 final size:12
Alignment explanation
Indices: 2944--3009 Score: 82
Period size: 12 Copynumber: 5.3 Consensus size: 12
2934 CCTAAATTGA
2944 AAAAAAGAAAAG
1 AAAAAAGAAAAG
2956 AAAAAAGAAAAG
1 AAAAAAGAAAAG
2968 -AAAAAGAAAACAGG
1 AAAAAAG-AAA-A-G
2982 AAAAGAA-AAAAG
1 AAAA-AAGAAAAG
2994 AAAAAAGAAAAG
1 AAAAAAGAAAAG
3006 AAAA
1 AAAA
3010 TAAGGTGGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
11 8 0.17
12 29 0.60
13 2 0.04
14 4 0.08
15 3 0.06
16 2 0.04
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:5605 original size:31 final size:30
Alignment explanation
Indices: 5564--5902 Score: 232
Period size: 31 Copynumber: 11.4 Consensus size: 30
5554 TATCTTATTT
*
5564 TCTTTCTTTCATTTATTTTTTATTTTCTTTA
1 TCTTTATTT-ATTTATTTTTTATTTTCTTTA
*
5595 TCTTTATTTCATTTGTTTTTTTATTGTT-TTTA
1 TCTTTATTT-ATTT-ATTTTTTATT-TTCTTTA
*
5627 TC-TTATTTTTTTATTTTTTTATTTTCTTTA
1 TCTTTATTTATTTA-TTTTTTATTTTCTTTA
* *
5657 -CCTTATTTTCTTTATTTTATT-TGTTT-TTTA
1 TCTTTA-TTTATTTATTTT-TTAT-TTTCTTTA
* *
5687 T-TTTCTTTATTTTATTTTTTATTTTTTTTA
1 TCTTTATTTA-TTTATTTTTTATTTTCTTTA
*
5717 TCTTTATTTATTTATTTATTTATTTTCTCTA
1 TCTTTATTTATTTATTT-TTTATTTTCTTTA
*
5748 TCTTTA--TCTTTATTTTTTATTTTC-TTA
1 TCTTTATTTATTTATTTTTTATTTTCTTTA
*
5775 T-TTTATTT-GTT-TTTTTTATTTTCTTTA
1 TCTTTATTTATTTATTTTTTATTTTCTTTA
* * *
5802 T-ATTACTTT-TTTA-TCTTTATTTTATTTA
1 TCTTTA-TTTATTTATTTTTTATTTTCTTTA
* * * *
5830 TTTTTATTTTTTTCTTTATCTT-TATTTCATTA
1 TCTTTATTTATTTATTT-T-TTAT-TTTCTTTA
*
5862 T-TTT-TTT-TTTATTTATCTTATTTTCTTCA
1 TCTTTATTTATTTATTT-T-TTATTTTCTTTA
5891 T-TTTATTTATTT
1 TCTTTATTTATTT
5903 TTATTACCTA
Statistics
Matches: 254, Mismatches: 26, Indels: 56
0.76 0.08 0.17
Matches are distributed among these distances:
26 16 0.06
27 12 0.05
28 32 0.13
29 46 0.18
30 59 0.23
31 63 0.25
32 24 0.09
33 2 0.01
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (30 bp):
TCTTTATTTATTTATTTTTTATTTTCTTTA
Found at i:5641 original size:61 final size:57
Alignment explanation
Indices: 5575--5904 Score: 257
Period size: 60 Copynumber: 5.6 Consensus size: 57
5565 CTTTCTTTCA
5575 TTTATTTTTTATTTTCTTTATCTTTATTTCATTTGTTTTTTTATTGTTTTTATCTTATTTT
1 TTTATTTTTTATTTTCTTTATCTTTATTT-ATTT-TTTTTTTATT-TTTTTATCTT-TTTT
* *
5636 TTTATTTTTTTATTTTCTTTA-CCTTATTT-TCTTTATTTTATT-TGTTTTTTATTTTCTTTAT
1 TTTA-TTTTTTATTTTCTTTATCTTTATTTAT-TTT-TTTT-TTAT-TTTTTTATCTT-TTT-T
* * * * *
5697 TTTATTTTTTATTTTTTTTATCTTTATTTATTTATTTATTTATTTTCTCTATCTTTATC
1 TTTATTTTTTATTTTCTTTATCTTTATTTATTT-TTTTTTTATTTT-TTTATCTTTTTT
* * *
5756 TTTATTTTTTATTTTC-TTAT-TTTA-TT-TGTTTTTTTTATTTTCTTTATATTACTTT
1 TTTATTTTTTATTTTCTTTATCTTTATTTATTTTTTTTTTATTTT-TTTATCTT-TTTT
* * * * **
5811 TTTA-TCTTTATTTTATTTATTTTTATTTTTTTCTTTATCTTTATTTCATTAT-TTTTTT
1 TTTATTTTTTATTTTCTTTATCTTTATTTATTT-TTT-T-TTTATTTTTTTATCTTTTTT
*
5869 TTTATTTATCTTATTTTCTTCAT-TTTATTTATTTTT
1 TTTATTT-T-TTATTTTCTTTATCTTTATTTATTTTT
5905 ATTACCTATT
Statistics
Matches: 219, Mismatches: 28, Indels: 46
0.75 0.10 0.16
Matches are distributed among these distances:
54 27 0.12
55 11 0.05
56 6 0.03
57 6 0.03
58 13 0.06
59 25 0.11
60 57 0.26
61 56 0.26
62 18 0.08
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (57 bp):
TTTATTTTTTATTTTCTTTATCTTTATTTATTTTTTTTTTATTTTTTTATCTTTTTT
Found at i:5643 original size:5 final size:5
Alignment explanation
Indices: 5545--5903 Score: 107
Period size: 5 Copynumber: 72.0 Consensus size: 5
5535 GTCCCTTCAC
* * * * * * *
5545 ATTTT AATTT ATCTT ATTTT -CTTT CTTTC ATTTAT TTTTT ATTTT -CTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT ATTTT ATTTT
* * * * *
5594 ATCTTT ATTTC ATTTGTT TTTTT ATTGT -TTTT ATCTT ATTTT TTTATT
1 AT-TTT ATTTT A-TT-TT ATTTT ATTTT ATTTT ATTTT ATTTT ATT-TT
* * ** * *
5642 TTTTT ATTTT -CTTT ACCTT ATTTT -CTTT ATTTT ATTTGT TTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT ATTTT
*
5691 -CTTT ATTTT ATTTTTT ATTTT -TTTT ATCTTT A-TTT A-TTT A-TTT
1 ATTTT ATTTT A--TTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT
* *
5734 A-TTT ATTTT -CTCT ATCTTT ATCTTT ATTTT -TTATT -TTCTT ATTTT
1 ATTTT ATTTT ATTTT AT-TTT AT-TTT ATTTT ATT-TT ATT-TT ATTTT
* *
5779 A-TTT GTTTT -TTTT ATTTT CTTTAT ATTACTT -TTTT ATCTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTT-T ATT--TT ATTTT AT-TTT ATTTT
* *
5825 A-TTT ATTTTT ATTTTT TTCTTT ATCTTT ATTTC ATTATT -TTTT -TTTT
1 ATTTT A-TTTT A-TTTT AT-TTT AT-TTT ATTTT ATT-TT ATTTT ATTTT
* * *
5872 A-TTT ATCTT ATTTT -CTTC ATTTT A-TTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
5904 TATTACCTAT
Statistics
Matches: 267, Mismatches: 51, Indels: 72
0.68 0.13 0.18
Matches are distributed among these distances:
4 71 0.27
5 121 0.45
6 67 0.25
7 7 0.03
8 1 0.00
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:5644 original size:9 final size:9
Alignment explanation
Indices: 5610--5904 Score: 123
Period size: 9 Copynumber: 30.4 Consensus size: 9
5600 ATTTCATTTG
5610 TTTTTTTAT
1 TTTTTTTAT
*
5619 TGTTTTTAT
1 TTTTTTTAT
*
5628 CTTATTTTTTT
1 -TT-TTTTTAT
5639 ATTTTTTTAT
1 -TTTTTTTAT
* *
5649 TTTCTTTACC
1 TTTTTTTA-T
* *
5659 TTATTTTCT
1 TTTTTTTAT
*
5668 TTATTTTATT
1 TTTTTTTA-T
5678 TGTTTTTTAT
1 T-TTTTTTAT
*
5688 TTTCTTTATTT
1 TTT-TTT-TAT
5699 TATTTTTTAT
1 T-TTTTTTAT
5709 TTTTTTTAT
1 TTTTTTTAT
*
5718 CTTTATTTATT
1 -TTTTTTTA-T
5729 TATTTATTTAT
1 T-TTT-TTTAT
* *
5740 TTTCTCTAT
1 TTTTTTTAT
5749 CTTTATCTTTA-
1 -TTT-T-TTTAT
5760 -TTTTTTA-
1 TTTTTTTAT
*
5767 TTTTCTTAT
1 TTTTTTTAT
* *
5776 TTTATTTGT
1 TTTTTTTAT
5785 TTTTTTTAT
1 TTTTTTTAT
5794 TTTCTTTATAT
1 TTT-TTT-TAT
5805 TACTTTTTTAT
1 T--TTTTTTAT
5816 CTTTATTTTAT
1 -TTT-TTTTAT
5827 TTATTTTTAT
1 TT-TTTTTAT
5837 TTTTTTCT-T
1 TTTTTT-TAT
* *
5846 TATCTTTAT
1 TTTTTTTAT
*
5855 TTCATTATT-T
1 TT--TTTTTAT
5865 TTTTTTTAT
1 TTTTTTTAT
* *
5874 TTATCTTAT
1 TTTTTTTAT
* *
5883 TTTCTTCAT
1 TTTTTTTAT
*
5892 TTTATTTAT
1 TTTTTTTAT
5901 TTTT
1 TTTT
5905 ATTACCTATT
Statistics
Matches: 215, Mismatches: 42, Indels: 58
0.68 0.13 0.18
Matches are distributed among these distances:
7 4 0.02
8 12 0.06
9 88 0.41
10 54 0.25
11 42 0.20
12 13 0.06
13 2 0.01
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:5740 original size:52 final size:50
Alignment explanation
Indices: 5574--5922 Score: 228
Period size: 52 Copynumber: 6.9 Consensus size: 50
5564 TCTTTCTTTC
*
5574 ATTTATTTTTTATTTTCTTTATCTTTATTTCATTT-GTTTTTTTATTGTT-TTT
1 ATTTATTTTTTATTTTCTTTAT-TTTATTT--TTTATTTTTTTTATT-TTATTT
* * *
5626 ATCTTATTTTTTTATTTT-TTTATTTTCTTTACCTTATTTTCTTTA---T-TTT
1 AT-TTA-TTTTTTATTTTCTTTATTTTATTT--TTTATTTTTTTTATTTTATTT
*
5675 ATTTGTTTTTTATTTTCTTTATTTTATTTTTTATTTTTTTTATCTTTATTT
1 ATTTATTTTTTATTTTCTTTATTTTATTTTTTATTTTTTTTAT-TTTATTT
* *
5726 ATTTATTTATTTATTTTCTCTATCTTTA-TCTTTATTTTTTATT-TTCTTATTTT
1 ATTTATTT-TTTATTTTCTTTAT-TTTATTTTTTATTTTTT-TTATT-TTA-TTT
* * *
5779 ATTTGTTTTTTTTATTTTCTTTATATTACTTTTTTA---TCTTTATTTTATTT
1 A-TT-TATTTTTTATTTTCTTTATTTTA-TTTTTTATTTTTTTTATTTTATTT
* *
5829 ATTT-TTATTT-TTTTCTTTATCTTTA--TTTCATTATTTTTT-TTTTATTT
1 ATTTATTTTTTATTTTCTTTAT-TTTATTTTTTATT-TTTTTTATTTTATTT
* ***
5876 ATCTTATTTTCTTCATTTTATTTATTTTTATTACCTATTTTTTTTAT
1 AT-TTATTTT-TT-ATTTTCTTTA-TTTTATTTTTTATTTTTTTTAT
5923 CTATTTTGAC
Statistics
Matches: 236, Mismatches: 28, Indels: 64
0.72 0.09 0.20
Matches are distributed among these distances:
44 4 0.02
46 21 0.09
47 29 0.12
48 20 0.08
49 11 0.05
50 7 0.03
51 16 0.07
52 54 0.23
53 35 0.15
54 30 0.13
55 9 0.04
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (50 bp):
ATTTATTTTTTATTTTCTTTATTTTATTTTTTATTTTTTTTATTTTATTT
Found at i:5793 original size:122 final size:123
Alignment explanation
Indices: 5545--5922 Score: 325
Period size: 122 Copynumber: 3.0 Consensus size: 123
5535 GTCCCTTCAC
* *
5545 ATTTTAATTTATCTTATTTTCTTTCTTTCA-TTTATTTTTTATTTTCTTTATCTTTATTTCATTT
1 ATTTT-ATTTATATTATTTT-TTTCTTT-ATTTTATTTTTTATTTTTTTTATCTTTATTTCATTT
* * * *
5609 GTTTTTTTATTGTTTTTATCTTATTTTTTTATTTTTTTATTTTCTTTACCTTATTTTCTTT
63 ATTTATTTATTGTTTCTATCTTATTTTTTTATTTTTTTATTATCTTTACCTTATTTTCTTT
*
5670 ATTTTATTTGT-TT-TTTATTTTCTTTATTTTATTTTTTATTTTTTTTATCTTTATTT-ATTTAT
1 ATTTTATTTATATTATTT-TTTTCTTTATTTTATTTTTTATTTTTTTTATCTTTATTTCATTTAT
* * * *
5732 TTATTTATT-TTCTCTATCTTTATCTTTATTT-TTTATTTTCTTAT-TTTA-TTTGTTTTTTTT
65 TTATTTATTGTT-TCTATC-TTAT-TTT-TTTATTT-TTTTATTATCTTTACCTTATTTTCTTT
*
5792 ATTTTCTTTATATTACTTTTTTATCTTTATTTTATTTATTTTTATTTTTTTCTTTATCTTTATTT
1 ATTTTATTTATATTA-TTTTTT-TCTTTATTTTA--T-TTTTTA--TTTTT-TTTATCTTTATTT
* * *
5857 CA-TTATTT-TTT-TT-TTATTTATCTTATTTTCTTCATTTTATTTATT-TTTATTACC-TATTT
58 CATTTATTTATTTATTGTT-TCTATCTTATTTT-TTTATTTT-TTTATTATCT-TTACCTTATTT
*
5916 TTTTT
119 TCTTT
5921 AT
1 AT
5923 CTATTTTGAC
Statistics
Matches: 211, Mismatches: 19, Indels: 42
0.78 0.07 0.15
Matches are distributed among these distances:
120 2 0.01
121 19 0.09
122 60 0.28
123 15 0.07
124 18 0.09
125 19 0.09
127 8 0.04
128 19 0.09
129 23 0.11
130 8 0.04
131 19 0.09
132 1 0.00
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (123 bp):
ATTTTATTTATATTATTTTTTTCTTTATTTTATTTTTTATTTTTTTTATCTTTATTTCATTTATT
TATTTATTGTTTCTATCTTATTTTTTTATTTTTTTATTATCTTTACCTTATTTTCTTT
Found at i:5829 original size:28 final size:26
Alignment explanation
Indices: 5635--5875 Score: 140
Period size: 28 Copynumber: 9.1 Consensus size: 26
5625 TATCTTATTT
* *
5635 TTTTATTT-TTTTATTTTCTTTACCTTA
1 TTTTATTTATATTATTTT-TTT-CTTTA
* * *
5662 TTTTCTTTATTTTATTTGTTT-TTTA
1 TTTTATTTATATTATTTTTTTCTTTA
* *
5687 TTTTCTTTATTTTATTTTTTAT-TTT-
1 TTTTATTTATATTATTTTTT-TCTTTA
* *
5712 TTTTATCTT-TATTTATTTATTTATTTA
1 TTTTAT-TTATA-TTATTTTTTTCTTTA
* * *
5739 TTTTCTCTATCTTTATCTTTATTT-TTTA
1 TTTTATTTAT-ATTAT-TTT-TTTCTTTA
* * *
5767 TTTT-CTTATTTTATTTGTTTTTTTTA
1 TTTTATTTATATTATTT-TTTTCTTTA
*
5793 TTTTCTTTATATTACTTTTTTATCTTTA
1 TTTTATTTATATTA-TTTTTT-TCTTTA
*
5821 TTTTATTTATTTTTATTTTTTTCTTTA
1 TTTTATTTA-TATTATTTTTTTCTTTA
*
5848 TCTTTATTT-CATTATTTTTTT-TTTA
1 T-TTTATTTATATTATTTTTTTCTTTA
5873 TTT
1 TTT
5876 ATCTTATTTT
Statistics
Matches: 177, Mismatches: 20, Indels: 37
0.76 0.09 0.16
Matches are distributed among these distances:
24 2 0.01
25 39 0.22
26 42 0.24
27 40 0.23
28 47 0.27
29 7 0.04
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTATTTATATTATTTTTTTCTTTA
Found at i:5870 original size:29 final size:27
Alignment explanation
Indices: 5666--5884 Score: 123
Period size: 26 Copynumber: 8.5 Consensus size: 27
5656 ACCTTATTTT
* *
5666 CTTTAT-TTTATTT-GTTTTTTATTTT
1 CTTTATCTTTATTTATTTTTTTTTTTT
5691 CTTTAT-TTTATTT-TTTATTTTTTTTAT
1 CTTTATCTTTATTTATTT-TTTTTTTT-T
* *
5718 CTTTA--TTTATTTATTTATTTATTTT
1 CTTTATCTTTATTTATTTTTTTTTTTT
* *
5743 CTCTATCTTTATCTT-TATTTTTTATTTT
1 CTTTATCTTTAT-TTAT-TTTTTTTTTTT
*
5771 C-TTAT-TTTATTTGTTTTTTTTATTTT
1 CTTTATCTTTATTTATTTTTTTT-TTTT
* * * * *
5797 CTTTAT-ATTACTT-TTTTATCTTTAT
1 CTTTATCTTTATTTATTTTTTTTTTTT
*
5822 -TTTA--TTTA-TT--TTTATTTTTTT
1 CTTTATCTTTATTTATTTTTTTTTTTT
5843 CTTTATCTTTATTTCATTATTTTTTTTTT
1 CTTTATCTTTATTT-ATT-TTTTTTTTTT
*
5872 ATTTATC-TTATTT
1 CTTTATCTTTATTT
5885 TCTTCATTTT
Statistics
Matches: 158, Mismatches: 18, Indels: 33
0.76 0.09 0.16
Matches are distributed among these distances:
21 9 0.06
22 6 0.04
23 3 0.02
24 8 0.05
25 33 0.21
26 37 0.23
27 27 0.17
28 20 0.13
29 15 0.09
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.77
Consensus pattern (27 bp):
CTTTATCTTTATTTATTTTTTTTTTTT
Found at i:5882 original size:28 final size:26
Alignment explanation
Indices: 5662--5884 Score: 126
Period size: 25 Copynumber: 8.7 Consensus size: 26
5652 CTTTACCTTA
* * *
5662 TTTTCTTTATTTTATTT-GTTTTTTA
1 TTTTCTTTATCTTATTTATTTTTTTT
*
5687 TTTTCTTTATTTTATTT-TTTATTTTT
1 TTTTCTTTATCTTATTTATTT-TTTTT
* *
5713 TTTATCTTTAT-TTATTTATTTATTTA
1 TTT-TCTTTATCTTATTTATTTTTTTT
* *
5739 TTTTCTCTATCTTTATCTT-TATTTTTTA
1 TTTTCTTTATC-TTAT-TTAT-TTTTTTT
* *
5767 TTTTC-TTATTTTATTTGTTTTTTTT
1 TTTTCTTTATCTTATTTATTTTTTTT
* * * *
5792 ATTTTCTTTATATTACTT-TTTTATCT
1 -TTTTCTTTATCTTATTTATTTTTTTT
* *
5818 TTAT-TTTAT-TTA-TT-TTTATTTT
1 TTTTCTTTATCTTATTTATTTTTTTT
*
5840 TTTC-TTTATCTTTATTTCATTATTTTTT
1 TTTTCTTTATC-TTATTT-ATT-TTTTTT
*
5868 TTTTATTTATCTTATTT
1 TTTTCTTTATCTTATTT
5885 TCTTCATTTT
Statistics
Matches: 160, Mismatches: 21, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
22 14 0.09
23 3 0.02
24 8 0.05
25 38 0.24
26 35 0.22
27 29 0.18
28 27 0.17
29 6 0.04
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTCTTTATCTTATTTATTTTTTTT
Found at i:5906 original size:29 final size:28
Alignment explanation
Indices: 5552--5856 Score: 65
Period size: 27 Copynumber: 10.9 Consensus size: 28
5542 CACATTTTAA
5552 TTTATCTTATTTTCTT-TCTTTCATTTATTT
1 TTTATCTTATTTTCTTAT-TTT-ATTT-TTT
* * * *
5582 TTTATTTTCTTTATCTTTATTTCA-TTTGT
1 TTTATCTTATTT-TC-TTATTTTATTTTTT
* *
5611 TTT-T-TTATTGTTTTTATCTTATTTTTT
1 TTTATCTTATT-TTCTTATTTTATTTTTT
* * ** *
5638 TATTTTTTTATTTTCTTTACCTTA-TTTTC
1 T-TTATCTTATTTTC-TTATTTTATTTTTT
* * *
5667 TTTATTTTA-TTTGTT-TTTTATT-TTC
1 TTTATCTTATTTTCTTATTTTATTTTTT
* *
5692 TTTATTTTATTTT-TTATTTT-TTTTATC
1 TTTATCTTATTTTCTTATTTTATTTT-TT
*
5719 TTTAT-TTATTTAT-TTA-TTTA-TTTTC
1 TTTATCTTATTT-TCTTATTTTATTTTTT
* *
5744 TCTATC-T-TTATCTTTATTTT-TTATTTT
1 TTTATCTTATTTTC-TTATTTTATT-TTTT
* * *
5771 CTTATTTTATTTGT-TTTTTTTATTTTCTT
1 TTTATCTTATTT-TCTTATTTTATTTT-TT
* * *
5800 TATATTACTTTTTTATCTTTATTTTATTTATT
1 TTTA-T-CTTATTT-TC-TTATTTTATTTTTT
5832 TTTAT-TT-TTTTCTTTATCTTTATTT
1 TTTATCTTATTTTC-TTAT-TTTATTT
5857 CATTATTTTT
Statistics
Matches: 211, Mismatches: 32, Indels: 66
0.68 0.10 0.21
Matches are distributed among these distances:
23 1 0.00
24 2 0.01
25 29 0.14
26 33 0.16
27 37 0.18
28 30 0.14
29 23 0.11
30 26 0.12
31 10 0.05
32 9 0.04
33 11 0.05
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.76
Consensus pattern (28 bp):
TTTATCTTATTTTCTTATTTTATTTTTT
Found at i:7563 original size:12 final size:12
Alignment explanation
Indices: 7548--7593 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
7538 CGGTTTTTTT
*
7548 ACCGGATAAAAA
1 ACCGGTTAAAAA
7560 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
7575 ACCGGTTAAAAA
1 ACCGGTTAAAAA
7587 ACCGGTT
1 ACCGGTT
7594 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:7575 original size:15 final size:13
Alignment explanation
Indices: 7554--7594 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
7544 TTTTACCGGA
7554 TAAAAAACCGGTT
1 TAAAAAACCGGTT
7567 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
7581 TAAAAAACCGGTT
1 TAAAAAACCGGTT
7594 T
1 T
7595 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:9976 original size:33 final size:33
Alignment explanation
Indices: 9922--10020 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
9912 TTTGTTTCAA
*
9922 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
1 TTATCAAACTTGAAAGTTTTTAAGTATTTGAAT
9954 TTATCAAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCAAACTTGAAAGTTTTTAAGTATTTGAAT
* *
9987 TTATCAAACTTGAAAGTATTTAAGTATTTCAAT
1 TTATCAAACTTGAAAGTTTTTAAGTATTTGAAT
10020 T
1 T
10021 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (33 bp):
TTATCAAACTTGAAAGTTTTTAAGTATTTGAAT
Found at i:10049 original size:13 final size:13
Alignment explanation
Indices: 10006--10060 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
9996 TTGAAAGTAT
10006 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
10019 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
10033 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
10046 TTAAGTATTTGAA
1 TTAAGTATTTCAA
10059 TT
1 TT
10061 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:10282 original size:21 final size:21
Alignment explanation
Indices: 10256--10312 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
10246 TGGAGCGTGG
*
10256 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
10277 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
10298 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
10313 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:10509 original size:15 final size:15
Alignment explanation
Indices: 10479--10534 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
10469 ATCTGGAATA
* *
10479 TTAAAATCGATTTTT
1 TTAAAACCGGTTTTT
*
10494 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
10509 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
10526 TTAAAACCG
1 TTAAAACCG
10535 AAACCGGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.61
17 13 0.39
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:10543 original size:21 final size:18
Alignment explanation
Indices: 10498--10531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10488 ATTTTTTTAT
10498 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
10515 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
10532 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:10651 original size:15 final size:17
Alignment explanation
Indices: 10625--10656 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10615 TTCTATGGGA
10625 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
10641 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
10657 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:11248 original size:28 final size:26
Alignment explanation
Indices: 11220--11285 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
11210 ATTAAATTTA
*
11220 AAAAATATTTCTTTATATTAACTT-ATT
1 AAAAATATTT-TAT-TATTAACTTAATT
*
11247 AAATA-ATTTTATTATTAACTTAATTT
1 AAAAATATTTTATTATTAACTTAA-TT
11273 AAAAATATTTTAT
1 AAAAATATTTTAT
11286 CTTTATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 9 0.27
25 3 0.09
26 10 0.30
27 11 0.33
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
AAAAATATTTTATTATTAACTTAATT
Found at i:11285 original size:24 final size:24
Alignment explanation
Indices: 11235--11285 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
11225 TATTTCTTTA
*
11235 TATTAACTTATTAAATAATTTTAT
1 TATTAACTTATTAAATAATATTAT
11259 TATTAACTTAATTTAAA-AATATT-T
1 TATTAACTT-A-TTAAATAATATTAT
11283 TAT
1 TAT
11286 CTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 13 0.54
25 6 0.25
26 5 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAACTTATTAAATAATATTAT
Found at i:11296 original size:27 final size:27
Alignment explanation
Indices: 11196--11298 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
11186 TTAAATTCAT
* * *
11196 AATATTTTATATATA-TTAAATTTAAA
1 AATATTTTATCTTTATTTTAATTTAAA
* * * *
11222 AA-ATATT-TCTTTATATTAACTTATTA
1 AATATTTTATCTTTATTTTAATTTA-AA
**
11248 AATAATTTTAT-TATTAACTTAATTTAAA
1 AAT-ATTTTATCT-TTATTTTAATTTAAA
11276 AATATTTTATCTTTATTTTAATT
1 AATATTTTATCTTTATTTTAATT
11299 ATTTATATAT
Statistics
Matches: 56, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
24 4 0.07
25 10 0.18
26 5 0.09
27 16 0.29
28 10 0.18
29 11 0.20
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATTTTATCTTTATTTTAATTTAAA
Found at i:16533 original size:24 final size:24
Alignment explanation
Indices: 16501--16548 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16491 GTTTTCCGGT
16501 ACTGTTGGCGGAGGCAAGAAAGTG
1 ACTGTTGGCGGAGGCAAGAAAGTG
16525 ACTGTTGGCGGAGGCAAGAAAGTG
1 ACTGTTGGCGGAGGCAAGAAAGTG
16549 GGAGTAGGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.42, T:0.17
Consensus pattern (24 bp):
ACTGTTGGCGGAGGCAAGAAAGTG
Found at i:16558 original size:24 final size:24
Alignment explanation
Indices: 16507--16558 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16497 CGGTACTGTT
* *
16507 GGCGGAGGCAAGAAAGTGACTGTT
1 GGCGGAGGCAAGAAAGTGACAGTA
**
16531 GGCGGAGGCAAGAAAGTGGGAGTA
1 GGCGGAGGCAAGAAAGTGACAGTA
16555 GGCG
1 GGCG
16559 ATGGTGAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.48, T:0.12
Consensus pattern (24 bp):
GGCGGAGGCAAGAAAGTGACAGTA
Found at i:25553 original size:18 final size:16
Alignment explanation
Indices: 25515--25545 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25505 ATTGTCAGTT
25515 AAAGAGACAAAGAAGA
1 AAAGAGACAAAGAAGA
25531 AAAGAGACAAA-AAGA
1 AAAGAGACAAAGAAGA
25546 TAACAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAGACAAAGAAGA
Found at i:26521 original size:27 final size:27
Alignment explanation
Indices: 26483--26541 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
26473 AAAACGTTAG
*
26483 GCACCTATTTTGCGAAACATTTTTTAA
1 GCACCTATTTTGCGAAACATTCTTTAA
26510 GCACCTATTTTGCGAAACATTCTTTAA
1 GCACCTATTTTGCGAAACATTCTTTAA
26537 GCACC
1 GCACC
26542 AAAAGTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (27 bp):
GCACCTATTTTGCGAAACATTCTTTAA
Found at i:28581 original size:20 final size:20
Alignment explanation
Indices: 28556--28600 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28546 AAATGTTGAA
28556 ACTTTTACAG-GAGTATCGAT
1 ACTTTT-CAGCGAGTATCGAT
* *
28576 ACTTTTGAGCTAGTATCGAT
1 ACTTTTCAGCGAGTATCGAT
28596 ACTTT
1 ACTTT
28601 CAGTCTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (20 bp):
ACTTTTCAGCGAGTATCGAT
Found at i:35512 original size:22 final size:22
Alignment explanation
Indices: 35479--35535 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
35469 AATAAACATA
*
35479 CTAATTTTTTTTTTGTAATTTTT
1 CTAA-TTTTTTTTTATAATTTTT
* *
35502 GTAATTTTTTTTTATATTTTTT
1 CTAATTTTTTTTTATAATTTTT
*
35524 CTGATTTTTTTT
1 CTAATTTTTTTT
35536 AAATTTAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (22 bp):
CTAATTTTTTTTTATAATTTTT
Found at i:35911 original size:32 final size:32
Alignment explanation
Indices: 35868--35935 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
35858 AGTAGTATTT
* *
35868 GTTTATTAACAGGTTAGTTCAAGTGGTAAACA
1 GTTTATCAACAGATTAGTTCAAGTGGTAAACA
*
35900 GTTTATCAACAGATTAGTTCAAGTGGTAAGCA
1 GTTTATCAACAGATTAGTTCAAGTGGTAAACA
35932 GTTT
1 GTTT
35936 GATATCACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (32 bp):
GTTTATCAACAGATTAGTTCAAGTGGTAAACA
Found at i:36645 original size:13 final size:14
Alignment explanation
Indices: 36627--36656 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36617 GAAATCAACT
36627 AATCAA-TGGATCG
1 AATCAATTGGATCG
36640 AATCAATTGGATCG
1 AATCAATTGGATCG
36654 AAT
1 AAT
36657 TTTTCTGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (14 bp):
AATCAATTGGATCG
Found at i:36951 original size:2 final size:2
Alignment explanation
Indices: 36944--36972 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36934 TTTTAAATAA
36944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36973 AAGAGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41897 original size:29 final size:29
Alignment explanation
Indices: 41811--41890 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
41801 CGCCATAGGA
41811 CGCCATGCAATCCAGGCGACCTTGGAGGT
1 CGCCATGCAATCCAGGCGACCTTGGAGGT
41840 CGCCATGCAATCCAGGCGACCTTGGAGGT
1 CGCCATGCAATCCAGGCGACCTTGGAGGT
*
41869 CGCCATGCAATCCGGGCGACCT
1 CGCCATGCAATCCAGGCGACCT
41891 CCAAGGTGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (29 bp):
CGCCATGCAATCCAGGCGACCTTGGAGGT
Found at i:42525 original size:21 final size:21
Alignment explanation
Indices: 42500--42543 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42490 AATCTAGTTA
42500 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
42521 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
42542 AT
1 AT
42544 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:42553 original size:28 final size:30
Alignment explanation
Indices: 42520--42582 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
42510 TAGTATAAAT
*
42520 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
42548 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
42578 TATTA
1 TATTA
42583 TATAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:43413 original size:26 final size:25
Alignment explanation
Indices: 43384--43442 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
43374 AAATCATATT
*
43384 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
43410 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
43436 ATTATTA
1 ATTATTA
43443 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:46318 original size:8 final size:8
Alignment explanation
Indices: 46295--46327 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
46285 AATGATTTAA
46295 TAATGATT
1 TAATGATT
46303 TAAT-ATT
1 TAATGATT
46310 TAATGATT
1 TAATGATT
*
46318 TGATGATT
1 TAATGATT
46326 TA
1 TA
46328 GTAATGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:46355 original size:26 final size:25
Alignment explanation
Indices: 46329--46686 Score: 266
Period size: 26 Copynumber: 14.4 Consensus size: 25
46319 GATGATTTAG
*
46329 TAATGATTTGATAATAATCATTATAG
1 TAATGATTT-ATAATAATCATTATAA
46355 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
46381 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
46407 AAATGA-TT-TAATAATGATT-T-A
1 TAATGATTTATAATAATCATTATAA
* * * *
46428 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTT-AT-A-ATAATCATTATAA
*
46453 TAATGATTTGATAATAATCATTATAG
1 TAATGATTT-ATAATAATCATTATAA
46479 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
46505 TAATAATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
*
46531 -AATGA-TT-TAATAATGATT-T-A
1 TAATGATTTATAATAATCATTATAA
* * * *
46551 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTT-AT-A-ATAATCATTATAA
46576 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
* *
46602 TAATGATTTTATAATAATTATT-TAG
1 TAATGA-TTTATAATAATCATTATAA
* * *
46627 TTATTATTTAGTAATTAT--TTATAA
1 TAATGATTTA-TAATAATCATTATAA
*
46651 TAATGATTTATAATAATGATTTATAA
1 TAATGATTTATAATAATCA-TTATAA
46677 TAATGATTTA
1 TAATGATTTA
46687 ATACTAACAA
Statistics
Matches: 275, Mismatches: 31, Indels: 52
0.77 0.09 0.15
Matches are distributed among these distances:
19 2 0.01
20 11 0.04
21 2 0.01
22 13 0.05
23 20 0.07
24 32 0.12
25 32 0.12
26 148 0.54
27 15 0.05
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:46544 original size:123 final size:124
Alignment explanation
Indices: 46272--46678 Score: 671
Period size: 123 Copynumber: 3.3 Consensus size: 124
46262 ATGTATTTAT
46272 TAATCATTATAAAAATGATTTAATAATGATTT-AATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
46336 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATAATTTAGTAA
46395 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
46460 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATAATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATAATTTAGTAA
46519 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
46583 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATAATTTAGTAA
* *
46641 TTAT--TTATAATAATGATTTATAATAATGATTTATAATA
1 TAATCATTATAAAAATGA-TT-TAATAATGATTTA-AATA
46679 ATGATTTAAT
Statistics
Matches: 270, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
120 4 0.01
121 6 0.02
122 19 0.07
123 137 0.51
124 104 0.39
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATAATTTAGTAA
Found at i:46659 original size:13 final size:13
Alignment explanation
Indices: 46638--46686 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
46628 TATTATTTAG
*
46638 TAATTATTTATAA
1 TAATGATTTATAA
46651 TAATGATTTATAA
1 TAATGATTTATAA
46664 TAATGATTTATAA
1 TAATGATTTATAA
46677 TAATGATTTA
1 TAATGATTTA
46687 ATACTAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:46809 original size:17 final size:17
Alignment explanation
Indices: 46784--46816 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46774 ACTAAATATT
*
46784 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
46801 TAATGATTTGATACTA
1 TAATGATTTGATACTA
46817 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:47747 original size:23 final size:23
Alignment explanation
Indices: 47721--47768 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
47711 TAAAATTACA
*
47721 AAAACAATAAAATTTATTTAAAT
1 AAAACAATAAAATTAATTTAAAT
* * *
47744 AAAATAATATAGTTAATTTAAAT
1 AAAACAATAAAATTAATTTAAAT
47767 AA
1 AA
47769 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAACAATAAAATTAATTTAAAT
Found at i:48989 original size:15 final size:14
Alignment explanation
Indices: 48963--48994 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
48953 TTTACAACAC
48963 TAACTTTAATATAA
1 TAACTTTAATATAA
48977 TAACTTATAATATAA
1 TAACTT-TAATATAA
48992 TAA
1 TAA
48995 ACTAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
TAACTTTAATATAA
Found at i:49002 original size:16 final size:16
Alignment explanation
Indices: 48969--49015 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
48959 ACACTAACTT
*
48969 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
48984 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
49000 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
49016 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:49252 original size:45 final size:44
Alignment explanation
Indices: 49175--49307 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 44
49165 TCAACAAACA
49175 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AA-ACAAACTAATTAAATAATTTTTT
* *
49223 TATATAACTAACTATTAACAATACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAA-ACAAACTAATTAAATAATTTTTT
49267 AACTAT-A-TAACTA-T--CAAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAACA-A-ACTAATTAAATAATTTTT
49308 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 3 0.04
40 4 0.05
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (44 bp):
AATATAACTAACTATTAACAAACAAACTAATTAAATAATTTTTT
Found at i:49335 original size:41 final size:40
Alignment explanation
Indices: 49197--49335 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 40
49187 CTATTTAACT
* * *
49197 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATT
1 AACATAAACTAATTAAATAA-TTTTTAACTAT-A-TAACTATA
* *
49239 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATAATTTTTAACTATATAACTAT-A
* * *
49283 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATAATTTTTAA-CTATATA-ACTATA
*
49324 AACTTAAACTAA
1 AACATAAACTAA
49336 CAATCATATA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
41 29 0.37
42 8 0.10
43 15 0.19
44 10 0.13
45 16 0.21
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (40 bp):
AACATAAACTAATTAAATAATTTTTAACTATATAACTATA
Found at i:49498 original size:4 final size:4
Alignment explanation
Indices: 49462--49527 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
49452 CCTTATCTCC
* ** **
49462 CTTT C-TT C-TT CTTA CTTT CCTTT CTCC CTTT CTTT CTTT CCTTT CTCC
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT CTTT
49510 CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CT
49528 CGGCTGCAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
3 6 0.12
4 35 0.71
5 8 0.16
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:49500 original size:21 final size:21
Alignment explanation
Indices: 49470--49528 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
49460 CCCTTTCTTC
*
49470 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
49491 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
49512 TTCTTTCTTT-CTTTCTC
1 TTCTTTCTTTCCTTTCTC
49529 GGCTGCAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 7 0.19
21 30 0.81
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:49561 original size:23 final size:23
Alignment explanation
Indices: 49531--49576 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
49521 TCTTTCTCGG
49531 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
49554 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
49577 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:49749 original size:36 final size:37
Alignment explanation
Indices: 49702--49775 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
49692 ACATGCATGC
49702 ATTGGGAGGTGTAGGC-ATGCAGCGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
49738 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
49775 A
1 A
49776 GGAATCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 16 0.43
37 21 0.57
ACGTcount: A:0.24, C:0.14, G:0.46, T:0.16
Consensus pattern (37 bp):
ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
Found at i:49858 original size:29 final size:29
Alignment explanation
Indices: 49826--49963 Score: 242
Period size: 29 Copynumber: 4.8 Consensus size: 29
49816 ATGGGAATGG
49826 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
49855 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
49884 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
49913 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
49942 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
49964 CTCTATTCCT
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 104 0.98
30 2 0.02
ACGTcount: A:0.22, C:0.32, G:0.31, T:0.14
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:50052 original size:61 final size:61
Alignment explanation
Indices: 49977--50169 Score: 298
Period size: 61 Copynumber: 3.1 Consensus size: 61
49967 TATTCCTGCA
49977 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
*
50038 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCGT
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
* * *
50099 GGGCTCGTATATGGCTCGTTGCATGCTCCCCA-TGGCTCGTATATGGCTCGTTGCATGCTCCCCA
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTC-TCTAT---TC-CTGCATGCTCCCCA
50163 T
61 T
50164 TGGCTC
1 TGGCTC
50170 TCTATTCCTG
Statistics
Matches: 121, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
60 6 0.05
61 95 0.79
64 2 0.02
65 18 0.15
ACGTcount: A:0.11, C:0.33, G:0.23, T:0.33
Consensus pattern (61 bp):
TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
Found at i:50150 original size:93 final size:92
Alignment explanation
Indices: 50024--50232 Score: 357
Period size: 93 Copynumber: 2.3 Consensus size: 92
50014 TCTCTATTCC
50024 TGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCA
1 TGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCA
* *
50089 TGCTCCCCGTGGGCTCGTATATGGCTCGT
66 TGCTCCCCATGGCCTCG--TATGGCTCGT
50118 TGCATGCTCCCCA-TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCA
1 TGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCA
*
50182 TGCTCCCCATTGCCTCGTATGGCTCGT
66 TGCTCCCCATGGCCTCGTATGGCTCGT
*
50209 TGCATCCTCCCCATTGGCTCGTAT
1 TGCATGCTCCCCATTGGCTCGTAT
50233 GACTCGTATA
Statistics
Matches: 110, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
91 22 0.20
92 10 0.09
93 65 0.59
94 13 0.12
ACGTcount: A:0.11, C:0.34, G:0.22, T:0.33
Consensus pattern (92 bp):
TGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCA
TGCTCCCCATGGCCTCGTATGGCTCGT
Found at i:50278 original size:12 final size:13
Alignment explanation
Indices: 50246--50280 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
50236 TCGTATATGG
50246 CTCGTATGTCACC
1 CTCGTATGTCACC
50259 CTCGTATGTCACC
1 CTCGTATGTCACC
50272 C-CGTATGTC
1 CTCGTATGTC
50281 GCCTGGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.31
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:50727 original size:60 final size:61
Alignment explanation
Indices: 50638--50760 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
50628 TAAAAATTAT
* * * *
50638 AAATGATTTTCTAATATAGGACGATTG-TTTGTTAAATTC-TTCGACTACTAAATGTTATAA
1 AAATAATTTTCTAATATAGGACGATTGTTTTATTAAATTCATT-GACTACTAAAAGTTAGAA
*
50698 AAATAATTTTCTAACTATAGGACGA-TGTTTTATTAAATTCATTGACTATTAAAAGTTAGAA
1 AAATAATTTTCTAA-TATAGGACGATTGTTTTATTAAATTCATTGACTACTAAAAGTTAGAA
50759 AA
1 AA
50761 TTATCACTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
60 15 0.27
61 38 0.69
62 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (61 bp):
AAATAATTTTCTAATATAGGACGATTGTTTTATTAAATTCATTGACTACTAAAAGTTAGAA
Found at i:50761 original size:60 final size:58
Alignment explanation
Indices: 50624--50761 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 58
50614 TTTATCTAGG
* * * *
50624 CTATTAAAAATTATAAATGATTTTCTAATATAGGACGATTGTTTGTTAAATTCTTCGA
1 CTATTAAAAGTTAAAAATAATTTTCTAATATAGGACGATTGTTTATTAAATTCTTCGA
* *
50682 CTACTAAATGTTATAAAAATAATTTTCTAACTATAGGACGA-TGTTTTATTAAATTCATT-GA
1 CTATTAAAAG-T-TAAAAATAATTTTCTAA-TATAGGACGATTG-TTTATTAAATTC-TTCGA
50743 CTATTAAAAGTTAGAAAAT
1 CTATTAAAAGTTA-AAAAT
50762 TATCACTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
58 7 0.11
59 3 0.05
60 23 0.35
61 31 0.47
62 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (58 bp):
CTATTAAAAGTTAAAAATAATTTTCTAATATAGGACGATTGTTTATTAAATTCTTCGA
Found at i:52093 original size:2 final size:2
Alignment explanation
Indices: 52086--52121 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52076 AAATAAATAA
52086 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
52122 GATAAAATTG
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:52363 original size:29 final size:29
Alignment explanation
Indices: 52317--52373 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
52307 AATTGTATTA
* *
52317 AACTTGTCACCTTCACGTGACAAGTTTCT
1 AACTTCTCACCTTCACGTAACAAGTTTCT
*
52346 AACTTCTCACC-TCTACGTAATAAGTTTC
1 AACTTCTCACCTTC-ACGTAACAAGTTTC
52374 ACTAATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (29 bp):
AACTTCTCACCTTCACGTAACAAGTTTCT
Found at i:56499 original size:29 final size:30
Alignment explanation
Indices: 56443--56500 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
56433 TTGTTCCCCA
* *
56443 CTCGATCGCTGTTCCCCCCTCGCTGCAGAC
1 CTCGATCGCTATTCCCCCCTCGATGCAGAC
*
56473 CTCGATCGCTATT-CCCCCTTGATGCAGA
1 CTCGATCGCTATTCCCCCCTCGATGCAGA
56501 GCTTGTGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.14, C:0.41, G:0.19, T:0.26
Consensus pattern (30 bp):
CTCGATCGCTATTCCCCCCTCGATGCAGAC
Found at i:56581 original size:17 final size:15
Alignment explanation
Indices: 56567--56599 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
56557 TATGATTTGC
56567 TGTGTATGTTGA-TT
1 TGTGTATGTTGATTT
56581 TGTGTATGTTGATGTT
1 TGTGTATGTTGAT-TT
56597 TGT
1 TGT
56600 TTTTGCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.71
16 5 0.29
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.58
Consensus pattern (15 bp):
TGTGTATGTTGATTT
Found at i:56584 original size:14 final size:14
Alignment explanation
Indices: 56567--56593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56557 TATGATTTGC
56567 TGTGTATGTTGATT
1 TGTGTATGTTGATT
56581 TGTGTATGTTGAT
1 TGTGTATGTTGAT
56594 GTTTGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (14 bp):
TGTGTATGTTGATT
Found at i:56828 original size:18 final size:20
Alignment explanation
Indices: 56791--56831 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56781 ACTAGGCTAT
*
56791 TATATATATGCTGATTTATA
1 TATATATATGCTGATGTATA
56811 TATATATATG-T-ATGTATA
1 TATATATATGCTGATGTATA
56829 TAT
1 TAT
56832 TGTATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (20 bp):
TATATATATGCTGATGTATA
Found at i:56877 original size:32 final size:32
Alignment explanation
Indices: 56815--56881 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
56805 TTTATATATA
* **
56815 TATATGTATGTATATATTGTATTTGTTGTTTG
1 TATATGTATGTATATATTGAATTTACTGTTTG
*
56847 TATATGTATGTATGT-TATGAATTTACTGTTTG
1 TATATGTATGTATATAT-TGAATTTACTGTTTG
56879 TAT
1 TAT
56882 GTTATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.24, C:0.01, G:0.18, T:0.57
Consensus pattern (32 bp):
TATATGTATGTATATATTGAATTTACTGTTTG
Found at i:56881 original size:22 final size:22
Alignment explanation
Indices: 56855--56947 Score: 147
Period size: 22 Copynumber: 4.4 Consensus size: 22
56845 TGTATATGTA
*
56855 TGTATGTTATGAATTTACTGTT
1 TGTATGTTATGAATTTGCTGTT
56877 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
56899 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
*
56921 TG-ATGTTATGTATTTGCTG--
1 TGTATGTTATGAATTTGCTGTT
56940 TGTATGTT
1 TGTATGTT
56948 GATTTGTGTG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 16 0.24
22 45 0.66
ACGTcount: A:0.18, C:0.04, G:0.23, T:0.55
Consensus pattern (22 bp):
TGTATGTTATGAATTTGCTGTT
Found at i:57650 original size:24 final size:24
Alignment explanation
Indices: 57605--57650 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
57595 AATACCTCAA
*
57605 TTGATCCACCTCTTAGTGCATCAG
1 TTGATCCACCTCTGAGTGCATCAG
57629 TTGATCCACCTCCTGAGT-CATC
1 TTGATCCACCT-CTGAGTGCATC
57651 CCCTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.33
Consensus pattern (24 bp):
TTGATCCACCTCTGAGTGCATCAG
Found at i:58045 original size:30 final size:30
Alignment explanation
Indices: 58005--58174 Score: 185
Period size: 30 Copynumber: 5.9 Consensus size: 30
57995 TCTTTTTGAT
* *
58005 TATGTAAGAAATATTTTATGGTTTGTGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
*
58035 TATGTTAGAAATATTAAATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* * *
58062 GATGTTCA-AAACATTATATGGTTTGTGGTT
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
*
58092 TATGTTAGAAATATTATATGGTTTGTCGAT-
1 TATGTTAGAAATATTATATGGTTTGT-GGTC
* *
58122 T-T-TTA-AAACATTATATAGTTTGTGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
58149 TATGTTAGAAATATTATATGGTTTGT
1 TATGTTAGAAATATTATATGGTTTGT
58175 ATTAAAGTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
26 2 0.02
27 36 0.31
28 8 0.07
29 8 0.07
30 59 0.51
31 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.46
Consensus pattern (30 bp):
TATGTTAGAAATATTATATGGTTTGTGGTC
Found at i:58087 original size:57 final size:57
Alignment explanation
Indices: 58021--58174 Score: 263
Period size: 57 Copynumber: 2.7 Consensus size: 57
58011 AGAAATATTT
*
58021 TATGGTTTGTGGTCTATGTTAGAAATATTAAATGGTTTGTCGATGTTCAAAACATTA
1 TATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAACATTA
* * *
58078 TATGGTTTGTGGTTTATGTTAGAAATATTATATGGTTTGTCGATTTTTAAAACATTA
1 TATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAACATTA
*
58135 TATAGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1 TATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
58175 ATTAAAGTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.47
Consensus pattern (57 bp):
TATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAACATTA
Found at i:59530 original size:31 final size:31
Alignment explanation
Indices: 59493--59551 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
59483 AGTTGTATGG
*
59493 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
59524 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
59552 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:67125 original size:90 final size:88
Alignment explanation
Indices: 66889--67215 Score: 373
Period size: 90 Copynumber: 3.7 Consensus size: 88
66879 TGGATTACTT
* * *
66889 CACTACTCTTCCGTGAAGATTTCATACTTTGTTGAAAAATCCGTTCCACTACTCTTTCGTGGA-A
1 CACTACTATTCCGTGAA-ATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCGTGGAGT
* * *
66953 ACTAAATTT-TGCTT---TTGCTT-
65 TC-AGATTTATGATTGAATTGCTTC
* * *
66973 CACTACTCTTACC-TGAAATTTGATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGT
1 CACTACTATT-CCGTGAAATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCGTGGAGT
*
67037 TCAGATTTATGATTGAATTCCCTTC
65 TCAGATTTATGATTGAATT-GCTTC
* *
67062 CACTACTATTCCGTGGAATTTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTTGTGGAGT
1 CACTACTATTCCGT-GAAATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCGTGGAGT
*
67127 TTAGATTTATGATTGAATTTGCTTC
65 TCAGATTTATGATTGAA-TTGCTTC
* ** *
67152 CACTACTATTCTGTGGAGTTTTCATAATTTGCTGAAAAATCCGTTCCACTACT-TTTCCGTGGAG
1 CACTACTATTCCGT-GAAATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTT-CGTGGAG
67216 AGCGAATTTT
Statistics
Matches: 212, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
83 47 0.22
84 19 0.09
85 2 0.01
87 2 0.01
88 5 0.02
89 13 0.06
90 122 0.58
91 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (88 bp):
CACTACTATTCCGTGAAATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCGTGGAGTT
CAGATTTATGATTGAATTGCTTC
Found at i:67172 original size:44 final size:44
Alignment explanation
Indices: 67015--67172 Score: 140
Period size: 44 Copynumber: 3.5 Consensus size: 44
67005 GAAAAATCCG
* * *
67015 TTCCACTACTCTTCCGTGGAGTTCAGATTTATGATTGAATTCCC
1 TTCCACTACTATTCCGTGGAGTTTAGATTTATGATTGAATTTCC
* * * * **
67059 TTCCACTACTATTCCGTGGAATTTTCATACTT-TG-CTGAAAAATCC
1 TTCCACTACTATTCCGTGG-AGTTT-AGATTTATGATTG-AATTTCC
* ** *
67104 GTTCCACTACTCTTTTGTGGAGTTTAGATTTATGATTGAATTTGC
1 -TTCCACTACTATTCCGTGGAGTTTAGATTTATGATTGAATTTCC
*
67149 TTCCACTACTATTCTGTGGAGTTT
1 TTCCACTACTATTCCGTGGAGTTT
67173 TCATAATTTG
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
44 46 0.53
45 19 0.22
46 22 0.25
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.42
Consensus pattern (44 bp):
TTCCACTACTATTCCGTGGAGTTTAGATTTATGATTGAATTTCC
Found at i:67214 original size:46 final size:44
Alignment explanation
Indices: 66999--67215 Score: 163
Period size: 46 Copynumber: 4.8 Consensus size: 44
66989 AATTTGATAC
* *
66999 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAG-TTCAGA
1 TTTGCTGAAAAATCCGTTCCACTACTATTCCGTGGAGTTTCAAA
* * * * * *
67042 TTT-ATGATTGAATTCCCTTCCACTACTATTCCGTGGAATTTTCATAC
1 TTTGCTGA--AAAATCCGTTCCACTACTATTCCGTGG-AGTTTCA-AA
* ** *
67089 TTTGCTGAAAAATCCGTTCCACTACTCTTTTGTGGAGTTT-AGA
1 TTTGCTGAAAAATCCGTTCCACTACTATTCCGTGGAGTTTCAAA
* ** ** *
67132 TTT-ATGATTGAATTTGCTTCCACTACTATTCTGTGGAGTTTTCATAA
1 TTTGCTGA-AAAATCCG-TTCCACTACTATTCCGTGGAG-TTTCA-AA
*
67179 TTTGCTGAAAAATCCGTTCCACTACTTTTCCGTGGAG
1 TTTGCTGAAAAATCCGTTCCACTACTATTCCGTGGAG
67216 AGCGAATTTT
Statistics
Matches: 129, Mismatches: 33, Indels: 21
0.70 0.18 0.11
Matches are distributed among these distances:
42 6 0.05
43 10 0.08
44 43 0.33
45 8 0.06
46 45 0.35
47 11 0.09
48 6 0.05
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (44 bp):
TTTGCTGAAAAATCCGTTCCACTACTATTCCGTGGAGTTTCAAA
Found at i:85133 original size:137 final size:137
Alignment explanation
Indices: 84887--85459 Score: 806
Period size: 137 Copynumber: 4.2 Consensus size: 137
84877 AACTGGTGTT
* * * * * *
84887 TGACATTGTTCCTTCATGATGAGAACGTCTGACCATTTTTGAAGATATTTGAGATAACAAGGTTC
1 TGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTC
** * * * ** * *
84952 CTTTGTGATGAGGACGTCTAGTTATCTGAGGATGACT-CAGCTCCTACCTGATGAGGAGTTCTGA
66 CTTCATGATGAGGACATCTAGTTATCTAAGAATGA-TGTTGCTCCTTCGTGATGAGGAGTTCTGA
85016 TCGGTGGA
130 TCGGTGGA
* * *
85024 TGACATTGTTCCTTTGTGATGAGGATGTCTGGCCATCTTTAAATATATTTGAGATAACACGGTTC
1 TGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTC
* *
85089 CTTCTTGATGAGGACATCTAGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGAT
66 CTTCATGATGAGGACATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGAT
85154 CGGTGGA
131 CGGTGGA
* * * *
85161 TGACATTGTTCCTTCATGATGAGTACGTCTGGCCATCTTTAAAGATATTTTAGATAACACTGTTC
1 TGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTC
* * * *
85226 TTTCATGATGAGGATATCTAGTTATCTAAGAATGATGTTGCTCTTTCGTGATGAGGAGTTCTTAT
66 CTTCATGATGAGGACATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGAT
85291 CGGTGGA
131 CGGTGGA
* *
85298 TGACATTGTTCCTTCGTGATGAGGACGTCTGACCATCTTTAAAGATATTTGAGATAACACTGTTC
1 TGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTC
* * * *
85363 TTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTTTGAT
66 CTTCATGATGAGGACATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGAT
*
85428 CAGTGGA
131 CGGTGGA
*
85435 TGACATTGTTCCTTTGTGATGAGGA
1 TGACATTGTTCCTTCGTGATGAGGA
85460 TGTATGGCTG
Statistics
Matches: 393, Mismatches: 42, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
136 1 0.00
137 392 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (137 bp):
TGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTC
CTTCATGATGAGGACATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGAT
CGGTGGA
Found at i:85454 original size:40 final size:40
Alignment explanation
Indices: 85404--85542 Score: 140
Period size: 40 Copynumber: 3.4 Consensus size: 40
85394 ATGATGTTGC
*
85404 TCCTTCGTGATGAGGAGTTTTGATCAGTGGATGACATTGT
1 TCCTTCGTGATGAGGAGTTCTGATCAGTGGATGACATTGT
* * *
85444 TCCTTTGTGATGAGGATGTATGGCTG-TCTA-AGGATGATA-TGAT
1 TCCTTCGTGATGAGGA-GT-T--CTGATC-AGTGGATGACATTG-T
** *
85487 TCCTTCGTGATGAGGAGTTCTGATTGGTAGATGACATTGT
1 TCCTTCGTGATGAGGAGTTCTGATCAGTGGATGACATTGT
85527 TCCTTCGTGATGAGGA
1 TCCTTCGTGATGAGGA
85543 TATTTGGCCA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
39 3 0.04
40 39 0.49
41 5 0.06
42 5 0.06
43 25 0.31
44 3 0.04
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (40 bp):
TCCTTCGTGATGAGGAGTTCTGATCAGTGGATGACATTGT
Found at i:92161 original size:20 final size:19
Alignment explanation
Indices: 92099--92167 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
92089 AGAAATGCAA
* *
92099 AAAATAAAAATGCAAATTG
1 AAAATACAAATGCAAAATG
*
92118 AACAATACAAAAGCAAACAT-
1 AA-AATACAAATGCAAA-ATG
92138 AAAAGTACAAATGCAAAATG
1 AAAA-TACAAATGCAAAATG
*
92158 AAAATGCAAA
1 AAAATACAAA
92168 GATGCGTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 11 0.27
20 29 0.71
21 1 0.02
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (19 bp):
AAAATACAAATGCAAAATG
Found at i:92343 original size:43 final size:43
Alignment explanation
Indices: 92263--92352 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
92253 GTACATCAAA
*
92263 CAAAACTTTACATATAGGGGATAACCTTCTCTCCTAACTTCTC
1 CAAAACTTTACATATAGGGGATAACATTCTCTCCTAACTTCTC
* * *
92306 CAAAACTTTACATATAGGGGATAA-ATTTTATTTCTAACTTCTC
1 CAAAACTTTACATATAGGGGATAACATTCT-CTCCTAACTTCTC
92349 CAAA
1 CAAA
92353 GACAATTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.07
43 39 0.93
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (43 bp):
CAAAACTTTACATATAGGGGATAACATTCTCTCCTAACTTCTC
Found at i:92866 original size:36 final size:36
Alignment explanation
Indices: 92810--92878 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
92800 TTTTACCGTA
* *
92810 GAATGCTTTTGGTATCAATCTAATAGGATCTTTATG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTATG
*
92846 GAATACTTTTGGTATTAATCTAACAGGATCTTT
1 GAATACTTTTGGTATCAATCTAACAGGATCTTT
92879 GTGTGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATCTAACAGGATCTTTATG
Found at i:95725 original size:3 final size:3
Alignment explanation
Indices: 95719--95744 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
95709 ATTTATTATT
95719 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
95745 TAAAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:96388 original size:21 final size:21
Alignment explanation
Indices: 96345--96388 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
96335 AAAACACATA
* *
96345 ATTTTATATTAACATCTATAT
1 ATTTTATATTAACATATAAAT
96366 ATTTTATAATTAA-ATATAAAT
1 ATTTTAT-ATTAACATATAAAT
96387 AT
1 AT
96389 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTATATTAACATATAAAT
Done.