Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 29
Found at i:2731529 original size:18 final size:18
Alignment explanation
Indices: 2731506--2731541 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2731496 AAGCCGGTTG
*
2731506 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2731524 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2731542 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2733990 original size:12 final size:12
Alignment explanation
Indices: 2733969--2734002 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2733959 GGTTGTGGGT
*
2733969 TTTGAGATTGTG
1 TTTGATATTGTG
2733981 TTTGATATTGTG
1 TTTGATATTGTG
*
2733993 TTTGGTATTG
1 TTTGATATTG
2734003 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2734779 original size:20 final size:20
Alignment explanation
Indices: 2734754--2734891 Score: 77
Period size: 20 Copynumber: 6.9 Consensus size: 20
2734744 TTGCGAAATT
2734754 AAATTCGCGTTGCGAATTCG
1 AAATTCGCGTTGCGAATTCG
* *
2734774 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTCG
** * *
2734793 ACTTTCGCGTCGCGAATTTGG
1 AAATTCGCGTTGCGAA-TTCG
* ** *
2734814 AAAATCGCAATGCGATTTAC-
1 AAATTCGCGTTGCGAATT-CG
* *
2734834 ATATTCGCGTTGCGAAATTGG
1 AAATTCGCGTTGCG-AATTCG
* *
2734855 AAACT-GGGTTGCGAAATT-G
1 AAATTCGCGTTGCG-AATTCG
*
2734874 GAATTCGCGTTGCGAATT
1 AAATTCGCGTTGCGAATT
2734892 TGTTGGTTAA
Statistics
Matches: 85, Mismatches: 27, Indels: 13
0.68 0.22 0.10
Matches are distributed among these distances:
19 23 0.27
20 44 0.52
21 18 0.21
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTCG
Found at i:2737398 original size:5 final size:5
Alignment explanation
Indices: 2737379--2737495 Score: 66
Period size: 5 Copynumber: 22.8 Consensus size: 5
2737369 TATATTTACT
* * *
2737379 TTTTA TTTT- TCTTA TTTTA TTTTA TTTGT- TTTT- TTTCTT TTTTC TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTT-TA TTTTA TTTTA
* *
2737428 TCTTTA TCTTT- TCTTA TTTTA -TTT- TTTTA TATTA GTTTTA TTTATA
1 T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT-TA
2737474 TATTTA TTTTCA TTTGTA TTTT
1 T-TTTA TTTT-A TTT-TA TTTT
2737496 CCTCTTGTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
4 15 0.16
5 42 0.46
6 31 0.34
7 3 0.03
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:2737414 original size:13 final size:12
Alignment explanation
Indices: 2737373--2737457 Score: 53
Period size: 13 Copynumber: 6.4 Consensus size: 12
2737363 TTTCCATATA
*
2737373 TTTACTTTTTATT
1 TTTA-TTTTTTTT
* *
2737386 TTTCTTATTTTAT
1 TTTATT-TTTTTT
2737399 TTTATTTGTTTTT
1 TTTATTT-TTTTT
* *
2737412 TTTCTTTTTTCT
1 TTTATTTTTTTT
2737424 TTTATCTTTATCTTT
1 TTTAT-TTT-T-TTT
2737439 TCTTATTTTATTTT
1 T-TTATTTT-TTTT
2737453 TTTAT
1 TTTAT
2737458 ATTAGTTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 11 0.19
13 29 0.51
14 5 0.09
15 8 0.14
16 4 0.07
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:2737512 original size:4 final size:4
Alignment explanation
Indices: 2737503--2737532 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2737493 TTTCCTCTTG
2737503 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2737533 ATGTATATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2737567 original size:5 final size:5
Alignment explanation
Indices: 2737552--2737772 Score: 52
Period size: 5 Copynumber: 43.0 Consensus size: 5
2737542 CAATTATTAG
* * *
2737552 TATTT TCTTT TATTT TATTCT TATTTT TATTT TATTT TGCTCGT TATCTT
1 TATTT TATTT TATTT TATT-T TA-TTT TATTT TATTT T-AT-TT TAT-TT
*
2737602 TATTT TGATTAT T-TTT TATTT T-TCTT CA-TT T-TTT TATTT CT-TTT
1 TATTT T-ATT-T TATTT TATTT TAT-TT TATTT TATTT TATTT -TATTT
* * * * *
2737646 GTTTTT TATGT T-CTT TATTT TA-TT TAGTT T-TTT TATTTT TATTT AGTTTTT
1 -TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT --TATTT
* * ** *
2737697 TATGTCT TTTCTT TATCT TATTT TCCTT T-TTT CA-TT TATTTT TATTT
1 TAT-T-T TAT-TT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT
* *
2737744 CA-TT TATTT TATTT T-TCTT TAGTT TATTT
1 TATTT TATTT TATTT TAT-TT TATTT TATTT
2737773 ATCTTCATTG
Statistics
Matches: 158, Mismatches: 31, Indels: 54
0.65 0.13 0.22
Matches are distributed among these distances:
4 26 0.16
5 85 0.54
6 33 0.21
7 14 0.09
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:2737581 original size:12 final size:11
Alignment explanation
Indices: 2737554--2737689 Score: 57
Period size: 11 Copynumber: 11.7 Consensus size: 11
2737544 ATTATTAGTA
*
2737554 TTTTCTTTTA-
1 TTTTATTTTAT
2737564 TTTTATTCTTAT
1 TTTTATT-TTAT
2737576 TTTTATTTTAT
1 TTTTATTTTAT
** *
2737587 TTTGCTCGTTAT
1 TTTTAT-TTTAT
*
2737599 CTTTATTTTGAT
1 TTTTATTTT-AT
*
2737611 TATT-TTTTAT
1 TTTTATTTTAT
*
2737621 TTTTCTTCATT-T
1 TTTTATT--TTAT
2737633 TTTTATTTCT-T
1 TTTTATTT-TAT
2737644 TTGTT-TTTTATGT
1 TT-TTATTTTA--T
2737657 TCTTTATTTTAT
1 T-TTTATTTTAT
*
2737669 TTAGTTTTTTTAT
1 TT--TTATTTTAT
2737682 TTTTATTT
1 TTTTATTT
2737690 AGTTTTTTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
10 13 0.14
11 32 0.33
12 29 0.30
13 16 0.17
14 6 0.06
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:2737584 original size:22 final size:21
Alignment explanation
Indices: 2737554--2737697 Score: 63
Period size: 22 Copynumber: 6.8 Consensus size: 21
2737544 ATTATTAGTA
*
2737554 TTTTCTTTTATTTTATTCTTAT
1 TTTTATTTTATTTT-TTCTTAT
*
2737576 TTTTATTTTATTTTGCTCGTTAT
1 TTTTATTTTATTTT-TTC-TTAT
*
2737599 CTTTATTTTGATTATTTT-TTAT
1 TTTTATTTT-ATT-TTTTCTTAT
* *
2737621 TTTT-CTTCA-TTTTT-TTAT
1 TTTTATTTTATTTTTTCTTAT
*
2737639 TTCTT-TTGTTTTTTATGTTCTT-T
1 TT-TTATT-TTATTT-T-TTCTTAT
*
2737662 ATTTTA-TTTAGTTTTT-TTAT
1 -TTTTATTTTATTTTTTCTTAT
2737682 TTTTA-TTTAGTTTTTT
1 TTTTATTTTA-TTTTTT
2737698 ATGTCTTTTC
Statistics
Matches: 95, Mismatches: 14, Indels: 28
0.69 0.10 0.20
Matches are distributed among these distances:
18 10 0.11
19 15 0.16
20 10 0.11
21 5 0.05
22 27 0.28
23 18 0.19
24 8 0.08
25 2 0.02
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTATTTTATTTTTTCTTAT
Found at i:2737603 original size:23 final size:22
Alignment explanation
Indices: 2737559--2737607 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2737549 TAGTATTTTC
* *
2737559 TTTTATTTTATTCTTATTTTTA
1 TTTTATTTTACTCTTATCTTTA
*
2737581 TTTTATTTTGCTCGTTATCTTTA
1 TTTTATTTTACTC-TTATCTTTA
2737604 TTTT
1 TTTT
2737608 GATTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTATTTTACTCTTATCTTTA
Found at i:2737645 original size:9 final size:8
Alignment explanation
Indices: 2737600--2737699 Score: 69
Period size: 9 Copynumber: 11.6 Consensus size: 8
2737590 GCTCGTTATC
2737600 TTTATTTT
1 TTTATTTT
*
2737608 GATTA-TTT
1 -TTTATTTT
2737616 TTTATTTT
1 TTTATTTT
2737624 TCTTCATTTT
1 T-TT-ATTTT
2737634 TTTATTTCT
1 TTTATTT-T
*
2737643 TTT-GTTT
1 TTTATTTT
*
2737650 TTTATGTTC
1 TTTAT-TTT
2737659 TTTATTTT
1 TTTATTTT
2737667 ATTTAGTTTT
1 -TTTA-TTTT
2737677 TTTATTTTT
1 TTTA-TTTT
*
2737686 ATTTAGTTT
1 -TTTATTTT
2737695 TTTAT
1 TTTAT
2737700 GTCTTTTCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
7 7 0.10
8 19 0.26
9 33 0.45
10 14 0.19
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:2737666 original size:16 final size:15
Alignment explanation
Indices: 2737610--2737774 Score: 57
Period size: 18 Copynumber: 9.7 Consensus size: 15
2737600 TTTATTTTGA
2737610 TTATTTTTTATTTTTCT
1 TTATTTTTTA--TTTCT
*
2737627 TCATTTTTTTATTTCTT
1 TTA-TTTTTTATTTC-T
*
2737644 TTGTTTTTTATGTTCT
1 TTATTTTTTAT-TTCT
*
2737660 TTATTTTATTTAGTTTTT
1 TTA-TTT-TTTA-TTTCT
2737678 TTATTTTTATTTAGTTT-T
1 TTA--TTT-TTTA-TTTCT
* *
2737696 TTATGTCTTTTCTTTAT
1 TTAT-T-TTTTATTTCT
*
2737713 CTTATTTTCCTTTTTTCAT
1 -TTATTTT--TTATTTC-T
2737732 TTA-TTTTTATTTCAT
1 TTATTTTTTATTTC-T
2737747 TTATTTTATT-TTTCT
1 TTATTTT-TTATTTCT
2737762 TTAGTTTATTTAT
1 TTA-TTT-TTTAT
2737775 CTTCATTGCC
Statistics
Matches: 120, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
15 15 0.12
16 33 0.28
17 23 0.19
18 34 0.28
19 15 0.12
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (15 bp):
TTATTTTTTATTTCT
Found at i:2737686 original size:33 final size:33
Alignment explanation
Indices: 2737614--2737687 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
2737604 TTTTGATTAT
* *
2737614 TTTTTATTTTTCTTCATTTTTTTATTTCTTTTGT
1 TTTTTA-TGTTCTTCATTTTTTTATTTCTTTTGA
*
2737648 TTTTTATGTTCTTTATTTTATTTAGTTT-TTTT-A
1 TTTTTATGTTCTTCATTTT-TTTA-TTTCTTTTGA
2737681 TTTTTAT
1 TTTTTAT
2737688 TTAGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 18 0.51
34 14 0.40
35 3 0.09
ACGTcount: A:0.12, C:0.05, G:0.04, T:0.78
Consensus pattern (33 bp):
TTTTTATGTTCTTCATTTTTTTATTTCTTTTGA
Found at i:2737687 original size:19 final size:18
Alignment explanation
Indices: 2737659--2737697 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
2737649 TTTTATGTTC
2737659 TTTATTTTATTTAGTTTT
1 TTTATTTTATTTAGTTTT
2737677 TTTATTTTTATTTAGTTTT
1 TTTA-TTTTATTTAGTTTT
2737696 TT
1 TT
2737698 ATGTCTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTATTTTATTTAGTTTT
Found at i:2738748 original size:5 final size:5
Alignment explanation
Indices: 2738729--2738844 Score: 66
Period size: 5 Copynumber: 22.8 Consensus size: 5
2738719 TATATTTACT
* *
2738729 TTTTA TTTT- TCTTA TTTTA TTTTA TTTGT- TTTT- TTCTT- TTTTC TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TT-TTA TTTTA TTTTA
* *
2738777 TCTTTA TCTTT- TCTTA TTTTA -TTT- TTTTA TATTA GTTTTA TTTATA
1 T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT-TA
2738823 TATTTA TTTTCA TTTGTA TTTT
1 T-TTTA TTTT-A TTT-TA TTTT
2738845 CCTCTTGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
4 16 0.18
5 44 0.48
6 28 0.31
7 3 0.03
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:2738748 original size:14 final size:14
Alignment explanation
Indices: 2738729--2738806 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 14
2738719 TATATTTACT
2738729 TTTTATTTTTCTTA
1 TTTTATTTTTCTTA
* *
2738743 TTTTATTTTATTTGTTT
1 TTTTA--TT-TTTCTTA
*
2738760 TTTTCTTTTTTCTTTTA
1 TTTT-ATTTTTC--TTA
2738777 TCTTTATCTTTTCTTA
1 T-TTTAT-TTTTCTTA
2738793 TTTTATTTTT-TTA
1 TTTTATTTTTCTTA
2738806 T
1 T
2738807 ATTAGTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 17
0.68 0.08 0.23
Matches are distributed among these distances:
13 4 0.08
14 9 0.18
15 8 0.16
16 8 0.16
17 13 0.26
18 8 0.16
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTCTTA
Found at i:2738762 original size:25 final size:26
Alignment explanation
Indices: 2738730--2738801 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
2738720 ATATTTACTT
2738730 TTTA-TTTTTCTTATTTTATTTTAT-
1 TTTATTTTTTCTTATTTTATTTTATC
*
2738754 TTGT-TTTTTTCTT-TTTTCTTTTATC
1 TT-TATTTTTTCTTATTTTATTTTATC
*
2738779 TTTATCTTTTCTTATTTTATTTT
1 TTTATTTTTTCTTATTTTATTTT
2738802 TTTATATTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 13 0.32
25 19 0.47
26 8 0.20
ACGTcount: A:0.11, C:0.08, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTATTTTTTCTTATTTTATTTTATC
Found at i:2738861 original size:4 final size:4
Alignment explanation
Indices: 2738852--2738877 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2738842 TTTCCTCTTG
2738852 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
2738878 ATGTATATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2738912 original size:5 final size:5
Alignment explanation
Indices: 2738897--2739117 Score: 52
Period size: 5 Copynumber: 43.0 Consensus size: 5
2738887 CAATTATTAG
* * *
2738897 TATTT TCTTT TATTT TATTCT TATTTT TATTT TATTT TGCTCGT TATCTT
1 TATTT TATTT TATTT TATT-T TA-TTT TATTT TATTT T-AT-TT TAT-TT
*
2738947 TATTT TGATTAT T-TTT TATTT T-TCTT CA-TT T-TTT TATTT CT-TTT
1 TATTT T-ATT-T TATTT TATTT TAT-TT TATTT TATTT TATTT -TATTT
* * * * *
2738991 GTTTTT TATGT T-CTT TATTT TA-TT TAGTT T-TTT TATTTT TATTT AGTTTTT
1 -TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT --TATTT
* * ** *
2739042 TATGTCT TTTCTT TATCT TATTT TCCTT T-TTT CA-TT TATTTT TATTT
1 TAT-T-T TAT-TT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT
* *
2739089 CA-TT TATTT TATTT T-TCTT TAGTT TATTT
1 TATTT TATTT TATTT TAT-TT TATTT TATTT
2739118 ATCTTCATTG
Statistics
Matches: 158, Mismatches: 31, Indels: 54
0.65 0.13 0.22
Matches are distributed among these distances:
4 26 0.16
5 85 0.54
6 33 0.21
7 14 0.09
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:2738926 original size:12 final size:11
Alignment explanation
Indices: 2738899--2739034 Score: 57
Period size: 11 Copynumber: 11.7 Consensus size: 11
2738889 ATTATTAGTA
*
2738899 TTTTCTTTTA-
1 TTTTATTTTAT
2738909 TTTTATTCTTAT
1 TTTTATT-TTAT
2738921 TTTTATTTTAT
1 TTTTATTTTAT
** *
2738932 TTTGCTCGTTAT
1 TTTTAT-TTTAT
*
2738944 CTTTATTTTGAT
1 TTTTATTTT-AT
*
2738956 TATT-TTTTAT
1 TTTTATTTTAT
*
2738966 TTTTCTTCATT-T
1 TTTTATT--TTAT
2738978 TTTTATTTCT-T
1 TTTTATTT-TAT
2738989 TTGTT-TTTTATGT
1 TT-TTATTTTA--T
2739002 TCTTTATTTTAT
1 T-TTTATTTTAT
*
2739014 TTAGTTTTTTTAT
1 TT--TTATTTTAT
2739027 TTTTATTT
1 TTTTATTT
2739035 AGTTTTTTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
10 13 0.14
11 32 0.33
12 29 0.30
13 16 0.17
14 6 0.06
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:2738929 original size:22 final size:21
Alignment explanation
Indices: 2738899--2739042 Score: 63
Period size: 22 Copynumber: 6.8 Consensus size: 21
2738889 ATTATTAGTA
*
2738899 TTTTCTTTTATTTTATTCTTAT
1 TTTTATTTTATTTT-TTCTTAT
*
2738921 TTTTATTTTATTTTGCTCGTTAT
1 TTTTATTTTATTTT-TTC-TTAT
*
2738944 CTTTATTTTGATTATTTT-TTAT
1 TTTTATTTT-ATT-TTTTCTTAT
* *
2738966 TTTT-CTTCA-TTTTT-TTAT
1 TTTTATTTTATTTTTTCTTAT
*
2738984 TTCTT-TTGTTTTTTATGTTCTT-T
1 TT-TTATT-TTATTT-T-TTCTTAT
*
2739007 ATTTTA-TTTAGTTTTT-TTAT
1 -TTTTATTTTATTTTTTCTTAT
2739027 TTTTA-TTTAGTTTTTT
1 TTTTATTTTA-TTTTTT
2739043 ATGTCTTTTC
Statistics
Matches: 95, Mismatches: 14, Indels: 28
0.69 0.10 0.20
Matches are distributed among these distances:
18 10 0.11
19 15 0.16
20 10 0.11
21 5 0.05
22 27 0.28
23 18 0.19
24 8 0.08
25 2 0.02
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTATTTTATTTTTTCTTAT
Found at i:2738948 original size:23 final size:22
Alignment explanation
Indices: 2738904--2738952 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2738894 TAGTATTTTC
* *
2738904 TTTTATTTTATTCTTATTTTTA
1 TTTTATTTTACTCTTATCTTTA
*
2738926 TTTTATTTTGCTCGTTATCTTTA
1 TTTTATTTTACTC-TTATCTTTA
2738949 TTTT
1 TTTT
2738953 GATTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTATTTTACTCTTATCTTTA
Found at i:2738990 original size:9 final size:8
Alignment explanation
Indices: 2738945--2739044 Score: 69
Period size: 9 Copynumber: 11.6 Consensus size: 8
2738935 GCTCGTTATC
2738945 TTTATTTT
1 TTTATTTT
*
2738953 GATTA-TTT
1 -TTTATTTT
2738961 TTTATTTT
1 TTTATTTT
2738969 TCTTCATTTT
1 T-TT-ATTTT
2738979 TTTATTTCT
1 TTTATTT-T
*
2738988 TTT-GTTT
1 TTTATTTT
*
2738995 TTTATGTTC
1 TTTAT-TTT
2739004 TTTATTTT
1 TTTATTTT
2739012 ATTTAGTTTT
1 -TTTA-TTTT
2739022 TTTATTTTT
1 TTTA-TTTT
*
2739031 ATTTAGTTT
1 -TTTATTTT
2739040 TTTAT
1 TTTAT
2739045 GTCTTTTCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
7 7 0.10
8 19 0.26
9 33 0.45
10 14 0.19
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:2739011 original size:16 final size:15
Alignment explanation
Indices: 2738955--2739119 Score: 57
Period size: 18 Copynumber: 9.7 Consensus size: 15
2738945 TTTATTTTGA
2738955 TTATTTTTTATTTTTCT
1 TTATTTTTTA--TTTCT
*
2738972 TCATTTTTTTATTTCTT
1 TTA-TTTTTTATTTC-T
*
2738989 TTGTTTTTTATGTTCT
1 TTATTTTTTAT-TTCT
*
2739005 TTATTTTATTTAGTTTTT
1 TTA-TTT-TTTA-TTTCT
2739023 TTATTTTTATTTAGTTT-T
1 TTA--TTT-TTTA-TTTCT
* *
2739041 TTATGTCTTTTCTTTAT
1 TTAT-T-TTTTATTTCT
*
2739058 CTTATTTTCCTTTTTTCAT
1 -TTATTTT--TTATTTC-T
2739077 TTA-TTTTTATTTCAT
1 TTATTTTTTATTTC-T
2739092 TTATTTTATT-TTTCT
1 TTATTTT-TTATTTCT
2739107 TTAGTTTATTTAT
1 TTA-TTT-TTTAT
2739120 CTTCATTGCC
Statistics
Matches: 120, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
15 15 0.12
16 33 0.28
17 23 0.19
18 34 0.28
19 15 0.12
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (15 bp):
TTATTTTTTATTTCT
Found at i:2739031 original size:33 final size:33
Alignment explanation
Indices: 2738959--2739032 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
2738949 TTTTGATTAT
* *
2738959 TTTTTATTTTTCTTCATTTTTTTATTTCTTTTGT
1 TTTTTA-TGTTCTTCATTTTTTTATTTCTTTTGA
*
2738993 TTTTTATGTTCTTTATTTTATTTAGTTT-TTTT-A
1 TTTTTATGTTCTTCATTTT-TTTA-TTTCTTTTGA
2739026 TTTTTAT
1 TTTTTAT
2739033 TTAGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 18 0.51
34 14 0.40
35 3 0.09
ACGTcount: A:0.12, C:0.05, G:0.04, T:0.78
Consensus pattern (33 bp):
TTTTTATGTTCTTCATTTTTTTATTTCTTTTGA
Found at i:2739032 original size:19 final size:18
Alignment explanation
Indices: 2739004--2739042 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
2738994 TTTTATGTTC
2739004 TTTATTTTATTTAGTTTT
1 TTTATTTTATTTAGTTTT
2739022 TTTATTTTTATTTAGTTTT
1 TTTA-TTTTATTTAGTTTT
2739041 TT
1 TT
2739043 ATGTCTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTATTTTATTTAGTTTT
Found at i:2739712 original size:17 final size:18
Alignment explanation
Indices: 2739690--2739738 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
2739680 GTTTCAGATT
*
2739690 CAGATTTCAATTCC-TGA
1 CAGATTTCAATTCCTTCA
2739707 CAGATTTCAATTCCTTCA
1 CAGATTTCAATTCCTTCA
*
2739725 TAGATTTCAATTCC
1 CAGATTTCAATTCC
2739739 CTCAGAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (18 bp):
CAGATTTCAATTCCTTCA
Found at i:2742497 original size:21 final size:21
Alignment explanation
Indices: 2742471--2742513 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2742461 TTTGAAACGA
2742471 GGGACTCATGGTTGTCATTGT
1 GGGACTCATGGTTGTCATTGT
2742492 GGGACTCATGGTTGTCATTGT
1 GGGACTCATGGTTGTCATTGT
2742513 G
1 G
2742514 TGTATCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.35, T:0.37
Consensus pattern (21 bp):
GGGACTCATGGTTGTCATTGT
Found at i:2744484 original size:23 final size:23
Alignment explanation
Indices: 2744458--2744505 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2744448 ATAAAGTACA
*
2744458 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2744481 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2744504 AT
1 AT
2744506 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2744957 original size:23 final size:23
Alignment explanation
Indices: 2744922--2744994 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2744912 ATACTTTACA
*
2744922 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2744945 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2744968 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2744991 ATAT
1 ATAT
2744995 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2745160 original size:431 final size:431
Alignment explanation
Indices: 2744572--2746489 Score: 3617
Period size: 431 Copynumber: 4.5 Consensus size: 431
2744562 TATTACATTA
*
2744572 TATTATATTAAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
2744637 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
2744701 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
2744766 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
2744831 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* *
2744896 TTTATAAAAATGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCTA
2744961 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
2745002 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
2745067 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
2745132 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
2745197 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
2745262 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* * *
2745327 TTTATAAAAATGATAGATACTTTACAATATAAGCACTACCTATTATATTATATAAACGCTACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCTA
2745392 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
2745433 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
2745498 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
2745563 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
*
2745628 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
2745693 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
2745758 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACTTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCTA
2745823 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
2745864 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
2745929 TTATGTTTTAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
2745994 AGTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
*
2746059 AATAATAATATATATCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
2746124 CTTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* * *
2746189 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACATATTACATTATATAAACGATATCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCTA
2746254 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
2746295 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
2746360 TTATGTTTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* * *
2746424 ATTTGCACAAAAAATTATTTGATTGTTTTGATACTTTATAAAATAATATTTAGAA-TTTAAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
2746488 AA
196 AA
2746490 CAACATTAAC
Statistics
Matches: 1461, Mismatches: 26, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
429 10 0.01
430 179 0.12
431 1272 0.87
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (431 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCTA
TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:2745380 original size:23 final size:23
Alignment explanation
Indices: 2745353--2745425 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2745343 ATACTTTACA
* *
2745353 ATATAAGCACTACCTATTATATT
1 ATATAAGCGCTACCTATTACATT
*
2745376 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2745399 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2745422 ATAT
1 ATAT
2745426 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2745819 original size:23 final size:23
Alignment explanation
Indices: 2745784--2745856 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2745774 ATACTTTACA
* *
2745784 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
2745807 ATATAAACGCTACTTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
2745830 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2745853 ATAT
1 ATAT
2745857 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2746255 original size:23 final size:23
Alignment explanation
Indices: 2746229--2746287 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2746219 AACCACTACA
*
2746229 TATTACATTATATAAACGATATC
1 TATTACATTATATAAACGATACC
* *
2746252 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACC
*
2746275 TATTACATCATAT
1 TATTACATTATAT
2746288 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (23 bp):
TATTACATTATATAAACGATACC
Found at i:2746762 original size:39 final size:39
Alignment explanation
Indices: 2746708--2746794 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2746698 TCAAGTTGTA
*
2746708 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
2746747 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
2746786 GATTTTGAT
1 GATTTTGAT
2746795 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:2747081 original size:24 final size:24
Alignment explanation
Indices: 2747054--2747101 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2747044 TAGTGGAGCC
* *
2747054 GAAATATATATTGAAACTCAAATT
1 GAAATATAAATTCAAACTCAAATT
* *
2747078 GAAATTTAAATTCAAACTCCAATT
1 GAAATATAAATTCAAACTCAAATT
2747102 ATATATGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (24 bp):
GAAATATAAATTCAAACTCAAATT
Found at i:2747514 original size:25 final size:25
Alignment explanation
Indices: 2747480--2747529 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2747470 ATTATTTTTC
* *
2747480 CAAATAATGTACCCATAGCAATGTT
1 CAAATAATGTACCCACAACAATGTT
2747505 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2747530 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2747839 original size:23 final size:23
Alignment explanation
Indices: 2747813--2747875 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2747803 ATATAACCAC
2747813 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2747836 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2747859 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2747876 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2748279 original size:25 final size:25
Alignment explanation
Indices: 2748222--2748287 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
2748212 CACTCAAAAG
*
2748222 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
2748247 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
2748272 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
2748288 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:2751282 original size:183 final size:183
Alignment explanation
Indices: 2750757--2751249 Score: 880
Period size: 183 Copynumber: 2.7 Consensus size: 183
2750747 TTAAAATTAC
* *
2750757 CGACACTTTTTTAAATGGTATCGACATATTTTTCTTCCAATTTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
2750822 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
2750887 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
2750940 CGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCAACACAAT
1 CGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
2751005 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2751070 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
2751123 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
2751187 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGGATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
2751250 ATAGCATTGC
Statistics
Matches: 298, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
183 295 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:2751655 original size:21 final size:21
Alignment explanation
Indices: 2751625--2751678 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2751615 GATAGATACT
*
2751625 TTACAATATAA-CCACTACCTA
1 TTACATTATAAGCCA-TACCTA
*
2751646 TTACATTATATAAGCGATACCTA
1 TTACA-T-TATAAGCCATACCTA
2751669 TTACATTATA
1 TTACATTATA
2751679 TAAGCGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 9 0.32
22 1 0.04
23 16 0.57
24 2 0.07
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (21 bp):
TTACATTATAAGCCATACCTA
Found at i:2751666 original size:23 final size:23
Alignment explanation
Indices: 2751640--2751702 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2751630 ATATAACCAC
2751640 TACCTATTACATTATATAAGCGA
1 TACCTATTACATTATATAAGCGA
*
2751663 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGA
* *
2751686 TACTTATTACATCATAT
1 TACCTATTACATTATAT
2751703 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGA
Found at i:2752088 original size:432 final size:431
Alignment explanation
Indices: 2751286--2752321 Score: 1941
Period size: 432 Copynumber: 2.4 Consensus size: 431
2751276 TTATAATATG
2751286 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
2751351 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
2751416 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAAAATTTTTAATTTAATAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAAAATTTTTAATTTAATAATA
*
2751481 ATATATATCGTAACGTAAAAAATAAATCATTAGATGCCTATAATTACTAAATTAATATCTTAAAA
196 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
*
2751546 CTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAATGAAAAAAGTATAGACACTTTTATAA
261 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATAGACACTTTTATAA
* *
2751611 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAGCGATACCTATTACATT
326 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATT
*
2751676 ATATAAGCGCTACTTATTACATCATATTTTTACCTATTATA
391 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
2751717 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
2751782 TCAATTTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TCAA-TTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
2751847 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAAAATTTTTAATTTAATAAT
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAAAATTTTTAATTTAATAAT
2751912 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
195 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
* *
2751977 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAGTATAGACACTTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATAGACACTTTTATA
2752042 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACAT
325 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACAT
2752107 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
2752149 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATAC-TTTTTTTAAAGATATGTAATTTATGT
*
2752214 TTCAA-TTTTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTA
65 TTCAATTTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
2752277 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
129 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
2752322 TAGAATTTAA
Statistics
Matches: 592, Mismatches: 10, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
430 2 0.00
431 168 0.28
432 392 0.66
433 30 0.05
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (431 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAAAATTTTTAATTTAATAATA
ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATAGACACTTTTATAA
AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:2752099 original size:23 final size:23
Alignment explanation
Indices: 2752062--2752134 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
2752052 ATACTTTACA
* *
2752062 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
2752085 ATATAAACGAC-ACCTATTACATT
1 ATATAAACG-CTACCTATTACATT
* *
2752108 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2752131 ATAT
1 ATAT
2752135 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2752535 original size:86 final size:86
Alignment explanation
Indices: 2752390--2752552 Score: 326
Period size: 86 Copynumber: 1.9 Consensus size: 86
2752380 TTATTGTTTT
2752390 TAATTTAATAATATGTAAGTTATGTAATAGGTAGCGCTTATATTTACCTATTTTATAAGTAAACC
1 TAATTTAATAATATGTAAGTTATGTAATAGGTAGCGCTTATATTTACCTATTTTATAAGTAAACC
2752455 GGTTTACTTATGTAAGTTATG
66 GGTTTACTTATGTAAGTTATG
2752476 TAATTTAATAATATGTAAGTTATGTAATAGGTAGCGCTTATATTTACCTATTTTATAAGTAAACC
1 TAATTTAATAATATGTAAGTTATGTAATAGGTAGCGCTTATATTTACCTATTTTATAAGTAAACC
2752541 GGTTTACTTATG
66 GGTTTACTTATG
2752553 CCACACGAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (86 bp):
TAATTTAATAATATGTAAGTTATGTAATAGGTAGCGCTTATATTTACCTATTTTATAAGTAAACC
GGTTTACTTATGTAAGTTATG
Found at i:2752983 original size:9 final size:9
Alignment explanation
Indices: 2752969--2753048 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
2752959 CTTGTTTGGA
2752969 TCATCATCT
1 TCATCATCT
2752978 TCATCATCAT
1 TCATCATC-T
*
2752988 CATCATCATCG
1 --TCATCATCT
2752999 TCATCATCT
1 TCATCATCT
* *
2753008 TCATCGTCA
1 TCATCATCT
* * *
2753017 GCTTCATCG
1 TCATCATCT
*
2753026 TCATCATCA
1 TCATCATCT
*
2753035 TCGTCATCT
1 TCATCATCT
2753044 TCATC
1 TCATC
2753049 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
9 45 0.83
10 1 0.02
12 8 0.15
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.38
Consensus pattern (9 bp):
TCATCATCT
Found at i:2752985 original size:12 final size:12
Alignment explanation
Indices: 2752972--2753060 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
2752962 GTTTGGATCA
* *
2752972 TCATCTTCATCA
1 TCATCGTCATCT
* *
2752984 TCATCATCATCA
1 TCATCGTCATCT
* *
2752996 TCGTCATCATCT
1 TCATCGTCATCT
*
2753008 TCATCGTCAGCT
1 TCATCGTCATCT
*
2753020 TCATCGTCATCA
1 TCATCGTCATCT
2753032 TCATCGTCATCT
1 TCATCGTCATCT
*
2753044 TCATCGTCAGCT
1 TCATCGTCATCT
2753056 TCATC
1 TCATC
2753061 TTCTGCGACC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:2752987 original size:6 final size:6
Alignment explanation
Indices: 2752968--2753048 Score: 81
Period size: 6 Copynumber: 13.5 Consensus size: 6
2752958 ACTTGTTTGG
* * * *
2752968 ATCATC ATCTTC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * * *
2753016 AGCTTC ATCGTC ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATC
2753049 GTCAGCTTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:2753024 original size:36 final size:36
Alignment explanation
Indices: 2752984--2753060 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
2752974 ATCTTCATCA
*
2752984 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
2753020 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
2753056 TCATC
1 TCATC
2753061 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:2753063 original size:6 final size:6
Alignment explanation
Indices: 2752972--2753063 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
2752962 GTTTGGATCA
* * * * * * *
2752972 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
2753020 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
2753064 TGCGACCGCT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:2754867 original size:198 final size:199
Alignment explanation
Indices: 2754529--2755263 Score: 1357
Period size: 199 Copynumber: 3.7 Consensus size: 199
2754519 TTTAAATTAG
2754529 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
2754593 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATATTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* *
2754658 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
2754723 AAAA
196 AAAA
* *
2754727 TATCGACACCAACTAAAA-AGTGTCGACACATTAGTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2754791 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
2754856 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
2754921 AAAA
196 AAAA
*
2754925 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATG
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2754990 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
2755055 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
2755120 AAAA
196 AAAA
* *
2755124 TATCGACACAAACTAAAATAGTATCGGCACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
2755189 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
2755254 TCGACACTTT
130 TCGACACTTT
2755264 ATGGTTGCAC
Statistics
Matches: 522, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
198 210 0.40
199 286 0.55
200 26 0.05
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:2755444 original size:19 final size:19
Alignment explanation
Indices: 2755398--2755444 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
2755388 TTATATTCAC
*
2755398 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
2755417 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
2755436 ATACAAAAT
1 ATACAAAAT
2755445 CCCTACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2757281 original size:32 final size:32
Alignment explanation
Indices: 2757239--2757299 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2757229 TTAATATCAC
*
2757239 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
2757271 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
2757300 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:2757358 original size:21 final size:21
Alignment explanation
Indices: 2757333--2757376 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2757323 CCCCTTATGC
2757333 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
2757354 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
2757375 CT
1 CT
2757377 TGATTGTCTT
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:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2759611 original size:17 final size:18
Alignment explanation
Indices: 2759589--2759631 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2759579 ATATATCCGG
2759589 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2759606 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2759626 TATCAT
1 TATCAT
2759632 ATTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2759891 original size:161 final size:162
Alignment explanation
Indices: 2759617--2759954 Score: 498
Period size: 161 Copynumber: 2.1 Consensus size: 162
2759607 ATCATTTTGA
* * * *
2759617 TACCGGTTTTATCATATTTTTACTTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
* *
2759682 ACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAAG
** * *
2759746 TATTGACACTTTCAATATATCCGGTAACGTTT
131 TACCGACACTTTAAATATATCCGGTAACGCTT
* *
2759778 TATCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
* ** *
2759843 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATTAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAAG
* * *
2759908 TACCGACACTTTAAATGTATCTGGTAGCGCTT
131 TACCGACACTTTAAATATATCCGGTAACGCTT
2759940 TACCGGTTTTATCAT
1 TACCGGTTTTATCAT
2759955 TTCTATACCG
Statistics
Matches: 156, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
161 112 0.72
162 44 0.28
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (162 bp):
TACCGGTTTTATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATTAAAG
TACCGACACTTTAAATATATCCGGTAACGCTT
Found at i:2760006 original size:161 final size:158
Alignment explanation
Indices: 2759617--2760010 Score: 346
Period size: 161 Copynumber: 2.4 Consensus size: 158
2759607 ATCATTTTGA
* * * * * ** * * *
2759617 TACCGGTTTTATCATATTTTTACTTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTATACCTGGTATATAGTTTTACATCGATACA-TGTTTT--AGGATCG
* *
2759682 ACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGT
63 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATAAAGT
** * *
2759747 ATTGACACTTTCAATATATCCGGTAACGTTT
128 ACCGACACTTTAAATATATCCGGTAACGCTT
* * * ** * *
2759778 TATCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGTTTTATCATATTTATACCTGGTATATAGTTTTACATCGATACATGTTTT---AGGATCG
* ** *
2759843 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATTAAAG
63 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATA-TAAAG
* * *
2759908 TACCGACACTTTAAATGTATCTGGTAGCGCTT
127 TACCGACACTTTAAATATATCCGGTAACGCTT
* * *
2759940 TACCGGTTTTATCAT-TTCTATACC-GGTTTTGTCATAGTTTTACAT-GTTATATCGTTTT-GGA
1 TACCGGTTTTATCATATT-TATACCTGG---TAT-ATAGTTTTACATCGATACAT-GTTTTAGGA
2760001 TCGACACATT
60 TCGACACATT
2760011 TTTTATTTGG
Statistics
Matches: 196, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
160 6 0.03
161 121 0.62
162 49 0.25
164 7 0.04
165 13 0.07
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (158 bp):
TACCGGTTTTATCATATTTATACCTGGTATATAGTTTTACATCGATACATGTTTTAGGATCGACA
CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATAAAGTACC
GACACTTTAAATATATCCGGTAACGCTT
Found at i:2760511 original size:225 final size:226
Alignment explanation
Indices: 2760084--2760570 Score: 825
Period size: 228 Copynumber: 2.2 Consensus size: 226
2760074 ACTTTTATAC
2760084 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATATAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATATAATTTATGTTTCAATTT
* *
2760149 TTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTTATTTACACAAAATTA
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATTA
2760214 TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATAT
131 TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATAT
*
2760279 -AATAATAAATATGTTTCCACAGTGAAATAA
196 AAATAATAAATATATTTCCACAGTGAAATAA
* * *
2760309 GTATGGACATTTTTATAAAAATGATATATATTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATATAATTTATGTTTCAATTT
*
2760374 TTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTT--ACACAAAAT
*
2760439 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
129 TATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
* *
2760504 GAT-AATAATAAATATATTTTCACAGTGAAATAA
193 TATAAATAATAAATATATTTCCACAGTGAAATAA
* *
2760537 GTATGGACACTTTTATAAAAAGGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
2760571 ACAATATAAC
Statistics
Matches: 245, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
225 113 0.46
227 18 0.07
228 114 0.47
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (226 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATATAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATTA
TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATAT
AAATAATAAATATATTTCCACAGTGAAATAA
Found at i:2760834 original size:11 final size:11
Alignment explanation
Indices: 2760818--2760842 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2760808 ATCCGGTACT
2760818 ACCGTATATTA
1 ACCGTATATTA
2760829 ACCGTATATTA
1 ACCGTATATTA
2760840 ACC
1 ACC
2760843 TGCCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:2766173 original size:3 final size:3
Alignment explanation
Indices: 2766167--2766207 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2766157 CGCCATTATT
2766167 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2766208 ATTCATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2774033 original size:46 final size:45
Alignment explanation
Indices: 2773948--2774034 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
2773938 TAAAATATTA
* * *
2773948 ATTAATAATTTAGTATTTTTTTATTGTTTATTAGAAAATTAATAG
1 ATTAATAATTTAGTATTTTTTTATTATCTATTACAAAATTAATAG
* *
2773993 ATTAGTAATTTA-TCATTTTTTCTATTATCTATTACTAAATTA
1 ATTAATAATTTAGT-ATTTTTT-TATTATCTATTACAAAATTA
2774035 GTAATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.03
45 18 0.51
46 16 0.46
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.54
Consensus pattern (45 bp):
ATTAATAATTTAGTATTTTTTTATTATCTATTACAAAATTAATAG
Found at i:2776846 original size:22 final size:22
Alignment explanation
Indices: 2776821--2776871 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2776811 ACGTGAGAAT
*
2776821 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
2776843 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
2776865 CACGGGT
1 CACGGGT
2776872 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:2776914 original size:23 final size:23
Alignment explanation
Indices: 2776888--2776931 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2776878 TCCTGCAAGG
2776888 CTGCACGTCCGCATGTGGGGGTC
1 CTGCACGTCCGCATGTGGGGGTC
*
2776911 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCCGCATGTGGGGG
2776932 GCATGCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.23
Consensus pattern (23 bp):
CTGCACGTCCGCATGTGGGGGTC
Found at i:2776938 original size:23 final size:23
Alignment explanation
Indices: 2776889--2776938 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2776879 CCTGCAAGGC
* *
2776889 TGCACGTCCGCATGTGGGGGTCC
1 TGCACGTCCGCATGTGGGGGGCA
*
2776912 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCCGCATGTGGGGGGCA
2776935 TGCA
1 TGCA
2776939 ACTGATGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.26, G:0.40, T:0.22
Consensus pattern (23 bp):
TGCACGTCCGCATGTGGGGGGCA
Found at i:2777141 original size:30 final size:30
Alignment explanation
Indices: 2777107--2777167 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2777097 CAATTACAGA
2777107 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
1 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
2777137 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
1 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
2777167 A
1 A
2777168 CAAAGCATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.39, T:0.20
Consensus pattern (30 bp):
AGCAGTGAGAGCTTGAGAGGGAGATTGATC
Found at i:2777715 original size:170 final size:171
Alignment explanation
Indices: 2777387--2777723 Score: 534
Period size: 170 Copynumber: 2.0 Consensus size: 171
2777377 TTTAGGGACA
* * *
2777387 TTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTATACTATGCTGG
1 TTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTATACTATGCTGG
*
2777452 AATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTAAAATTTATGGATTAAATTGC
66 AATTTAGTATTAGAATGCTTAATTGGTTAAATTAGAAAGAATTTAAAATTTATGGATTAAATTGC
*
2777517 TAACTTTGAAAATGTTGAGAACCAAATAGTAATTAGGATCG
131 AAACTTTGAAAATGTTGAGAACCAAATAGTAATTAGGATCG
* * * *
2777558 TTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTATACTATGCTTG
1 TTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTATACTATGCTGG
* *
2777623 AATTTAGTATTA-AATGCTTAATTGGTTAAATTTGAAAGAATTTATAATTTA-GTGATTAAATTG
66 AATTTAGTATTAGAATGCTTAATTGGTTAAATTAGAAAGAATTTAAAATTTATG-GATTAAATTG
* *
2777686 CAAAGTTTGAAAATGTTGAGAAGCAAATAGTAATTAGG
130 CAAACTTTGAAAATGTTGAGAACCAAATAGTAATTAGG
2777724 GATAATTTTA
Statistics
Matches: 152, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
169 1 0.01
170 81 0.53
171 70 0.46
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (171 bp):
TTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTATACTATGCTGG
AATTTAGTATTAGAATGCTTAATTGGTTAAATTAGAAAGAATTTAAAATTTATGGATTAAATTGC
AAACTTTGAAAATGTTGAGAACCAAATAGTAATTAGGATCG
Found at i:2780166 original size:47 final size:47
Alignment explanation
Indices: 2780101--2780869 Score: 705
Period size: 47 Copynumber: 17.5 Consensus size: 47
2780091 AGTAATTATT
*
2780101 ATTAAATTATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
2780146 ATTAAATCATTAAATCATTAAATCATT-AA--AA-TA--ATT--ATT
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
2780185 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
2780232 ATT--A------AA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* * * *
2780269 ATTAAATCATTAAATCATTAAATCATTAAA-TCATTA-AAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAA--ATC
2780316 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* *
2780363 ATTAAATCATTAAATCATTAAATCATTAAAATAATAATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* *
2780410 ATTAAATCATTAAATCATTAAATCATTAAAATAATAATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* * * *
2780457 ATTAAATCATTAAAGTAATT--ATTATTAAA-TCATTAAATCATTAAATC
1 ATTAAATCATTAAA-TCATTAAATCATTAAAGTAATT--ATTATTAAATC
* * * *
2780504 ATTAAAGTAATT--ATTATTAAATCATTAAAGTTAA--ATCATTAAAGTA
1 ATTAAA-TCATTAAATCATTAAATCATTAAAG-TAATTATTATTAAA-TC
* * *
2780550 ATT--ATTATTAAATCATTAAATCATTAAA-TCATTAAATCATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATT--ATTATTAAATC
* * * *
2780596 ATTAAATCATTAAAGTAATT--ATTATTAAA-TCATTAAATCATTAAATC
1 ATTAAATCATTAAA-TCATTAAATCATTAAAGTAATT--ATTATTAAATC
2780643 A-T---T-A---AA--ATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
2780680 ATTAAATCATTAAATCATTAAATCATT-AA--AA-TA--ATT--ATT
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
2780719 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
2780766 ATT--A------AA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
2780803 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
2780850 ATTAAA--GTTAAATCATTAAA
1 ATTAAATCATTAAATCATTAAA
2780870 GTAATTATTA
Statistics
Matches: 611, Mismatches: 40, Indels: 146
0.77 0.05 0.18
Matches are distributed among these distances:
36 3 0.00
37 77 0.13
38 9 0.01
39 70 0.11
40 4 0.01
41 7 0.01
42 6 0.01
43 15 0.02
44 5 0.01
45 76 0.12
46 27 0.04
47 281 0.46
48 21 0.03
49 10 0.02
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (47 bp):
ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
Found at i:2780189 original size:39 final size:39
Alignment explanation
Indices: 2780146--2780929 Score: 774
Period size: 39 Copynumber: 19.4 Consensus size: 39
2780136 TTATTAAATC
2780146 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
*
2780185 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* *
2780224 ATTAAATCATTAAA--GTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
*
2780261 ATTAAATCATTAAATCATTAAATCATTAAATCATTAAATCATT
1 ATTAAATCATTAAATCATTAAATCATTAAA--A-T-AATTATT
* *
2780304 AAAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 --ATTAA--ATCATTAAATCATTAAATCA-T---T-A--AAA-TAATTATT
2780355 ATTAAATCATTAAATCATTAAATCATTAAATCATTAAAATAATAATT
1 ATTAAATCATTAAATCATTAAATCATTAAA--A-T--AAT--T-ATT
* **
2780402 ATTAAATCATTAAATCATTAAATCATT-AAATCATTAAA
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* * *
2780440 ATAATAATTATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTA-AATCATTAAATCATTAAATCATTAAAATAATTATT
*
2780480 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* *
2780519 ATTAAATCATTAAA--GTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* *
2780556 ATTAAATCATTAAATCATTAAATCATT-AAATCATTAAATC
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATT--ATT
* * * *
2780596 ATTAAATCATTAAAGTAATT--ATTATT-AAATCATTAAATC
1 ATTAAATCATTAAA-TCATTAAATCATTAAAATAATT--ATT
*
2780635 ATTAAATCATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAATCATT-AA--AA-TA--ATT--ATT
2780680 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
*
2780719 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* *
2780758 ATTAAATCATTAAA--GTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
2780795 ATTAAATCATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCA-T---T-A--AAA-TAATTATT
* *
2780842 ATTAAATCATTAAA--GTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
* *
2780879 ATTAAATCATTAAA--GTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
2780916 ATTAAATCATTAAA
1 ATTAAATCATTAAA
2780930 GTTAAATAAT
Statistics
Matches: 654, Mismatches: 39, Indels: 106
0.82 0.05 0.13
Matches are distributed among these distances:
36 3 0.00
37 167 0.26
38 17 0.03
39 240 0.37
40 31 0.05
41 10 0.02
42 6 0.01
43 12 0.02
44 8 0.01
45 34 0.05
46 8 0.01
47 101 0.15
48 1 0.00
49 4 0.01
51 7 0.01
52 3 0.00
54 2 0.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (39 bp):
ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
Found at i:2780972 original size:8 final size:8
Alignment explanation
Indices: 2779981--2780957 Score: 750
Period size: 8 Copynumber: 128.8 Consensus size: 8
2779971 AGTAATTATT
2779981 ATTAAATC
1 ATTAAATC
2779989 ATTAAA--
1 ATTAAATC
*
2779995 ATAAAATC
1 ATTAAATC
2780003 ATTAAA--
1 ATTAAATC
* *
2780009 ATTAAGTA
1 ATTAAATC
*
2780017 ATT--ATT
1 ATTAAATC
*
2780023 ATTAAATT
1 ATTAAATC
2780031 ATTAAA--
1 ATTAAATC
2780037 ATTAAATC
1 ATTAAATC
*
2780045 ATTAAAGTA
1 ATTAAA-TC
*
2780054 ATT--ATT
1 ATTAAATC
2780060 ATTAAATC
1 ATTAAATC
2780068 ATT-AA--
1 ATTAAATC
2780073 ATTAAATC
1 ATTAAATC
2780081 ATTAAA--
1 ATTAAATC
* *
2780087 ATTAAGTA
1 ATTAAATC
*
2780095 ATT--ATT
1 ATTAAATC
*
2780101 ATTAAATT
1 ATTAAATC
2780109 ATTAAA--
1 ATTAAATC
2780115 ATTAAATC
1 ATTAAATC
*
2780123 ATTAAAGTA
1 ATTAAA-TC
*
2780132 ATT--ATT
1 ATTAAATC
2780138 ATTAAATC
1 ATTAAATC
2780146 ATTAAATC
1 ATTAAATC
2780154 ATTAAATC
1 ATTAAATC
2780162 ATTAAATC
1 ATTAAATC
*
2780170 ATTAAAATA
1 ATT-AAATC
*
2780179 ATT--ATT
1 ATTAAATC
2780185 ATTAAATC
1 ATTAAATC
2780193 ATTAAATC
1 ATTAAATC
2780201 ATTAAATC
1 ATTAAATC
*
2780209 ATTAAAGTA
1 ATTAAA-TC
*
2780218 ATT--ATT
1 ATTAAATC
2780224 ATTAAATC
1 ATTAAATC
2780232 ATTAAA--
1 ATTAAATC
*
2780238 GTTAAATC
1 ATTAAATC
*
2780246 ATTAAAGTA
1 ATTAAA-TC
*
2780255 ATT--ATT
1 ATTAAATC
2780261 ATTAAATC
1 ATTAAATC
2780269 ATTAAATC
1 ATTAAATC
2780277 ATTAAATC
1 ATTAAATC
2780285 ATTAAATC
1 ATTAAATC
2780293 ATTAAATC
1 ATTAAATC
*
2780301 ATTAAAGTA
1 ATTAAA-TC
*
2780310 ATT--ATT
1 ATTAAATC
2780316 ATTAAATC
1 ATTAAATC
2780324 ATTAAATC
1 ATTAAATC
2780332 ATTAAATC
1 ATTAAATC
*
2780340 ATTAAAGTA
1 ATTAAA-TC
*
2780349 ATT--ATT
1 ATTAAATC
2780355 ATTAAATC
1 ATTAAATC
2780363 ATTAAATC
1 ATTAAATC
2780371 ATTAAATC
1 ATTAAATC
2780379 ATTAAATC
1 ATTAAATC
2780387 ATTAAA--
1 ATTAAATC
* *
2780393 ATAATAATT
1 ATTA-AATC
2780402 ATTAAATC
1 ATTAAATC
2780410 ATTAAATC
1 ATTAAATC
2780418 ATTAAATC
1 ATTAAATC
2780426 ATTAAATC
1 ATTAAATC
2780434 ATTAAA--
1 ATTAAATC
* *
2780440 ATAATAATT
1 ATTA-AATC
2780449 ATTAAATC
1 ATTAAATC
2780457 ATTAAATC
1 ATTAAATC
*
2780465 ATTAAAGTA
1 ATTAAA-TC
*
2780474 ATT--ATT
1 ATTAAATC
2780480 ATTAAATC
1 ATTAAATC
2780488 ATTAAATC
1 ATTAAATC
2780496 ATTAAATC
1 ATTAAATC
*
2780504 ATTAAAGTA
1 ATTAAA-TC
*
2780513 ATT--ATT
1 ATTAAATC
2780519 ATTAAATC
1 ATTAAATC
2780527 ATTAAA--
1 ATTAAATC
*
2780533 GTTAAATC
1 ATTAAATC
*
2780541 ATTAAAGTA
1 ATTAAA-TC
*
2780550 ATT--ATT
1 ATTAAATC
2780556 ATTAAATC
1 ATTAAATC
2780564 ATTAAATC
1 ATTAAATC
2780572 ATTAAATC
1 ATTAAATC
2780580 ATTAAATC
1 ATTAAATC
2780588 ATTAAATC
1 ATTAAATC
2780596 ATTAAATC
1 ATTAAATC
*
2780604 ATTAAAGTA
1 ATTAAA-TC
*
2780613 ATT--ATT
1 ATTAAATC
2780619 ATTAAATC
1 ATTAAATC
2780627 ATTAAATC
1 ATTAAATC
2780635 ATTAAATC
1 ATTAAATC
2780643 ATTAAA--
1 ATTAAATC
2780649 ATTAAATC
1 ATTAAATC
*
2780657 ATTAAAGTA
1 ATTAAA-TC
*
2780666 ATT--ATT
1 ATTAAATC
2780672 ATTAAATC
1 ATTAAATC
2780680 ATTAAATC
1 ATTAAATC
2780688 ATTAAATC
1 ATTAAATC
2780696 ATTAAATC
1 ATTAAATC
*
2780704 ATTAAAATA
1 ATT-AAATC
*
2780713 ATT--ATT
1 ATTAAATC
2780719 ATTAAATC
1 ATTAAATC
2780727 ATTAAATC
1 ATTAAATC
2780735 ATTAAATC
1 ATTAAATC
*
2780743 ATTAAAGTA
1 ATTAAA-TC
*
2780752 ATT--ATT
1 ATTAAATC
2780758 ATTAAATC
1 ATTAAATC
2780766 ATTAAA--
1 ATTAAATC
*
2780772 GTTAAATC
1 ATTAAATC
*
2780780 ATTAAAGTA
1 ATTAAA-TC
*
2780789 ATT--ATT
1 ATTAAATC
2780795 ATTAAATC
1 ATTAAATC
2780803 ATTAAATC
1 ATTAAATC
2780811 ATTAAATC
1 ATTAAATC
2780819 ATTAAATC
1 ATTAAATC
*
2780827 ATTAAAGTA
1 ATTAAA-TC
*
2780836 ATT--ATT
1 ATTAAATC
2780842 ATTAAATC
1 ATTAAATC
2780850 ATTAAA--
1 ATTAAATC
*
2780856 GTTAAATC
1 ATTAAATC
*
2780864 ATTAAAGTA
1 ATTAAA-TC
*
2780873 ATT--ATT
1 ATTAAATC
2780879 ATTAAATC
1 ATTAAATC
2780887 ATTAAA--
1 ATTAAATC
*
2780893 GTTAAATC
1 ATTAAATC
*
2780901 ATTAAAGTA
1 ATTAAA-TC
*
2780910 ATT--ATT
1 ATTAAATC
2780916 ATTAAATC
1 ATTAAATC
2780924 ATTAAA--
1 ATTAAATC
* *
2780930 GTTAAATA
1 ATTAAATC
*
2780938 ATT--ATT
1 ATTAAATC
2780944 ATTAAATC
1 ATTAAATC
2780952 ATTAAA
1 ATTAAA
2780958 GTTAAATAAT
Statistics
Matches: 794, Mismatches: 82, Indels: 186
0.75 0.08 0.18
Matches are distributed among these distances:
5 3 0.00
6 158 0.20
7 22 0.03
8 527 0.66
9 84 0.11
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:2784344 original size:17 final size:18
Alignment explanation
Indices: 2784322--2784355 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2784312 ACCAACTTGC
2784322 TTCAGACGAATC-CACGT
1 TTCAGACGAATCTCACGT
2784339 TTCAGACGAATCTCACG
1 TTCAGACGAATCTCACG
2784356 CTTCGGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (18 bp):
TTCAGACGAATCTCACGT
Found at i:2785331 original size:12 final size:12
Alignment explanation
Indices: 2785303--2785344 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
2785293 CGTTAACCCC
2785303 CTTCTTCTTATTT
1 CTTCTTCTTA-TT
*
2785316 CTTCTACTTATT
1 CTTCTTCTTATT
2785328 CTTCTTCTTATT
1 CTTCTTCTTATT
2785340 CTTCT
1 CTTCT
2785345 CTCACACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTCTTCTTATT
Found at i:2791218 original size:129 final size:129
Alignment explanation
Indices: 2791058--2791315 Score: 444
Period size: 129 Copynumber: 2.0 Consensus size: 129
2791048 ACACCAGAAC
*
2791058 GTTGTATATGACCAGCATCTTCAGTACCATTCCTAGGGAATGATTCTTCAGCCCCACTCCCAGGC
1 GTTGTATATGACCAGCATCTTCAGTACCATTCCTAAGGAATGATTCTTCAGCCCCACTCCCAGGC
* * * * *
2791123 GGTGGTTCTTCGGTAACACTCCCAGGTGGTGTAGAGTGTATAGGAACATCTGCCGAGTTAGTAG
66 AGTGATTCTTCAGCAACACTCCCAGGTGGTGTAGAGTGTATAGGAACATCTGCCGAGTCAGTAG
*
2791187 GTTGTATATGACCAGCATCTTCAGTACCATTCCTAAGGAATGATTCTTCAGCCCCACTCCCATGC
1 GTTGTATATGACCAGCATCTTCAGTACCATTCCTAAGGAATGATTCTTCAGCCCCACTCCCAGGC
*
2791252 AGTGATTCTTCAGCAACACTCCCAGGTGGTGTAGAGTGTATAGGAACATCTGTCGAGTCAGTAG
66 AGTGATTCTTCAGCAACACTCCCAGGTGGTGTAGAGTGTATAGGAACATCTGCCGAGTCAGTAG
2791316 AAACTTATGC
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (129 bp):
GTTGTATATGACCAGCATCTTCAGTACCATTCCTAAGGAATGATTCTTCAGCCCCACTCCCAGGC
AGTGATTCTTCAGCAACACTCCCAGGTGGTGTAGAGTGTATAGGAACATCTGCCGAGTCAGTAG
Found at i:2795915 original size:15 final size:16
Alignment explanation
Indices: 2795895--2795935 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2795885 GTTTACTTCA
*
2795895 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
2795910 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
2795926 GAATGATTCA
1 GAATGATTCA
2795936 GAGGCTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:2796775 original size:29 final size:29
Alignment explanation
Indices: 2796733--2796800 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
2796723 TTTTGCCTGA
2796733 TAAATTCTGATGGATTGGATACCATTGAC
1 TAAATTCTGATGGATTGGATACCATTGAC
2796762 TAAATTCTGATGGATTGGATACCATTGAC
1 TAAATTCTGATGGATTGGATACCATTGAC
2796791 TAAATTCTGA
1 TAAATTCTGA
2796801 ACTCTAGGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (29 bp):
TAAATTCTGATGGATTGGATACCATTGAC
Found at i:2819292 original size:36 final size:36
Alignment explanation
Indices: 2819246--2819507 Score: 263
Period size: 36 Copynumber: 7.4 Consensus size: 36
2819236 AGCAAAGTCA
*
2819246 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGA-ATAGTGAAGCAAACC
* *
2819282 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
*
2819318 ATCCT-AAGCC-TCATCG--GAATAGTGAAGCAAACC
1 AT-CTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* * *
2819351 ATCTGAAGCC-TCACCGGAGAATAGTGAAGCAATCA
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
*
2819386 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* *
2819422 ATCAT-AAGTCTTCACC-AGAGAGTAGTGAAGCAAACC
1 ATC-TGAAGCCTTCACCGA-AGAATAGTGAAGCAAACC
* * * *
2819458 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTGAAGCCTTCACCGAAGAA-TAGTGAAGCA-AACC
* *
2819495 ATTTTAAGCCTTC
1 ATCTGAAGCCTTC
2819508 TCAGAAGAGT
Statistics
Matches: 197, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
32 2 0.01
33 29 0.15
35 33 0.17
36 116 0.59
37 17 0.09
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (36 bp):
ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
Found at i:2819381 original size:104 final size:108
Alignment explanation
Indices: 2819246--2819489 Score: 318
Period size: 104 Copynumber: 2.3 Consensus size: 108
2819236 AGCAAAGTCA
* * *
2819246 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTGAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
* *
2819311 GCAAACCATCCTAAG-CCTCATC-G-GAATAGTGAAGCAAACC
66 GCAAACCATCATAAGTCCTCACCAGAGAATAGTGAAGCAAACC
* *
2819351 ATCTGAAGCC-TCACCGGAGA-ATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGA
1 ATCTGAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGA
* *
2819414 AGCAAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
65 AGCAAACCATCATAAGTCCTCACCAGAGAATAGTGAAGCAAACC
* * * * *
2819458 ATCTTAAGTCTTCACCAAAAAGTAGTGAAGCA
1 ATCTGAAGCCTTCACCGAAGAGAAGTGAAGCA
2819490 GATCCATTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
103 1 0.01
104 62 0.53
105 14 0.12
106 1 0.01
107 24 0.20
108 16 0.14
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (108 bp):
ATCTGAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAACCATCATAAGTCCTCACCAGAGAATAGTGAAGCAAACC
Found at i:2819793 original size:51 final size:52
Alignment explanation
Indices: 2819676--2820291 Score: 540
Period size: 51 Copynumber: 11.6 Consensus size: 52
2819666 TGAAGATATA
* *
2819676 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGA-GGT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTGAAGAGATGTT
* * *
2819728 CTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTT
1 C-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGAAGAGATGTT
*
2819780 CGAGTTCTATACTCCCTAAAGAAAGATGGAGCGAGGAGCGAACCCGTTTAA-AGATGTT
1 CGAGTTCTATACTCCCTAAAG-AA-A--GA--G-GGAGCGAACCCGTTGAAGAGATGTT
* * *
2819838 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATG-T
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTGAAGAGATGTT
* *
2819890 CTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTT
1 C-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGAAGAGATGTT
* *
2819942 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGACTAT-TT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC-GTTGAAGA-GATGTT
* * * *
2819995 -GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTG-A-AGATCTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTGAAGAGATGTT
* * ** *
2820045 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTGAAG-AGAT-GTT
* * * * *
2820100 CGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATT
1 CGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCG-TT-GAAGAGA-TGTT
* * * *
2820156 CGAGTTCTATACTCCTTAAAGAAA-A---AGGGAATCCGCTT-ACAGAAGATTATT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTGA-AG-AGA-TGTT
* * * *
2820207 CAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGT-TGAAG-AGATGTT
* * * *
2820261 CGAGTTCCATAATCCCTAGAGAAATAGGGAG
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAG
2820292 TAGACGCAAT
Statistics
Matches: 471, Mismatches: 58, Indels: 68
0.79 0.10 0.11
Matches are distributed among these distances:
49 3 0.01
50 4 0.01
51 157 0.33
52 53 0.11
53 83 0.18
54 40 0.08
55 40 0.08
56 45 0.10
57 5 0.01
58 38 0.08
59 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (52 bp):
CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGAAGAGATGTT
Found at i:2819943 original size:162 final size:156
Alignment explanation
Indices: 2819668--2820291 Score: 658
Period size: 162 Copynumber: 3.9 Consensus size: 156
2819658 GAAGCAAATG
* * *
2819668 AAGA-TATACGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCTAA
1 AAGACTATTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGA-TTCTAA
2819732 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAG-AGATGTTCGAGTTCTATACTCCC
65 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAAGATGTTCGAGTTCTATACTCCC
2819796 TAAAGAAAGATGGAGCGAGGAGCGAACCCGTTTA
130 TAAAG-AA-A--GA--G-GGAGCGAACCCGTTTA
* * *
2819830 AAGA-TGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGA
1 AAGACTATTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAT-TCTAA
2819894 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAG-AGATGTTCGAGTTCTATACTCCC
65 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAAGATGTTCGAGTTCTATACTCCC
* *
2819958 TAAAGAAAGAGGGAGCGAACCCATTTG
130 TAAAGAAAGAGGGAGCGAACCCGTTTA
* * * * ** *
2819985 AAGACTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGATCTTC-GAG
1 AAGACTATTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATTCTAAG
* * ** *
2820049 TTCTATACTCCCT-GAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATTCGAGTTCTATACT
66 TTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCG--TGAAGAAGAT-GTTCGAGTTCTATACT
* *
2820113 TCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAA
127 CCCT-AAAGAAAGAGGGAGCGAACCCGTTT---A
* * * * * *
2820147 AAGATTATTCGAGTTCTATACTCCTTAAAGAAA-AA-G-G-GAATCCGCTT-ACAGAAGATTATT
1 AAGACTATTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGA-AG-AGATT-CT
* * *
2820207 CAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTCGAGTTCCATA
63 -AAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--GAAGAAGATGTTCGAGTTCTATA
* * *
2820272 ATCCCTAGAGAAATAGGGAG
125 CTCCCTAAAGAAAGAGGGAG
2820292 TAGACGCAAT
Statistics
Matches: 395, Mismatches: 48, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
153 1 0.00
154 34 0.09
155 20 0.05
156 50 0.13
157 5 0.01
158 30 0.08
159 27 0.07
160 15 0.04
161 19 0.05
162 193 0.49
163 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (156 bp):
AAGACTATTCGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATTCTAAG
TTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAAGATGTTCGAGTTCTATACTCCCT
AAAGAAAGAGGGAGCGAACCCGTTTA
Found at i:2820170 original size:265 final size:263
Alignment explanation
Indices: 2819667--2820243 Score: 651
Period size: 265 Copynumber: 2.2 Consensus size: 263
2819657 TGAAGCAAAT
* * *
2819667 GAAGA-TATACGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCTA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGAGA-GTCTA
*
2819731 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTCTATACTCCC
65 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATCTTCGAGTTCTATACTCCC
* *
2819796 TAAAGAAAGATGGAGCGAGGAGCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAA
130 TAAAGAAAGA-GGA-CGAGGAGCGAACCCGTTTAAAGATATTCGAGTTCCATACTCCTGAAAGAA
* * * *
2819861 AGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA
193 AGAAGGAGCAAACCCGTTTCAAAAGATGTCTGAGTTCCATACTCCCTAAAGAAA-A---AGCGAA
2819926 CCCG-TGA-A
254 CCCGCTGACA
* * * *
2819934 G-AGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGACTA-TTTG
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGA-GAGTCTA
*
2819996 AGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTG-A-AGATCTTCGAGTTCTATACTC
65 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATCTTCGAGTTCTATACTC
* * *
2820059 CCTGAAG-AA-A-GA-G-GGAGCGAGCCCGTTTTCAGAAGATCATTCGAGTTCTATACTTCCTGA
128 CCTAAAGAAAGAGGACGAGGAGCGAACCCG-TTT-A-AAGAT-ATTCGAGTTCCATAC-TCCTGA
* * * *
2820119 AAGAAAGAGGGAGCAAACCCGTTTCCAAAAGAT-TATTCGAGTTCTATACTCCTTAAAGAAAAAG
188 AAGAAAGAAGGAGCAAACCCGTTT-CAAAAGATGT-CT-GAGTTCCATACTCCCTAAAGAAAAAG
* * *
2820183 GGAATCCGCTTACA
250 CGAACCCGCTGACA
* *
2820197 GAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACC
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACC
2820244 TGTAAGAAGA
Statistics
Matches: 267, Mismatches: 28, Indels: 32
0.82 0.09 0.10
Matches are distributed among these distances:
258 11 0.04
259 4 0.01
260 1 0.00
261 15 0.06
262 15 0.06
263 31 0.12
264 13 0.05
265 122 0.46
266 51 0.19
267 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (263 bp):
GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGAGAGTCTAA
GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATCTTCGAGTTCTATACTCCCT
AAAGAAAGAGGACGAGGAGCGAACCCGTTTAAAGATATTCGAGTTCCATACTCCTGAAAGAAAGA
AGGAGCAAACCCGTTTCAAAAGATGTCTGAGTTCCATACTCCCTAAAGAAAAAGCGAACCCGCTG
ACA
Found at i:2820177 original size:107 final size:101
Alignment explanation
Indices: 2819666--2820280 Score: 427
Period size: 104 Copynumber: 5.8 Consensus size: 101
2819656 GTGAAGCAAA
* * * * * * **
2819666 TGAAGATATACGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGA-GGTCT
1 TGAAGACATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT-AAAAGATATTC-
* *
2819730 AAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--
64 GAGTTCTATACTCCCT--AGAAAGAGGGAGCGAACCCGTT
* * *
2819768 TGAAGAGATGTTCGAGTTCTATACTCCCTAAAGAAAGATGGAGCGAGGAGCGAACCCGTTT-AAA
1 TGAAGACA--TTCGAGTTCCATACTCCCTAGAG-AA-A--GA--G-GGAGCGAACCCGTTTAAAA
* * * *
2819832 GATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
57 GATATTCGAGTTCTATACTCCCT--AGAAAGAGGGAGCGAACCCGTT
* * * *
2819879 TGAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTTC
1 TGAAGACAT-TC-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAAGATATTC
*
2819943 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATT
64 GAGTTCTATACTCCCT--AGAAAGAGGGAGCGAACCCGTT
* * * *
2819983 TGAAGACTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTT-GAAGATCTTCG
1 TGAAGAC-ATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAAGATATTCG
*
2820047 AGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTT
65 AGTTCTATACTCCCT--AGAAAGAGGGAGCGAACCCG-TT
* * * *
2820087 TCAGAAGATCATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGAT
1 T--GAAGA-CATTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTT--AAAAGA-
* *** * *
2820152 TATTCGAGTTCTATACT-CCT-TAAAGAAAAAGGGAATCCGCTT
59 TATTCGAGTTCTATACTCCCTAGAAAGAGGGAGCGAACCCG-TT
* * * * * ** *
2820194 ACAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATG
1 --TGAAGA-CATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT-TTAA-AAGATA
* *
2820259 TTCGAGTTCCATAATCCCTAGA
61 TTCGAGTTCTATACTCCCTAGA
2820281 GAAATAGGGA
Statistics
Matches: 425, Mismatches: 56, Indels: 59
0.79 0.10 0.11
Matches are distributed among these distances:
102 7 0.02
103 80 0.19
104 90 0.21
105 21 0.05
106 50 0.12
107 64 0.15
108 2 0.00
109 40 0.09
110 14 0.03
111 57 0.13
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (101 bp):
TGAAGACATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAAGATATTCGA
GTTCTATACTCCCTAGAAAGAGGGAGCGAACCCGTT
Found at i:2820340 original size:55 final size:55
Alignment explanation
Indices: 2820280--2820730 Score: 617
Period size: 55 Copynumber: 8.3 Consensus size: 55
2820270 TAATCCCTAG
* * * *
2820280 AGAAATAGGGAGTAGACGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
2820335 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
2820390 AGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
*
2820443 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
2820498 AGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
*
2820551 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * * *
2820606 AGAAATAGGGGGCAGATGCGATGGATGAAGA-TGGT-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * * *
2820659 AGAAATAGGGAGTAGACCCGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
1 AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
2820714 AGGAATAAGGAGCAGAC
1 AGAAATAGGGGGCAGAC
2820731 ACGTTTTCAA
Statistics
Matches: 352, Mismatches: 38, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
53 138 0.39
54 10 0.03
55 204 0.58
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (55 bp):
AGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:2820745 original size:108 final size:108
Alignment explanation
Indices: 2820280--2820730 Score: 722
Period size: 108 Copynumber: 4.2 Consensus size: 108
2820270 TAATCCCTAG
* * * *
2820280 AGAAATAGGGAGTAGACGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGG
*
2820345 GGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
64 GGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
2820390 AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
1 AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
2820455 CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
66 CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
2820498 AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
1 AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
2820563 CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
66 CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * *
2820606 AGAAATAGGGGGCAGATGCGATGGATGAAGATGGTGGGTCTTATACTCTCTGAAGAAATAGGGAG
1 AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
* * * * *
2820671 TAGACCCGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
66 CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
2820714 AGGAATAAGGAGCAGAC
1 AGAAATAGGGGGCAGAC
2820731 ACGTTTTCAA
Statistics
Matches: 322, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
108 291 0.90
109 1 0.00
110 30 0.09
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (108 bp):
AGAAATAGGGGGCAGACGCAATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGG
CAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:2821013 original size:1 final size:1
Alignment explanation
Indices: 2821007--2821033 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2820997 ACCATCGGAT
2821007 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2821034 GAGGTCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2824893 original size:2 final size:2
Alignment explanation
Indices: 2824888--2824932 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2824878 ACATAAAAAA
2824888 AT AT AT -T AT -T A- 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
2824927 AT AT AT
1 AT AT AT
2824933 TCATCTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2825203 original size:71 final size:71
Alignment explanation
Indices: 2825122--2825266 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
2825112 AATTTATAAA
2825122 ATATTAAATTATAAATTACTAAACATATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAAT
1 ATATTAAATTATAAATTACTAAACATATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAAT
2825187 TAAAAT
66 TAAAAT
2825193 ATATTAAATTATAAATTACTAAACATATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAAT
1 ATATTAAATTATAAATTACTAAACATATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAAT
2825258 TAAAAT
66 TAAAAT
2825264 ATA
1 ATA
2825267 ATATTTGCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (71 bp):
ATATTAAATTATAAATTACTAAACATATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAAT
TAAAAT
Found at i:2825260 original size:23 final size:23
Alignment explanation
Indices: 2825105--2825262 Score: 95
Period size: 23 Copynumber: 6.7 Consensus size: 23
2825095 GATGAGTACC
*
2825105 ATAAATTAATTTATAAAATATTAAATT
1 ATAAATTAA-TTA-AAAAT-CTAAA-T
* * * *
2825132 ATAAATT-ACTAAACATATAATT
1 ATAAATTAATTAAAAATCTAAAT
*
2825154 ATAAATTAGTTAAAAATCTAAAT
1 ATAAATTAATTAAAAATCTAAAT
* * *
2825177 GTAATTTAATTAAAATATATTAAATT
1 ATAAATTAATTAAAA-AT-CTAAA-T
* * * *
2825203 ATAAATT-ACTAAACATATAATT
1 ATAAATTAATTAAAAATCTAAAT
*
2825225 ATAAATTAGTTAAAAATCTAAAT
1 ATAAATTAATTAAAAATCTAAAT
* *
2825248 GTAATTTAATTAAAA
1 ATAAATTAATTAAAA
2825263 TATAATATTT
Statistics
Matches: 99, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
22 16 0.16
23 50 0.51
24 8 0.08
25 11 0.11
26 7 0.07
27 7 0.07
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (23 bp):
ATAAATTAATTAAAAATCTAAAT
Found at i:2825920 original size:29 final size:25
Alignment explanation
Indices: 2825887--2825950 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
2825877 AGATAATTTA
2825887 TTAATTTAAAATATGTAAAATGATACATT
1 TTAATTTAAAATAT-T-AAAT-ATAC-TT
*
2825916 TTAATTATAACATATTAAATATACTT
1 TTAATT-TAAAATATTAAATATACTT
*
2825942 TTATTTTAA
1 TTAATTTAA
2825951 TTTTTGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 3 0.09
26 7 0.22
27 4 0.12
28 4 0.12
29 7 0.22
30 7 0.22
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (25 bp):
TTAATTTAAAATATTAAATATACTT
Found at i:2827598 original size:23 final size:23
Alignment explanation
Indices: 2827572--2827626 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2827562 ACAAAAAATA
2827572 TGTCATAAAGACAGAGAAAAACG
1 TGTCATAAAGACAGAGAAAAACG
2827595 TGTCATAAAGACAGAGAAAAACG
1 TGTCATAAAGACAGAGAAAAACG
2827618 TGTCATAAA
1 TGTCATAAA
2827627 AGTATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.51, C:0.13, G:0.20, T:0.16
Consensus pattern (23 bp):
TGTCATAAAGACAGAGAAAAACG
Found at i:2828182 original size:16 final size:16
Alignment explanation
Indices: 2828161--2828191 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2828151 TAATTATTTT
2828161 AGAATTTATAAATAAA
1 AGAATTTATAAATAAA
*
2828177 AGAATTTATGAATAA
1 AGAATTTATAAATAA
2828192 TTTAAGTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
AGAATTTATAAATAAA
Found at i:2828426 original size:14 final size:14
Alignment explanation
Indices: 2828404--2828448 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2828394 AAAATACCCT
2828404 AAACTCTAAATCTTA
1 AAAC-CTAAATCTTA
*
2828419 AAACCTAAATCCTA
1 AAACCTAAATCTTA
* *
2828433 AACCCTAAACCTTA
1 AAACCTAAATCTTA
2828447 AA
1 AA
2828449 TCAACATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCTAAATCTTA
Found at i:2828737 original size:12 final size:12
Alignment explanation
Indices: 2828722--2828767 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2828712 CGGTTTTTTT
*
2828722 ACCGGATAAAAA
1 ACCGGTTAAAAA
2828734 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
2828749 ACCGGTTAAAAA
1 ACCGGTTAAAAA
2828761 ACCGGTT
1 ACCGGTT
2828768 TTTATCCGAA
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:2828749 original size:15 final size:13
Alignment explanation
Indices: 2828728--2828768 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
2828718 TTTTACCGGA
2828728 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2828741 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
2828755 TAAAAAACCGGTT
1 TAAAAAACCGGTT
2828768 T
1 T
2828769 TTATCCGAAA
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:2831082 original size:21 final size:21
Alignment explanation
Indices: 2831058--2831097 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2831048 TTTATTTTAT
2831058 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2831079 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2831098 AACCTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2831144 original size:33 final size:33
Alignment explanation
Indices: 2831092--2831190 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2831082 TTTGTTTCAA
*
2831092 TTATCGAACCT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2831124 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2831157 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2831190 T
1 T
2831191 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 10 0.16
33 52 0.84
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2831219 original size:13 final size:13
Alignment explanation
Indices: 2831176--2831230 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2831166 TTGGAAGTAT
2831176 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2831189 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2831203 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2831216 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2831229 TT
1 TT
2831231 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:2831476 original size:21 final size:21
Alignment explanation
Indices: 2831426--2831482 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2831416 TGGAGCGTGG
*
2831426 GGGAATCGATACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
2831447 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
*
2831468 GGGAATCGGTTCCCT
1 GGGAATCGGTACCCT
2831483 AAGTGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (21 bp):
GGGAATCGGTACCCTCTCATA
Found at i:2831674 original size:15 final size:15
Alignment explanation
Indices: 2831647--2831702 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2831637 ATATGGAATA
*
2831647 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2831662 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
2831677 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
2831694 TTAAAACCG
1 TTAAAACCG
2831703 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2831711 original size:21 final size:18
Alignment explanation
Indices: 2831666--2831699 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2831656 GTTTTTTTAT
2831666 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
2831683 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
2831700 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:2833002 original size:10 final size:10
Alignment explanation
Indices: 2832987--2833018 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
2832977 CTGACTGCAT
2832987 AAAATTTAAA
1 AAAATTTAAA
2832997 AAAATTTAAA
1 AAAATTTAAA
2833007 AAAATTTAAA
1 AAAATTTAAA
2833017 AA
1 AA
2833019 TAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:2839956 original size:73 final size:73
Alignment explanation
Indices: 2839837--2839983 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
2839827 CGCAAGTTCC
2839837 GGCAGGGTCTCAAGAACGAGTGGGAATCAACATCCATGTGTGCAAGTTTCTAAGTGTGGTGGACC
1 GGCAGGGTCTCAAGAACGAGTGGGAATCAACATCCATGTGTGCAAGTTTCTAAGTGTGGTGGACC
2839902 TGTCCGGG
66 TGTCCGGG
2839910 GGCAGGGTCTCAAGAACGAGTGGGAATCAACATCCATGTGTGCAAGTTTCTAAGTGTGGTGGACC
1 GGCAGGGTCTCAAGAACGAGTGGGAATCAACATCCATGTGTGCAAGTTTCTAAGTGTGGTGGACC
2839975 TGTCCGGG
66 TGTCCGGG
2839983 G
1 G
2839984 TTCGAAGAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (73 bp):
GGCAGGGTCTCAAGAACGAGTGGGAATCAACATCCATGTGTGCAAGTTTCTAAGTGTGGTGGACC
TGTCCGGG
Found at i:2841240 original size:22 final size:22
Alignment explanation
Indices: 2841207--2841255 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
2841197 TCTTCTACGT
*
2841207 TTGTTAGTTATAAGATATTGGC
1 TTGTTAGTTATAAGATATTAGC
2841229 TTGTTA-TGTATAAGATATTAGC
1 TTGTTAGT-TATAAGATATTAGC
2841251 TTGTT
1 TTGTT
2841256 TGGTTAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (22 bp):
TTGTTAGTTATAAGATATTAGC
Found at i:2841269 original size:20 final size:20
Alignment explanation
Indices: 2841244--2841305 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2841234 ATGTATAAGA
2841244 TATTAGCTTGTTTGGTTAGT
1 TATTAGCTTGTTTGGTTAGT
* * *
2841264 TATTAGTTTGTTAGATTAGT
1 TATTAGCTTGTTTGGTTAGT
**
2841284 TGGTA-CTTCGTTT-GTTAGT
1 TATTAGCTT-GTTTGGTTAGT
2841303 TAT
1 TAT
2841306 AAGTTGGTAC
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.18, C:0.05, G:0.23, T:0.55
Consensus pattern (20 bp):
TATTAGCTTGTTTGGTTAGT
Found at i:2841301 original size:24 final size:25
Alignment explanation
Indices: 2841269--2841317 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
2841259 TTAGTTATTA
*
2841269 GTTTGTTAG-ATTAGTTGGTACTTC
1 GTTTGTTAGTATAAGTTGGTACTTC
2841293 GTTTGTTAGTTATAAGTTGGTACTT
1 GTTTGTTAG-TATAAGTTGGTACTT
2841318 TTGATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.51
Consensus pattern (25 bp):
GTTTGTTAGTATAAGTTGGTACTTC
Found at i:2842598 original size:121 final size:121
Alignment explanation
Indices: 2842384--2842625 Score: 484
Period size: 121 Copynumber: 2.0 Consensus size: 121
2842374 CCTGTGTTAG
2842384 AAGTGGAAGCTAAGGGTGTTCAAATCCAATCCAATTCAAAAAAATAATTGAAAACCGATTCAAAA
1 AAGTGGAAGCTAAGGGTGTTCAAATCCAATCCAATTCAAAAAAATAATTGAAAACCGATTCAAAA
2842449 AACCGAAACTGATTTAGTGTGTTTGGTTTTATTTAATAAAATTGATTGGTCCGATT
66 AACCGAAACTGATTTAGTGTGTTTGGTTTTATTTAATAAAATTGATTGGTCCGATT
2842505 AAGTGGAAGCTAAGGGTGTTCAAATCCAATCCAATTCAAAAAAATAATTGAAAACCGATTCAAAA
1 AAGTGGAAGCTAAGGGTGTTCAAATCCAATCCAATTCAAAAAAATAATTGAAAACCGATTCAAAA
2842570 AACCGAAACTGATTTAGTGTGTTTGGTTTTATTTAATAAAATTGATTGGTCCGATT
66 AACCGAAACTGATTTAGTGTGTTTGGTTTTATTTAATAAAATTGATTGGTCCGATT
2842626 CGGTTTCGGT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (121 bp):
AAGTGGAAGCTAAGGGTGTTCAAATCCAATCCAATTCAAAAAAATAATTGAAAACCGATTCAAAA
AACCGAAACTGATTTAGTGTGTTTGGTTTTATTTAATAAAATTGATTGGTCCGATT
Found at i:2847122 original size:34 final size:33
Alignment explanation
Indices: 2847060--2847131 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
2847050 ACCTTACAAC
* *
2847060 TCCCTAGTTTTTCCGGGCTAAACTAGAAC-GTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACTGTT
* *
2847092 TCCCTAGCTTTTACACGGGATAAGCTAGAACTTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACTGTT
2847127 TCCCT
1 TCCCT
2847132 TTACAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 14 0.42
35 7 0.21
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACTGTT
Found at i:2847516 original size:20 final size:20
Alignment explanation
Indices: 2847491--2847569 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
2847481 TCGTCCATGA
*
2847491 ATGCACATCAGGATGCATCG
1 ATGCACAGCAGGATGCATCG
*
2847511 ATGCACAGCAGTATGCATCG
1 ATGCACAGCAGGATGCATCG
2847531 ATGCACAGCAGGATGCATCG
1 ATGCACAGCAGGATGCATCG
**
2847551 ATGCACAAAAGGATGCATC
1 ATGCACAGCAGGATGCATC
2847570 TATACACTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (20 bp):
ATGCACAGCAGGATGCATCG
Found at i:2847643 original size:42 final size:42
Alignment explanation
Indices: 2847597--2847691 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
2847587 CGGTGTTTGA
* *
2847597 GTGCATGGATGCACTGCATGG-TGCATCGATGCACTAGT-GCAG
1 GTGCATGGATGCACTACAGGGATGCATCGATGCACT-GTAG-AG
* * *
2847639 GTGCATCGATGCACTACAGGGATGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTACAGGGATGCATCGATGCACTGTAGAG
2847681 GTGCATGGATG
1 GTGCATGGATG
2847692 TACTTTGACA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 31 0.69
43 14 0.31
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
GTGCATGGATGCACTACAGGGATGCATCGATGCACTGTAGAG
Found at i:2847644 original size:22 final size:23
Alignment explanation
Indices: 2847611--2847654 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
2847601 ATGGATGCAC
2847611 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
2847634 TGCA-GGTGCATCGATGCACTA
1 TGCATGGTGCATCGATGCACTA
2847655 CAGGGATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:2847670 original size:21 final size:20
Alignment explanation
Indices: 2847597--2847691 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 20
2847587 CGGTGTTTGA
* *
2847597 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTACAGG
*
2847617 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACTA---CAGG
*
2847639 GTGCATCGATGCACTACAGG
1 GTGCATGGATGCACTACAGG
**
2847659 GATGCATGGATGCACTGTAGGG
1 G-TGCATGGATGCACTACA-GG
2847681 GTGCATGGATG
1 GTGCATGGATG
2847692 TACTTTGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.03
20 16 0.25
21 24 0.38
22 20 0.31
23 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTACAGG
Found at i:2847826 original size:29 final size:31
Alignment explanation
Indices: 2847776--2847835 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
2847766 AAACTTTGAA
2847776 TAAATTCAATTAAGTG-AAAAAA-CATTTTG
1 TAAATTCAATTAAGTGAAAAAAACCATTTTG
**
2847805 TAAATTCAATTCAAGT-CCAAAAACCATTTTG
1 TAAATTCAATT-AAGTGAAAAAAACCATTTTG
2847836 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTAAGTGAAAAAAACCATTTTG
Found at i:2847844 original size:34 final size:29
Alignment explanation
Indices: 2847776--2847835 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
2847766 AAACTTTGAA
*
2847776 TAAATTCAATTAAGTGAAAAAACATTTTG
1 TAAATTCAATTAAGTCAAAAAACATTTTG
*
2847805 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGT-CAAAAAACATTTTG
2847836 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 4 0.15
31 12 0.44
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTAAGTCAAAAAACATTTTG
Found at i:2849698 original size:13 final size:13
Alignment explanation
Indices: 2849666--2849691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2849656 TCCATGTGGA
2849666 ACGAGCCGAAGGT
1 ACGAGCCGAAGGT
2849679 ACGAGCCGAAGGT
1 ACGAGCCGAAGGT
2849692 GGAAGCCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.38, T:0.08
Consensus pattern (13 bp):
ACGAGCCGAAGGT
Found at i:2860320 original size:21 final size:21
Alignment explanation
Indices: 2860287--2860362 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 21
2860277 GAGTGCTGTA
*
2860287 AACCGATTTGACCGGTTTTC-
1 AACCGGTTTGACCGGTTTTCG
*
2860307 AACCGGTTCTGACCTG-TTTCG
1 AACCGGTT-TGACCGGTTTTCG
* *
2860328 AACCGGTTTGATCGG--TCCG
1 AACCGGTTTGACCGGTTTTCG
*
2860347 AACCAGTTTGACCGGT
1 AACCGGTTTGACCGGT
2860363 CTGACCCGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.35
20 16 0.35
21 14 0.30
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (21 bp):
AACCGGTTTGACCGGTTTTCG
Found at i:2860389 original size:19 final size:19
Alignment explanation
Indices: 2860365--2860412 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2860355 TGACCGGTCT
2860365 GACCCGACCCAACTGACCC
1 GACCCGACCCAACTGACCC
*
2860384 GACCCGACCCGACTGACCC
1 GACCCGACCCAACTGACCC
2860403 GACCCCGACC
1 GA-CCCGACC
2860413 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.23, C:0.54, G:0.19, T:0.04
Consensus pattern (19 bp):
GACCCGACCCAACTGACCC
Found at i:2863260 original size:23 final size:23
Alignment explanation
Indices: 2863217--2863261 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2863207 GATCAATCGC
*
2863217 TTATATTTCTTTTATTTTTTATA
1 TTATATTTATTTTATTTTTTATA
*
2863240 TTATA-TTATTTTGTTTATTTAT
1 TTATATTTATTTTATTT-TTTAT
2863262 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATATTTATTTTATTTTTTATA
Found at i:2863991 original size:32 final size:31
Alignment explanation
Indices: 2863955--2864031 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2863945 CGGGGCCGTG
* *
2863955 GGGCCTACCTAAGAACACATTTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
2863987 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
2864018 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
2864032 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:2864014 original size:63 final size:63
Alignment explanation
Indices: 2863908--2864031 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
2863898 CCCTAAAGGA
* * ** *
2863908 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* * *
2863971 ACATTTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
2864032 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:2864958 original size:29 final size:29
Alignment explanation
Indices: 2864917--2865107 Score: 215
Period size: 29 Copynumber: 6.6 Consensus size: 29
2864907 CACATTCGAA
*
2864917 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
*
2864946 AATTCCCAGAATGTCAC-CTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
** *
2864974 -ATTTTCAGAATGTCACCTTTTTTTCAAAAT
1 AATTCCCAGAATGTCA-C-ATTTTTCAAAAT
* *
2865004 ATTTCCCAGAATGTCACATTTTTTAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* * * *
2865033 ATTTCCTAGAATATCACAATTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
2865062 ATTTCCCAGAATGTCACAATTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
2865091 AATTTCCAAAATGTCAC
1 AATTCCCAGAATGTCAC
2865108 CGGGTCGGGT
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
27 13 0.09
28 11 0.08
29 92 0.66
30 11 0.08
31 12 0.09
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:2865010 original size:58 final size:58
Alignment explanation
Indices: 2864926--2865108 Score: 237
Period size: 58 Copynumber: 3.2 Consensus size: 58
2864916 AAATTCCCAA
* * *
2864926 AATGTCA-CATTTTTCAAAATAATTCCCAGAATGTCAC-CTTTTCAAAATATTTTCAG
1 AATGTCACCATTTTTCAAAATATTTCCCAGAATGTCACAATTTTCAAAATATTTCCAG
* * *
2864982 AATGTCACCTTTTTTTCAAAATATTTCCCAGAATGTCACATTTTTTAAAATATTTCCTAG
1 AATGTCACC-ATTTTTCAAAATATTTCCCAGAATGTCACAATTTTCAAAATATTTCC-AG
* * *
2865042 AATATCA-CAATTTTCAAAATATTTCCCAGAATGTCACAATTTTCAAAATAATTTCCAA
1 AATGTCACCATTTTTCAAAATATTTCCCAGAATGTCACAATTTTCAAAAT-ATTTCCAG
2865100 AATGTCACC
1 AATGTCACC
2865109 GGGTCGGGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
56 7 0.06
57 1 0.01
58 71 0.65
59 22 0.20
60 8 0.07
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.38
Consensus pattern (58 bp):
AATGTCACCATTTTTCAAAATATTTCCCAGAATGTCACAATTTTCAAAATATTTCCAG
Found at i:2865085 original size:87 final size:88
Alignment explanation
Indices: 2864919--2865107 Score: 251
Period size: 87 Copynumber: 2.2 Consensus size: 88
2864909 CATTCGAAAA
* * *
2864919 TTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCTTTTCAAAATATTTTCAGAA
1 TTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATATCACATTTTCAAAATATTTCCAGAA
**
2864984 TGTCACCTTTTTTTCAAAAT-AT
66 TGTCACCTAATTTTCAAAATAAT
* * * *
2865006 TTCCCAGAATGTCACATTTTTTAAAATATTTCCTAGAATATCACAATTTTCAAAATATTTCCCAG
1 TTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATATCAC-ATTTTCAAAATATTT-CCAG
2865071 AATGTCA-C-AATTTTCAAAATAAT
64 AATGTCACCTAATTTTCAAAATAAT
2865094 TT-CCAAAATGTCAC
1 TTCCCAAAATGTCAC
2865108 CGGGTCGGGT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
87 60 0.67
88 19 0.21
89 10 0.11
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.38
Consensus pattern (88 bp):
TTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATATCACATTTTCAAAATATTTCCAGAA
TGTCACCTAATTTTCAAAATAAT
Done.