Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 25 of 91
Found at i:4458394 original size:18 final size:18
Alignment explanation
Indices: 4458371--4458687 Score: 136
Period size: 18 Copynumber: 17.9 Consensus size: 18
4458361 ATTATTTGTG
*
4458371 AATCTTTGAACTTTTACA
1 AATCTTTGAACTTTTGCA
4458389 AATCTTTGAA-TTCTTGCA
1 AATCTTTGAACTT-TTGCA
* * *
4458407 AATCTTTGCATTTTTGGA
1 AATCTTTGAACTTTTGCA
*
4458425 AATCTTTGAACTCTTGCA
1 AATCTTTGAACTTTTGCA
* *
4458443 AATATTTGAA-TTCTTACA
1 AATCTTTGAACTT-TTGCA
*
4458461 AATCTTTGAACTCTTGCA
1 AATCTTTGAACTTTTGCA
* * * *
4458479 TATCATTGAATTTTTGTA
1 AATCTTTGAACTTTTGCA
* * **
4458497 AATCTTTAAACTCTTATA
1 AATCTTTGAACTTTTGCA
* **
4458515 AATCATTGAA-TTCTTGTG
1 AATCTTTGAACTT-TTGCA
* *
4458533 AATGTTTAAAC---TG--
1 AATCTTTGAACTTTTGCA
* * *
4458546 ATTTTTTGAACTTTTACA
1 AATCTTTGAACTTTTGCA
*
4458564 AATCATTGAA-TTCTTGCA
1 AATCTTTGAACTT-TTGCA
* * *
4458582 AATTTTTGAACTATTGCT
1 AATCTTTGAACTTTTGCA
* * *
4458600 AGTTTTTGAACTCTTGCA
1 AATCTTTGAACTTTTGCA
* **
4458618 AATCATTGAA-TTCTTGTG
1 AATCTTTGAACTT-TTGCA
* * **
4458636 AATTTTTAAATTCTTTCACA
1 AATCTTTGAA--CTTTTGCA
*
4458656 AATCTTTG--CTTTTGTA
1 AATCTTTGAACTTTTGCA
4458672 AATCTTTGAACTTTTG
1 AATCTTTGAACTTTTG
4458688 TGAATCTTTA
Statistics
Matches: 215, Mismatches: 65, Indels: 38
0.68 0.20 0.12
Matches are distributed among these distances:
13 8 0.04
15 2 0.01
16 14 0.07
17 7 0.03
18 171 0.80
19 4 0.02
20 7 0.03
21 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.46
Consensus pattern (18 bp):
AATCTTTGAACTTTTGCA
Found at i:4458412 original size:36 final size:36
Alignment explanation
Indices: 4458371--4458683 Score: 178
Period size: 36 Copynumber: 8.8 Consensus size: 36
4458361 ATTATTTGTG
* *
4458371 AATCTTTGAACTTTTACAAATCTTTGAATTCTTGCA
1 AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
* * *
4458407 AATCTTTGCATTTTTGGAAATCTTTGAACTCTTGCA
1 AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
* *
4458443 AATATTTGAA-TTCTTACAAATCTTTGAACTCTTGCA
1 AATCTTTGAACTT-TTGCAAATCTTTGAACTCTTGCA
* * * * * **
4458479 TATCATTGAATTTTTGTAAATCTTTAAACTCTTATA
1 AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
* ** * *
4458515 AATCATTGAA-TTCTTGTGAATGTTT-AA-AC-TG--
1 AATCTTTGAACTT-TTGCAAATCTTTGAACTCTTGCA
* * * * *
4458546 ATTTTTTGAACTTTTACAAATCATTGAATTCTTGCA
1 AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
* * * * *
4458582 AATTTTTGAACTATTGCTAGTTTTTGAACTCTTGCA
1 AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
* ** * * * *
4458618 AATCATTGAA-TTCTTGTGAATTTTTAAATTCTTTCACA
1 AATCTTTGAACTT-TTGCAAATCTTTGAACTC-TT-GCA
*
4458656 AATCTTTG--CTTTTGTAAATCTTTGAACT
1 AATCTTTGAACTTTTGCAAATCTTTGAACT
4458684 TTTGTGAATC
Statistics
Matches: 211, Mismatches: 53, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
31 14 0.07
32 4 0.02
33 2 0.01
34 3 0.01
35 7 0.03
36 166 0.79
37 6 0.03
38 9 0.04
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (36 bp):
AATCTTTGAACTTTTGCAAATCTTTGAACTCTTGCA
Found at i:4458488 original size:54 final size:54
Alignment explanation
Indices: 4458371--4458633 Score: 169
Period size: 54 Copynumber: 5.0 Consensus size: 54
4458361 ATTATTTGTG
* * * * * *
4458371 AATCTTTGAACTTTTACAAATCTTTGAATTCTTGCAAATCTTTGCATTTTTGGA
1 AATCATTGAACTTTTGCAAATCTTTGAATTCTTACAAATCTTTGAATTCTTGCA
* * * *
4458425 AATCTTTGAACTCTTGCAAATATTTGAATTCTTACAAATCTTTGAACTCTTGCA
1 AATCATTGAACTTTTGCAAATCTTTGAATTCTTACAAATCTTTGAATTCTTGCA
* * * * * * * **
4458479 TATCATTGAATTTTTGTAAATCTTTAAACTCTTATAAATCATTGAATTCTTGTG
1 AATCATTGAACTTTTGCAAATCTTTGAATTCTTACAAATCTTTGAATTCTTGCA
** * * * *
4458533 AATGTTTAAAC---TG--ATTTTTTGAACTT-TTACAAATCATTGAATTCTTGCA
1 AATCATTGAACTTTTGCAAATCTTTGAA-TTCTTACAAATCTTTGAATTCTTGCA
** * * * * * * *
4458582 AATTTTTGAACTATTGCTAGTTTTTGAACTCTTGCAAATCATTGAATTCTTG
1 AATCATTGAACTTTTGCAAATCTTTGAATTCTTACAAATCTTTGAATTCTTG
4458634 TGAATTTTTA
Statistics
Matches: 164, Mismatches: 38, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
49 36 0.22
50 1 0.01
51 2 0.01
52 2 0.01
53 1 0.01
54 122 0.74
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (54 bp):
AATCATTGAACTTTTGCAAATCTTTGAATTCTTACAAATCTTTGAATTCTTGCA
Found at i:4458573 original size:103 final size:103
Alignment explanation
Indices: 4458447--4458645 Score: 249
Period size: 103 Copynumber: 1.9 Consensus size: 103
4458437 CTTGCAAATA
* * * *
4458447 TTTGAATTCTTACAAATCTTTGAACTCTTGCATATCATTGAATTTTTG-TAAATCTTTAAACTCT
1 TTTGAATTCTTACAAATCATTGAACTCTTGCAAATCATTGAACTATTGCT-AATCTTTAAACTCT
*
4458511 TATAAATCATTGAATTCTTGTGAATGTTTAAACTGATTT
65 TACAAATCATTGAATTCTTGTGAATGTTTAAACTGATTT
* ** * * *
4458550 TTTGAACTT-TTACAAATCATTGAATTCTTGCAAATTTTTGAACTATTGCTAGTTTTTGAACTCT
1 TTTGAA-TTCTTACAAATCATTGAACTCTTGCAAATCATTGAACTATTGCTAATCTTTAAACTCT
* *
4458614 TGCAAATCATTGAATTCTTGTGAATTTTTAAA
65 TACAAATCATTGAATTCTTGTGAATGTTTAAA
4458646 TTCTTTCACA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 78 0.96
104 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (103 bp):
TTTGAATTCTTACAAATCATTGAACTCTTGCAAATCATTGAACTATTGCTAATCTTTAAACTCTT
ACAAATCATTGAATTCTTGTGAATGTTTAAACTGATTT
Found at i:4458674 original size:16 final size:17
Alignment explanation
Indices: 4458655--4458696 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
4458645 ATTCTTTCAC
4458655 AAATCTTTG-CTTTTGT
1 AAATCTTTGACTTTTGT
4458671 AAATCTTTGAACTTTTGT
1 AAATCTTTG-ACTTTTGT
*
4458689 GAATCTTT
1 AAATCTTT
4458697 AAATGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (17 bp):
AAATCTTTGACTTTTGT
Found at i:4458806 original size:18 final size:18
Alignment explanation
Indices: 4458783--4458825 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4458773 TTGCAAACCA
*
4458783 TTGAATTTTAGCATATTT
1 TTGAATTTTAACATATTT
*
4458801 TTGAATTTTAACATGTTT
1 TTGAATTTTAACATATTT
*
4458819 TTCAATT
1 TTGAATT
4458826 GTGAATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (18 bp):
TTGAATTTTAACATATTT
Found at i:4462036 original size:17 final size:16
Alignment explanation
Indices: 4461998--4462038 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
4461988 ATGAATGATA
*
4461998 AAATTATTTTAATAAT
1 AAATTATTTCAATAAT
4462014 ACAATTATTTCAATAATT
1 A-AATTATTTCAATAA-T
4462032 AAATTAT
1 AAATTAT
4462039 CATAATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTATTTCAATAAT
Found at i:4465158 original size:20 final size:20
Alignment explanation
Indices: 4465130--4465167 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4465120 TAGAATAAAA
4465130 TTTTCAATT-TTATGTTAAGT
1 TTTTCAATTATTAT-TTAAGT
*
4465150 TTTTTAATTATTATTTAA
1 TTTTCAATTATTATTTAA
4465168 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTCAATTATTATTTAAGT
Found at i:4465524 original size:13 final size:13
Alignment explanation
Indices: 4465506--4465531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4465496 TTTTTATAAA
4465506 TAATTAAATTAAT
1 TAATTAAATTAAT
4465519 TAATTAAATTAAT
1 TAATTAAATTAAT
4465532 GTCCGAATTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:4466033 original size:13 final size:13
Alignment explanation
Indices: 4466015--4466039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4466005 TAATTAGAAG
4466015 TTAATTTAATATT
1 TTAATTTAATATT
4466028 TTAATTTAATAT
1 TTAATTTAATAT
4466040 AATTTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTTAATATT
Found at i:4466114 original size:29 final size:27
Alignment explanation
Indices: 4466081--4466163 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
4466071 ATTACATTTT
*
4466081 AATTATATATAAATATAATATTATTATTA
1 AATTATATATAAATATAATATTA--AGTA
4466110 AATTAATATATTAAATAGTAAT-TTAAGTA
1 AATT-ATATA-TAAATA-TAATATTAAGTA
* *
4466139 ATATAATATATAAATATAAAATTAA
1 A-ATTATATATAAATATAATATTAA
4466164 ATAATAACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.07
28 10 0.22
29 13 0.28
30 7 0.15
31 9 0.20
32 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTATATATAAATATAATATTAAGTA
Found at i:4466163 original size:28 final size:29
Alignment explanation
Indices: 4466085--4466169 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 29
4466075 CATTTTAATT
* *
4466085 ATATATAAATATAATATTATTATTAA-ATTA
1 ATATATAAATATAAAATTA--AATAATATTA
* *
4466115 ATATATTAAATAGT-AATTTAAGTAATA-TA
1 ATATA-TAAATA-TAAAATTAAATAATATTA
4466144 ATATATAAATATAAAATTAAATAATA
1 ATATATAAATATAAAATTAAATAATA
4466170 ACAAAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 17 0.37
29 11 0.24
30 6 0.13
31 10 0.22
32 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATATAAATATAAAATTAAATAATATTA
Found at i:4466658 original size:24 final size:24
Alignment explanation
Indices: 4466631--4466685 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
4466621 ATTTATCTTA
*
4466631 TATTTTATATAAAAAAT-TATAATT
1 TATTTTATA-AAAAAATATAAAATT
* *
4466655 TATTTCGATAACAAAATATAAAATT
1 TATTT-TATAAAAAAATATAAAATT
4466680 TATTTT
1 TATTTT
4466686 TATTTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTTTATAAAAAAATATAAAATT
Found at i:4466679 original size:25 final size:23
Alignment explanation
Indices: 4466639--4466684 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
4466629 TATATTTTAT
*
4466639 ATAAAAAATTATAATTTATTTCG
1 ATAAAAAATTAAAATTTATTTCG
4466662 ATAACAAAATATAAAATTTATTT
1 ATAA-AAAAT-TAAAATTTATTT
4466685 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAAAAATTAAAATTTATTTCG
Found at i:4466769 original size:20 final size:20
Alignment explanation
Indices: 4466728--4466774 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4466718 AATTTTAATC
**
4466728 TATATTATTTTCATATTTTA
1 TATATTATTTTCATATCATA
*
4466748 TATATTATTTTTATATCATA
1 TATATTATTTTCATATCATA
4466768 TA-ATTAT
1 TATATTAT
4466775 GACATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTATTTTCATATCATA
Found at i:4479219 original size:81 final size:80
Alignment explanation
Indices: 4479088--4479332 Score: 333
Period size: 75 Copynumber: 3.1 Consensus size: 80
4479078 CTAAAAACCT
* * *
4479088 AACCCTAACCCTAACCTTAAGCCAAACCTTAAATCTTAAATCAAGCCTT-AACCAAGACCTAATT
1 AACCC-AAACCTAACCCTAAGCCAAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAATT
4479152 CCAACTTGAAACCCTA
65 CCAACTTGAAACCCTA
* *
4479168 AACCCAAAAACCTAACCCTAACCCTAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAAT
1 AACCC--AAACCTAACCCTAAGCCAAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAAT
* *
4479233 TCCAA-TTCAAAACCCTT
64 TCCAACTT-GAAACCCTA
*
4479250 AA--C---CCTAACCCTAAGTCAAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAATTC
1 AACCCAAACCTAACCCTAAGCCAAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAATTC
4479310 CAACTTGAAACCCTA
66 CAACTTGAAACCCTA
4479325 AACCCAAA
1 AACCCAAA
4479333 TTACGTTATC
Statistics
Matches: 143, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
75 66 0.46
76 2 0.01
77 1 0.01
80 6 0.04
81 40 0.28
82 28 0.20
ACGTcount: A:0.42, C:0.33, G:0.04, T:0.21
Consensus pattern (80 bp):
AACCCAAACCTAACCCTAAGCCAAACCTTAAATCTTAAACCAAGCCTTAAACCAAGACCTAATTC
CAACTTGAAACCCTA
Found at i:4484067 original size:7 final size:7
Alignment explanation
Indices: 4484054--4484110 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
4484044 GAAGAAAATT
4484054 GAAAAAA
1 GAAAAAA
*
4484061 GAGAAAA
1 GAAAAAA
*
4484068 CAAAAAA
1 GAAAAAA
4484075 -AAAAAA
1 GAAAAAA
*
4484081 CAAAAAGA
1 GAAAAA-A
4484089 GAAAAAA
1 GAAAAAA
4484096 GAAAAAA
1 GAAAAAA
4484103 GAACAAAA
1 GAA-AAAA
4484111 TGATAAAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
6 6 0.14
7 27 0.63
8 10 0.23
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:4484085 original size:26 final size:25
Alignment explanation
Indices: 4484056--4484110 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
4484046 AGAAAATTGA
4484056 AAAAAGAGAAAACAAAAAAAAAAAAC
1 AAAAAGAGAAAA-AAAAAAAAAAAAC
* *
4484082 AAAAAGAGAAAAAAGAAAAAAGAAC
1 AAAAAGAGAAAAAAAAAAAAAAAAC
4484107 AAAA
1 AAAA
4484111 TGATAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (25 bp):
AAAAAGAGAAAAAAAAAAAAAAAAC
Found at i:4485593 original size:21 final size:20
Alignment explanation
Indices: 4485564--4485602 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4485554 TGATAATGTG
*
4485564 ATGATAAATCTAATTTTATC
1 ATGATAAATCTAAATTTATC
*
4485584 ATGATTAAATTTAAATTTA
1 ATGA-TAAATCTAAATTTA
4485603 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ATGATAAATCTAAATTTATC
Found at i:4485637 original size:21 final size:20
Alignment explanation
Indices: 4485595--4485638 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4485585 TGATTAAATT
*
4485595 TAAATTTAAATTTTTTAAGA
1 TAAATTTAAATTTTTCAAGA
* *
4485615 TAAATTTTATATTTTTCATGA
1 TAAA-TTTAAATTTTTCAAGA
4485636 TAA
1 TAA
4485639 TTCTAGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
TAAATTTAAATTTTTCAAGA
Found at i:4486358 original size:15 final size:15
Alignment explanation
Indices: 4486338--4486368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4486328 ATTTAGTTAA
*
4486338 TTTATTTATTTCAAT
1 TTTATTTATTCCAAT
4486353 TTTATTTATTCCAAT
1 TTTATTTATTCCAAT
4486368 T
1 T
4486369 GATTCTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTTATTCCAAT
Found at i:4490700 original size:22 final size:22
Alignment explanation
Indices: 4490619--4491169 Score: 173
Period size: 22 Copynumber: 24.8 Consensus size: 22
4490609 AGTAATTAGT
*
4490619 ATAACTTAATAGT-AATT-ATCA
1 ATAACTTAATAGTAAATTAAT-G
**
4490640 ATAACTTAATAACAAATT-ATG
1 ATAACTTAATAGTAAATTAATG
* **
4490661 TATAACTTAAAAAAAAATTAATG
1 -ATAACTTAATAGTAAATTAATG
*
4490684 ATAACTTAATAGTAAATGAATG
1 ATAACTTAATAGTAAATTAATG
* * * *
4490706 ATAATTTAGTAATTAA-TAACTG
1 ATAACTTAATAGTAAATTAA-TG
* * * *
4490728 ATAACTTAGTAGTAAATCAGTA
1 ATAACTTAATAGTAAATTAATG
* * *
4490750 ATAACATAATAATAAA-TACATA
1 ATAACTTAATAGTAAATTA-ATG
* * *
4490772 ATAATTTAATAGTAAATCAATT
1 ATAACTTAATAGTAAATTAATG
** *
4490794 ATAA--T-ATAGT-TGTAAATG
1 ATAACTTAATAGTAAATTAATG
* **
4490812 CATAACCATATAGTAGTAAATTAAAA
1 -ATAA-C-T-TAATAGTAAATTAATG
* ** *
4490838 ATATCTTAATAAAAAATAAATG
1 ATAACTTAATAGTAAATTAATG
* * * *
4490860 ATAACTTAATAGTCAATCATTA
1 ATAACTTAATAGTAAATTAATG
* * *
4490882 ATAATTTAATAATAAATCAATG
1 ATAACTTAATAGTAAATTAATG
* *
4490904 A-AAATTCAATAGTAAATTAGTG
1 ATAACTT-AATAGTAAATTAATG
* *
4490926 ATAATTTAATAATGAACTATTAAAT-
1 ATAACTTAATAGT-AA--ATT-AATG
* * *
4490951 AGTAA-TTAATTGTTAAGAGTAAATC
1 A-TAACTTAATAG-TAA-A-TTAATG
* * *
4490976 ATAA-ATAATTTAGTGTAAATCAAAG
1 ATAACTTAA--TA--GTAAATTAATG
4491001 ATAACTTAATAGTAAA-TAATTG
1 ATAACTTAATAGTAAATTAA-TG
* * * *
4491023 ATAATTTAGTAGTTAATTATTG
1 ATAACTTAATAGTAAATTAATG
* * * *
4491045 AAAACTTAAAAATAAATCAAT-
1 ATAACTTAATAGTAAATTAATG
* * * *
4491066 CTATCTTAATAGTAAATCATTG
1 ATAACTTAATAGTAAATTAATG
* * * *
4491088 ATAACTTAATAGTTAATCAGTA
1 ATAACTTAATAGTAAATTAATG
4491110 ATAACTTAATAGTAAATT-ATGG
1 ATAACTTAATAGTAAATTAAT-G
* *
4491132 ATAATTTAATA-TAAATCAATG
1 ATAACTTAATAGTAAATTAATG
*
4491153 ATAACTTAGTAGTAAAT
1 ATAACTTAATAGTAAAT
4491170 CATATTAAGT
Statistics
Matches: 385, Mismatches: 109, Indels: 71
0.68 0.19 0.13
Matches are distributed among these distances:
18 4 0.01
19 9 0.02
20 1 0.00
21 51 0.13
22 247 0.64
23 14 0.04
24 14 0.04
25 27 0.07
26 14 0.04
27 3 0.01
28 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATG
Found at i:4490898 original size:88 final size:83
Alignment explanation
Indices: 4490662--4490898 Score: 204
Period size: 88 Copynumber: 2.7 Consensus size: 83
4490652 CAAATTATGT
* * * * *
4490662 ATAACTTAAAAAAAAATTAATGATAACTTAATAGTAAATGAATGATAATTTAGTAATTAATAACT
1 ATAACTTAATAAAAAATAAATGATAACTTAATAGTAAAT-CATTATAA-TT--TAA-TAATAAAT
**
4490727 GATAACTTAGTAGTAAATCAGTA
61 GATAACTTAGTAGTAAATCAAAA
* * * * * * * **
4490750 ATAACATAATAATAAATACATAATAATTTAATAGTAAATCAATTATAATATAGTTGTAAATGCAT
1 ATAACTTAATAAAAAATAAATGATAACTTAATAGTAAATC-ATTATAATTTAATAATAAATG-AT
*
4490815 AACCATATAGTAGTAAATTAAAA
64 AA-C-T-TAGTAGTAAATCAAAA
* *
4490838 ATATCTTAATAAAAAATAAATGATAACTTAATAGTCAATCATTAATAATTTAATAATAAAT
1 ATAACTTAATAAAAAATAAATGATAACTTAATAGTAAATCATT-ATAATTTAATAATAAAT
4490899 CAATGAAAAT
Statistics
Matches: 115, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
84 6 0.05
85 6 0.05
86 1 0.01
87 5 0.04
88 97 0.84
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (83 bp):
ATAACTTAATAAAAAATAAATGATAACTTAATAGTAAATCATTATAATTTAATAATAAATGATAA
CTTAGTAGTAAATCAAAA
Found at i:4491128 original size:87 final size:87
Alignment explanation
Indices: 4490990--4491173 Score: 208
Period size: 87 Copynumber: 2.1 Consensus size: 87
4490980 ATAATTTAGT
* * * * * * *
4490990 GTAAATCAAAGATAACTTAATAGTAAATAATTGATAATTTAGTAGTTAATTATTGAAAACTTAAA
1 GTAAATCATAGATAACTTAATAGTAAATAAGTAATAACTTAATAGTAAATTATGGAAAA-TTAAA
* *
4491055 AATAAATCAAT-CTATCTTAATA
65 AATAAATCAATGATAACTTAATA
* * * * * *
4491077 GTAAATCATTGATAACTTAATAGTTAATCAGTAATAACTTAATAGTAAATTATGGATAATTTAAT
1 GTAAATCATAGATAACTTAATAGTAAATAAGTAATAACTTAATAGTAAATTATGGAAAATTAAAA
*
4491142 ATAAATCAATGATAACTTAGTA
66 ATAAATCAATGATAACTTAATA
4491164 GTAAATCATA
1 GTAAATCATA
4491174 TTAAGTAGTA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
86 14 0.18
87 65 0.82
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (87 bp):
GTAAATCATAGATAACTTAATAGTAAATAAGTAATAACTTAATAGTAAATTATGGAAAATTAAAA
ATAAATCAATGATAACTTAATA
Found at i:4491135 original size:44 final size:43
Alignment explanation
Indices: 4490990--4491172 Score: 145
Period size: 43 Copynumber: 4.2 Consensus size: 43
4490980 ATAATTTAGT
** * * *
4490990 GTAAATCAAAGATAACTTAATAGTAAAT-AATTGATAATTTAGTA
1 GTAAATCATGGATAACTTAATA-TAAATCAA-TAATAACTTAATA
* * * * * * *
4491034 GTTAATTATTGAAAACTTAAAAATAAATCAAT-CTATCTTAATA
1 GTAAATCATGGATAACTT-AATATAAATCAATAATAACTTAATA
* * *
4491077 GTAAATCATTGATAACTTAATAGTTAATCAGTAATAACTTAATA
1 GTAAATCATGGATAACTTAATA-TAAATCAATAATAACTTAATA
* * * *
4491121 GTAAATTATGGATAATTTAATATAAATCAATGATAACTTAGTA
1 GTAAATCATGGATAACTTAATATAAATCAATAATAACTTAATA
4491164 GTAAATCAT
1 GTAAATCAT
4491173 ATTAAGTAGT
Statistics
Matches: 109, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
42 3 0.03
43 54 0.50
44 47 0.43
45 5 0.05
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (43 bp):
GTAAATCATGGATAACTTAATATAAATCAATAATAACTTAATA
Found at i:4491294 original size:22 final size:22
Alignment explanation
Indices: 4491269--4491320 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
4491259 TCTTATAATG
*
4491269 GTAAATCATTGATAATTTAGTA
1 GTAAATCATTGATAACTTAGTA
4491291 GTAAAGT-ATTGATAACTTAGTA
1 GTAAA-TCATTGATAACTTAGTA
4491313 GTAAATCA
1 GTAAATCA
4491321 CCAAAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (22 bp):
GTAAATCATTGATAACTTAGTA
Found at i:4491355 original size:22 final size:21
Alignment explanation
Indices: 4491280--4491384 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
4491270 TAAATCATTG
* * *
4491280 ATAATTTAGTAGTAAAGTATTG
1 ATAATTTAATAGTAAA-TACTA
* * *
4491302 ATAACTTAGTAGTAAATCACCA
1 ATAATTTAATAGTAAAT-ACTA
* *
4491324 AAAATGTAATAGTAAATAACTA
1 ATAATTTAATAGTAAAT-ACTA
*
4491346 ATAATTTAATTGTAAATTGA-TA
1 ATAATTTAATAGTAAA-T-ACTA
*
4491368 ATAATTTAATAATAAAT
1 ATAATTTAATAGTAAAT
4491385 TAGTTAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
21 2 0.03
22 61 0.94
23 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (21 bp):
ATAATTTAATAGTAAATACTA
Found at i:4491479 original size:22 final size:21
Alignment explanation
Indices: 4491420--4491593 Score: 72
Period size: 22 Copynumber: 8.2 Consensus size: 21
4491410 TAAATTATCG
* *
4491420 ATAAATTACTAATAAATCAATT
1 ATAACTTAATAATAAATC-ATT
*
4491442 ATAACTTTATAATAAATCATT
1 ATAACTTAATAATAAATCATT
* * *
4491463 AATCACTTAATAGTAAATCATCA
1 -ATAACTTAATAATAAATCAT-T
* * * *
4491486 ACAATTTAATCATAAGTCATT
1 ATAACTTAATAATAAATCATT
**
4491507 CATAACTTAATGGT-AAT--TT
1 -ATAACTTAATAATAAATCATT
* *
4491526 AT--TTTAATGATAAATCATT
1 ATAACTTAATAATAAATCATT
*
4491545 CATGAA-TTAGTAATAAATCATT
1 -AT-AACTTAATAATAAATCATT
* * *
4491567 AATAATTTAGTAATAAATAATT
1 -ATAACTTAATAATAAATCATT
4491589 GATAA
1 -ATAA
4491594 TTTGTCATAA
Statistics
Matches: 115, Mismatches: 26, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
16 7 0.06
17 3 0.03
18 2 0.02
19 4 0.03
20 2 0.02
21 7 0.06
22 90 0.78
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (21 bp):
ATAACTTAATAATAAATCATT
Found at i:4491594 original size:22 final size:22
Alignment explanation
Indices: 4491551--4491640 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
4491541 CATTCATGAA
* *
4491551 TTAGTAATAAATCATTAATAAT
1 TTAGTAATAAATAATTGATAAT
4491573 TTAGTAATAAATAATTGATAAT
1 TTAGTAATAAATAATTGATAAT
* * * * *
4491595 TT-GTCATAAATCACTGACAAC
1 TTAGTAATAAATAATTGATAAT
4491616 TTAGTAATAAATTAA-TGATAAT
1 TTAGTAATAAA-TAATTGATAAT
4491638 TTA
1 TTA
4491641 ATTGTTCATC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
21 16 0.29
22 37 0.67
23 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.39
Consensus pattern (22 bp):
TTAGTAATAAATAATTGATAAT
Found at i:4491605 original size:43 final size:43
Alignment explanation
Indices: 4491557--4491639 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
4491547 TGAATTAGTA
* * *
4491557 ATAAATCATTAATAATTTAGTAATAAA-TAATTGATAATTTGTC
1 ATAAATCACTAACAACTTAGTAATAAATTAA-TGATAATTTGTC
*
4491600 ATAAATCACTGACAACTTAGTAATAAATTAATGATAATTT
1 ATAAATCACTAACAACTTAGTAATAAATTAATGATAATTT
4491640 AATTGTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 32 0.91
44 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (43 bp):
ATAAATCACTAACAACTTAGTAATAAATTAATGATAATTTGTC
Found at i:4492055 original size:22 final size:22
Alignment explanation
Indices: 4492028--4492179 Score: 82
Period size: 22 Copynumber: 7.0 Consensus size: 22
4492018 ACAAATATAG
4492028 TAGTAAATCATAAATAATTTAA
1 TAGTAAATCATAAATAATTTAA
* *
4492050 TAGTAAAT--TAATGATAATGTAG
1 TAGTAAATCATAA--ATAATTTAA
* * * * *
4492072 TATTTAATCGTTAA-AACTTAA
1 TAGTAAATCATAAATAATTTAA
* * * *
4492093 AAGTAAATGA-ATATAAATTAA
1 TAGTAAATCATAAATAATTTAA
*
4492114 TAGTAAATCATTAATAATTTAA
1 TAGTAAATCATAAATAATTTAA
* * *
4492136 TAGTTAATCAGT-GATAACGTT-A
1 TAGTAAATCA-TAAATAA-TTTAA
*
4492158 TGGTAAATCATAAATAATTTAA
1 TAGTAAATCATAAATAATTTAA
4492180 CATAAATTAA
Statistics
Matches: 92, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
20 4 0.04
21 26 0.28
22 57 0.62
23 3 0.03
24 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (22 bp):
TAGTAAATCATAAATAATTTAA
Found at i:4492297 original size:22 final size:22
Alignment explanation
Indices: 4492269--4492342 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
4492259 AAAAATTAAG
*
4492269 TAGTAAATCAATGATAATATAA
1 TAGTAAATCAATAATAATATAA
*
4492291 TAGTAAAT-ACATAATAACATAA
1 TAGTAAATCA-ATAATAATATAA
* *
4492313 TAGTAAA-CTAATAATAATTTAG
1 TAGTAAATC-AATAATAATATAA
4492335 TAGTAAAT
1 TAGTAAAT
4492343 TATTTTGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 1 0.02
22 41 0.95
23 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (22 bp):
TAGTAAATCAATAATAATATAA
Found at i:4492403 original size:22 final size:22
Alignment explanation
Indices: 4492378--4492502 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
4492368 TAAATTGTCA
4492378 ATAAATTAATAATAAATCAATT
1 ATAAATTAATAATAAATCAATT
*
4492400 AT-AATTTATAATAAATC-ATT
1 ATAAATTAATAATAAATCAATT
* * * *
4492420 AGCAACTTAATAGTAAATC-ATCA
1 A-TAAATTAATAATAAATCAAT-T
* * * * *
4492443 ATAATTTATTAGTAAATTATTT
1 ATAAATTAATAATAAATCAATT
*
4492465 ATAAATTAGTAATAAATCAA-T
1 ATAAATTAATAATAAATCAATT
*
4492486 ATAATTTAA-AAGTAAAT
1 ATAAATTAATAA-TAAAT
4492503 TATTGATAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
20 6 0.08
21 27 0.34
22 44 0.56
23 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAATTAATAATAAATCAATT
Found at i:4492500 original size:65 final size:65
Alignment explanation
Indices: 4492375--4492526 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 65
4492365 TATTAAATTG
* * * * *
4492375 TCAATAAATTAATAATAAATCAATTATAATTTATAATAAATCATTAGCAACTTAATAGTAAATCA
1 TCAATAATTTAATAGTAAATCAATTATAAATTATAATAAATCAATAGCAACTTAAAAGTAAATCA
* * * * * *
4492440 TCAATAATTTATTAGTAAATTATTTATAAATTAGTAATAAATCAATA-TAATTTAAAAGTAAATT
1 TCAATAATTTAATAGTAAATCAATTATAAATTA-TAATAAATCAATAGCAACTTAAAAGTAAATC
4492504 A
65 A
** *
4492505 TTGATAATTTAGTAGTAAATCA
1 TCAATAATTTAATAGTAAATCA
4492527 CTGATAACAT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 59 0.83
66 12 0.17
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (65 bp):
TCAATAATTTAATAGTAAATCAATTATAAATTATAATAAATCAATAGCAACTTAAAAGTAAATCA
Found at i:4492503 original size:43 final size:43
Alignment explanation
Indices: 4492378--4492526 Score: 142
Period size: 43 Copynumber: 3.4 Consensus size: 43
4492368 TAAATTGTCA
*
4492378 ATAAATTAATAATAAATCAATTATAATTTATAA-TAAATCA-TT
1 ATAAATTAATAATAAATCAA-TATAATTTATAAGTAAATTATTT
* * * *
4492420 AGCAACTTAATAGTAAATC-ATCAATAATTTATTAGTAAATTATTT
1 A-TAAATTAATAATAAATCAAT--ATAATTTATAAGTAAATTATTT
* * *
4492465 ATAAATTAGTAATAAATCAATATAATTTAAAAGTAAATTATTG
1 ATAAATTAATAATAAATCAATATAATTTATAAGTAAATTATTT
* * *
4492508 ATAATTTAGTAGTAAATCA
1 ATAAATTAATAATAAATCA
4492527 CTGATAACAT
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 60 0.69
44 19 0.22
45 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (43 bp):
ATAAATTAATAATAAATCAATATAATTTATAAGTAAATTATTT
Found at i:4492512 original size:22 final size:22
Alignment explanation
Indices: 4492426--4492548 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 22
4492416 CATTAGCAAC
* **
4492426 TTAATAGTAAATCATCAATAAT
1 TTAATAGTAAATTATTGATAAT
* * *
4492448 TTATTAGTAAATTATTTATAAA
1 TTAATAGTAAATTATTGATAAT
* * * *
4492470 TTAGTAATAAATCAAT-ATAAT
1 TTAATAGTAAATTATTGATAAT
*
4492491 TTAAAAGTAAATTATTGATAAT
1 TTAATAGTAAATTATTGATAAT
* * * *
4492513 TTAGTAGTAAATCACTGATAAC
1 TTAATAGTAAATTATTGATAAT
*
4492535 ATAATAGTAAATTA
1 TTAATAGTAAATTA
4492549 ATGAAAACAT
Statistics
Matches: 77, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
21 15 0.19
22 62 0.81
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (22 bp):
TTAATAGTAAATTATTGATAAT
Found at i:4492543 original size:87 final size:87
Alignment explanation
Indices: 4492378--4492548 Score: 204
Period size: 87 Copynumber: 2.0 Consensus size: 87
4492368 TAAATTGTCA
*
4492378 ATAAATTAATAATAAATCAATTATAATTTATAATAAATCATTAGCAACTTAATAGTAAATCATCA
1 ATAAATTAATAATAAATCAATTATAATTTAAAATAAATCATTAGCAACTTAATAGTAAATCATCA
** *
4492443 ATAATTTATTAGTAAATTATTT
66 ATAACATAATAGTAAATTATTT
* * * * *
4492465 ATAAATTAGTAATAAATCAA-TATAATTTAAAAGTAAATTATT-GATAATTTAGTAGTAAATCA-
1 ATAAATTAATAATAAATCAATTATAATTTAAAA-TAAATCATTAG-CAACTTAATAGTAAATCAT
*
4492527 CTGATAACATAATAGTAAATTA
64 C-AATAACATAATAGTAAATTA
4492549 ATGAAAACAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 13 0.18
87 58 0.82
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (87 bp):
ATAAATTAATAATAAATCAATTATAATTTAAAATAAATCATTAGCAACTTAATAGTAAATCATCA
ATAACATAATAGTAAATTATTT
Found at i:4492557 original size:22 final size:22
Alignment explanation
Indices: 4492517--4492572 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4492507 GATAATTTAG
* *
4492517 TAGTAAATCACTGATAACATAA
1 TAGTAAATCAATGAAAACATAA
*
4492539 TAGTAAATTAATGAAAACATAA
1 TAGTAAATCAATGAAAACATAA
* *
4492561 TTGTCAATCAAT
1 TAGTAAATCAAT
4492573 TAATAATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
TAGTAAATCAATGAAAACATAA
Found at i:4492857 original size:21 final size:20
Alignment explanation
Indices: 4492825--4492864 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4492815 AATTTTATTA
4492825 ATAATTACCAAAAATATATC
1 ATAATTACCAAAAATATATC
* *
4492845 ATAAGTTAGCAAAATTATAT
1 ATAA-TTACCAAAAATATAT
4492865 GAAACATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATTACCAAAAATATATC
Found at i:4493008 original size:21 final size:21
Alignment explanation
Indices: 4492979--4493034 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
4492969 AAACTAACAT
4492979 AAAATGTTACCAAAATTGTATC
1 AAAA-GTTACCAAAATTGTATC
*
4493001 AAAAGTTATCC-AAATTTTATC
1 AAAAGTTA-CCAAAATTGTATC
*
4493022 AAAAGTTATCAAA
1 AAAAGTTACCAAA
4493035 TTTTAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 6 0.20
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAGTTACCAAAATTGTATC
Found at i:4493036 original size:20 final size:21
Alignment explanation
Indices: 4492991--4493044 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
4492981 AATGTTACCA
*
4492991 AAATTGTATCAAAAGTTATCC
1 AAATTTTATCAAAAGTTATCC
4493012 AAATTTTATCAAAAGTTAT-C
1 AAATTTTATCAAAAGTTATCC
*
4493032 AAATTTTAACAAA
1 AAATTTTATCAAA
4493045 TATTATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (21 bp):
AAATTTTATCAAAAGTTATCC
Found at i:4497428 original size:12 final size:12
Alignment explanation
Indices: 4497411--4497435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4497401 TCAATCATTG
4497411 TGTTAAAAACAT
1 TGTTAAAAACAT
4497423 TGTTAAAAACAT
1 TGTTAAAAACAT
4497435 T
1 T
4497436 ATGCTCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TGTTAAAAACAT
Found at i:4502439 original size:28 final size:28
Alignment explanation
Indices: 4502408--4502463 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4502398 TGTAAAGGAC
*
4502408 GTAACCATGTAAGAAATGAGTAATGGGA
1 GTAACCATGTAACAAATGAGTAATGGGA
4502436 GTAACCATGTAACAAATGAGTAATGGGA
1 GTAACCATGTAACAAATGAGTAATGGGA
4502464 ATTCTGCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.21
Consensus pattern (28 bp):
GTAACCATGTAACAAATGAGTAATGGGA
Found at i:4507987 original size:37 final size:37
Alignment explanation
Indices: 4507897--4507990 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 37
4507887 TTGTTACTCA
* * * *
4507897 TAATAAAATTA-AAATAAAATTTAAAATATCTATACT
1 TAATATAATTACATATAAAATATAAAATATATATACT
*** * *
4507933 TAATATAATTTTTTATAAAATATAAAATATATCTATT
1 TAATATAATTACATATAAAATATAAAATATATATACT
*
4507970 TAATATTATTACATATAAAAT
1 TAATATAATTACATATAAAAT
4507991 TTATTCCCAA
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
36 9 0.20
37 36 0.80
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (37 bp):
TAATATAATTACATATAAAATATAAAATATATATACT
Found at i:4508225 original size:17 final size:18
Alignment explanation
Indices: 4508188--4508236 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
4508178 AAATAATGTA
4508188 TTATTTATATAG-CACATG
1 TTATTTATAT-GTCACATG
4508206 TTATTTATATGTCA-ATG
1 TTATTTATATGTCACATG
*
4508223 TTATTCATATGTCA
1 TTATTTATATGTCA
4508237 TCAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (18 bp):
TTATTTATATGTCACATG
Found at i:4510170 original size:22 final size:21
Alignment explanation
Indices: 4510145--4510185 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4510135 CTCTTACTCA
4510145 TAATTCGTGATATCATTTAATT
1 TAATTCGT-ATATCATTTAATT
* *
4510167 TAATTTGTTTATCATTTAA
1 TAATTCGTATATCATTTAA
4510186 CTATCATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
TAATTCGTATATCATTTAATT
Found at i:4510542 original size:12 final size:12
Alignment explanation
Indices: 4510510--4510542 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4510500 ATCAAACTTG
4510510 AAAAAAA-TCCA
1 AAAAAAATTCCA
4510521 ATAAAAAATTCCA
1 A-AAAAAATTCCA
4510534 AAAAAAATT
1 AAAAAAATT
4510543 AAATTTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 14 0.70
13 5 0.25
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAATTCCA
Found at i:4514422 original size:12 final size:12
Alignment explanation
Indices: 4514405--4514430 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4514395 AGTTTGGAAT
4514405 ATAAAATTATTA
1 ATAAAATTATTA
4514417 ATAAAATTATTA
1 ATAAAATTATTA
4514429 AT
1 AT
4514431 TTAAGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAAAATTATTA
Found at i:4514803 original size:13 final size:12
Alignment explanation
Indices: 4514787--4514820 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
4514777 TTTTAAATAA
4514787 ATTAAATAAAATT
1 ATTAAATAAAA-T
4514800 ATTAAATAAAAT
1 ATTAAATAAAAT
4514812 ATTTAAATA
1 A-TTAAATA
4514821 TCAGAGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:4515242 original size:18 final size:19
Alignment explanation
Indices: 4515221--4515258 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4515211 TATATATTAT
4515221 ATAATATAAAT-ATTAAAA
1 ATAATATAAATAATTAAAA
*
4515239 ATAATATATATAATTAAAA
1 ATAATATAAATAATTAAAA
4515258 A
1 A
4515259 AAAAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAATATAAATAATTAAAA
Found at i:4516147 original size:12 final size:12
Alignment explanation
Indices: 4516132--4516163 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4516122 GTAAATTACA
4516132 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
4516144 AAAAACAAAAAC
1 AAAAAAAAAAAC
4516156 AAAAAAAA
1 AAAAAAAA
4516164 GAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:4516161 original size:21 final size:20
Alignment explanation
Indices: 4516131--4516169 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4516121 AGTAAATTAC
4516131 AAAAAAAAAAAACAAAAACA
1 AAAAAAAAAAAACAAAAACA
*
4516151 AAAACAAAAAAAAGAAAAA
1 AAAA-AAAAAAAACAAAAA
4516170 TATCAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.90, C:0.08, G:0.03, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAACAAAAACA
Found at i:4519066 original size:5 final size:6
Alignment explanation
Indices: 4519054--4519079 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4519044 ATTAATTATA
4519054 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
4519080 TTGCATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:4521209 original size:21 final size:21
Alignment explanation
Indices: 4521168--4521206 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
4521158 TATTATATTT
4521168 TTTCTTTTCTCTTTTTCTTTC
1 TTTCTTTTCTCTTTTTCTTTC
4521189 TTTCTTTT-T-TTTTTCTTT
1 TTTCTTTTCTCTTTTTCTTT
4521207 TTCAGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTCTTTTCTCTTTTTCTTTC
Found at i:4522961 original size:15 final size:15
Alignment explanation
Indices: 4522938--4522970 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4522928 AATGCCTAAA
*
4522938 AAATTTCTAGGTAAG
1 AAATCTCTAGGTAAG
4522953 AAATCTCTAGGTAAG
1 AAATCTCTAGGTAAG
4522968 AAA
1 AAA
4522971 AGGTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (15 bp):
AAATCTCTAGGTAAG
Found at i:4530570 original size:16 final size:17
Alignment explanation
Indices: 4530533--4530573 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4530523 TTATTTTACT
4530533 TTTCATTTTCTCATTTCA
1 TTTCATTTTCT-ATTTCA
4530551 --TCATTTTCT-TTTCA
1 TTTCATTTTCTATTTCA
4530565 TTTCATTTT
1 TTTCATTTT
4530574 TGTGTACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.24
16 16 0.76
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTCATTTTCTATTTCA
Found at i:4534971 original size:66 final size:66
Alignment explanation
Indices: 4534865--4534992 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
4534855 GATGAGATTT
* *
4534865 TTAAAGTTGTTGAGCCTCTGCTGAGAGAAGTTTTTTCAAGATAAATTTTTAAAGTTGTTGAGTCT
1 TTAAAGTTGTTGAGCCTCTACTGAGAGAAGCTTTTTCAAGATAAATTTTTAAAGTTGTTGAGTCT
4534930 C
66 C
* * *
4534931 TTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTGAG
1 TTAAAGTTGTTGAGCCTCTACTGAGAGAAGCTTTTTCAAGATAAATTTTTAAAGTTGTTGAG
4534993 CCTTTATTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (66 bp):
TTAAAGTTGTTGAGCCTCTACTGAGAGAAGCTTTTTCAAGATAAATTTTTAAAGTTGTTGAGTCT
C
Found at i:4534987 original size:48 final size:48
Alignment explanation
Indices: 4534931--4535356 Score: 378
Period size: 48 Copynumber: 8.8 Consensus size: 48
4534921 GTTGAGTCTC
*
4534931 TTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATGAATTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTT
* * *
4534979 TTAAAGTTGTTGAGCCTT-TA-TTGAAAGAAGCTTTTTTAAGATGAA-TT
1 TTAAAGTTGTTGAG-CTTCTACTT-AGAGGAGCTTTTTCAAGATGAATTT
* * *
4535026 TTAAAGTTGTTGAG-TCTCTGCTTAGAGGAGCTTTTCCAAGATGTTAAAATT
1 TTAAAGTTGTTGAGCT-TCTACTTAGAGGAGCTTTTTCAAGATG---AATTT
* * * * *
4535077 TTAAAGTTGTCGAGCTTCTACTTATAAGAGCTTTTTCAATATGATAGTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGA-ATTT
* * * * * *
4535126 TTAAAGTTATTGAGCCTCTGCTGAGATGAGCTTTTTCAAGATGGATTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTT
* ** * * * * *
4535174 TTAAAATTGTCAAGCCTATGCTTAGAAGAGCTTTTCCAGAATGATGAA-TT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTC--AA-GATGAATTT
* *
4535224 TTAAAGTTATTGAGCATCTACTTAGAGGAG-TTTTTCCAAGATGAATTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTT-CAAGATGAATTT
* * * *
4535272 TTAAAGTTATTGAGCCTCTGCTTAGAGGAGTTTTTTCAAGATGAATTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTT
* * * *
4535320 TTAAAGTTGCTGAGCCTCTGCTTAGAGAAGCCTTTTT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAG-CTTTTT
4535357 AAATTTTCAA
Statistics
Matches: 310, Mismatches: 50, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.00
46 1 0.00
47 40 0.13
48 141 0.45
49 55 0.18
50 29 0.09
51 42 0.14
52 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (48 bp):
TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTT
Found at i:4535275 original size:98 final size:96
Alignment explanation
Indices: 4534931--4535356 Score: 423
Period size: 98 Copynumber: 4.4 Consensus size: 96
4534921 GTTGAGTCTC
* * * *
4534931 TTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTGAGCCT
1 TTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTCGAGCCT
** *
4534996 -TTATT-GAAAGAAGCTTTTT-TAAGATGAATT
66 CTGCTTAG-AAG-AGCTTTTTCAAAGATGAATT
* * *
4535026 TTAAAGTTGTTGAGTCTCTGCTTAGAGGAGCTTTTCCAAGATGTTAAAATTTTAAAGTTGTCGAG
1 TTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATG---AATTTTTAAAGTTGTCGAG
* * * *
4535091 CTTCTACTTATAAGAGCTTTTTCAATATGAT-AGTT
63 CCTCTGCTTAGAAGAGCTTTTTCAA-A-GATGAATT
* * * * * *
4535126 TTAAAGTTATTGAGCCTCTGCTGAGATGAGCTTTTTCAAGATGGATTTTTAAAATTGTCAAGCCT
1 TTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTCGAGCCT
* *
4535191 ATGCTTAGAAGAGCTTTTCCAGAATGATGAATT
66 CTGCTTAGAAGAGCTTTTTCA-AA-GATGAATT
* * * * *
4535224 TTAAAGTTATTGAGCATCTACTTAGAGGAG-TTTTTCCAAGATGAATTTTTAAAGTTATTGAGCC
1 TTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTT-CAAGATGAATTTTTAAAGTTGTCGAGCC
* *
4535288 TCTGCTTAGAGGAGTTTTTTC-AAGATGAATTT
65 TCTGCTTAGAAGAGCTTTTTCAAAGATGAA-TT
* *
4535320 TTAAAGTTGCTGAGCCTCTGCTTAGAGAAGCCTTTTT
1 TTAAAGTTGTTGAGCCTCTGCTTAGAGGAG-CTTTTT
4535357 AAATTTTCAA
Statistics
Matches: 271, Mismatches: 46, Indels: 25
0.79 0.13 0.07
Matches are distributed among these distances:
95 44 0.16
96 29 0.11
97 44 0.16
98 102 0.38
99 7 0.03
100 42 0.15
101 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (96 bp):
TTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTCGAGCCT
CTGCTTAGAAGAGCTTTTTCAAAGATGAATT
Found at i:4535336 original size:146 final size:146
Alignment explanation
Indices: 4534931--4535345 Score: 500
Period size: 146 Copynumber: 2.8 Consensus size: 146
4534921 GTTGAGTCTC
* *
4534931 TTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTGAGCCT
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTATTGAGCCT
** * * * *
4534996 -TTATTGAAAGAAGCTTTTTT-AAGATGAA-TTTTAAAGTTGTTGAGTCTCTGCTTAGAGGAGCT
66 CTGCTT-AGAGGAG-TTTTTTCAAGATGAATTTTTAAAGTTG-TGAGCCTCTGCTTAGAAGAGCT
*
4535058 TTTCCAAGATGTTAAAATT
128 TTTCCAAGATGATAAAATT
* * * * *
4535077 TTAAAGTTGTCGAGCTTCTACTTATAAGAGCTTTTTCAATATGATAGTTTTAAAGTTATTGAGCC
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGA-ATTTTTAAAGTTATTGAGCC
* * * * * * *
4535142 TCTGCTGAGATGAGCTTTTTCAAGATGGATTTTTAAAATTGTCAAGCCTATGCTTAGAAGAGCTT
65 TCTGCTTAGAGGAGTTTTTTCAAGATGAATTTTTAAAGTTGT-GAGCCTCTGCTTAGAAGAGCTT
*
4535207 TTCC-AGAATGAT-GAATT
129 TTCCAAG-ATGATAAAATT
* *
4535224 TTAAAGTTATTGAGCATCTACTTAGAGGAG-TTTTTCCAAGATGAATTTTTAAAGTTATTGAGCC
1 TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTT-CAAGATGAATTTTTAAAGTTATTGAGCC
4535288 TCTGCTTAGAGGAGTTTTTTCAAGATGAATTTTTAAAGTTGCTGAGCCTCTGCTTAGA
65 TCTGCTTAGAGGAGTTTTTTCAAGATGAATTTTTAAAGTTG-TGAGCCTCTGCTTAGA
4535346 GAAGCCTTTT
Statistics
Matches: 225, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
146 117 0.52
147 70 0.31
148 38 0.17
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.40
Consensus pattern (146 bp):
TTAAAGTTGTTGAGCTTCTACTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTATTGAGCCT
CTGCTTAGAGGAGTTTTTTCAAGATGAATTTTTAAAGTTGTGAGCCTCTGCTTAGAAGAGCTTTT
CCAAGATGATAAAATT
Found at i:4535380 original size:44 final size:44
Alignment explanation
Indices: 4535332--4535455 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
4535322 AAAGTTGCTG
*
4535332 AGCCTCTGCTTAGAGAAGCCTTTTTAAATTTTCAAAAGTCGTTA
1 AGCCTCTACTTAGAGAAGCCTTTTTAAATTTTCAAAAGTCGTTA
* * * *
4535376 AGCCTTTACTTAGA-AGAGCCTCTTTAAATTTTCAAAAGTTGTTG
1 AGCCTCTACTTAGAGA-AGCCTTTTTAAATTTTCAAAAGTCGTTA
* * *
4535420 AGCCTCTACTCAGAGGAGCC-TTTAAAATTTTCAAAA
1 AGCCTCTACTTAGAGAAGCCTTTTTAAATTTTCAAAA
4535456 ATGTTGTTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 15 0.22
44 53 0.78
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (44 bp):
AGCCTCTACTTAGAGAAGCCTTTTTAAATTTTCAAAAGTCGTTA
Found at i:4535633 original size:18 final size:19
Alignment explanation
Indices: 4535610--4535654 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
4535600 CCATTTTGTA
4535610 TTTATTTTATTATTT-TTT
1 TTTATTTTATTATTTCTTT
*
4535628 TTTATTTT-TTTTTTCTTT
1 TTTATTTTATTATTTCTTT
*
4535646 TTTAGTTTA
1 TTTATTTTA
4535655 GCTCGACAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTATTTTATTATTTCTTT
Found at i:4538369 original size:16 final size:16
Alignment explanation
Indices: 4538347--4538399 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
4538337 ATCCTAAAAT
*
4538347 CTAAAACCTTGCAACC
1 CTAAAACCTTGAAACC
* *
4538363 TTAAAACTTTGAAACC
1 CTAAAACCTTGAAACC
*
4538379 CTAAAACC-TAAAACC
1 CTAAAACCTTGAAACC
4538394 CTAAAA
1 CTAAAA
4538400 TTACTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (16 bp):
CTAAAACCTTGAAACC
Found at i:4540988 original size:3 final size:3
Alignment explanation
Indices: 4540980--4541014 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4540970 AAATATTTTC
4540980 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4541015 ATTTTCTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4543658 original size:16 final size:16
Alignment explanation
Indices: 4543638--4543697 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
4543628 AATATATATA
4543638 ATAAAAAAATAAAAATC
1 ATAAAAAAA-AAAAATC
*
4543655 -TAAAACAAAAAAATC
1 ATAAAAAAAAAAAATC
4543670 ATAAAAATTAAAAAAA-C
1 ATAAAAA--AAAAAAATC
4543687 A-AAAATAAAAA
1 ATAAAA-AAAAA
4543698 TGAAAAGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 11 0.30
16 16 0.43
17 3 0.08
18 7 0.19
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (16 bp):
ATAAAAAAAAAAAATC
Found at i:4543665 original size:21 final size:21
Alignment explanation
Indices: 4543640--4543723 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
4543630 TATATATAAT
4543640 AAAAAAATAAAAATCTAAAACAA
1 AAAAAAATAAAAAT-TAAAA-AA
*
4543663 AAAAATCATAAAAATTAAAAAA
1 AAAAA-AATAAAAATTAAAAAA
* * *
4543685 ACAAAAATAAAAATGAAAAGA
1 AAAAAAATAAAAATTAAAAAA
**
4543706 TGAAAAA-AAAAATTAAAA
1 AAAAAAATAAAAATTAAAA
4543724 TTTTAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.19
21 18 0.35
22 6 0.12
23 10 0.19
24 8 0.15
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (21 bp):
AAAAAAATAAAAATTAAAAAA
Found at i:4543834 original size:17 final size:15
Alignment explanation
Indices: 4543803--4543847 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
4543793 TTTTGAATTA
*
4543803 AAATATCAA-ATAAT
1 AAATATTAATATAAT
4543817 AAATTTATTAATATAAT
1 AAA--TATTAATATAAT
4543834 AAATATTAATATAA
1 AAATATTAATATAA
4543848 AATTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 11 0.41
16 5 0.19
17 8 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTAATATAAT
Found at i:4544699 original size:6 final size:7
Alignment explanation
Indices: 4544681--4544706 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4544671 AAAATATATT
4544681 TAAAAAA
1 TAAAAAA
4544688 TAAAAAA
1 TAAAAAA
4544695 TAAAAAA
1 TAAAAAA
4544702 TAAAA
1 TAAAA
4544707 TGAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:4545915 original size:12 final size:12
Alignment explanation
Indices: 4545890--4545930 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4545880 TTAATAAAGC
4545890 AAAA-AGAA-AA
1 AAAAGAGAAGAA
4545900 AAAAGAGAAGAA
1 AAAAGAGAAGAA
*
4545912 AAAAGAAAAGACA
1 AAAAGAGAAGA-A
4545925 AAAAGA
1 AAAAGA
4545931 CAAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 12 0.44
13 7 0.26
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAGAA
Found at i:4545952 original size:16 final size:16
Alignment explanation
Indices: 4545885--4545943 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
4545875 CTAACTTAAT
4545885 AAAG-CAAAAAGAAAAA
1 AAAGACAAAAAG-AAAA
*
4545901 AAAGAGAAGAAA-AAAGA
1 AAAGACAA-AAAGAAA-A
*
4545918 AAAGACAAAAAGACAA
1 AAAGACAAAAAGAAAA
4545934 AAAGA-AAAAA
1 AAAGACAAAAA
4545944 ATATAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
15 5 0.14
16 16 0.44
17 12 0.33
18 3 0.08
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGACAAAAAGAAAA
Found at i:4550169 original size:70 final size:70
Alignment explanation
Indices: 4550055--4550195 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 70
4550045 GTCTTTAATG
* * *
4550055 CTTAGTAATTTTGCCATATTTTGAGGATCAATCCTTGTTAATTGAGGTTTGATCCCTATTCTTAG
1 CTTAGTAATTTTACCATATTTTGAGGATCAATCCTTGTTAATTGAGGATTGATCCCTATTCGTAG
4550120 AGGAT
66 AGGAT
*
4550125 CTTAGTAATTTTACCATATTTTGAGGATCAATCCTTGTTGATTGAGGATTGATCCCTATTCGTAG
1 CTTAGTAATTTTACCATATTTTGAGGATCAATCCTTGTTAATTGAGGATTGATCCCTATTCGTAG
4550190 AGGAT
66 AGGAT
4550195 C
1 C
4550196 GATCCTTCCC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (70 bp):
CTTAGTAATTTTACCATATTTTGAGGATCAATCCTTGTTAATTGAGGATTGATCCCTATTCGTAG
AGGAT
Found at i:4550788 original size:32 final size:32
Alignment explanation
Indices: 4550742--4550830 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
4550732 CAATTACATA
* ** *
4550742 TTCACAACTTTCAAATTAACAAATTCCACCAAAT
1 TTCACAA-TATCAAATCCACAAATTCCAAC-AAT
4550776 TT-ACAATATCAAATCCACAAATTCCAACAAT
1 TTCACAATATCAAATCCACAAATTCCAACAAT
*
4550807 TTCACAATTTCAAATCCACAAATT
1 TTCACAATATCAAATCCACAAATT
4550831 GCATGCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.10
32 38 0.78
33 4 0.08
34 2 0.04
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (32 bp):
TTCACAATATCAAATCCACAAATTCCAACAAT
Found at i:4551640 original size:22 final size:23
Alignment explanation
Indices: 4551592--4551644 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
4551582 GGAGTAAGGA
*
4551592 AAGAGAAGGGAGGAGAAAGAAAT
1 AAGAGAAGGGAGGAGAAAGAAAG
* *
4551615 AAGA-AAGGGAGGAGAATGGAAG
1 AAGAGAAGGGAGGAGAAAGAAAG
4551637 AAGAGAAG
1 AAGAGAAG
4551645 TGATGTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (23 bp):
AAGAGAAGGGAGGAGAAAGAAAG
Found at i:4554893 original size:23 final size:23
Alignment explanation
Indices: 4554867--4554912 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4554857 ATTAATTCAA
4554867 ATTAAATAAAATATTACAATTTG
1 ATTAAATAAAATATTACAATTTG
* *
4554890 ATTAAATCAAATATTATAATTTG
1 ATTAAATAAAATATTACAATTTG
4554913 GTTCAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTAAATAAAATATTACAATTTG
Found at i:4555190 original size:16 final size:15
Alignment explanation
Indices: 4555167--4555209 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
4555157 CATCTCACAT
4555167 TTTAATCATTTTGAA
1 TTTAATCATTTTGAA
4555182 TTTAGATCATTTTGAA
1 TTTA-ATCATTTTGAA
*
4555198 TTCAATTCATTT
1 TTTAA-TCATTT
4555210 CATATATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTAATCATTTTGAA
Found at i:4555653 original size:26 final size:25
Alignment explanation
Indices: 4555593--4555641 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4555583 TTTTACTCGA
4555593 AAGAAGATGGGAATTATATCAAATT
1 AAGAAGATGGGAATTATATCAAATT
* *
4555618 AAAAAGATGGGTATTAATATCAAA
1 AAGAAGATGGGAATT-ATATCAAA
4555642 ATTTGAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (25 bp):
AAGAAGATGGGAATTATATCAAATT
Found at i:4559766 original size:5 final size:5
Alignment explanation
Indices: 4559756--4559780 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4559746 GAGTCAATTA
4559756 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
4559781 TTTTTATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:4560152 original size:21 final size:20
Alignment explanation
Indices: 4560071--4560156 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 20
4560061 TTCGATAACC
* *
4560071 TTTGATAAAATTTTGGTAACT
1 TTTGATACAATTTTAGTAA-T
* *
4560092 TTCGATACAGTTTTAGTAAT
1 TTTGATACAATTTTAGTAAT
* * *
4560112 TTATGACATAAGTTTAGTAAT
1 TT-TGATACAATTTTAGTAAT
*
4560133 TATTGATACAATTTTGGTAAT
1 T-TTGATACAATTTTAGTAAT
4560154 TTT
1 TTT
4560157 TAATAAAATT
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.10
21 44 0.88
22 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.48
Consensus pattern (20 bp):
TTTGATACAATTTTAGTAAT
Found at i:4560173 original size:21 final size:21
Alignment explanation
Indices: 4560126--4560173 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
4560116 GACATAAGTT
* * *
4560126 TAGTAATTATTGATACAATTT
1 TAGTAATTATTAATAAAATTA
* *
4560147 TGGTAATTTTTAATAAAATTA
1 TAGTAATTATTAATAAAATTA
4560168 TAGTAA
1 TAGTAA
4560174 CCTCTTGAGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (21 bp):
TAGTAATTATTAATAAAATTA
Found at i:4560220 original size:20 final size:22
Alignment explanation
Indices: 4560193--4560242 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
4560183 TTAGTTTTAG
4560193 TAATATTTT-GATAACTTA-TGA
1 TAATATTTTCGATAA-TTATTGA
4560214 T-ATATTTTCGATAATTATTGA
1 TAATATTTTCGATAATTATTGA
4560235 TAATATTT
1 TAATATTT
4560243 GTATTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.38
21 10 0.38
22 6 0.23
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATATTTTCGATAATTATTGA
Found at i:4560509 original size:22 final size:22
Alignment explanation
Indices: 4560471--4560562 Score: 80
Period size: 22 Copynumber: 4.1 Consensus size: 22
4560461 CAACTTTATC
* *
4560471 ATTTACTACTAAA-TTATTAATG
1 ATTTATTA-TAAAGTTATCAATG
*
4560493 ATTTGTTATAAAGTTAT-AACTG
1 ATTTATTATAAAGTTATCAA-TG
* * * *
4560515 ATTTACTATTAATTTATCAATA
1 ATTTATTATAAAGTTATCAATG
4560537 ATTTATTATAAAAGTTATCAATG
1 ATTTATTAT-AAAGTTATCAATG
4560560 ATT
1 ATT
4560563 AACTAATTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
21 6 0.11
22 34 0.62
23 15 0.27
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTTATTATAAAGTTATCAATG
Found at i:4560521 original size:44 final size:45
Alignment explanation
Indices: 4560471--4560567 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
4560461 CAACTTTATC
* * *
4560471 ATTTACTACTAAATTATTAATGATTTGTTAT-AAAGTTAT-AACTG
1 ATTTACTACTAAATTATCAATAATTTATTATAAAAGTTATCAA-TG
* *
4560515 ATTTACTATTAATTTATCAATAATTTATTATAAAAGTTATCAATG
1 ATTTACTACTAAATTATCAATAATTTATTATAAAAGTTATCAATG
*
4560560 ATTAACTA
1 ATTTACTA
4560568 ATTTACTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 26 0.58
45 17 0.38
46 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (45 bp):
ATTTACTACTAAATTATCAATAATTTATTATAAAAGTTATCAATG
Found at i:4560637 original size:22 final size:22
Alignment explanation
Indices: 4560568--4561061 Score: 171
Period size: 22 Copynumber: 22.4 Consensus size: 22
4560558 TGATTAACTA
* * * *
4560568 ATTTACTACTAAAGTATCACTT
1 ATTTACTATTAAATTATCAATG
* * * *
4560590 ATTTACAACTAAATTATTAACG
1 ATTTACTATTAAATTATCAATG
*
4560612 ATTTACTATTAAATTATCAATA
1 ATTTACTATTAAATTATCAATG
** * *
4560634 ATTTACTATTATGTTAT-TATAC
1 ATTTACTATTAAATTATCAAT-G
* ** *
4560656 ATTTA-TCACTATGTTATCATTG
1 ATTTACT-ATTAAATTATCAATG
** *
4560678 ATTTACTACTTAGCTT-TCAATT
1 ATTTACTA-TTAAATTATCAATG
* ** * * *
4560700 ATTTATTACAAAATTAACCATA
1 ATTTACTATTAAATTATCAATG
* * * * * *
4560722 ACTCATTATTAAGTTATCATTT
1 ATTTACTATTAAATTATCAATG
* *
4560744 ATTTA-TATTAAATTATCCATA
1 ATTTACTATTAAATTATCAATG
* * *
4560765 ATTTACTATTAAGTTATCATTA
1 ATTTACTATTAAATTATCAATG
* * * **
4560787 ATTAATTATTAAGTTATTTATG
1 ATTTACTATTAAATTATCAATG
* *
4560809 ATTAACTACTATTAAGTTAT-ATTG
1 ATT---TACTATTAAATTATCAATG
* * * *
4560833 ATTTTCTTTTAATTTTTCAATG
1 ATTTACTATTAAATTATCAATG
* *
4560855 ATTAACTATTAAATTATCATTG
1 ATTTACTATTAAATTATCAATG
**
4560877 ATTTACTATTAAATTATTTATG
1 ATTTACTATTAAATTATCAATG
*
4560899 ATTTACTACTAAATTTATCAACTG
1 ATTTACTATTAAA-TTATCAA-TG
* *
4560923 A-TTACTATTAAACTGA--AACCG
1 ATTTACTATTAAA-TTATCAA-TG
* * * *
4560944 ATTTATTATTAATTTATCACTA
1 ATTTACTATTAAATTATCAATG
* *
4560966 ATTTACTATTAAGTTATCATAGG
1 ATTTACTATTAAATTATCA-ATG
* * *
4560989 ATTTATTATTAAGTTATCAATT
1 ATTTACTATTAAATTATCAATG
* * * * *
4561011 ATTAACTACTAAATTATTATTT
1 ATTTACTATTAAATTATCAATG
* *
4561033 ATTT-TTATT-AATCTATCATTG
1 ATTTACTATTAAAT-TATCAATG
4561054 ATTTACTA
1 ATTTACTA
4561062 ATATATTGCT
Statistics
Matches: 345, Mismatches: 108, Indels: 38
0.70 0.22 0.08
Matches are distributed among these distances:
20 3 0.01
21 53 0.15
22 227 0.66
23 42 0.12
24 8 0.02
25 12 0.03
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCAATG
Found at i:4560764 original size:43 final size:44
Alignment explanation
Indices: 4560710--4560803 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 44
4560700 ATTTATTACA
* * * *
4560710 AAATTAACCATAACTCATTATTAAGTTATCATTTATTTA-TATT
1 AAATTATCCATAACTCACTATTAAGTTATCATTAATTAATTATT
* *
4560753 AAATTATCCATAATTTACTATTAAGTTATCATTAATTAATTATT
1 AAATTATCCATAACTCACTATTAAGTTATCATTAATTAATTATT
*
4560797 AAGTTAT
1 AAATTAT
4560804 TTATGATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 33 0.77
44 10 0.23
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (44 bp):
AAATTATCCATAACTCACTATTAAGTTATCATTAATTAATTATT
Found at i:4560822 original size:90 final size:90
Alignment explanation
Indices: 4560728--4560909 Score: 222
Period size: 90 Copynumber: 2.0 Consensus size: 90
4560718 CATAACTCAT
* * * *
4560728 TATTAAGTTATCATTTA-TTTATATTAAATTATCCATAATTTACTATTAAGTTATCATTAATTAA
1 TATTAAGTTAT-ATTGATTTTATATTAAATTATCAATAATTAACTATTAAATTATCATTAATTAA
* *
4560792 TTATTAAGTTATTTATGATTAACTAC
65 CTATTAAATTATTTATGATTAACTAC
* * * * * * *
4560818 TATTAAGTTATATTGATTTTCTTTTAATTTTTCAATGATTAACTATTAAATTATCATTGATTTAC
1 TATTAAGTTATATTGATTTTATATTAAATTATCAATAATTAACTATTAAATTATCATTAATTAAC
*
4560883 TATTAAATTATTTATGATTTACTAC
66 TATTAAATTATTTATGATTAACTAC
4560908 TA
1 TA
4560910 AATTTATCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 4 0.05
90 73 0.95
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (90 bp):
TATTAAGTTATATTGATTTTATATTAAATTATCAATAATTAACTATTAAATTATCATTAATTAAC
TATTAAATTATTTATGATTAACTAC
Found at i:4561444 original size:22 final size:22
Alignment explanation
Indices: 4561357--4561489 Score: 76
Period size: 22 Copynumber: 6.1 Consensus size: 22
4561347 ATCAATATTA
* * *
4561357 TATCACTAATTTATGAATTATT
1 TATCACTAAGTTATTAATGATT
* * *
4561379 TGTCATTAAGTTATAAATGATT
1 TATCACTAAGTTATTAATGATT
* * * * *
4561401 TACCAATCA-TTGTTAGTGATT
1 TATCACTAAGTTATTAATGATT
*
4561422 TATCACTAAGTTATTAATAATT
1 TATCACTAAGTTATTAATGATT
*
4561444 TATTA-TAAAGTTA-TAATTGATT
1 TATCACT-AAGTTATTAA-TGATT
* *
4561466 TA-CTACTAATTTACTAATGATT
1 TATC-ACTAAGTTATTAATGATT
4561488 TA
1 TA
4561490 CTAAAAAGTT
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
21 19 0.23
22 60 0.72
23 4 0.05
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (22 bp):
TATCACTAAGTTATTAATGATT
Found at i:4561489 original size:44 final size:44
Alignment explanation
Indices: 4561417--4561509 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
4561407 TCATTGTTAG
* * *
4561417 TGATTTATCACTAAGTTATTAATAATTTATTATAAAGTTAT-AA
1 TGATTTATCACTAAGTTACTAATAATTTACTAAAAAGTTATCAA
* *
4561460 TTGATTTA-CTACTAATTTACTAATGATTTACTAAAAAGTTATCAA
1 -TGATTTATC-ACTAAGTTACTAATAATTTACTAAAAAGTTATCAA
4561505 TGATT
1 TGATT
4561510 ATATGATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 39 0.93
45 2 0.05
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (44 bp):
TGATTTATCACTAAGTTACTAATAATTTACTAAAAAGTTATCAA
Found at i:4561506 original size:22 final size:22
Alignment explanation
Indices: 4561429--4561509 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
4561419 ATTTATCACT
* * * *
4561429 AAGTTATTAATAATTTATTATA
1 AAGTTATCAATGATTTACTAAA
**
4561451 AAGTTAT-AATTGATTTACTACT
1 AAGTTATCAA-TGATTTACTAAA
*
4561473 AATTTA-CTAATGATTTACTAAA
1 AAGTTATC-AATGATTTACTAAA
4561495 AAGTTATCAATGATT
1 AAGTTATCAATGATT
4561510 ATATGATTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 42 0.89
23 3 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (22 bp):
AAGTTATCAATGATTTACTAAA
Found at i:4561526 original size:96 final size:96
Alignment explanation
Indices: 4561417--4561601 Score: 212
Period size: 96 Copynumber: 1.9 Consensus size: 96
4561407 TCATTGTTAG
* * ** * *
4561417 TGATTTATCACTAAGTTATTAATAATTTATTATAAAGTTATAATTGATTTACTACTAAT-TTACT
1 TGATTTATCACTAAATTATCAATAATTTACAATAAAGTTATAAGTAATTTACTA-TAATATTACT
4561481 AATGATTTACTAAAAAGTTATCAATGATTATA
65 AATGATTTACTAAAAAGTTATCAATGATTATA
* * * * *
4561513 TGATTTAGT-ACTAAATTATCACTAATTTACAATTAAGTTATTAGTAATTTACTATTATATTATT
1 TGATTTA-TCACTAAATTATCAATAATTTACAATAAAGTTATAAGTAATTTACTATAATATTACT
* **
4561577 AGTGATTTACTATTAAGTTATCAAT
65 AATGATTTACTAAAAAGTTATCAAT
4561602 TTACTACTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
95 3 0.04
96 69 0.95
97 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (96 bp):
TGATTTATCACTAAATTATCAATAATTTACAATAAAGTTATAAGTAATTTACTATAATATTACTA
ATGATTTACTAAAAAGTTATCAATGATTATA
Found at i:4561553 original size:22 final size:22
Alignment explanation
Indices: 4561528--4561631 Score: 101
Period size: 22 Copynumber: 4.9 Consensus size: 22
4561518 TAGTACTAAA
* *
4561528 TTATCACTAATTTACAATTAAG
1 TTATCAGTAATTTACTATTAAG
*
4561550 TTATTAGTAATTTACTATTATA-
1 TTATCAGTAATTTACTATTA-AG
* *
4561572 TTATTAGTGATTTACTATTAAG
1 TTATCAGTAATTTACTATTAAG
*
4561594 TTATC---AATTTACTACTAA-
1 TTATCAGTAATTTACTATTAAG
*
4561612 TTATCAGTTATTTACTATTA
1 TTATCAGTAATTTACTATTA
4561632 TATATATTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
18 5 0.07
19 11 0.16
21 11 0.16
22 40 0.59
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.49
Consensus pattern (22 bp):
TTATCAGTAATTTACTATTAAG
Found at i:4561605 original size:19 final size:19
Alignment explanation
Indices: 4561526--4561647 Score: 72
Period size: 22 Copynumber: 6.1 Consensus size: 19
4561516 TTTAGTACTA
*
4561526 AATTATCACTAATTTACAATT
1 AATTATCA-T-ATTTACTATT
*
4561547 AAGTTATTAGTAATTTACTATT
1 AA-TTATCA-T-ATTTACTATT
*
4561569 ATATTATTAGTGATTTACTATT
1 A-ATTATCA-T-ATTTACTATT
*
4561591 AAGTTATCA-ATTTACTACT
1 AA-TTATCATATTTACTATT
4561610 AATTATCAGTTATTTACTATT
1 AATTATCA--TATTTACTATT
*
4561631 -A-TAT-ATATTTATTATT
1 AATTATCATATTTACTATT
4561647 A
1 A
4561648 TTTTATTATT
Statistics
Matches: 86, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
16 10 0.12
18 7 0.08
19 14 0.16
20 1 0.01
21 12 0.14
22 41 0.48
23 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (19 bp):
AATTATCATATTTACTATT
Found at i:4561617 original size:18 final size:19
Alignment explanation
Indices: 4561581--4561617 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4561571 ATTATTAGTG
*
4561581 ATTTACTATTAAGTTATCA
1 ATTTACTACTAAGTTATCA
4561600 ATTTACTACTAA-TTATCA
1 ATTTACTACTAAGTTATCA
4561618 GTTATTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTACTACTAAGTTATCA
Found at i:4561670 original size:26 final size:26
Alignment explanation
Indices: 4561641--4561701 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
4561631 ATATATATTT
* *
4561641 ATTATTATTTTATTATTGAT-TTAATA
1 ATTATTATTTAATTATTGATCTGAA-A
*
4561667 ATTAATT-TTTAATTATTTATCTGAAA
1 ATT-ATTATTTAATTATTGATCTGAAA
4561693 ATTATTATT
1 ATTATTATT
4561702 GATTTACCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 3 0.10
26 20 0.69
27 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTATTATTTAATTATTGATCTGAAA
Found at i:4561791 original size:22 final size:22
Alignment explanation
Indices: 4561766--4562045 Score: 132
Period size: 22 Copynumber: 13.0 Consensus size: 22
4561756 AAATTAATGC
*
4561766 ATGATTTATTATTAAGTTATCA
1 ATGATTTACTATTAAGTTATCA
* *
4561788 ATGATTAACTATTATGTTATCA
1 ATGATTTACTATTAAGTTATCA
*
4561810 ATGATTTACTAATAAGTTATGC-
1 ATGATTTACTATTAAGTTAT-CA
* *
4561832 -TGATTTACTTTTAAGTTTTCA
1 ATGATTTACTATTAAGTTATCA
* * * *
4561853 ACGGA-TAACTACTAAATTATCA
1 A-TGATTTACTATTAAGTTATCA
* *
4561875 ATTATTTACTATTAATTTAT-A
1 ATGATTTACTATTAAGTTATCA
* **
4561896 ATTAATTTACTATTAAGTTATTT
1 A-TGATTTACTATTAAGTTATCA
* *
4561919 ATTATTTACTACT-A--T-T-A
1 ATGATTTACTATTAAGTTATCA
* * * *
4561936 ATTAATTACTATTAAACTGA--A
1 ATGATTTACTATT-AAGTTATCA
* **
4561957 ACTCATTTACTATTAAACTATCA
1 A-TGATTTACTATTAAGTTATCA
* * * *
4561980 TTAATTTACTATTAAATTATTA
1 ATGATTTACTATTAAGTTATCA
* * *
4562002 TTGATTTATTACTAAGTTATCA
1 ATGATTTACTATTAAGTTATCA
* * *
4562024 ATAATTAACTACTAAGTTATCA
1 ATGATTTACTATTAAGTTATCA
4562046 TTTATTTTTT
Statistics
Matches: 196, Mismatches: 47, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
17 11 0.06
18 1 0.01
19 2 0.01
20 1 0.01
21 25 0.13
22 151 0.77
23 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
ATGATTTACTATTAAGTTATCA
Found at i:4561846 original size:65 final size:66
Alignment explanation
Indices: 4561762--4561916 Score: 156
Period size: 65 Copynumber: 2.4 Consensus size: 66
4561752 TATTAAATTA
* * **
4561762 ATGCATGATTTATTATTAAGTTATCAA-TGATTAACTATTATGTTATCAATGATTTACTAATAAG
1 ATGCATGATTTATTATTAAGTTATCAACGGA-TAACTACTAAATTATCAATGATTTACTAATAAG
4561826 TT
65 TT
* * * *
4561828 ATGC-TGATTTACTT-TTAAGTTTTCAACGGATAACTACTAAATTATCAATTATTTACTATTAAT
1 ATGCATGATTTA-TTATTAAGTTATCAACGGATAACTACTAAATTATCAATGATTTACTAATAAG
4561891 TT
65 TT
* * *
4561893 AT-AATTAATTTACTATTAAGTTAT
1 ATGCA-TGATTTATTATTAAGTTAT
4561917 TTATTATTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
65 50 0.69
66 22 0.31
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (66 bp):
ATGCATGATTTATTATTAAGTTATCAACGGATAACTACTAAATTATCAATGATTTACTAATAAGT
T
Found at i:4561910 original size:11 final size:11
Alignment explanation
Indices: 4561878--4561929 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
4561868 ATTATCAATT
4561878 ATTTACTATTA
1 ATTTACTATTA
4561889 ATTTA-TAATTA
1 ATTTACT-ATTA
4561900 ATTTACTATTA
1 ATTTACTATTA
* *
4561911 AGTTATTTATT-
1 ATTTA-CTATTA
4561922 ATTTACTA
1 ATTTACTA
4561930 CTATTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 3 0.09
11 26 0.76
12 5 0.15
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTACTATTA
Found at i:4562250 original size:22 final size:22
Alignment explanation
Indices: 4562205--4562261 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4562195 ATTATCATTC
* * * *
4562205 ATTTATTATTAAGTTATTACTA
1 ATTTACTAATAAGTTATAAATA
*
4562227 ATTTACTACTAAGTTATAAATA
1 ATTTACTAATAAGTTATAAATA
4562249 A-TTACTAATAAGT
1 ATTTACTAATAAGT
4562262 ATAGACACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTACTAATAAGTTATAAATA
Found at i:4565134 original size:8 final size:8
Alignment explanation
Indices: 4565121--4565152 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
4565111 AATTTTTGTT
4565121 AATAAAAA
1 AATAAAAA
4565129 AAT-AAAA
1 AATAAAAA
4565136 AATAAAAA
1 AATAAAAA
4565144 AATAAAAA
1 AATAAAAA
4565152 A
1 A
4565153 GAAAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:4565135 original size:7 final size:7
Alignment explanation
Indices: 4565125--4565168 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
4565115 TTTGTTAATA
4565125 AAAAAAT
1 AAAAAAT
4565132 AAAAAAT
1 AAAAAAT
4565139 AAAAAAAT
1 -AAAAAAT
*
4565147 AAAAAAG
1 AAAAAAT
*
4565154 AAAAAAG
1 AAAAAAT
4565161 AAAAAAT
1 AAAAAAT
4565168 A
1 A
4565169 GGTAGTTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:4565141 original size:15 final size:15
Alignment explanation
Indices: 4565121--4565168 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
4565111 AATTTTTGTT
4565121 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
4565136 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
* *
4565151 AA-GAAAAAAGAAAA
1 AATAAAAAAATAAAA
4565165 AATA
1 AATA
4565169 GGTAGTTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.10
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:4570051 original size:9 final size:10
Alignment explanation
Indices: 4570037--4570096 Score: 65
Period size: 9 Copynumber: 6.2 Consensus size: 10
4570027 TAATGGATGG
*
4570037 AAAAAATAAA
1 AAAAAATGAA
4570047 AAAAAAT-AA
1 AAAAAATGAA
4570056 AAAAAATGAAGA
1 AAAAAATG-A-A
4570068 AAAAAATG--
1 AAAAAATGAA
4570076 AAAAAAT-AA
1 AAAAAATGAA
4570085 AAAAAATGAA
1 AAAAAATGAA
4570095 AA
1 AA
4570097 GGAAAACTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.16
9 16 0.36
10 11 0.25
11 1 0.02
12 9 0.20
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:4571123 original size:21 final size:20
Alignment explanation
Indices: 4571078--4571123 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4571068 CTAGATTATC
*
4571078 ACATTTGCATCATTGAGAAA
1 ACATTTGCATCATTGACAAA
* *
4571098 ACATTTGCATTATTGATCATA
1 ACATTTGCATCATTGA-CAAA
4571119 ACATT
1 ACATT
4571124 CATTGTATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATTTGCATCATTGACAAA
Found at i:4571203 original size:22 final size:21
Alignment explanation
Indices: 4571178--4571232 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
4571168 TCTTTTGATG
* *
4571178 AGAATTTTTGAGTTGTCAAATA
1 AGAATCTTTGAATT-TCAAATA
* *
4571200 AGAAGCTTTGAATTTCAAATG
1 AGAATCTTTGAATTTCAAATA
4571221 AGAATCTTTGAA
1 AGAATCTTTGAA
4571233 GTATGAAACC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
AGAATCTTTGAATTTCAAATA
Found at i:4571298 original size:21 final size:21
Alignment explanation
Indices: 4571260--4571331 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
4571250 TATTGAATGT
4571260 GAATCTTTGAA-CTCAAATAA
1 GAATCTTTGAATCTCAAATAA
* *
4571280 GAATCTTTGAATTTCAAATGA
1 GAATCTTTGAATCTCAAATAA
*
4571301 GGATCTTTGAATCTCAAATAA
1 GAATCTTTGAATCTCAAATAA
4571322 GAATCTTTGA
1 GAATCTTTGA
4571332 GGTGTGAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
20 11 0.24
21 34 0.76
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
GAATCTTTGAATCTCAAATAA
Found at i:4571366 original size:100 final size:100
Alignment explanation
Indices: 4571178--4571410 Score: 313
Period size: 100 Copynumber: 2.3 Consensus size: 100
4571168 TCTTTTGATG
* * * * * *
4571178 AGAATTTTTGAGTTGTCAAATAAGAAGCTTTGAATTTCAAATGAGAATCTTTGAAGTATGAAACC
1 AGAATCTTTGAATT-TCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAAGTATGAAACC
* ** ** *
4571243 CAAAATTTATTGAATGTGAATCTTTGAACTCAAATA
65 CAAAATTTATCGAATAAGAATCTTCAAACTCAAAAA
* * * *
4571279 AGAATCTTTGAATTTCAAATGAGGATCTTTGAATCTCAAATAAGAATCTTTGAGGTGTGAAACCT
1 AGAATCTTTGAATTTCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAAGTATGAAACCC
4571344 AAAATTTATCGAATAAGAATCTTCAAACTCAAAAA
66 AAAATTTATCGAATAAGAATCTTCAAACTCAAAAA
4571379 AGAATCTTTGAATTTCAAATGAGAATCTTTGA
1 AGAATCTTTGAATTTCAAATGAGAATCTTTGA
4571411 GGTGTGAAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 103 0.90
101 12 0.10
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (100 bp):
AGAATCTTTGAATTTCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAAGTATGAAACCC
AAAATTTATCGAATAAGAATCTTCAAACTCAAAAA
Found at i:4571376 original size:79 final size:79
Alignment explanation
Indices: 4571275--4571466 Score: 240
Period size: 79 Copynumber: 2.4 Consensus size: 79
4571265 TTTGAACTCA
* ** *
4571275 AATAAGAATCTTTGAATTTCAAATGAGGATCTTTGAATCTCAAATAAGAATCTTTGAGGTGTGAA
1 AATAAGAATC-TTCAAACTCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAGGTGTGAA
*
4571340 ACCTAAAATTTATCG
65 ACCAAAAATTTATCG
** * *
4571355 AATAAGAATCTTCAAACTCAAAAAAGAATCTTTGAATTTCAAATGAGAATCTTTGAGGTGTGAAA
1 AATAAGAATCTTCAAACTCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAGGTGTGAAA
* *
4571420 TCAAAAATTTGTCG
66 CCAAAAATTTATCG
** * *
4571434 AATGTGAATCTTCGAGCTCAAATGAGAATCTTT
1 AATAAGAATCTTCAAACTCAAATGAGAATCTTT
4571467 AAAGTGTGAA
Statistics
Matches: 95, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 85 0.89
80 10 0.11
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (79 bp):
AATAAGAATCTTCAAACTCAAATGAGAATCTTTGAATCTCAAATAAGAATCTTTGAGGTGTGAAA
CCAAAAATTTATCG
Found at i:4571864 original size:42 final size:42
Alignment explanation
Indices: 4571801--4571929 Score: 149
Period size: 42 Copynumber: 3.1 Consensus size: 42
4571791 GATCATCAAT
* *
4571801 GAGC-TTTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA-AA
1 GAGCATTTTTATTTTTCAAAGTTGTGATGCCTCTATTTAGAA
*
4571841 GGAGCATTTTTATTTTTCAAAGTTGTGATGCCTTTATTTAGAA
1 -GAGCATTTTTATTTTTCAAAGTTGTGATGCCTCTATTTAGAA
* * *
4571884 GAGCATTTATT-TTTCTCAAAGTTGTTGA-ACTTCTATTTAGAA
1 GAGCATTT-TTATTTTTCAAAGTTG-TGATGCCTCTATTTAGAA
4571926 GAGC
1 GAGC
4571930 TTTGTTTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.05
42 66 0.86
43 7 0.09
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (42 bp):
GAGCATTTTTATTTTTCAAAGTTGTGATGCCTCTATTTAGAA
Found at i:4580134 original size:19 final size:20
Alignment explanation
Indices: 4580108--4580156 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
4580098 TGATGGTTGT
4580108 AACAAAAAAAAAAAAT-AAA
1 AACAAAAAAAAAAAATAAAA
* **
4580127 ACCAAAAACCAAAAATAAAA
1 AACAAAAAAAAAAAATAAAA
4580147 AACAAAAAAA
1 AACAAAAAAA
4580157 CGAAAATGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.04
Consensus pattern (20 bp):
AACAAAAAAAAAAAATAAAA
Found at i:4580979 original size:27 final size:26
Alignment explanation
Indices: 4580918--4580979 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
4580908 GAAAGAAGGC
* *
4580918 AAAAAA-AAATGAGGAAAAAATAAAA
1 AAAAAAGAAATGAAGAAAAAAGAAAA
* *
4580943 AGAAAGGAAATGAAGAATAAAAGAAAA
1 AAAAAAGAAATGAAGAA-AAAAGAAAA
4580970 AAAAAAGAAA
1 AAAAAAGAAA
4580980 AGAAATGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 4 0.14
26 9 0.31
27 16 0.55
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (26 bp):
AAAAAAGAAATGAAGAAAAAAGAAAA
Found at i:4583027 original size:36 final size:36
Alignment explanation
Indices: 4582987--4583143 Score: 104
Period size: 36 Copynumber: 4.3 Consensus size: 36
4582977 CCCGATCATT
4582987 TTCTTATTTTTTTGACTTGTAGTGTCATCCCAGACA
1 TTCTTATTTTTTTGACTTGTAGTGTCATCCCAGACA
* ** * **
4583023 TTCTT-TATTTTTTGACTTGTGGTGTTGTCCCGGTTA
1 TTCTTAT-TTTTTTGACTTGTAGTGTCATCCCAGACA
* * * * *
4583059 TGTTTTAATTTTATGACTTGTGGTGTTATCCCA-ATCA
1 T-TCTTATTTTTTTGACTTGTAGTGTCATCCCAGA-CA
* * * * *
4583096 CTCTT-TATTTTTTAACTTGCAGTGTCATCCTAGTCA
1 TTCTTAT-TTTTTTGACTTGTAGTGTCATCCCAGACA
4583132 TTCTTTATTTTT
1 TTC-TTATTTTT
4583144 GAGTTATGTT
Statistics
Matches: 89, Mismatches: 24, Indels: 15
0.70 0.19 0.12
Matches are distributed among these distances:
35 1 0.01
36 55 0.62
37 32 0.36
38 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (36 bp):
TTCTTATTTTTTTGACTTGTAGTGTCATCCCAGACA
Found at i:4583198 original size:36 final size:37
Alignment explanation
Indices: 4583132--4583257 Score: 111
Period size: 38 Copynumber: 3.5 Consensus size: 37
4583122 ATCCTAGTCA
*
4583132 TTCTTTA-TTTTTGAGTTATGTTGTCATCTCGATC-G
1 TTCTTTATTTTTTGACTTATGTTGTCATCTCGATCAG
**
4583167 TTCTTTATTTTTTGACTTATAG-TGTTGTCTCGATCATG
1 TTCTTTATTTTTTGACTTAT-GTTGTCATCTCGATCA-G
* * * * *
4583205 TTCTTTATTATTTGACTCACGATT-TAATCTCGATTA-
1 TTCTTTATTTTTTGACTTATG-TTGTCATCTCGATCAG
4583241 TT-TTTATTTTTTGACTT
1 TTCTTTATTTTTTGACTT
4583258 GTGGTTTAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
35 20 0.27
36 24 0.32
37 2 0.03
38 27 0.36
39 1 0.01
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.56
Consensus pattern (37 bp):
TTCTTTATTTTTTGACTTATGTTGTCATCTCGATCAG
Found at i:4583219 original size:38 final size:35
Alignment explanation
Indices: 4583132--4583221 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 35
4583122 ATCCTAGTCA
*
4583132 TTCTTTATTTTTGAGTTATGTTGTCATCTCGATCG
1 TTCTTTATTTTTGACTTATGTTGTCATCTCGATCG
**
4583167 TTCTTTATTTTTTGACTTATAG-TGTTGTCTCGATCATG
1 TTCTTTA-TTTTTGACTTAT-GTTGTCATCTCGATC--G
4583205 TTCTTTATTATTTGACT
1 TTCTTTATT-TTTGACT
4583222 CACGATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 7 0.15
36 22 0.47
37 3 0.06
38 15 0.32
ACGTcount: A:0.16, C:0.13, G:0.14, T:0.57
Consensus pattern (35 bp):
TTCTTTATTTTTGACTTATGTTGTCATCTCGATCG
Found at i:4583254 original size:35 final size:35
Alignment explanation
Indices: 4583194--4583292 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
4583184 TATAGTGTTG
*
4583194 TCTCGATCATGTTCTTTATTATTTGACTCACGATTTAA
1 TCTCGATCA--TT-TTTATTTTTTGACTCACGATTTAA
* *** *
4583232 TCTCGATTATTTTTATTTTTTGACTTGTGGTTTAA
1 TCTCGATCATTTTTATTTTTTGACTCACGATTTAA
* * *
4583267 TTTCGGTCATTTTTATATTTTGACTC
1 TCTCGATCATTTTTATTTTTTGACTC
4583293 GTAGTTCAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 40 0.80
36 2 0.04
38 8 0.16
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.55
Consensus pattern (35 bp):
TCTCGATCATTTTTATTTTTTGACTCACGATTTAA
Found at i:4583351 original size:34 final size:34
Alignment explanation
Indices: 4583279--4583351 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
4583269 TCGGTCATTT
* * * *
4583279 TTATATTTTGACTCGTAGTTCAATCTTAATTTCT
1 TTATTTTTTGACTCGTAATTCAATCTTAATCTCG
**
4583313 TTATTTTTTGACTCGTAATTCAATCTTGGTCTCG
1 TTATTTTTTGACTCGTAATTCAATCTTAATCTCG
4583347 TTATT
1 TTATT
4583352 CTCCAACTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (34 bp):
TTATTTTTTGACTCGTAATTCAATCTTAATCTCG
Found at i:4583502 original size:35 final size:35
Alignment explanation
Indices: 4583421--4583583 Score: 102
Period size: 35 Copynumber: 4.6 Consensus size: 35
4583411 AATCCTTCTG
* *
4583421 ACTTACGGTTCAGTCCTAGTCATATTTATTTCTTG
1 ACTTACGGTTCAATCCTAGTCATATTTATTTCTTC
* * *
4583456 ACTCACAGTTCAATCCTGGTCAT-TTTCATTAT-TTC
1 ACTTACGGTTCAATCCTAGTCATATTT-ATT-TCTTC
* * *
4583491 ACTTACGGTTCAAT-CTTGATCATATTTATTTTTTTG
1 ACTTACGGTTCAATCCTAG-TCATATTTA-TTTCTTC
* * * * *
4583527 ACTTGCAGTTTAATCCTAATCAT-TTCTATCTTC-TA
1 ACTTACGGTTCAATCCTAGTCATATT-TAT-TTCTTC
* *
4583562 ACTTATGGTTCAGTCCTAGTCA
1 ACTTACGGTTCAATCCTAGTCA
4583584 CCGTTATTCT
Statistics
Matches: 97, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
34 6 0.06
35 62 0.64
36 27 0.28
37 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (35 bp):
ACTTACGGTTCAATCCTAGTCATATTTATTTCTTC
Found at i:4583566 original size:71 final size:71
Alignment explanation
Indices: 4583415--4583752 Score: 194
Period size: 70 Copynumber: 4.8 Consensus size: 71
4583405 AATCCAAATC
* **
4583415 CTTCTGACTTACGGTTCAGTCCTAGTCATATTTATTTCTTGACTCACAGTTCAATCCTGGTCATT
1 CTTCT-ACTTACGGTTCAATCCTAGTCATATTTATTTCTTGACTCACAGTTCAATCCTAATCATT
4583480 TTCATTAT
65 TTCA-TAT
* * ** *
4583488 -TTC-ACTTACGGTTCAAT-CTTGATCATATTTATTTTTTTGACTTGCAGTTTAATCCTAATCA-
1 CTTCTACTTACGGTTCAATCCTAG-TCATATTTA-TTTCTTGACTCACAGTTCAATCCTAATCAT
4583549 TTTC-TAT
64 TTTCATAT
* * *** ** * * *
4583556 CTTCTAACTTATGGTTCAGTCCTAGTCACCGTTA-TTCTTTGACTCGTAGTTAAATTCTAGTCA-
1 CTTCT-ACTTACGGTTCAATCCTAGTCATATTTATTTC-TTGACTCACAGTTCAATCCTAATCAT
*
4583619 TCTC-TAT
64 TTTCATAT
** * * * **
4583626 CTTCTTACTTGTGGCTCAATTCC-AGTCATATTTATTT-TGTGACTCACGGTTTAATCCTGGTCA
1 CTTC-TACTTACGGTTCAA-TCCTAGTCATATTTATTTCT-TGACTCACAGTTCAATCCTAATCA
4583689 TTTTCAT-T
63 TTTTCATAT
* * * * * * * * *
4583697 TTTCAACTTGCAGTTCAGTCTTAATCATATTTATTTCTTTGAGTCATAGTTCAATC
1 CTTCTACTTACGGTTCAATCCTAGTCATATTTATTTC-TTGACTCACAGTTCAATC
4583753 TCAATTATTT
Statistics
Matches: 203, Mismatches: 46, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
68 3 0.01
69 11 0.05
70 114 0.56
71 67 0.33
72 8 0.04
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (71 bp):
CTTCTACTTACGGTTCAATCCTAGTCATATTTATTTCTTGACTCACAGTTCAATCCTAATCATTT
TCATAT
Found at i:4583868 original size:211 final size:211
Alignment explanation
Indices: 4583415--4583945 Score: 522
Period size: 211 Copynumber: 2.5 Consensus size: 211
4583405 AATCCAAATC
* * * * * *
4583415 CTTCTGACTTACGGTTCAGTCCTAGTCATATTTATTTCTTGACTCACAGTTCAATCCTGGTCATT
1 CTTCTTACTTATGGCTCAATCCCAGTCATATTTATTTCTTGACTCACAGTTTAATCCTGGTCATT
* * * * ** *
4583480 TTCATTATTTC-ACTTACGGTTCAATCTTGATCATATTTATTTTTTTGACTTGCAGTTTAATCCT
66 TTCATT-TTTCAACTTACAGTTCAGTCTTAATCATATTTATTTCTTTGACTCACAGTTCAATCCT
* * * * *
4583544 AATCATTTCTATCTTCTAACTTATGGTTCAGTCCTAGTCACCGTTATTCTTTGACTCGTAGTTAA
130 AATCATTTCTATCTTCTAACTTATGATTCAATCCCAGTCACCATTATTATTTGACTCGTAGTTAA
* *
4583609 ATTCTAGTCATCTCTAT
195 ATTCTAGCCATCTATAT
* * *
4583626 CTTCTTACTTGTGGCTCAATTCCAGTCATATTTATTT-TGTGACTCACGGTTTAATCCTGGTCAT
1 CTTCTTACTTATGGCTCAATCCCAGTCATATTTATTTCT-TGACTCACAGTTTAATCCTGGTCAT
* * *
4583690 TTTCATTTTTCAACTTGCAGTTCAGTCTTAATCATATTTATTTCTTTGAGTCATAGTTCAAT-CT
65 TTTCATTTTTCAACTTACAGTTCAGTCTTAATCATATTTATTTCTTTGACTCACAGTTCAATCCT
* * * * * ** * * *
4583754 CAATTATTTTTATCTTTTGACTTGT-ATCTCAATCCCAGTCATTATTATTATTTTACTTGTGGTT
130 -AATCATTTCTATCTTCTAACTTATGAT-TCAATCCCAGTCACCATTATTATTTGACTCGTAGTT
*
4583818 CAATCTCT-GCCATCTATAT
193 AAAT-TCTAGCCATCTATAT
* ** * *
4583837 CTT-TTGACTTATGGCTTAATCCC-GATCATATTTATTTCTCAACTCACAGTTTAAT-TTCAGTC
1 CTTCTT-ACTTATGGCTCAATCCCAG-TCATATTTATTTCTTGACTCACAGTTTAATCCT-GGTC
* * *
4583899 ATTTT-ATTATTCAACTTACAGTTCAGTCTTAGTCATTTTTATTTCTT
63 ATTTTCATTTTTCAACTTACAGTTCAGTCTTAATCATATTTATTTCTT
4583946 CAACTCGTGA
Statistics
Matches: 262, Mismatches: 49, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
210 50 0.19
211 208 0.79
212 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (211 bp):
CTTCTTACTTATGGCTCAATCCCAGTCATATTTATTTCTTGACTCACAGTTTAATCCTGGTCATT
TTCATTTTTCAACTTACAGTTCAGTCTTAATCATATTTATTTCTTTGACTCACAGTTCAATCCTA
ATCATTTCTATCTTCTAACTTATGATTCAATCCCAGTCACCATTATTATTTGACTCGTAGTTAAA
TTCTAGCCATCTATAT
Found at i:4583905 original size:34 final size:34
Alignment explanation
Indices: 4583862--4583951 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 34
4583852 TTAATCCCGA
*
4583862 TCATATTTATTTCTCAACTCACAGTTTAAT-TTCAG
1 TCAT-TTTATTTCTCAACTCACAGTTCAATCTT-AG
* *
4583897 TCATTTTATTAT-TCAACTTACAGTTCAGTCTTAG
1 TCATTTTATT-TCTCAACTCACAGTTCAATCTTAG
4583931 TCATTTTTATTTCTTCAACTC
1 TCA-TTTTATTTC-TCAACTC
4583952 GTGATTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
34 26 0.57
35 14 0.30
36 6 0.13
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (34 bp):
TCATTTTATTTCTCAACTCACAGTTCAATCTTAG
Found at i:4584183 original size:35 final size:35
Alignment explanation
Indices: 4584117--4584204 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 35
4584107 ATCTCTATCT
* * * * *
4584117 TCGACTTATGGCTCAGTCTCGGTTATATTTATTTA
1 TCGACTTGTGACTCAATCTAGGTAATATTTATTTA
* *
4584152 TCGACTTGTGACTCAATCTAGGTAATTTTTATTTT
1 TCGACTTGTGACTCAATCTAGGTAATATTTATTTA
* * *
4584187 TTGATTTGTGATTCAATC
1 TCGACTTGTGACTCAATC
4584205 CTGATCATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (35 bp):
TCGACTTGTGACTCAATCTAGGTAATATTTATTTA
Found at i:4585265 original size:145 final size:145
Alignment explanation
Indices: 4585115--4585455 Score: 389
Period size: 145 Copynumber: 2.4 Consensus size: 145
4585105 AAGCTTAAAT
* * ** * *
4585115 TTTCATGAAACTTTTTAAATATCAATTTTATAACATTTCATGATTTTTGGTACATTTAAAATTAT
1 TTTCATGAAACTTTTCAAATATTAATTTTATAACATTTCATGATTTTTGGTACACCTAAAATCAC
* * * *
4585180 AGCAATACCCCGAAAAAT-GTGATATTACCAAAATACTCTTAT-AGAGGTATTTTCATAATTTGA
66 AGCAATACCCC-AAAAATCATAAAATTACCAAAATACCCTTATAAG-GGTATTTTCATAATTTGA
* * *
4585243 CTTTTTTGAACTCAAAA
129 CCTTCTCGAACTCAAAA
** * *
4585260 TTTCATGAAACTTTTCAGCTATTAATTTTATAACATTTCATAATTTTTGGTACACCTGAAATCAC
1 TTTCATGAAACTTTTCAAATATTAATTTTATAACATTTCATGATTTTTGGTACACCTAAAATCAC
* * *
4585325 AGTAGTACCCCAAAAATCATAAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGGCC
66 AGCAATACCCCAAAAATCATAAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACC
* *
4585390 TTCTCGAGCTCAAAT
131 TTCTCGAACTCAAAA
* ** * * * *
4585405 TTTTACAAAACTTTTCATATCTTAATTTCATAATATTTCATGATTTTTGGT
1 TTTCATGAAACTTTTCAAATATTAATTTTATAACATTTCATGATTTTTGGT
4585456 GTTTTAAAAT
Statistics
Matches: 163, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
144 6 0.04
145 155 0.95
146 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (145 bp):
TTTCATGAAACTTTTCAAATATTAATTTTATAACATTTCATGATTTTTGGTACACCTAAAATCAC
AGCAATACCCCAAAAATCATAAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACC
TTCTCGAACTCAAAA
Done.