Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 22 of 27
Found at i:3723367 original size:48 final size:48
Alignment explanation
Indices: 3723310--3723414 Score: 185
Period size: 48 Copynumber: 2.2 Consensus size: 48
3723300 GTTTTTATGT
3723310 CATTTCATGTCATTTTAGACATTTTCCATGACTTAGGGATTTTCAT-A
1 CATTTCATGTCATTTTAGACATTTTCCATGACTTAGGGATTTTCATAA
*
3723357 CATTTTCATGTCATTTTAGTCATTTTCCATGACTTAGGGATTTTCATAA
1 CA-TTTCATGTCATTTTAGACATTTTCCATGACTTAGGGATTTTCATAA
3723406 CATTTCATG
1 CATTTCATG
3723415 CATATTTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 2 0.04
48 50 0.91
49 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (48 bp):
CATTTCATGTCATTTTAGACATTTTCCATGACTTAGGGATTTTCATAA
Found at i:3723543 original size:58 final size:58
Alignment explanation
Indices: 3723481--3723607 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
3723471 ATAAATTTTG
* * * *
3723481 ATGTCATTTTTCATGA-TCAAGGGACTTTG-ATGCAATTTTTTGAATTTTGATCTCATTT
1 ATGTCATTTTCCATAACT-AAGGGAC-TTGAATGCAATTTTATGAATTTTGATATCATTT
* *
3723539 ATGTCAGTTTCCATAACTTAGGGACTTGAATGCAATTTTATGAATTTTGATATCATTT
1 ATGTCATTTTCCATAACTAAGGGACTTGAATGCAATTTTATGAATTTTGATATCATTT
3723597 A-GATCATTTTC
1 ATG-TCATTTTC
3723608 TTAAATTTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 4 0.07
58 54 0.92
59 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (58 bp):
ATGTCATTTTCCATAACTAAGGGACTTGAATGCAATTTTATGAATTTTGATATCATTT
Found at i:3723615 original size:30 final size:30
Alignment explanation
Indices: 3723581--3723637 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3723571 CAATTTTATG
3723581 AATTTTGATATCATTT-AGATCATTTTCTTA
1 AATTTTGATATCATTTAAG-TCATTTTCTTA
*
3723611 AATTTTGATGTCATTTAAGTCATTTTC
1 AATTTTGATATCATTTAAGTCATTTTC
3723638 CATAATTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (30 bp):
AATTTTGATATCATTTAAGTCATTTTCTTA
Found at i:3723640 original size:88 final size:87
Alignment explanation
Indices: 3723515--3723691 Score: 250
Period size: 88 Copynumber: 2.0 Consensus size: 87
3723505 CTTTGATGCA
* *
3723515 ATTTTTTGAATTTTGATCTCATTTATGTCAGTTTCCATAACTT-AGGGACTT-GAATGCAATTTT
1 ATTTTTTAAATTTTGATCTCATTTAAGTCAGTTTCCATAA-TTGAGGGACTTAG-ATGCAATTTT
*
3723578 ATGAATTTTGATATCATTTAGATC
64 ATAAATTTTGATATCATTTAGATC
* * *
3723602 ATTTTCTTAAATTTTGATGTCATTTAAGTCATTTTCCATAATTGAGGGACTTAGATGTAATTTTA
1 ATTTT-TTAAATTTTGATCTCATTTAAGTCAGTTTCCATAATTGAGGGACTTAGATGCAATTTTA
*
3723667 TAAATTTTGATATCATTTAGGTC
65 TAAATTTTGATATCATTTAGATC
3723690 AT
1 AT
3723692 ATTCCATGTG
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
87 7 0.09
88 72 0.90
89 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (87 bp):
ATTTTTTAAATTTTGATCTCATTTAAGTCAGTTTCCATAATTGAGGGACTTAGATGCAATTTTAT
AAATTTTGATATCATTTAGATC
Found at i:3727773 original size:22 final size:22
Alignment explanation
Indices: 3727748--3727800 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
3727738 ATTTACGAGA
3727748 TACCCTAAACCTGGGATTGTGG
1 TACCCTAAACCTGGGATTGTGG
3727770 TACCCTAAACCTGGGATTGTGG
1 TACCCTAAACCTGGGATTGTGG
3727792 TACCCTAAA
1 TACCCTAAA
3727801 GAATCCTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (22 bp):
TACCCTAAACCTGGGATTGTGG
Found at i:3731670 original size:21 final size:21
Alignment explanation
Indices: 3731629--3731672 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3731619 CTCTCCTTTA
* *
3731629 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3731650 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3731671 TC
1 TC
3731673 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3733473 original size:13 final size:13
Alignment explanation
Indices: 3733455--3733480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3733445 ATAATCACCC
3733455 TGTATCGATACAA
1 TGTATCGATACAA
3733468 TGTATCGATACAA
1 TGTATCGATACAA
3733481 AGAAAGATAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3735570 original size:15 final size:15
Alignment explanation
Indices: 3735550--3735580 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3735540 ATTTCGTTTG
*
3735550 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3735565 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3735580 G
1 G
3735581 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3737411 original size:21 final size:21
Alignment explanation
Indices: 3737382--3737426 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3737372 AAGTTTTCAT
*
3737382 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3737402 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3737424 TTT
1 TTT
3737427 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3739671 original size:13 final size:13
Alignment explanation
Indices: 3739653--3739678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3739643 CAATTTTTTG
3739653 TGTATCGATACAT
1 TGTATCGATACAT
3739666 TGTATCGATACAT
1 TGTATCGATACAT
3739679 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3741232 original size:20 final size:20
Alignment explanation
Indices: 3741207--3741244 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3741197 ATATCAATAC
3741207 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
3741227 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
3741245 ACTGGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:3744711 original size:18 final size:18
Alignment explanation
Indices: 3744690--3744727 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3744680 TAGCTTAACC
3744690 TAATTTATAATGTATAAA
1 TAATTTATAATGTATAAA
3744708 TAATTTATAATGTATAAA
1 TAATTTATAATGTATAAA
3744726 TA
1 TA
3744728 CATAGTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TAATTTATAATGTATAAA
Found at i:3748729 original size:88 final size:88
Alignment explanation
Indices: 3748562--3748735 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 88
3748552 TTAACTTTGA
* * * * * *
3748562 GGAAACTCCAGCCCTATTACGTCGAAGGGATCTTCTAATCCCGTTCTTCATATGAAAACTCAAAT
1 GGAAACTCCAACCCTACTACGTCGAAGGGATCCTCCAATCCCGTTCTTCATAAGAAAACTCAAAG
*
3748627 TTTCACTTCGTATAATTTTATAG
66 TTTCACTTCATATAATTTTATAG
* * *
3748650 GGAAACTCCAACCCTACTAC-TCTGAGGGGATCCTCCAA-CCCTGTTTTTCATAAGAAAACTCGA
1 GGAAACTCCAACCCTACTACGTC-GAAGGGATCCTCCAATCCC-GTTCTTCATAAGAAAACTCAA
*
3748713 AGTTTCTCTTCATATAATTTTAT
64 AGTTTCACTTCATATAATTTTAT
3748736 TTTTAGGAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 68 0.93
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (88 bp):
GGAAACTCCAACCCTACTACGTCGAAGGGATCCTCCAATCCCGTTCTTCATAAGAAAACTCAAAG
TTTCACTTCATATAATTTTATAG
Found at i:3748916 original size:103 final size:105
Alignment explanation
Indices: 3748737--3749044 Score: 318
Period size: 103 Copynumber: 2.9 Consensus size: 105
3748727 TAATTTTATT
* * * * *
3748737 TTTAGGAAAACTCTAACCCCACAACTTCGAGGGTATACTCTAGCCCCGTTCTAAAAAAAAACTCA
1 TTTAGGAAAACTCTAACCCCACTACTTCGAGGGGACACTCCAGCCCCATTCTAAAAAAAAACTCA
*
3748802 AATTTACTTTTTGTTCCTAAA-ATTTTCA-AATCTTTGAC
66 AATTTACTTTTTGTTCCTAAATATTTTCATAATATTTGAC
* * * *
3748840 TTTAGGAAAACTCTAACCCCACTA-TTCTGAGGGGACACTCCAG-TCCATTCTTCATAAAAACCT
1 TTTAGGAAAACTCTAACCCCACTACTTC-GAGGGGACACTCCAGCCCCATTC-TAAAAAAAAACT
* *
3748903 TAAATTTACTTTTTGTTTCTAAATATTTTCATAATATTTGAC
64 CAAATTTACTTTTTGTTCCTAAATATTTTCATAATATTTGAC
* * * * * * * * ** *
3748945 TTTAGGGAAACTCCAACCCTACTACTCCGAAGGGAAACTTCAACCTCTTTCTCTATAAAAAAACT
1 TTTAGGAAAACTCTAACCCCACTACTTCGAGGGGACACTCCAGCC-CCAT-TCTAAAAAAAAACT
* * *
3749010 CAAATTTTCTCTTTGTTTCTAAATATTTTCATAAT
64 CAAATTTACTTTTTGTTCCTAAATATTTTCATAAT
3749045 TTTATCTTTG
Statistics
Matches: 167, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
102 8 0.05
103 65 0.39
104 7 0.04
105 41 0.25
106 2 0.01
107 42 0.25
108 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (105 bp):
TTTAGGAAAACTCTAACCCCACTACTTCGAGGGGACACTCCAGCCCCATTCTAAAAAAAAACTCA
AATTTACTTTTTGTTCCTAAATATTTTCATAATATTTGAC
Found at i:3749112 original size:107 final size:107
Alignment explanation
Indices: 3748786--3749097 Score: 298
Period size: 106 Copynumber: 3.0 Consensus size: 107
3748776 CTAGCCCCGT
* * * * *
3748786 TCTAAAAAAAAACTCAAATTTACTTTTTGTTCCTAAA-ATTTTCA-AATCTTTGACTTTAGGAAA
1 TCTACAAAAAAACTCAAATTTACTCTTTGTTTCTAAATATTTTCATAATATTTGACTTTAGGGAA
* * * * * * * ** *
3748849 ACTCTAACCCCACTATTCTGAGGGGACACTCC-AGTCCATTC
66 ACTCCAACCCTACTACTCCGAAGAGAAACTCCAACCCCTTTC
* * *
3748890 T-T-CATAAAAACCTTAAATTTACTTTTTGTTTCTAAATATTTTCATAATATTTGACTTTAGGGA
1 TCTACA-AAAAAACTCAAATTTACTCTTTGTTTCTAAATATTTTCATAATATTTGACTTTAGGGA
* * *
3748953 AACTCCAACCCTACTACTCCGAAGGGAAACTTCAACCTCTTTC
65 AACTCCAACCCTACTACTCCGAAGAGAAACTCCAACCCCTTTC
* * *
3748996 TCTATAAAAAAACTCAAATTTTCTCTTTGTTTCTAAATATTTTCATAAT-TTT-ATCTTTGGGGA
1 TCTACAAAAAAACTCAAATTTACTCTTTGTTTCTAAATATTTTCATAATATTTGA-CTTTAGGGA
* * *
3749059 AACTCCAATCCC-ACTTCTCTGAAGAGATACTCCAACCCC
65 AACTCCAA-CCCTACTACTCCGAAGAGAAACTCCAACCCC
3749098 GTTTTTACCC
Statistics
Matches: 171, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
102 1 0.01
103 29 0.17
104 8 0.05
105 43 0.25
106 46 0.27
107 43 0.25
108 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (107 bp):
TCTACAAAAAAACTCAAATTTACTCTTTGTTTCTAAATATTTTCATAATATTTGACTTTAGGGAA
ACTCCAACCCTACTACTCCGAAGAGAAACTCCAACCCCTTTC
Found at i:3750593 original size:26 final size:25
Alignment explanation
Indices: 3750557--3750655 Score: 101
Period size: 26 Copynumber: 3.8 Consensus size: 25
3750547 AAAGAGTCTA
*
3750557 ATTAAAAATTCAATGTATAAAGTTT
1 ATTAAAAATTCAATGTAAAAAGTTT
* *
3750582 GATTAAAAATTCTATCTAAAAAGTTT
1 -ATTAAAAATTCAATGTAAAAAGTTT
* *
3750608 AAATAAAAATTCAATGTAAAAAATTT
1 -ATTAAAAATTCAATGTAAAAAGTTT
*
3750634 ATGTAAAAAATCTAAT-TAAAAA
1 AT-TAAAAATTC-AATGTAAAAA
3750656 TTCTTATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
25 1 0.02
26 57 0.93
27 3 0.05
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (25 bp):
ATTAAAAATTCAATGTAAAAAGTTT
Found at i:3750603 original size:13 final size:13
Alignment explanation
Indices: 3750559--3750659 Score: 59
Period size: 13 Copynumber: 7.8 Consensus size: 13
3750549 AGAGTCTAAT
*
3750559 TAAAAATTCAATG
1 TAAAAATTCTATG
*
3750572 TATAAAGTT-TGAT-
1 TA-AAAATTCT-ATG
*
3750585 TAAAAATTCTATC
1 TAAAAATTCTATG
**
3750598 TAAAAAGTT-TAAA
1 TAAAAA-TTCTATG
*
3750611 TAAAAATTCAATG
1 TAAAAATTCTATG
3750624 TAAAAAATT-TATG
1 T-AAAAATTCTATG
*
3750637 TAAAAAATCTAAT-
1 TAAAAATTCT-ATG
3750650 TAAAAATTCT
1 TAAAAATTCT
3750660 TATATAAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
12 15 0.22
13 35 0.51
14 18 0.26
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (13 bp):
TAAAAATTCTATG
Found at i:3750662 original size:27 final size:26
Alignment explanation
Indices: 3750612--3750745 Score: 117
Period size: 27 Copynumber: 5.0 Consensus size: 26
3750602 AAGTTTAAAT
* *
3750612 AAAAATTCAATGTAAAAAATTTATGTA
1 AAAAATTTAAT-TAAAAATTTTATGTA
* *
3750639 AAAAATCTAATTAAAAATTCTTATATA
1 AAAAATTTAATTAAAAATT-TTATGTA
* * *
3750666 AAGAATTTGATT-AAAATTTGATGTGTA
1 AAAAATTTAATTAAAAATTT--TATGTA
*
3750693 AAAAGTTTAATTAAAAATTTTATTTGTA
1 AAAAATTTAATTAAAAATTTTA--TGTA
* *
3750721 AAAAGTTTAATTAAAAATTCTATGT
1 AAAAATTTAATTAAAAATTTTATGT
3750746 TTAAAAGGTG
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
25 1 0.01
26 17 0.20
27 37 0.43
28 32 0.37
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (26 bp):
AAAAATTTAATTAAAAATTTTATGTA
Found at i:3750709 original size:13 final size:13
Alignment explanation
Indices: 3750691--3750737 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3750681 ATTTGATGTG
3750691 TAAAAAGTTTAAT
1 TAAAAAGTTTAAT
* *
3750704 TAAAAATTTTATTT
1 TAAAAAGTTTA-AT
3750718 GTAAAAAGTTTAAT
1 -TAAAAAGTTTAAT
3750732 TAAAAA
1 TAAAAA
3750738 TTCTATGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 16 0.57
14 2 0.07
15 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (13 bp):
TAAAAAGTTTAAT
Found at i:3750720 original size:28 final size:28
Alignment explanation
Indices: 3750611--3750863 Score: 127
Period size: 28 Copynumber: 9.3 Consensus size: 28
3750601 AAAGTTTAAA
* *
3750611 TAAAAA-TTCAATGTAAAAAATTTA--TG
1 TAAAAAGTTTAAT-TAAAAATTTTATTTG
* * *
3750637 TAAAAAATCTAATTAAAAATTCTTA--TA
1 TAAAAAGTTTAATTAAAAATT-TTATTTG
* * *
3750664 TAAAGAA-TTTGATT-AAAATTTGATGTG
1 TAAA-AAGTTTAATTAAAAATTTTATTTG
3750691 TAAAAAGTTTAATTAAAAATTTTATTTG
1 TAAAAAGTTTAATTAAAAATTTTATTTG
*
3750719 TAAAAAGTTTAATTAAAAATTCTATGTT-
1 TAAAAAGTTTAATTAAAAATTTTAT-TTG
* * * * * *
3750747 TAAAAGGTGTGATTGAAAATTTCATGTG
1 TAAAAAGTTTAATTAAAAATTTTATTTG
* * *
3750775 T-GAGAGTTAAATT-AAAATTTTATATT-
1 TAAAAAGTTTAATTAAAAATTTTAT-TTG
* * * * **
3750801 TAAAAGGTCTAATTGAAAATTTAATGGG
1 TAAAAAGTTTAATTAAAAATTTTATTTG
* *
3750829 T-GAAAGTTTAATTAAAAATTATATATT-
1 TAAAAAGTTTAATTAAAAATTTTAT-TTG
3750856 TAAAAAGT
1 TAAAAAGT
3750864 CTCATGGAAA
Statistics
Matches: 168, Mismatches: 44, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
25 2 0.01
26 31 0.18
27 61 0.36
28 72 0.43
29 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (28 bp):
TAAAAAGTTTAATTAAAAATTTTATTTG
Found at i:3750752 original size:55 final size:55
Alignment explanation
Indices: 3750722--3750901 Score: 200
Period size: 55 Copynumber: 3.3 Consensus size: 55
3750712 TTATTTGTAA
* * * * *
3750722 AAAGTTTAATTAAAAATTCTATGTTTAAAAGGTGTGATTGAAAATTTCATGTGTG
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGTGTG
* * * *
3750777 AGAGTTAAATT-AAAATTTTATATTTAAAAGGTCTAATTGAAAATTTAATGGGTG
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGTGTG
* * * ** * *
3750831 AAAGTTTAATTAAAAATTATATATTTAAAAAGTCTCATGGAAAATTCCATGTATA
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGTGTG
*
3750886 AAAGTTCAATTAAAAA
1 AAAGTTTAATTAAAAA
3750902 GTTTAATTAA
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
54 46 0.44
55 58 0.56
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.37
Consensus pattern (55 bp):
AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGTGTG
Found at i:3750805 original size:54 final size:55
Alignment explanation
Indices: 3750722--3750876 Score: 195
Period size: 54 Copynumber: 2.8 Consensus size: 55
3750712 TTATTTGTAA
* * * * * *
3750722 AAAGTTTAATTAAAAATTCTATGTTTAAAAGGTGTGATTGAAAATTTCATGTGTG
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGGGTG
* * *
3750777 AGAGTTAAATT-AAAATTTTATATTTAAAAGGTCTAATTGAAAATTTAATGGGTG
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGGGTG
* * *
3750831 AAAGTTTAATTAAAAATTATATATTTAAAAAGTCTCATGGAAAATT
1 AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATT
3750877 CCATGTATAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 46 0.54
55 39 0.46
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.39
Consensus pattern (55 bp):
AAAGTTTAATTAAAAATTATATATTTAAAAGGTCTAATTGAAAATTTAATGGGTG
Found at i:3750922 original size:68 final size:68
Alignment explanation
Indices: 3750831--3750970 Score: 174
Period size: 68 Copynumber: 2.0 Consensus size: 68
3750821 TTAATGGGTG
* **
3750831 AAAGTTTAATTAAAAATTATATATTTAAAAAGTCTCATGGAAAATTC-CATGTATAAAAGTTCAA
1 AAAGTTTAATTAAAAATTATATATGTAAAAAGTCAAATGGAAAATTCACATGTA-AAAAGTTCAA
3750895 TTAA
65 TTAA
* * * * *
3750899 AAAGTTTAATTAAGAATTTTATATGTAAAACGTCAAATTGAAAATTCTACATGTAAAAAGTTTAA
1 AAAGTTTAATTAAAAATTATATATGTAAAAAGTCAAATGGAAAATTC-ACATGTAAAAAGTTCAA
*
3750964 TTGA
65 TTAA
3750968 AAA
1 AAA
3750971 TTCTATTTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 40 0.66
69 15 0.25
70 6 0.10
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (68 bp):
AAAGTTTAATTAAAAATTATATATGTAAAAAGTCAAATGGAAAATTCACATGTAAAAAGTTCAAT
TAA
Found at i:3750965 original size:28 final size:28
Alignment explanation
Indices: 3750896--3750990 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
3750886 AAAGTTCAAT
*
3750896 TAAAAAGTTTAATT-AAGAATTTTATATG
1 TAAAAAGTTTAATTGAA-AATTCTATATG
* ** *
3750924 TAAAACGTCAAATTGAAAATTCTACATG
1 TAAAAAGTTTAATTGAAAATTCTATATG
*
3750952 TAAAAAGTTTAATTGAAAATTCTATTTG
1 TAAAAAGTTTAATTGAAAATTCTATATG
*
3750980 TAAAAAATTTA
1 TAAAAAGTTTA
3750991 GTAAAAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 53 0.96
29 2 0.04
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (28 bp):
TAAAAAGTTTAATTGAAAATTCTATATG
Found at i:3750998 original size:28 final size:28
Alignment explanation
Indices: 3750939--3750998 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3750929 CGTCAAATTG
* **
3750939 AAAATTCTACATGTAAAAAGTTTAATTG
1 AAAATTCTACATGTAAAAAATTTAATAA
** *
3750967 AAAATTCTATTTGTAAAAAATTTAGTAA
1 AAAATTCTACATGTAAAAAATTTAATAA
3750995 AAAA
1 AAAA
3750999 AATCTATATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (28 bp):
AAAATTCTACATGTAAAAAATTTAATAA
Found at i:3751444 original size:16 final size:18
Alignment explanation
Indices: 3751405--3751446 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3751395 ATGTGAATTA
3751405 TTAATATATAAAAATTAAT
1 TTAA-ATATAAAAATTAAT
*
3751424 ATAAATAT-AAAA-TAAT
1 TTAAATATAAAAATTAAT
3751440 TTAAATA
1 TTAAATA
3751447 CGATTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 4 0.19
19 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATATAAAAATTAAT
Found at i:3759074 original size:259 final size:259
Alignment explanation
Indices: 3758602--3759138 Score: 970
Period size: 259 Copynumber: 2.1 Consensus size: 259
3758592 TTATTATGTT
* *
3758602 AAAA-AAATTAATATAATATTACATTACCTTTTTCTTTTAGGAGGAGAGTTATGGTCTCGTGACA
1 AAAATAAAGTAATTTAATATTACATTACCTTTTTCTTTTAGGAGGAGAGTTATGGTCTCGTGACA
* *
3758666 AGTGGTATTAGAGCCAACTTTTAATTGTCTAATTTCATGCCGAGCGCCGTAATTCCTGATTCCAT
66 AGTGGTATTAGAGCCAACCTTTAATTATCTAATTTCATGCCGAGCGCCGTAATTCCTGATTCCAT
*
3758731 GCCAAACATCACAAGGATGGGATCCGAAAAAATAGTGGAGAAACCTATGACAAGACCATCACGAG
131 GCCAAACATCACAAGGATGGGATCCGAAAAAATAGTGGAGAAACCTATGAAAAGACCATCACGAG
3758796 ATTGGATGCTATAAAGATAAAAAAATTAAGTTGAACTTTAATTCTTTTTTATTTTTGATTTTTG
196 ATTGGATGCTATAAAGATAAAAAAATTAAGTTGAACTTTAATTCTTTTTTATTTTTGATTTTTG
*
3758860 AAAATAAAGTAATTTAATATTACATTA-CTTTCTTCTTTTGGGAGGAGAGTTATGGTCTCGTGAC
1 AAAATAAAGTAATTTAATATTACATTACCTTT-TTCTTTTAGGAGGAGAGTTATGGTCTCGTGAC
*
3758924 AAGTGGTATTAGAGCCAACCTTTAATTATCTAATTTCATGCCGAGCGTCGTAATTCCTGATTCCA
65 AAGTGGTATTAGAGCCAACCTTTAATTATCTAATTTCATGCCGAGCGCCGTAATTCCTGATTCCA
*
3758989 TGCCAAACATCACAAGGATGGGATCCGAAAAAATAGTGGAGAAGCCTATGAAAAGACCATCACGA
130 TGCCAAACATCACAAGGATGGGATCCGAAAAAATAGTGGAGAAACCTATGAAAAGACCATCACGA
*
3759054 GATTGGGTGCTATAAAGATAAAAAAATTAAGTTGAACTTTAATTCTTTTTTATTTTTGATTTTTG
195 GATTGGATGCTATAAAGATAAAAAAATTAAGTTGAACTTTAATTCTTTTTTATTTTTGATTTTTG
3759119 AAAATAAAGTAATTTAATAT
1 AAAATAAAGTAATTTAATAT
3759139 AAACTTTTAA
Statistics
Matches: 268, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
258 8 0.03
259 260 0.97
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (259 bp):
AAAATAAAGTAATTTAATATTACATTACCTTTTTCTTTTAGGAGGAGAGTTATGGTCTCGTGACA
AGTGGTATTAGAGCCAACCTTTAATTATCTAATTTCATGCCGAGCGCCGTAATTCCTGATTCCAT
GCCAAACATCACAAGGATGGGATCCGAAAAAATAGTGGAGAAACCTATGAAAAGACCATCACGAG
ATTGGATGCTATAAAGATAAAAAAATTAAGTTGAACTTTAATTCTTTTTTATTTTTGATTTTTG
Found at i:3766263 original size:8 final size:8
Alignment explanation
Indices: 3766246--3766297 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
3766236 ATTTGATATT
3766246 AATA-AAA
1 AATATAAA
3766253 AATATAAA
1 AATATAAA
3766261 AATA-AAA
1 AATATAAA
3766268 TAATAT-AA
1 -AATATAAA
3766276 AATA-AGAA
1 AATATA-AA
3766284 AATATAAA
1 AATATAAA
3766292 AATATA
1 AATATA
3766298 TACATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 11 0.28
8 27 0.69
9 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (8 bp):
AATATAAA
Found at i:3766266 original size:15 final size:15
Alignment explanation
Indices: 3766246--3766295 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
3766236 ATTTGATATT
3766246 AATAAAAAATATAAA
1 AATAAAAAATATAAA
3766261 AATAAAATAATAT-AA
1 AATAAAA-AATATAAA
3766276 AATAAGAAAATATAAA
1 AATAA-AAAATATAAA
3766292 AATA
1 AATA
3766296 TATACATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AATAAAAAATATAAA
Found at i:3766277 original size:23 final size:24
Alignment explanation
Indices: 3766245--3766297 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3766235 TATTTGATAT
*
3766245 TAATAAAAAATATA-AAAATA-AAA
1 TAATATAAAATA-AGAAAATATAAA
3766268 TAATATAAAATAAGAAAATATAAA
1 TAATATAAAATAAGAAAATATAAA
3766292 -AATATA
1 TAATATA
3766298 TACATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.85
24 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
TAATATAAAATAAGAAAATATAAA
Found at i:3776452 original size:20 final size:19
Alignment explanation
Indices: 3776410--3776463 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
3776400 CACATCCAGA
*
3776410 TGTATCAATACATGATCAT
1 TGTATCGATACATGATCAT
3776429 TGTATCGATACATGCA-CAAT
1 TGTATCGATACATG-ATC-AT
3776449 TGTATCGATACATGA
1 TGTATCGATACATGA
3776464 AACTGGCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:3779256 original size:13 final size:13
Alignment explanation
Indices: 3779238--3779262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3779228 TAAAATATCA
3779238 TCATACTAATATT
1 TCATACTAATATT
3779251 TCATACTAATAT
1 TCATACTAATAT
3779263 GGCCCATAGA
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:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TCATACTAATATT
Found at i:3781025 original size:20 final size:20
Alignment explanation
Indices: 3781000--3781067 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3780990 ATGTATCAAT
3781000 ATAATGTATTGATACTTTGA
1 ATAATGTATTGATACTTTGA
* *
3781020 ATAATGCATCGATAC----A
1 ATAATGTATTGATACTTTGA
3781036 AT-A--TATTGATACTTTGA
1 ATAATGTATTGATACTTTGA
3781053 ATAATGTATTGATAC
1 ATAATGTATTGATAC
3781068 ATATGAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
13 7 0.19
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
20 22 0.59
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (20 bp):
ATAATGTATTGATACTTTGA
Found at i:3781067 original size:33 final size:33
Alignment explanation
Indices: 3780977--3781068 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
3780967 ATTATCTATC
* * *
3780977 GATACTTTGAATAATGTATCAATATAATGTATT
1 GATACTTTGAATAATGTATCGATACAATATATT
*
3781010 GATACTTTGAATAATGCATCGATACAATATATT
1 GATACTTTGAATAATGTATCGATACAATATATT
*
3781043 GATACTTTGAATAATGTATTGATACA
1 GATACTTTGAATAATGTATCGATACA
3781069 TATGAGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (33 bp):
GATACTTTGAATAATGTATCGATACAATATATT
Found at i:3784515 original size:26 final size:26
Alignment explanation
Indices: 3784486--3784550 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
3784476 TGAGAAACAG
3784486 GGTTAGAGTATCCTTCGGAACAATAA
1 GGTTAGAGTATCCTTCGGAACAATAA
*
3784512 GGTTAGAGTATCCTTCGGAACAATAG
1 GGTTAGAGTATCCTTCGGAACAATAA
*
3784538 GGTTGGAGTATCC
1 GGTTAGAGTATCC
3784551 CGTGAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (26 bp):
GGTTAGAGTATCCTTCGGAACAATAA
Found at i:3787023 original size:20 final size:20
Alignment explanation
Indices: 3786951--3787023 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
3786941 GTCAAAACTT
3786951 AAAATATATCGATACAATGAA
1 AAAATATATCGATACAAT-AA
* *
3786972 AAAATGTATCGA-AC-CT--
1 AAAATATATCGATACAATAA
* *
3786988 AGAATATATTGATACAATAA
1 AAAATATATCGATACAATAA
*
3787008 AAAATGTATCGATACA
1 AAAATATATCGATACA
3787024 TTTTCTTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
16 9 0.23
17 2 0.05
18 1 0.03
19 1 0.03
20 15 0.38
21 11 0.28
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAATATATCGATACAATAA
Found at i:3787099 original size:20 final size:21
Alignment explanation
Indices: 3787076--3787129 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3787066 CATTTCAGAC
3787076 ATGTATCAATACATTCACTT-
1 ATGTATCAATACATTCACTTG
**
3787096 ATGTATTGATACATTCACTTG
1 ATGTATCAATACATTCACTTG
* *
3787117 TTGCATCAATACA
1 ATGTATCAATACA
3787130 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTATCAATACATTCACTTG
Found at i:3788727 original size:20 final size:20
Alignment explanation
Indices: 3788704--3788776 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3788694 ACAATTCAAA
3788704 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3788724 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3788745 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3788765 GTATCGATACAT
1 GTATCGATACAT
3788777 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3788748 original size:21 final size:21
Alignment explanation
Indices: 3788722--3788797 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3788712 ACATGTTGCA
3788722 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3788743 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3788763 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
3788784 TTGTATCGATACAT
1 ATGTATCGATACAT
3788798 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3788755 original size:41 final size:41
Alignment explanation
Indices: 3788704--3788797 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3788694 ACAATTCAAA
*
3788704 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
3788745 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3788786 GTATCGATACAT
1 GTATCGATACAT
3788798 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3788854 original size:13 final size:13
Alignment explanation
Indices: 3788836--3788861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3788826 TACAGCAAGT
3788836 ATGTATCGATACA
1 ATGTATCGATACA
3788849 ATGTATCGATACA
1 ATGTATCGATACA
3788862 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3790612 original size:45 final size:45
Alignment explanation
Indices: 3790563--3790654 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
3790553 TTCAAGAATT
* *
3790563 TTAATAAAACCAAAAATCACTAAATCAATCCATGAATCAACCAGA
1 TTAATAAAACCAAAAATCACCAAATCAATACATGAATCAACCAGA
* * *
3790608 TTAATTATACCAAAAATCACCAAATCAATACATGAATCAATCAGA
1 TTAATAAAACCAAAAATCACCAAATCAATACATGAATCAACCAGA
3790653 TT
1 TT
3790655 GGTTATCACC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.24
Consensus pattern (45 bp):
TTAATAAAACCAAAAATCACCAAATCAATACATGAATCAACCAGA
Found at i:3791797 original size:22 final size:20
Alignment explanation
Indices: 3791767--3791818 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
3791757 TACTTCATAT
3791767 AAAT-ATTATTAAATAATTATC
1 AAATAATTATTAAAT--TTATC
*
3791788 AAATAATTATTTAATTTATC
1 AAATAATTATTAAATTTATC
3791808 AAA-AATTATTA
1 AAATAATTATTA
3791819 TTTAGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 8 0.29
21 4 0.14
22 9 0.32
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAATTATTAAATTTATC
Found at i:3794194 original size:21 final size:22
Alignment explanation
Indices: 3794159--3794218 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
3794149 CAAAGAAGCC
*
3794159 TAAATT-TATTAATACATTTAG
1 TAAATTGTATTGATACATTTAG
3794180 -AAATTGTATTGATACA-TTAG
1 TAAATTGTATTGATACATTTAG
*
3794200 TAAA-TGTATTGATGCATTT
1 TAAATTGTATTGATACATTT
3794219 GGCCATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (22 bp):
TAAATTGTATTGATACATTTAG
Found at i:3795326 original size:493 final size:493
Alignment explanation
Indices: 3794400--3795385 Score: 1972
Period size: 493 Copynumber: 2.0 Consensus size: 493
3794390 TGTTACGAGC
3794400 TTTACTTTCTTATGTTATGAATTGTTTCATGGTGCCTAAAGCCTTAAGTGAGGAGATTACAAAGA
1 TTTACTTTCTTATGTTATGAATTGTTTCATGGTGCCTAAAGCCTTAAGTGAGGAGATTACAAAGA
3794465 TCATAAGGAAACATTAGTGGACTAGTAAAAAAGACAGAATTGGGATACATGGGCTTAGTTAGGAT
66 TCATAAGGAAACATTAGTGGACTAGTAAAAAAGACAGAATTGGGATACATGGGCTTAGTTAGGAT
3794530 AACATGTGCGTTCCTAAGAACATGGGCGAACTCATGTTTAGAAATATTCAAGATTTCAACATGGC
131 AACATGTGCGTTCCTAAGAACATGGGCGAACTCATGTTTAGAAATATTCAAGATTTCAACATGGC
3794595 TATCTTGACGAAACAAGGAGACTTACTAACATTCCAGATTCATCGACAGAGTACACATAGCCAAA
196 TATCTTGACGAAACAAGGAGACTTACTAACATTCCAGATTCATCGACAGAGTACACATAGCCAAA
3794660 TATTTTCCATTCAATGATTTCATGAAAACAAAGCTAGGTGGGCAAACTTCATTCACGTGGAGGAG
261 TATTTTCCATTCAATGATTTCATGAAAACAAAGCTAGGTGGGCAAACTTCATTCACGTGGAGGAG
3794725 CATTTGGACAGCTGAGGTGGTACTACAGCAAGGTGTTTGGTGGAGGGTTTGTAATGGAAGATCAA
326 CATTTGGACAGCTGAGGTGGTACTACAGCAAGGTGTTTGGTGGAGGGTTTGTAATGGAAGATCAA
3794790 TCAAGATTTGGGGTGACAATTGGCTTCCCACATAAGATTCTTTCAAGATTGTTACAGGAGGATCG
391 TCAAGATTTGGGGTGACAATTGGCTTCCCACATAAGATTCTTTCAAGATTGTTACAGGAGGATCG
3794855 ATTAAAAGTGTTGAAAAGGTAGAGGAGCTTATTGATGG
456 ATTAAAAGTGTTGAAAAGGTAGAGGAGCTTATTGATGG
3794893 TTTACTTTCTTATGTTATGAATTGTTTCATGGTGCCTAAAGCCTTAAGTGAGGAGATTACAAAGA
1 TTTACTTTCTTATGTTATGAATTGTTTCATGGTGCCTAAAGCCTTAAGTGAGGAGATTACAAAGA
3794958 TCATAAGGAAACATTAGTGGACTAGTAAAAAAGACAGAATTGGGATACATGGGCTTAGTTAGGAT
66 TCATAAGGAAACATTAGTGGACTAGTAAAAAAGACAGAATTGGGATACATGGGCTTAGTTAGGAT
3795023 AACATGTGCGTTCCTAAGAACATGGGCGAACTCATGTTTAGAAATATTCAAGATTTCAACATGGC
131 AACATGTGCGTTCCTAAGAACATGGGCGAACTCATGTTTAGAAATATTCAAGATTTCAACATGGC
3795088 TATCTTGACGAAACAAGGAGACTTACTAACATTCCAGATTCATCGACAGAGTACACATAGCCAAA
196 TATCTTGACGAAACAAGGAGACTTACTAACATTCCAGATTCATCGACAGAGTACACATAGCCAAA
3795153 TATTTTCCATTCAATGATTTCATGAAAACAAAGCTAGGTGGGCAAACTTCATTCACGTGGAGGAG
261 TATTTTCCATTCAATGATTTCATGAAAACAAAGCTAGGTGGGCAAACTTCATTCACGTGGAGGAG
3795218 CATTTGGACAGCTGAGGTGGTACTACAGCAAGGTGTTTGGTGGAGGGTTTGTAATGGAAGATCAA
326 CATTTGGACAGCTGAGGTGGTACTACAGCAAGGTGTTTGGTGGAGGGTTTGTAATGGAAGATCAA
3795283 TCAAGATTTGGGGTGACAATTGGCTTCCCACATAAGATTCTTTCAAGATTGTTACAGGAGGATCG
391 TCAAGATTTGGGGTGACAATTGGCTTCCCACATAAGATTCTTTCAAGATTGTTACAGGAGGATCG
3795348 ATTAAAAGTGTTGAAAAGGTAGAGGAGCTTATTGATGG
456 ATTAAAAGTGTTGAAAAGGTAGAGGAGCTTATTGATGG
3795386 GAACAATATG
Statistics
Matches: 493, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
493 493 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (493 bp):
TTTACTTTCTTATGTTATGAATTGTTTCATGGTGCCTAAAGCCTTAAGTGAGGAGATTACAAAGA
TCATAAGGAAACATTAGTGGACTAGTAAAAAAGACAGAATTGGGATACATGGGCTTAGTTAGGAT
AACATGTGCGTTCCTAAGAACATGGGCGAACTCATGTTTAGAAATATTCAAGATTTCAACATGGC
TATCTTGACGAAACAAGGAGACTTACTAACATTCCAGATTCATCGACAGAGTACACATAGCCAAA
TATTTTCCATTCAATGATTTCATGAAAACAAAGCTAGGTGGGCAAACTTCATTCACGTGGAGGAG
CATTTGGACAGCTGAGGTGGTACTACAGCAAGGTGTTTGGTGGAGGGTTTGTAATGGAAGATCAA
TCAAGATTTGGGGTGACAATTGGCTTCCCACATAAGATTCTTTCAAGATTGTTACAGGAGGATCG
ATTAAAAGTGTTGAAAAGGTAGAGGAGCTTATTGATGG
Found at i:3803358 original size:16 final size:16
Alignment explanation
Indices: 3803337--3803367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3803327 TTTGGCATAA
3803337 CATTTTCAACTAATAG
1 CATTTTCAACTAATAG
*
3803353 CATTTTCAAGTAATA
1 CATTTTCAACTAATA
3803368 TTACCTAGTG
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:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (16 bp):
CATTTTCAACTAATAG
Found at i:3808162 original size:137 final size:137
Alignment explanation
Indices: 3807904--3808151 Score: 365
Period size: 137 Copynumber: 1.8 Consensus size: 137
3807894 CAGTTATGAA
* * * * *
3807904 AAAATTATGAAAATGCCCCTAGAGGATACCTTTGACTTAGAAGTGCTCGATACCCCTGAAGGACT
1 AAAATTATGAAAATGCCCCTAGAGGATACCTTTGACTTAAAAGTGCCCAATAACCCTCAAGGACT
* * *
3807969 TAAAAATGATTATAGATGGGATGAACCGATTCTACATACCCACCTTCAACATAAAAGCAGACTCG
66 TAAAAATGATTATAGATAGGATGAACCGATCCTAAATACCCACCTTCAACATAAAAGCAGACTCG
3808034 ATTCTAG
131 ATTCTAG
**
3808041 AAAATTATGAAAATGCCTTTAG-GGAATACCTTTGA-TGTAAAAGTGCCCAATAACCCTCAAGGA
1 AAAATTATGAAAATGCCCCTAGAGG-ATACCTTTGACT-TAAAAGTGCCCAATAACCCTCAAGGA
*
3808104 CTTAAAAATGATTATAGATAGGATGAACCTATCCTAAATACCCACCTT
64 CTTAAAAATGATTATAGATAGGATGAACCGATCCTAAATACCCACCTT
3808152 TGGCATAAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
136 3 0.03
137 95 0.97
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (137 bp):
AAAATTATGAAAATGCCCCTAGAGGATACCTTTGACTTAAAAGTGCCCAATAACCCTCAAGGACT
TAAAAATGATTATAGATAGGATGAACCGATCCTAAATACCCACCTTCAACATAAAAGCAGACTCG
ATTCTAG
Found at i:3808399 original size:149 final size:150
Alignment explanation
Indices: 3808125--3808415 Score: 363
Period size: 149 Copynumber: 1.9 Consensus size: 150
3808115 TTATAGATAG
* ** ** * * *
3808125 GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGTGGACCCAGTGATGACCTAAGACTCGG
1 GATGAACCTATCCTAAATACACACCTTCAGCATAAAAGCAGACCCAGTGATCAACTAAGACTCGA
** * *
3808190 TTCTAAAAAATTACAAAAATACCCCTAAGGGATACTTTCGATGTAAAAGTGCCTGATACCCTTAA
66 TTCTAAAAAATTACAAAAATACCCCTAAAAGATACTTTCGACGTAAAAGTACCTGATACCCTTAA
* *
3808255 AGGGCTTAAAAAGGTAAAAA
131 AAGACTTAAAAAGGTAAAAA
* * *
3808275 GATGAACCTATCCTAAATGCACACCTTCAGCATAGAAGCAGACCTAGTGA-CAACT-AGAACTCG
1 GATGAACCTATCCTAAATACACACCTTCAGCATAAAAGCAGACCCAGTGATCAACTAAG-ACTCG
* * *
3808338 ATTCTAAAAAATTACAAAAATACCCCTAAAAGATA-TCTTCGACGTAGAAGTATCTGGTACCCTT
65 ATTCTAAAAAATTACAAAAATACCCCTAAAAGATACT-TTCGACGTAAAAGTACCTGATACCCTT
3808402 AAAAGACTTAAAAA
129 AAAAGACTTAAAAA
3808416 AAAGGATTAT
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
148 3 0.03
149 74 0.62
150 42 0.35
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (150 bp):
GATGAACCTATCCTAAATACACACCTTCAGCATAAAAGCAGACCCAGTGATCAACTAAGACTCGA
TTCTAAAAAATTACAAAAATACCCCTAAAAGATACTTTCGACGTAAAAGTACCTGATACCCTTAA
AAGACTTAAAAAGGTAAAAA
Found at i:3810896 original size:164 final size:162
Alignment explanation
Indices: 3810726--3811215 Score: 544
Period size: 165 Copynumber: 3.0 Consensus size: 162
3810716 ATATTATTTG
3810726 AATTTTAAAAATTTTAAACTGATGAAAATACCCCTAAAAAAATTTATGGA-ATAGAAAACTC-GA
1 AATTTTAAAAATTTTAAA-TGATGAAAAT-CCCCT-AAAAAATTTATGGAGA-AGAAAACTCTGA
* * ** *
3810789 TTTTTTAAAACAGA-AACATTTTGAA-GAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGA
62 TTTTTGAAAACAGAGAA-ATTCT-AAGGAAAAATGAAAAACTCATGAAAATGAATGAATTTTTCA
* * * *
3810852 AAACCGATTTAATAATGGTTATATGATAATATTTGATA
125 AAACTGATTTAATGATGATTAGATGATAATATTTGATA
* * **
3810890 AATTTTAAAAATTTTGAATCGATGACAATCCTCCTAAAAAATTTACAGAGAAGAAAACTCTGTAT
1 AATTTTAAAAATTTTAAAT-GATGAAAATCC-CCTAAAAAATTTATGGAGAAGAAAACTCTG-AT
* * * * *
3810955 TTTGGAAATA-GGAGGAATTCTAAGGAATAATGAAAAATTCATGAAAATGAATGAATTTTTCAAA
63 TTTTGAAA-ACAGAGAAATTCTAAGGAAAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAA
* *
3811019 ACTAATTTAATGATGATTAGA-GATAATATTTGATG
127 ACTGATTTAATGATGATTAGATGATAATATTTGATA
* * *
3811054 AATTTTAAAAAATTTAAATTGATGAAAATCCTCTCGAAAAATTTATGGAGAAGAAAACTCTG-TA
1 AATTTTAAAAATTTTAAA-TGATGAAAATCCCCT-AAAAAATTTATGGAGAAGAAAACTCTGAT-
* * * *
3811118 TTTTGAAAACAAGAGAAATTCTAAGGAAAAAAAGAAAAACTTATGAAAATGAATAAATTTTTTAA
63 TTTTGAAAAC-AGAGAAATTCTAAGG-AAAAATGAAAAACTCATGAAAATGAATGAATTTTTCAA
*
3811183 AATTGATTTAATGATGATTAGATGATAATATTT
126 AACTGATTTAATGATGATTAGATGATAATATTT
3811216 AAAGAATTTT
Statistics
Matches: 273, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
162 2 0.01
163 33 0.12
164 108 0.40
165 118 0.43
166 12 0.04
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (162 bp):
AATTTTAAAAATTTTAAATGATGAAAATCCCCTAAAAAATTTATGGAGAAGAAAACTCTGATTTT
TGAAAACAGAGAAATTCTAAGGAAAAATGAAAAACTCATGAAAATGAATGAATTTTTCAAAACTG
ATTTAATGATGATTAGATGATAATATTTGATA
Found at i:3811260 original size:164 final size:162
Alignment explanation
Indices: 3810823--3811262 Score: 442
Period size: 165 Copynumber: 2.7 Consensus size: 162
3810813 AGAAAAATTC
* * * ** * * *
3810823 AAAACTCATGAAAATGAATGAATTTTTGAAAACCGATTTAATAATGGTTATATGATAATATTTGA
1 AAAATTCATGAAAATGAATAAATTTTTCAAAACTAATTTAATGATGATTAGA-GATAATATTT-A
* ** * *
3810888 TA-AATTTTAAAAATTTTGAATCGATGACAATC-CTCCTAAAAAATTTACAGAGAAGAAAACTCT
64 AAGAATTTTAAAAA-TTAAAATTGATGAAAATCTCTCC--AAAAATTTACAGAGAAGAAAACTCT
* * * * * *
3810951 GTATTTTGGAAATAGGAGGAATTCTAAGGAATAATGA
126 GTATTTTGAAAACAAGAGAAATTCTAAGGAAAAAAGA
* * *
3810988 AAAATTCATGAAAATGAATGAATTTTTCAAAACTAATTTAATGATGATTAGAGATAATATTTGAT
1 AAAATTCATGAAAATGAATAAATTTTTCAAAACTAATTTAATGATGATTAGAGATAATATTTAAA
* * **
3811053 GAATTTTAAAAAATTTAAATTGATGAAAATCCTCTCGAAAAATTTATGGAGAAGAAAACTCTGTA
66 GAATTTT-AAAAATTAAAATTGATGAAAAT-CTCTCCAAAAATTTACAGAGAAGAAAACTCTGTA
3811118 TTTTGAAAACAAGAGAAATTCTAAGGAAAAAAAGA
129 TTTTGAAAACAAGAGAAATTCTAAGG-AAAAAAGA
* * *
3811153 AAAACTT-ATGAAAATGAATAAATTTTTTAAAATTGATTTAATGATGATTAGATGATAATATTTA
1 AAAA-TTCATGAAAATGAATAAATTTTTCAAAACTAATTTAATGATGATTAGA-GATAATATTTA
* *
3811217 AAGAATTTT-GATATTCAAAACTTGA-GAAAAT-TCTGCCAAAAATTTA
64 AAGAATTTTAAAAATT-AAAA-TTGATGAAAATCTCT-CCAAAAATTTA
3811263 ATGAGTAAAA
Statistics
Matches: 233, Mismatches: 32, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
163 3 0.01
164 92 0.39
165 111 0.48
166 27 0.12
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (162 bp):
AAAATTCATGAAAATGAATAAATTTTTCAAAACTAATTTAATGATGATTAGAGATAATATTTAAA
GAATTTTAAAAATTAAAATTGATGAAAATCTCTCCAAAAATTTACAGAGAAGAAAACTCTGTATT
TTGAAAACAAGAGAAATTCTAAGGAAAAAAGA
Found at i:3813300 original size:43 final size:43
Alignment explanation
Indices: 3813252--3813338 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
3813242 AACAATTCGA
3813252 GAGCTTTTTATGAAAGGTTTCATACATCAAGAGGTTTATTCCT
1 GAGCTTTTTATGAAAGGTTTCATACATCAAGAGGTTTATTCCT
3813295 GAGCTTTTTATGAAAGGTTTCATACATCAAGAGGTTTATTCCT
1 GAGCTTTTTATGAAAGGTTTCATACATCAAGAGGTTTATTCCT
3813338 G
1 G
3813339 GAAAATGACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.39
Consensus pattern (43 bp):
GAGCTTTTTATGAAAGGTTTCATACATCAAGAGGTTTATTCCT
Found at i:3816571 original size:12 final size:12
Alignment explanation
Indices: 3816556--3816581 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3816546 AATATGACTA
3816556 TTCCAAAAGTTG
1 TTCCAAAAGTTG
3816568 TTCCAAAAGTTG
1 TTCCAAAAGTTG
3816580 TT
1 TT
3816582 AGGAACTTGG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (12 bp):
TTCCAAAAGTTG
Found at i:3824324 original size:13 final size:13
Alignment explanation
Indices: 3824306--3824346 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
3824296 ACAACATTCC
3824306 TTGTATCGATACA
1 TTGTATCGATACA
3824319 TTGTATCGATACA
1 TTGTATCGATACA
*
3824332 ATGTATCGATACA
1 TTGTATCGATACA
3824345 TT
1 TT
3824347 AGGTACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3826846 original size:13 final size:13
Alignment explanation
Indices: 3826828--3826854 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3826818 ACATGCTGCT
3826828 TTGTATCGATACA
1 TTGTATCGATACA
3826841 TTGTATCGATACA
1 TTGTATCGATACA
3826854 T
1 T
3826855 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3826851 original size:33 final size:32
Alignment explanation
Indices: 3826809--3826873 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3826799 CACACCCAGA
*
3826809 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
3826842 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
3826874 GGATAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:3826863 original size:19 final size:19
Alignment explanation
Indices: 3826839--3826895 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
3826829 TGTATCGATA
*
3826839 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
3826858 CATTGTATCGATACATGGAT
1 CATTGTATCGATACAT-GAT
*
3826878 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
3826896 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:3826884 original size:20 final size:20
Alignment explanation
Indices: 3826835--3826894 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3826825 GCTTTGTATC
3826835 GATACATTGTATCGATACAT-
1 GATA-ATTGTATCGATACATG
* *
3826855 GTTCATTGTATCGATACATG
1 GATAATTGTATCGATACATG
3826875 GATAATTGTATCGATACATG
1 GATAATTGTATCGATACATG
3826895 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (20 bp):
GATAATTGTATCGATACATG
Found at i:3829789 original size:85 final size:87
Alignment explanation
Indices: 3829652--3829847 Score: 240
Period size: 85 Copynumber: 2.3 Consensus size: 87
3829642 TTTTATGTAG
* * * *
3829652 AACGAGGTTAGAGTATCCCTTTA-AAGTAGTGAGGGTAGAGTTTCCCCGAGGATAAAATTACAAA
1 AACGAGGTTAGAGTATCCCCTTAGAAGTAATGAGGGTAAAGTTTCCCCAAGGATAAAATTACAAA
**
3829716 GGGATATTTGA-TTTTTT-AAA
66 GAAATATTTGATTTTTTTGAAA
* *
3829736 AAGCGAGGTTAGAGTATCCCCTTAGAAG-AAT-AGGGATAAAGTTTCCCTAAGGATAAAATTATA
1 AA-CGAGGTTAGAGTATCCCCTTAGAAGTAATGAGGG-TAAAGTTTCCCCAAGGATAAAATTACA
3829799 AAGAAATATTTGATTTTTTTGAAA
64 AAGAAATATTTGATTTTTTTGAAA
* * *
3829823 AACGAGGTTGGAGTGTTCCCTTAGA
1 AACGAGGTTAGAGTATCCCCTTAGA
3829848 GGAGTGGAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
84 6 0.06
85 56 0.58
86 29 0.30
87 5 0.05
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (87 bp):
AACGAGGTTAGAGTATCCCCTTAGAAGTAATGAGGGTAAAGTTTCCCCAAGGATAAAATTACAAA
GAAATATTTGATTTTTTTGAAA
Found at i:3829867 original size:86 final size:85
Alignment explanation
Indices: 3829654--3829871 Score: 219
Period size: 85 Copynumber: 2.6 Consensus size: 85
3829644 TTATGTAGAA
* * * * *
3829654 CGAGGTTAGAGTATCCCTTTA-AAGTAGTGAGG-GTAGAGTTTCCCCGAGGATAAAATTACAAAG
1 CGAGGTTAGAGTATCCCCTTAGAAG-AAT-AGGAATAAAGTTTCCCCAAGGATAAAATTACAAAG
**
3829717 GGATATTTGATTTTTTAAAAAG
64 AAATATTTGATTTTTTAAAAAG
* * *
3829739 CGAGGTTAGAGTATCCCCTTAGAAGAATAGGGATAAAGTTTCCCTAAGGATAAAATTATAAAGAA
1 CGAGGTTAGAGTATCCCCTTAGAAGAATAGGAATAAAGTTTCCCCAAGGATAAAATTACAAAGAA
3829804 ATATTTGATTTTTTTGAAAAA-
66 ATATTTGA-TTTTTT-AAAAAG
* * * * * *
3829825 CGAGGTTGGAGTGTTCCCTTAGAGGAGT-GGAAATGAAGTTTCCCCAA
1 CGAGGTTAGAGTATCCCCTTAGAAGAATAGG-AATAAAGTTTCCCCAA
3829872 AAGTAAAATT
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
84 3 0.03
85 58 0.52
86 45 0.41
87 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (85 bp):
CGAGGTTAGAGTATCCCCTTAGAAGAATAGGAATAAAGTTTCCCCAAGGATAAAATTACAAAGAA
ATATTTGATTTTTTAAAAAG
Found at i:3835520 original size:19 final size:20
Alignment explanation
Indices: 3835477--3835550 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3835467 CACATCCAGA
* *
3835477 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
*
3835497 TGTATCGATACATGCT-CAT
1 TGTATCGATACATGATGCAT
*
3835516 TGTATCGATACAT-ATACAAT
1 TGTATCGATACATGATGC-AT
*
3835536 TCTATCGATACATGA
1 TGTATCGATACATGA
3835551 AACTGGCAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.02
19 16 0.35
20 28 0.61
21 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:3835596 original size:13 final size:13
Alignment explanation
Indices: 3835578--3835603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3835568 CTAAGTGAAA
3835578 TGTATCGATACAT
1 TGTATCGATACAT
3835591 TGTATCGATACAT
1 TGTATCGATACAT
3835604 GGTAAAAAGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3840051 original size:16 final size:16
Alignment explanation
Indices: 3840015--3840045 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3840005 AAAGGCTTTC
*
3840015 AAAATTTTTCATAGAA
1 AAAATTTTTAATAGAA
3840031 AAAATTTTTAATAGA
1 AAAATTTTTAATAGA
3840046 GGAAATGTTG
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:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAATTTTTAATAGAA
Found at i:3841410 original size:20 final size:23
Alignment explanation
Indices: 3841385--3841443 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 23
3841375 AATTTTTTAG
3841385 AATGTATCGATACAT-T-G-AAT
1 AATGTATCGATACATCTGGAAAT
3841405 AATGTATCGATACATCTGGAAAAT
1 AATGTATCGATACATCTGG-AAAT
3841429 AGATGTATCGATACA
1 A-ATGTATCGATACA
3841444 ATGTTCTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
20 15 0.44
21 1 0.03
22 1 0.03
24 4 0.12
25 13 0.38
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (23 bp):
AATGTATCGATACATCTGGAAAT
Found at i:3844114 original size:20 final size:19
Alignment explanation
Indices: 3844064--3844116 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3844054 TATCCATACG
* *
3844064 TTGTATCGATACATGCTCA
1 TTGTATCGATACATACACA
* *
3844083 TTGTACCAATACATACACAA
1 TTGTATCGATACATACAC-A
3844103 TTGTATCGATACAT
1 TTGTATCGATACAT
3844117 GAAACTGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATACACA
Found at i:3846081 original size:2 final size:2
Alignment explanation
Indices: 3846074--3846103 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3846064 GAGTTAGATT
3846074 TA TA TA TA TA TA TA TA TA TA TGA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T
3846104 GTATGATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3850372 original size:79 final size:78
Alignment explanation
Indices: 3850274--3850976 Score: 462
Period size: 79 Copynumber: 8.9 Consensus size: 78
3850264 TAAAAATAGG
* * * *
3850274 GGAGTATCCCATTGAAAATAATAGGGTTGGAGTATCTCTAATGATGGAAAATCTATGTTTTGGAA
1 GGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCTAATG-TGGAAAATCTATGTTTTAGAA
3850339 ATAAAACCGGGGTT
65 ATAAAACCGGGGTT
* *** * * * ** *
3850353 GGAGTATCCCCTTGGAAATAACAACATTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTT--AC
1 GGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCC-CTAATGTGGAAAATCTATGTTTTAGAA
*
3850416 ATAAAACCGGGATT
65 ATAAAACCGGGGTT
* ** ** * * * **
3850430 GAAGTATCCCCTCAAAAATAATGGGGGTTGGAGTATCCTCGATTATCAAAAAT-TGATGTTTTAG
1 GGAGTATCCCCTTGAAAATAA-CAGGGTTGGAGTATCC-CTAATGTGGAAAATCT-ATGTTTTAG
** *
3850494 AAATAAAATTGGGGTA
63 AAATAAAACCGGGGTT
* ** ** *
3850510 GGAGTATCCCC-TCAGAAATAATGGGGTTGGAGTATCCCCGATGATAGAAAATC-AGGTGTTTTA
1 GGAGTATCCCCTTGA-AAATAACAGGGTTGGAGTATCCCTAATG-TGGAAAATCTA--TGTTTTA
**
3850573 GAAATAAAACCAAGGTT
62 GAAATAAAACCGGGGTT
* * * * * * *
3850590 GGATTAT-CCCTTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT-TGGTGTTTTAG
1 GGAGTATCCCCTT-GAAAATAACAGGGTTGGAGTAT-CCCTAATGTGGAAAATCT-ATGTTTTAG
**
3850653 AAATAAAATGGGGGTT
63 AAATAAAACCGGGGTT
* * *
3850669 GGAGTGTCCCCTTGAAAATAACAGGGTTAGAGTATTCCC-GATGGTGGAAAAT-TGATGTTTTAG
1 GGAGTATCCCCTTGAAAATAACAGGGTTGGAGTA-TCCCTAAT-GTGGAAAATCT-ATGTTTTAG
*
3850732 AAATAAAATCGGGGTT
63 AAATAAAACCGGGGTT
** * * * * * *
3850748 GGAGTAT-CTTTTCGAAAATAATAGAGTTGGAGTATCCTCGATTGTGGGAAAT-TAGTGTTTTGG
1 GGAGTATCCCCTT-GAAAATAACAGGGTTGGAGTATCC-CTAATGTGGAAAATCTA-TGTTTTAG
*
3850811 AAA-AAAACTGGGGGTT
63 AAATAAAAC-CGGGGTT
* * ** *
3850827 GGAGTATCCCCTTAAAAATAA-AGGGGTTGGAGTATCCCTGATTGTGGAAAATCGGTGTTATAGA
1 GGAGTATCCCCTTGAAAATAACA-GGGTTGGAGTATCCCT-AATGTGGAAAATCTATGTTTTAGA
* *
3850891 AATAAAACTGTGGTT
64 AATAAAACCGGGGTT
* * * * **
3850906 GGAGTAT-CCCTTCGGAAATAACAGTGATGGAGTATCCCTAATGGTGAAAAATCGGTGTTTTAGA
1 GGAGTATCCCCTT-GAAAATAACAGGGTTGGAGTATCCCTAAT-GTGGAAAATCTATGTTTTAGA
3850970 AATAAAA
64 AATAAAA
3850977 ACACCAATGA
Statistics
Matches: 492, Mismatches: 101, Indels: 62
0.75 0.15 0.09
Matches are distributed among these distances:
77 31 0.06
78 54 0.11
79 303 0.62
80 98 0.20
81 6 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (78 bp):
GGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCTAATGTGGAAAATCTATGTTTTAGAAA
TAAAACCGGGGTT
Found at i:3850806 original size:158 final size:157
Alignment explanation
Indices: 3850274--3850976 Score: 679
Period size: 158 Copynumber: 4.5 Consensus size: 157
3850264 TAAAAATAGG
* * * *
3850274 GGAGTATCCCATT-GAAAATAATAGGGTTGGAGTAT-CTCTAATGATGGAAAATCTA-TGTTTTG
1 GGAGTATCCC-TTCGAAAATAATAGGGTTGGAGTATCCTCGATTG-TGAAAAAT-TAGTGTTTTA
** * *** * *
3850336 GAAATAAAACCGGGGTTGGAGTATCCCCTTGGAAATAACAACATTGGAGTATCCTCGATTGTGAA
63 GAAATAAAATGGGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCC-CGATGGTGGA
* *
3850401 AAATCGGTGTTTT--ACATAAAACCGGGATT
127 AAATCGGTGTTTTAGAAATAAAACCGGGGTT
* * * * * *
3850430 GAAGTATCCCCTCAAAAATAATGGGGGTTGGAGTATCCTCGATTATCAAAAATT-GATGTTTTAG
1 GGAGTATCCCTTCGAAAATAAT-AGGGTTGGAGTATCCTCGATTGTGAAAAATTAG-TGTTTTAG
* * * ** * *
3850494 AAATAAAATTGGGGTAGGAGTATCCCC-TCAGAAATAATGGGGTTGGAGTATCCCCGATGATAGA
64 AAATAAAATGGGGGTTGGAGTATCCCCTTGA-AAATAACAGGGTTGGAGTAT-CCCGATGGTGGA
**
3850558 AAATCAGGTGTTTTAGAAATAAAACCAAGGTT
127 AAATC-GGTGTTTTAGAAATAAAACCGGGGTT
* * ** * *
3850590 GGATTATCCCTTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAA
1 GGAGTATCCCTTCGAAAATAATAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAA
* *
3850655 ATAAAATGGGGGTTGGAGTGTCCCCTTGAAAATAACAGGGTTAGAGTATTCCCGATGGTGGAAAA
66 ATAAAATGGGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTA-TCCCGATGGTGGAAAA
* * *
3850720 TTGATGTTTTAGAAATAAAATCGGGGTT
130 TCGGTGTTTTAGAAATAAAACCGGGGTT
** * ** *
3850748 GGAGTATCTTTTCGAAAATAATAGAGTTGGAGTATCCTCGATTGTGGGAAATTAGTGTTTTGGAA
1 GGAGTATCCCTTCGAAAATAATAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAA
* *
3850813 A-AAAACTGGGGGTTGGAGTATCCCCTTAAAAATAA-AGGGGTTGGAGTATCCCTGATTGTGGAA
66 ATAAAA-TGGGGGTTGGAGTATCCCCTTGAAAATAACA-GGGTTGGAGTATCCC-GATGGTGGAA
* * *
3850876 AATCGGTGTTATAGAAATAAAACTGTGGTT
128 AATCGGTGTTTTAGAAATAAAACCGGGGTT
* * * * * * **
3850906 GGAGTATCCCTTCGGAAATAACAGTGATGGAGTATCC-CTAATGGTGAAAAATCGGTGTTTTAGA
1 GGAGTATCCCTTCGAAAATAATAGGGTTGGAGTATCCTC-GATTGTGAAAAATTAGTGTTTTAGA
3850970 AATAAAA
65 AATAAAA
3850977 ACACCAATGA
Statistics
Matches: 445, Mismatches: 84, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
155 1 0.00
156 19 0.04
157 85 0.19
158 212 0.48
159 94 0.21
160 34 0.08
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (157 bp):
GGAGTATCCCTTCGAAAATAATAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAA
ATAAAATGGGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCGATGGTGGAAAAT
CGGTGTTTTAGAAATAAAACCGGGGTT
Found at i:3850808 original size:237 final size:235
Alignment explanation
Indices: 3850274--3850976 Score: 740
Period size: 237 Copynumber: 3.0 Consensus size: 235
3850264 TAAAAATAGG
* * *
3850274 GGAGTATCCCATTGAAAATAATAGGGTTGGAGTAT-CTCTAATGATGGAAAATCTA-TGTTTTGG
1 GGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCTC-GATGATGGAAAAT-TAGTGTTTTGG
** **** *
3850337 AAATAAAACCGGGGTTGGAGTATCCCCTTGGAAATAACAACATTGGAGTATCCTCGATTGTGAAA
64 AAATAAAACCGGGGTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAA
* * * * ** **
3850402 AATCGGTGTTTT--ACATAAAACCGGGATTGAAGTATCCCCTCAAAAATAATGGGGGTTGGAGTA
129 AATCGGTGTTTTAGAAATAAAA-TGGGGTTGGAGTATCCCCTTGAAAATAA-CAGGGTTGGAGTA
** * *
3850465 TCCTCGATTATCAAAAATTGATGTTTTAGAAATAAAATTGGGGTA
192 TCC-CGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTA
* * * * *
3850510 GGAGTATCCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATGATAGAAAATCAGGTGTTTTAG
1 GGAGTATCCCCTCGA-AAATAATAGGGTTGGAGTATCCTCGATGATGGAAAATTA-GTGTTTTGG
** *
3850574 AAATAAAACCAAGGTTGGATTAT-CCCTTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAA
64 AAATAAAACCGGGGTTGGAGTATCCCCTT-AAAAATAACGGGGTTGGAGTATCCCCGATTGTGAA
* * *
3850638 AAATTGGTGTTTTAGAAATAAAATGGGGGTTGGAGTGTCCCCTTGAAAATAACAGGGTTAGAGTA
128 AAATCGGTGTTTTAGAAATAAAAT-GGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTA
* *
3850703 TTCCCGATGGTGGAAAATTGATGTTTTAGAAATAAAATCGGGGTT
192 -TCCCGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTA
*** * *
3850748 GGAGTATCTTTTCGAAAATAATAGAGTTGGAGTATCCTCGATTG-TGGGAAATTAGTGTTTTGGA
1 GGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCTCGA-TGATGGAAAATTAGTGTTTTGGA
* * * *
3850812 AA-AAAACTGGGGGTTGGAGTATCCCCTTAAAAATAAAGGGGTTGGAGTATCCCTGATTGTGGAA
65 AATAAAAC-CGGGGTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAA
* * * * *
3850876 AATCGGTGTTATAGAAATAAAACTGTGGTTGGAGTAT-CCCTTCGGAAATAACAGTGATGGAGTA
129 AATCGGTGTTTTAGAAATAAAA-TGGGGTTGGAGTATCCCCTT-GAAAATAACAGGGTTGGAGTA
* * *
3850940 TCCCTAATGGTGAAAAATCGGTGTTTTAGAAATAAAA
192 TCCC-GATGGTGAAAAATTGATGTTTTAGAAATAAAA
3850977 ACACCAATGA
Statistics
Matches: 387, Mismatches: 64, Indels: 31
0.80 0.13 0.06
Matches are distributed among these distances:
235 2 0.01
236 60 0.16
237 199 0.51
238 91 0.24
239 35 0.09
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (235 bp):
GGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCTCGATGATGGAAAATTAGTGTTTTGGAA
ATAAAACCGGGGTTGGAGTATCCCCTTAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAA
TCGGTGTTTTAGAAATAAAATGGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCC
GATGGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTA
Found at i:3852241 original size:36 final size:36
Alignment explanation
Indices: 3852137--3852243 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 36
3852127 TTTTTGACAC
*
3852137 ACAAA-ACAACATATATCATGGAGGATAGAAATCCA
1 ACAAACACAACATATATCATGGAGGATAGAAATGCA
3852172 ACAAACACAACATATATCATGGAGGATAGAAATGCA
1 ACAAACACAACATATATCATGGAGGATAGAAATGCA
* *
3852208 ACAAACATAACATATATCACGGAGGATAGAAATGCA
1 ACAAACACAACATATATCATGGAGGATAGAAATGCA
3852244 TGAACCAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 5 0.07
36 63 0.93
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (36 bp):
ACAAACACAACATATATCATGGAGGATAGAAATGCA
Found at i:3853548 original size:41 final size:41
Alignment explanation
Indices: 3853479--3853556 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
3853469 TAAAATCTAG
*
3853479 AATGTATCGATATATTGAAAAATGTATCGATACAAATAGTC
1 AATGTATCGATATATTGAAAAATATATCGATACAAATAGTC
* ***
3853520 AATGTATCGATATATTTACTTATATATCGATACAAAT
1 AATGTATCGATATATTGAAAAATATATCGATACAAAT
3853557 TGTAGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (41 bp):
AATGTATCGATATATTGAAAAATATATCGATACAAATAGTC
Found at i:3854165 original size:75 final size:75
Alignment explanation
Indices: 3854098--3854237 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 75
3854088 TGAAAGGGTA
*
3854098 TCCTACTC-TCTGACGATAAAGGAAAAT-GAGTACATCCTGTTCTTC-GAGGACAAAGGAAAAGA
1 TCCTACTCAT-TGACGACAAAGGAAAATGGAGTACATCCTGTTCTTCAG-GGACAAAGGAAAAGA
3854160 GAATGAAATAGG
64 GAATGAAATAGG
* * * * * *
3854172 TCTTGCTCATTGAGGACAAAGGAAAATGGAGTACATCCTGTTTTTCAGGGACACAGGAAAAAAGA
1 TCCTACTCATTGACGACAAAGGAAAATGGAGTACATCCTGTTCTTCAGGGACAAAGGAAAAGAGA
3854237 A
66 A
3854238 AATGAAGTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
74 21 0.38
75 34 0.61
76 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (75 bp):
TCCTACTCATTGACGACAAAGGAAAATGGAGTACATCCTGTTCTTCAGGGACAAAGGAAAAGAGA
ATGAAATAGG
Found at i:3854320 original size:44 final size:44
Alignment explanation
Indices: 3854228--3854331 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
3854218 AGGGACACAG
* * * *
3854228 GAAAA-AAGAAAATGAAGTGTGTCCCGCTCTTTGAGGACAAAAA
1 GAAAAGAAGGAAATGAGGTGCGTCCCGCTCTTTAAGGACAAAAA
* *
3854271 GAAAAGACA-GAAATGAGGTGCGTCCTGCTCTTTAAGGAC-AAAG
1 GAAAAGA-AGGAAATGAGGTGCGTCCCGCTCTTTAAGGACAAAAA
3854314 GTAAAAGAAGGAAATGAG
1 G-AAAAGAAGGAAATGAG
3854332 TCATGCTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 10 0.20
44 40 0.78
45 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.17
Consensus pattern (44 bp):
GAAAAGAAGGAAATGAGGTGCGTCCCGCTCTTTAAGGACAAAAA
Found at i:3854862 original size:120 final size:120
Alignment explanation
Indices: 3854337--3855056 Score: 690
Period size: 120 Copynumber: 5.9 Consensus size: 120
3854327 ATGAGTCATG
* * * * * *
3854337 CTCTTTAAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTT-GAAAAA-AAAACGTCTTGCTCT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAATGTCATGCTCT
* * *
3854400 TTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAGATGGAAAAGGAAAGAGGCGTCTTG
66 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TT----T-G-AAAGGAAAG-TGCG--TTA
* * * * *
3854465 CTCTTGGAGGACTAGAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAAAG-AAGTGACATGCTCT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAATGTCATGCTCT
* * * * *
3854529 TTAAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAATATC-CTA
66 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGT-GCGTTA
* * * *
3854584 CTCTTTG-GGGCTTAGAAGGTGCCACCAGCTTGTATGGGCTTTAAAAAAAG-AAGTGTCATGCTC
1 CTCTTTGAGGAC-TAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAATGTCATGCTC
* *
3854647 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAG-GCGTCCTA
65 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAAGTGCGT--TA
* ** ** * * * *
3854705 CTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGAGAAAACGTCCTACTTT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAATGTCATGCTCT
* ** * *
3854770 TTGACGACTGGAAGGTGCCACCAACTTGTGTGGGATTTGAAAGGAAAGTGCGTTG
66 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTGCGTTA
* * ** *
3854825 CTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGGTTT-AAAAGGGAAAGATGTCCTGCTC
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAA-ATGTCATGCTC
* * *
3854889 TCTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTC-CTA
65 TTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTG-CGTTA
* ** * *
3854945 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAG--GGTGTCCTGG
1 CTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA--AAAGAAAATGTCATGC
* *
3855007 TCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAA
63 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA
3855057 AGGCATCATG
Statistics
Matches: 497, Mismatches: 78, Indels: 42
0.81 0.13 0.07
Matches are distributed among these distances:
118 4 0.01
119 104 0.21
120 189 0.38
121 48 0.10
122 63 0.13
123 3 0.01
124 1 0.00
128 38 0.08
129 47 0.09
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (120 bp):
CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAATGTCATGCTCT
TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTGCGTTA
Found at i:3855083 original size:61 final size:61
Alignment explanation
Indices: 3854335--3855085 Score: 724
Period size: 61 Copynumber: 12.3 Consensus size: 61
3854325 AAATGAGTCA
* * * *
3854335 TGCTCTTTAAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTGAAAA--AAAA-ACGTCT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCC
*
3854394 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAGATGGAAAAGGAAAGAGGC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TT----T--AAAAGGAAA-AGGC
*
3854459 GTCT
58 GTCC
* * * * * * * *
3854463 TGCTCTTGGAGGACTAGAAGGTGCCACCAGCTTGTGTAGGCTTTAAAA--AAAGAAGTGACA
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-AGGCGTCC
* * * **
3854523 TGCTCTTTAAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAA--TATCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * * * * * *
3854582 TACTCTTTG-GGGCTTAGAAGGTGCCACCAGCTTGTATGGGCTTTAAAA--AAAGAAGTGTCA
1 TGCTCTTTGAGGAC-TAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-AGGCGTCC
*
3854642 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGCGTCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * ** *
3854703 TACTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGAGAAA-ACGTCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCGTCC
* * * ** * *
3854764 TACTTTTTGACGACTGGAAGGTGCCACCAACTTGTGTGGGATTTGAAAGG-AAAGTGCGT--
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-GCGTCC
* * * * **
3854823 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGGTTTAAAAGGGAAAGATGTCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
3854884 TGCTCTCTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAA-GTGTCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * * *
3854943 TACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAGGGTGTCC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * *
3855004 TGGTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCA
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
3855065 TGCTTTTTGAGGATTAAAAGG
1 TGCTCTTTGAGGACTAAAAGG
3855086 ATAAAAGGTT
Statistics
Matches: 582, Mismatches: 83, Indels: 52
0.81 0.12 0.07
Matches are distributed among these distances:
57 3 0.01
58 4 0.01
59 177 0.30
60 101 0.17
61 230 0.40
62 13 0.02
64 2 0.00
65 5 0.01
67 3 0.01
68 3 0.01
69 41 0.07
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (61 bp):
TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
Found at i:3856071 original size:14 final size:14
Alignment explanation
Indices: 3856052--3856111 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
3856042 CATAGGTAGG
3856052 TTCTTTTTACTTTT
1 TTCTTTTTACTTTT
* *
3856066 TTCTTTCTAGTTTT
1 TTCTTTTTACTTTT
* *
3856080 TGTTTTTTTTCTTTT
1 T-TCTTTTTACTTTT
3856095 TT-TTTGTTGACTTTT
1 TTCTTT-TT-ACTTTT
3856110 TT
1 TT
3856112 TTGGCGAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
13 3 0.08
14 16 0.44
15 17 0.47
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.78
Consensus pattern (14 bp):
TTCTTTTTACTTTT
Found at i:3856109 original size:22 final size:23
Alignment explanation
Indices: 3856058--3856111 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
3856048 TAGGTTCTTT
3856058 TTACTTTTTTCTTTCTAGTTTTTG
1 TTACTTTTTTCTTTCTA-TTTTTG
3856082 TT--TTTTTTCTTT-T-TTTTTG
1 TTACTTTTTTCTTTCTATTTTTG
3856101 TTGACTTTTTT
1 TT-ACTTTTTT
3856112 TTGGCGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 8 0.30
21 1 0.04
22 16 0.59
24 2 0.07
ACGTcount: A:0.06, C:0.09, G:0.07, T:0.78
Consensus pattern (23 bp):
TTACTTTTTTCTTTCTATTTTTG
Found at i:3865714 original size:20 final size:21
Alignment explanation
Indices: 3865675--3865714 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3865665 GTTTTGTATA
3865675 AATGTTTTCAAGTCTTAAATCG
1 AATGTTTTCAAG-CTTAAATCG
3865697 AATGTTTTCAAG-TTAAAT
1 AATGTTTTCAAGCTTAAAT
3865715 TACTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
AATGTTTTCAAGCTTAAATCG
Found at i:3877817 original size:79 final size:79
Alignment explanation
Indices: 3877751--3878454 Score: 617
Period size: 79 Copynumber: 8.8 Consensus size: 79
3877741 GGGGTTCGAA
* *
3877751 TATCCTCTTAGAAATAACGAGGTTGGAGTATCCTTGATGATGGAAAATCGGTGTTTT-GAAAATA
1 TATCCCCTTAGAAATAACGAGGTTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAG-AAATA
3877815 AAATCGAGGTTGGAG
65 AAATCGAGGTTGGAG
* ** * *
3877830 TATCCCCTCAGAAATAACGGAGGTTTAAGTATCCTTAATTATGGAAAATCGATGTTTTA-AAATA
1 TATCCCCTTAGAAATAAC-GAGGTTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAGAAATA
* *
3877894 AAACCAAGGTT-GACG
65 AAATCGAGGTTGGA-G
* * * * * * *
3877909 TATCTCCTCAAAAATAACAAGGTTAGAGTAT-CTTCGATGATAGAAAATTGATGTTTTAGAAATA
1 TATCCCCTTAGAAATAACGAGGTTGGAGTATCCTT-GATGATGGAAAATCGATGTTTTAGAAATA
3877973 AAATCGAGGTTGGAG
65 AAATCGAGGTTGGAG
* * * * *** * *
3877988 TATCCCCTCAAAAATAAAGGGGTTGGAGTATCCCCAATTAATGAAAAATCGATGTTTTAGAAATA
1 TATCCCCTTAGAAATAACGAGGTTGGAGTATCCTTGA-TGATGGAAAATCGATGTTTTAGAAATA
* *
3878053 AAACCAAGGTTGGAG
65 AAATCGAGGTTGGAG
* * * * *
3878068 TGT-CTCTTCGAAAATAACGGGGTTGGAGTATCCTTGATCGA-GGAAAATC-AGTGTTTTAGGAA
1 TATCCCCTTAG-AAATAACGAGGTTGGAGTATCCTTGAT-GATGGAAAATCGA-TGTTTTAGAAA
*
3878130 TAAAATCGGGGTTGGAG
63 TAAAATCGAGGTTGGAG
* * * * * *
3878147 TGT-CCCTTAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCAATGTTTTAGAAATA
1 TATCCCCTT-AGAAATAACGAGGTTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAGAAATA
* *
3878211 AAATCAAGGTTTGAG
65 AAATCGAGGTTGGAG
* * ** * *
3878226 TATCCCC-TCGAAAATAACG-GGAATGGAGTATCCCCGATGGTAGAAAATCGATGTTTT-GAAAA
1 TATCCCCTTAG-AAATAACGAGG-TTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAG-AAA
3878288 TAAAATCGAGGGTTGGAG
63 TAAAATCGA-GGTTGGAG
* * * * * *
3878306 TATCCCCTCAGAAATAACGAGGTTGGAGTATCCTCGATTG-TGAAAAATTGGTATTTTAGAAATA
1 TATCCCCTTAGAAATAACGAGGTTGGAGTATCCTTGA-TGATGGAAAATCGATGTTTTAGAAATA
*
3878370 AAATCGGGGTTGGAG
65 AAATCGAGGTTGGAG
* * * *
3878385 TATCCCCTATGGTGAAA-AATCG-GTGTTGGAGTATCCCTGATGGTGGAAAATCGGTGTTTTAGA
1 TATCCCCT-T--AGAAATAA-CGAG-GTTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAGA
3878448 AATAAAA
61 AATAAAA
3878455 ACATCAATGA
Statistics
Matches: 512, Mismatches: 84, Indels: 55
0.79 0.13 0.08
Matches are distributed among these distances:
77 3 0.01
78 36 0.07
79 258 0.50
80 160 0.31
81 11 0.02
82 44 0.09
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
TATCCCCTTAGAAATAACGAGGTTGGAGTATCCTTGATGATGGAAAATCGATGTTTTAGAAATAA
AATCGAGGTTGGAG
Found at i:3877977 original size:158 final size:157
Alignment explanation
Indices: 3877762--3878338 Score: 691
Period size: 158 Copynumber: 3.6 Consensus size: 157
3877752 ATCCTCTTAG
* *
3877762 AAATAACGAGGTTGGAGTATCCTTGATGATGGAAAATCGGTGTTTTGAAAATAAAATCGAGGTTG
1 AAATAACGAGGTTGGAGTATCCTTGATGATAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTG
* ** *
3877827 GAGTATCCCCTCAGAAATAACGGAGGTTTAAGTATCCTTAATTATGGAAAATCGATGTTTTA-AA
66 GAGTATCCCCTCAAAAATAACGG-GGTTGGAGTATCCCTAATTATGGAAAATCGATGTTTTAGAA
*
3877891 ATAAAACCAAGGTTGACGTATCTCCTCAA
130 ATAAAACCAAGGTTGA-GTATCTCCTCGA
* * *
3877920 AAATAACAAGGTTAGAGTAT-CTTCGATGATAGAAAATTGATGTTTT-AGAAATAAAATCGAGGT
1 AAATAACGAGGTTGGAGTATCCTT-GATGATAGAAAATCGATGTTTTGA-AAATAAAATCGAGGT
* * *
3877983 TGGAGTATCCCCTCAAAAATAAAGGGGTTGGAGTATCCCCAATTAATGAAAAATCGATGTTTTAG
64 TGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTAATT-ATGGAAAATCGATGTTTTAG
* *
3878048 AAATAAAACCAAGGTTGGAGTGTCTCTTCGA
128 AAATAAAACCAAGGTT-GAGTATCTCCTCGA
* * * *
3878079 AAATAACGGGGTTGGAGTATCCTTGATCGA-GGAAAATC-AGTGTTTT-AGGAATAAAATCGGGG
1 AAATAACGAGGTTGGAGTATCCTTGAT-GATAGAAAATCGA-TGTTTTGA-AAATAAAATCGAGG
* * * * ** *
3878141 TTGGAGTGTCCCTTAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCAATGTTTTAG
63 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTAATTATGGAAAATCGATGTTTTAG
* *
3878206 AAATAAAATCAAGGTTTGAGTATCCCCTCGA
128 AAATAAAACCAAGG-TTGAGTATCTCCTCGA
* ** *
3878237 AAATAACG-GGAATGGAGTATCCCCGATGGTAGAAAATCGATGTTTTGAAAATAAAATCGAGGGT
1 AAATAACGAGG-TTGGAGTATCCTTGATGATAGAAAATCGATGTTTTGAAAATAAAATCGA-GGT
* *
3878301 TGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCC
64 TGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCC
3878339 TCGATTGTGA
Statistics
Matches: 357, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
157 22 0.06
158 179 0.50
159 149 0.42
160 7 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (157 bp):
AAATAACGAGGTTGGAGTATCCTTGATGATAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTG
GAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTAATTATGGAAAATCGATGTTTTAGAAA
TAAAACCAAGGTTGAGTATCTCCTCGA
Found at i:3878372 original size:238 final size:236
Alignment explanation
Indices: 3877774--3878454 Score: 732
Period size: 238 Copynumber: 2.9 Consensus size: 236
3877764 ATAACGAGGT
** * *
3877774 TGGAGTATCCTTGATGATGGAAAATCGGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATG-TAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTC
** * * * * **
3877839 AGAAATAACGGAGGTTTAAGTATCCTTAATTATGGAAAATCGATGTTTTA-AAATAAAACCAAGG
65 AGAAATAAC-GAGGTTGGAGTATCCTTGATTGTGGAAAATCGGTGTTTTAGAAATAAAATCGGGG
* ** * * * * *
3877903 TT-GACGTATCTCC-TCAAAAATAACAAGGTTAGAGTAT-CTTCGATGATAGAAAATTGATGTTT
129 TTGGA-GTATC-CCTTAAAAAATAACGGGGTTGGAGTATCCCT-GATGGTGGAAAATCGATGTTT
* **
3877965 TAGAAATAAAATCGAGGTTGGAGTATCCCCTCAAAAATAAAGGGGT
191 TAGAAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAAAGGGAA
* * * * *
3878011 TGGAGTATCCCCAAT-TAATGAAAAATCGATGTTTT-AGAAATAAAACCAAGGTTGGAGTGTCTC
1 TGGAGTATCCCCGATGT-A-G-AAAATCGATGTTTTGA-AAATAAAATCGAGGTTGGAGTATCCC
* * * * * *
3878074 TTC-GAAAATAACGGGGTTGGAGTATCCTTGATCGAGGAAAATCAGTGTTTTAGGAATAAAATCG
62 CTCAG-AAATAACGAGGTTGGAGTATCCTTGATTGTGGAAAATCGGTGTTTTAGAAATAAAATCG
* *
3878138 GGGTTGGAGTGTCCCTTAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCAATGTTT
126 GGGTTGGAGTATCCCTTAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCGATGTTT
* * *
3878203 TAGAAATAAAATCAAGGTTTGAGTATCCCCTCGAAAATAACGGGAA
191 TAGAAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAAAGGGAA
3878249 TGGAGTATCCCCGATGGTAGAAAATCGATGTTTTGAAAATAAAATCGAGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGAT-GTAGAAAATCGATGTTTTGAAAATAAAATCGA-GGTTGGAGTATCCCCT
* * * *
3878314 CAGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGGG
64 CAGAAATAACGAGGTTGGAGTATCCTTGATTGTGGAAAATCGGTGTTTTAGAAATAAAATCGGGG
* * *
3878379 TTGGAGTATCCCCTATGGTGAAAAAT--CGGTGTTGGAGTATCCCTGATGGTGGAAAATCGGTGT
129 TTGGAGTAT-CCC--T--TAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCGATGT
3878442 TTTAGAAATAAAA
189 TTTAGAAATAAAA
3878455 ACATCAATGA
Statistics
Matches: 366, Mismatches: 59, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
235 1 0.00
237 72 0.20
238 228 0.62
239 9 0.02
240 1 0.00
241 48 0.13
243 7 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (236 bp):
TGGAGTATCCCCGATGTAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTCA
GAAATAACGAGGTTGGAGTATCCTTGATTGTGGAAAATCGGTGTTTTAGAAATAAAATCGGGGTT
GGAGTATCCCTTAAAAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCGATGTTTTAGAA
ATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAAAGGGAA
Found at i:3878439 original size:31 final size:31
Alignment explanation
Indices: 3878369--3878442 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
3878359 TTTTAGAAAT
*
3878369 AAAATCGGGGTTGGAGTATCCCCTATGGTGA
1 AAAATCGGTGTTGGAGTATCCCCTATGGTGA
*
3878400 AAAATCGGTGTTGGAGTAT-CCCTGATGGTGG
1 AAAATCGGTGTTGGAGTATCCCCT-ATGGTGA
3878431 AAAATCGGTGTT
1 AAAATCGGTGTT
3878443 TTAGAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (31 bp):
AAAATCGGTGTTGGAGTATCCCCTATGGTGA
Found at i:3880860 original size:20 final size:20
Alignment explanation
Indices: 3880826--3880866 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3880816 GTTAAAACCG
** *
3880826 AGAATGTATTGATACACTGA
1 AGAATGTATCAATACAATGA
3880846 AGAATGTATCAATACAATGA
1 AGAATGTATCAATACAATGA
3880866 A
1 A
3880867 AAAAAATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (20 bp):
AGAATGTATCAATACAATGA
Found at i:3887134 original size:166 final size:163
Alignment explanation
Indices: 3886942--3887653 Score: 573
Period size: 166 Copynumber: 4.3 Consensus size: 163
3886932 TTTTAATTCC
* * * * * *
3886942 AAAATTCCTTAAATATTATCATTTAATCACCATTATATCAGTTTTGAAAATTTTCTTTTATTTTA
1 AAAATTCATCAAATATTATTATTTAATCACTATTAAATCAGTTTT-AAAATTTTCATTTATTTTA
* * * * * * *** *
3887007 TGAGTTATTGATTTTCTTTTGGAATCCCTCATATTTTTGAAACAAAGAGTTTCCCACTCCATAAA
65 TGAGTT-TTGATTTTCTTTTGAAAT-TCTCCTATTTTCGAAATATAGAGTTTTTTACTCCGTAAA
3887072 TATTTTCGA-GAGTATTTTTTTTGGTTTTTAATTTTT
128 TATTTTCGAGGAG-ATTTTTTTTGGTTTTTAATTTTT
* * ** *
3887108 AAAATTCATAAAATATTATTATTTAATTCA-TATTAAATCAAATTTTAAAA-AATCATTCATTTT
1 AAAATTCATCAAATATTATTATTTAA-TCACTATTAAATC-AGTTTTAAAATTTTCATTTA-TTT
* ** * * * **
3887171 TATGAGTTTTTCATTTTTCCCTTGAAATTCTCCCATTTCCGAAATATTGAGTTTTTTACTTTGTA
63 TATGAG-TTTTGA-TTTTCTTTTGAAATTCTCCTATTTTCGAAATATAGAGTTTTTTACTCCGTA
* *
3887236 AATATTTT-TAGGAGCATTTCTCTTT-GTTTTTAATTTTT
126 AATATTTTCGAGGAG-ATTT-TTTTTGGTTTTTAATTTTT
* *
3887274 AAAATTCATCAAATATTATTATTTACTC-CATATTAAATCAGTTTTCAAATTTTCATTTATTTTC
1 AAAATTCATCAAATATTATTATTTAATCAC-TATTAAATCAGTTTTAAAATTTTCATTTATTTT-
* * * *
3887338 ATGAGTTTTGAATTTTTTCTTTGAAATTATCCTATTTTCAAAATATGGAGTTTTTTACTCCGTAA
64 ATGAGTTTTG-ATTTTCT-TTTGAAATTCTCCTATTTTCGAAATATAGAGTTTTTTACTCCGTAA
* * * *
3887403 ATGTTTTCGAGGAGATATTTCTTGGTTTTTAATTTCT
127 ATATTTTCGAGGAGATTTTTTTTGGTTTTTAATTTTT
* **
3887440 AAAATTCATCAAATATTATTATTTAATC-CATATTAAATCAATTTTAAAAAATTCATTTATTTTC
1 AAAATTCATCAAATATTATTATTTAATCAC-TATTAAATCAGTTTTAAAATTTTCATTTATTTT-
* * * * * * * **
3887504 ATGAATTTTGAATTTTTTTTTGAAATTTTCCTGTTTT-TAAAAATTGAGTTTTCTT-CTTTGTAA
64 ATGAGTTTTG-ATTTTCTTTTGAAATTCTCCTATTTTCGAAATATAGAGTTTT-TTACTCCGTAA
* * * ** *
3887567 ATGTTTTCGGAGG-GATTTTTCTTGGCTTAAAAGTTTT
127 ATATTTTC-GAGGAGATTTTTTTTGGTTTTTAATTTTT
* * * * *
3887604 AAAACTCATCTAATATTATCATTAAACTC-CCATTAAATCAGTTTTGAAAA
1 AAAATTCATCAAATATTATTATTTAA-TCACTATTAAATCAGTTTT-AAAA
3887654 ATTCAAATTA
Statistics
Matches: 447, Mismatches: 80, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
164 79 0.18
165 61 0.14
166 277 0.62
167 30 0.07
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (163 bp):
AAAATTCATCAAATATTATTATTTAATCACTATTAAATCAGTTTTAAAATTTTCATTTATTTTAT
GAGTTTTGATTTTCTTTTGAAATTCTCCTATTTTCGAAATATAGAGTTTTTTACTCCGTAAATAT
TTTCGAGGAGATTTTTTTTGGTTTTTAATTTTT
Found at i:3893908 original size:52 final size:52
Alignment explanation
Indices: 3893834--3893972 Score: 215
Period size: 52 Copynumber: 2.7 Consensus size: 52
3893824 AAATTTAGCT
* *
3893834 GAATGAATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACTCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACCCA
* * *
3893886 GAATGTATCGATACGATTAAGAATGTATCGATACATTTATGTCAAAAACCCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACCCA
* *
3893938 AAATGTATTGATACAATGAAGAATGTATCGATACA
1 GAATGTATCGATACAATGAAGAATGTATCGATACA
3893973 ATGAAGAATG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (52 bp):
GAATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAAACCCA
Found at i:3893964 original size:20 final size:20
Alignment explanation
Indices: 3893939--3893992 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3893929 AAAAACCCAA
*
3893939 AATGTATTGATACAATGAAG
1 AATGTATCGATACAATGAAG
3893959 AATGTATCGATACAATGAAG
1 AATGTATCGATACAATGAAG
*
3893979 AATGTATCAATACA
1 AATGTATCGATACA
3893993 TTTTCTTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAAG
Found at i:3895559 original size:51 final size:52
Alignment explanation
Indices: 3895501--3895639 Score: 217
Period size: 51 Copynumber: 2.7 Consensus size: 52
3895491 TTTGGAAAGA
3895501 AAATGTATCGATACATTTTTCATTGTATCAATACATTCTAGG-TTTTAACCT
1 AAATGTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTTAACCT
* *
3895552 AAATGTATCGATACATTCTTCATTGTATCAATACATTCTAGGTTTTTGACCT
1 AAATGTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTTAACCT
* * * *
3895604 AAACGTTTTGATACATTTTTCAATGTATCAATACAT
1 AAATGTATCGATACATTTTTCATTGTATCAATACAT
3895640 ACAGGTAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 41 0.51
52 39 0.49
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTTAACCT
Found at i:3895631 original size:52 final size:51
Alignment explanation
Indices: 3895505--3895639 Score: 207
Period size: 52 Copynumber: 2.6 Consensus size: 51
3895495 GAAAGAAAAT
*
3895505 GTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTAACCTAAAT
1 GTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTAACCTAAAC
* *
3895556 GTATCGATACATTCTTCATTGTATCAATACATTCTAGGTTTTTGACCTAAAC
1 GTATCGATACATTTTTCATTGTATCAATACATTCTAGG-TTTTAACCTAAAC
* * *
3895608 GTTTTGATACATTTTTCAATGTATCAATACAT
1 GTATCGATACATTTTTCATTGTATCAATACAT
3895640 ACAGGTAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
51 37 0.49
52 39 0.51
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (51 bp):
GTATCGATACATTTTTCATTGTATCAATACATTCTAGGTTTTAACCTAAAC
Found at i:3898146 original size:19 final size:19
Alignment explanation
Indices: 3898122--3898257 Score: 85
Period size: 20 Copynumber: 6.7 Consensus size: 19
3898112 TTACCACTGT
* *
3898122 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGATAA
3898141 TTGTATCGATACATGGATAA
1 TTGTATCGATACAT-GATAA
*
3898161 TTGTATCGATACATGA-GA
1 TTGTATCGATACATGATAA
* * * ** **
3898179 TTAGCAGTAGCTACCTTACCACTGT
1 TT-GTA-TCGATA-C--ATGA-TAA
3898204 TTGTATCGATACATGATACA
1 TTGTATCGATACATGATA-A
*
3898224 ATGTATCGATACATGATTAA
1 TTGTATCGATACATGA-TAA
3898244 TTGTATCGATACAT
1 TTGTATCGATACAT
3898258 TGCTTATAAC
Statistics
Matches: 89, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
18 3 0.03
19 19 0.21
20 52 0.58
21 3 0.03
22 1 0.01
23 6 0.07
24 2 0.02
25 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGATAA
Found at i:3898177 original size:82 final size:82
Alignment explanation
Indices: 3898040--3898257 Score: 366
Period size: 82 Copynumber: 2.6 Consensus size: 82
3898030 ATGCTTTACA
* *
3898040 TTGTATCGATACATGTTCATTGTATCGATACATGGATAATTATATCAATACATGAGATTACCAGT
1 TTGTATCGATACATGTTCATTGTATCGATACATGGATAATTGTATCGATACATGAGATTACCAGT
3898105 AGCTACCTTACCACTGT
66 AGCTACCTTACCACTGT
*
3898122 TTGTATCGATACATGTTCATTGTATCGATACATGGATAATTGTATCGATACATGAGATTAGCAGT
1 TTGTATCGATACATGTTCATTGTATCGATACATGGATAATTGTATCGATACATGAGATTACCAGT
3898187 AGCTACCTTACCACTGT
66 AGCTACCTTACCACTGT
* *
3898204 TTGTATCGATACATGATACAATGTATCGATACAT-GATTAATTGTATCGATACAT
1 TTGTATCGATACATG-TTCATTGTATCGATACATGGA-TAATTGTATCGATACAT
3898258 TGCTTATAAC
Statistics
Matches: 129, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
82 96 0.74
83 33 0.26
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (82 bp):
TTGTATCGATACATGTTCATTGTATCGATACATGGATAATTGTATCGATACATGAGATTACCAGT
AGCTACCTTACCACTGT
Found at i:3906597 original size:40 final size:40
Alignment explanation
Indices: 3906522--3906598 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
3906512 CAAAATATGA
**
3906522 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTAGGC
1 AAATTTGCCTGCATGTATCGATACAAAGAATAGTGTAGGC
3906562 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTA
1 AAATTTGCCTGCATGTATCGATACAAAGAAT-AGTGTA
3906599 TCGATACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (40 bp):
AAATTTGCCTGCATGTATCGATACAAAGAATAGTGTAGGC
Found at i:3906613 original size:13 final size:13
Alignment explanation
Indices: 3906595--3906619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3906585 CAAAGATCAG
3906595 TGTATCGATACAA
1 TGTATCGATACAA
3906608 TGTATCGATACA
1 TGTATCGATACA
3906620 TTTTATATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3906698 original size:13 final size:13
Alignment explanation
Indices: 3906680--3906704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3906670 CAAAGATCAG
3906680 TGTATCGATACAA
1 TGTATCGATACAA
3906693 TGTATCGATACA
1 TGTATCGATACA
3906705 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3906701 original size:85 final size:86
Alignment explanation
Indices: 3906558--3906726 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 86
3906548 TGAATAGTGT
3906558 AGGCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTT
1 AGGCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTT
* *
3906623 TA-TATTGTATCGATACATCG
66 GAGTAATGTATCGATACATCG
3906643 AGGCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTT
1 AGGCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTT
3906708 GAGTAATGTATCGATACAT
66 GAGTAATGTATCGATACAT
3906727 TTTTTGGCAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
85 66 0.81
86 15 0.19
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (86 bp):
AGGCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTT
GAGTAATGTATCGATACATCG
Found at i:3906782 original size:33 final size:33
Alignment explanation
Indices: 3906745--3906811 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3906735 AGTAGCTTAA
3906745 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3906778 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3906811 A
1 A
3906812 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3906785 original size:13 final size:13
Alignment explanation
Indices: 3906767--3906791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3906757 CAAAAAAATA
3906767 TGTATCGATACAT
1 TGTATCGATACAT
3906780 TGTATCGATACA
1 TGTATCGATACA
3906792 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3907542 original size:32 final size:33
Alignment explanation
Indices: 3907506--3907568 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
3907496 TGCCAGTTTC
* *
3907506 ATGTATTGATACAATG-AACATGTATCGATATA
1 ATGTATCGATACAAAGCAACATGTATCGATATA
*
3907538 ATGTATCGATACAAAGCAGCATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
3907569 CATCTGGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATATA
Found at i:3912259 original size:20 final size:19
Alignment explanation
Indices: 3912236--3912308 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
3912226 CACACCCAGA
*
3912236 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
3912256 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
3912275 TGTATCGATACATG-GACAAT
1 TGTATCGATACATGTG-C-AT
*
3912295 TTTATCGATACATG
1 TGTATCGATACATG
3912309 AAACTGGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:3913992 original size:3 final size:3
Alignment explanation
Indices: 3913986--3914018 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3913976 TAAAGAAGAA
*
3913986 GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3914019 TTGGATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3920391 original size:19 final size:19
Alignment explanation
Indices: 3920331--3920392 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
3920321 AAAGGGGAGA
*
3920331 AGATAATCGTTTAAGGGGG
1 AGATAATTGTTTAAGGGGG
** * *
3920350 AGAATTTTTTTTTAAAGGAGG
1 AG-ATAATTGTTT-AAGGGGG
3920371 AGATAATTGTTTAAGGGGG
1 AGATAATTGTTTAAGGGGG
3920390 AGA
1 AGA
3920393 AAAACGAAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 11 0.34
20 13 0.41
21 8 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (19 bp):
AGATAATTGTTTAAGGGGG
Found at i:3920954 original size:19 final size:19
Alignment explanation
Indices: 3920911--3921002 Score: 130
Period size: 19 Copynumber: 4.7 Consensus size: 19
3920901 CACACCCAGA
* *
3920911 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TTCAT
3920931 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
3920950 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
3920969 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
3920989 TGTATCGATACATG
1 TGTATCGATACATG
3921003 AAACTGGCAG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 37 0.55
20 30 0.45
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:3920955 original size:39 final size:39
Alignment explanation
Indices: 3920911--3921002 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
3920901 CACACCCAGA
* **
3920911 TGTATCGATACATGCTGCTTTGTATCGATACATGTTC-AT
1 TGTATCGATACATG-TGCATTGTATCGATACATGGACAAT
*
3920950 TGTATCGATACATGTTCATTGTATCGATACATGGACAAT
1 TGTATCGATACATGTGCATTGTATCGATACATGGACAAT
3920989 TGTATCGATACATG
1 TGTATCGATACATG
3921003 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 18 0.38
39 30 0.62
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (39 bp):
TGTATCGATACATGTGCATTGTATCGATACATGGACAAT
Found at i:3921995 original size:13 final size:13
Alignment explanation
Indices: 3921977--3922002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3921967 CAATTTTTTG
3921977 TGTATCGATACAT
1 TGTATCGATACAT
3921990 TGTATCGATACAT
1 TGTATCGATACAT
3922003 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3922067 original size:21 final size:21
Alignment explanation
Indices: 3922041--3922116 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3922031 CTGCCAAGAA
*
3922041 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3922062 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3922082 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3922103 ATGTATCGATACAT
1 ATGTATCGATACAT
3922117 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3922087 original size:20 final size:20
Alignment explanation
Indices: 3922062--3922134 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3922052 CATCTTTTTT
3922062 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3922082 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3922103 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3922123 ATGTATCGATAC
1 ATGTATCGATAC
3922135 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3922098 original size:41 final size:41
Alignment explanation
Indices: 3922041--3922134 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3922031 CTGCCAAGAA
*
3922041 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3922082 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3922123 ATGTATCGATAC
1 ATGTATCGATAC
3922135 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:3924485 original size:21 final size:21
Alignment explanation
Indices: 3924461--3924507 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3924451 TTTGATGCTG
3924461 ATTTTG-A-TGAAGAACGAAGT
1 ATTTTGAAGTGAAGAAC-AAGT
3924481 -TATTTGAAGTGAAGAACAAGT
1 AT-TTTGAAGTGAAGAACAAGT
3924502 ATTTTG
1 ATTTTG
3924508 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAGAACAAGT
Found at i:3924646 original size:13 final size:13
Alignment explanation
Indices: 3924628--3924666 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3924618 ATAATCACCC
*
3924628 TGTATCGATACAG
1 TGTATCGATACAA
3924641 TGTATCGATACAA
1 TGTATCGATACAA
3924654 TGTATCGATACAA
1 TGTATCGATACAA
3924667 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3924677 original size:20 final size:20
Alignment explanation
Indices: 3924652--3924730 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
3924642 GTATCGATAC
3924652 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
3924672 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
3924697 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
3924716 ACATGTATCGATACA
1 A-ATGTATCGATACA
3924731 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:3926766 original size:15 final size:15
Alignment explanation
Indices: 3926746--3926776 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3926736 ATTTCGTTTG
*
3926746 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3926761 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3926776 G
1 G
3926777 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3930857 original size:13 final size:13
Alignment explanation
Indices: 3930839--3930864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3930829 CAATTTTTTG
3930839 TGTATCGATACAT
1 TGTATCGATACAT
3930852 TGTATCGATACAT
1 TGTATCGATACAT
3930865 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3930929 original size:21 final size:21
Alignment explanation
Indices: 3930903--3930978 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3930893 CTGCCAAGAA
*
3930903 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3930924 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3930944 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3930965 ATGTATCGATACAT
1 ATGTATCGATACAT
3930979 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3930949 original size:20 final size:20
Alignment explanation
Indices: 3930924--3930996 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3930914 CATCTTTTTT
3930924 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3930944 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3930965 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3930985 ATGTATCGATAC
1 ATGTATCGATAC
3930997 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3930960 original size:41 final size:41
Alignment explanation
Indices: 3930903--3930996 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3930893 CTGCCAAGAA
*
3930903 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3930944 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3930985 ATGTATCGATAC
1 ATGTATCGATAC
3930997 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:3934020 original size:21 final size:22
Alignment explanation
Indices: 3933971--3934047 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
3933961 AGATTTGACA
* * * *
3933971 AAGGGAGAGAAATGCCTTGATT
1 AAGGGGGAGAAATTCTTTAATT
*
3933993 AAGGGGGAGAAATT-TTTTATT
1 AAGGGGGAGAAATTCTTTAATT
*
3934014 AAAGGGGAGAAATTCTTTAATT
1 AAGGGGGAGAAATTCTTTAATT
3934036 AAGGGGGAGAAA
1 AAGGGGGAGAAA
3934048 AATGAAAACT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 18 0.38
22 29 0.62
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.26
Consensus pattern (22 bp):
AAGGGGGAGAAATTCTTTAATT
Found at i:3934596 original size:19 final size:19
Alignment explanation
Indices: 3934572--3934625 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
3934562 CATACCCAGA
* *
3934572 TGTATCGATACATGTTCAT
1 TGTATCGATACATGATAAT
3934591 TGTATCGATACATAGATAAT
1 TGTATCGATACAT-GATAAT
3934611 TGTATCGATACATGA
1 TGTATCGATACATGA
3934626 GATTAGTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:3934690 original size:13 final size:13
Alignment explanation
Indices: 3934669--3934721 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
3934659 CAATACATGG
*
3934669 TACAATGTATCGA
1 TACATTGTATCGA
3934682 TACATTGTATCGA
1 TACATTGTATCGA
3934695 TACA-TG-AT-G-
1 TACATTGTATCGA
3934704 -A-ATTGTATCGA
1 TACATTGTATCGA
3934715 TACATTG
1 TACATTG
3934722 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3934698 original size:33 final size:33
Alignment explanation
Indices: 3934653--3934721 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3934643 CTACCACTGT
*
3934653 TTGTATCAATACATGGT-ACAATGTATCGATACA
1 TTGTATCAATACATGATGA-AATGTATCGATACA
* *
3934686 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAAATGTATCGATACA
3934719 TTG
1 TTG
3934722 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCAATACATGATGAAATGTATCGATACA
Found at i:3936230 original size:13 final size:13
Alignment explanation
Indices: 3936212--3936237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3936202 TACAGCAAGT
3936212 ATGTATCGATACA
1 ATGTATCGATACA
3936225 ATGTATCGATACA
1 ATGTATCGATACA
3936238 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3938484 original size:21 final size:21
Alignment explanation
Indices: 3938451--3938495 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3938441 TTGCAAGTTG
*
3938451 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3938473 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3938493 AAA
1 AAA
3938496 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3940319 original size:15 final size:15
Alignment explanation
Indices: 3940299--3940328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3940289 AAAAATGTCT
*
3940299 AAAATGAGGAAGCTC
1 AAAATGAAGAAGCTC
3940314 AAAATGAAGAAGCTC
1 AAAATGAAGAAGCTC
3940329 CAAACGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AAAATGAAGAAGCTC
Done.