Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 14 of 21
Found at i:1528558 original size:112 final size:112
Alignment explanation
Indices: 1528371--1528572 Score: 289
Period size: 112 Copynumber: 1.8 Consensus size: 112
1528361 ATTTCAGAAC
* * * *
1528371 TGATAGGATACATACCCCATTTTCCTAGGCACGAATAGATCGGGTTGTATAAAACATGAATTTCT
1 TGATAAGATACATACCCCATTTTCCTAAGCACGAATAGATCAGGTTGAATAAAACATGAATTTCT
1528436 TTGAAAATCAGACAAAGTTGATGTTGTTTGATCAAACATTTCACTAG
66 TTGAAAATCAGACAAAGTTGATGTTGTTTGATCAAACATTTCACTAG
* * * * * *
1528483 TGATAAGATACATGCCCTATTTTTCTAAGTACGAA-AGGATCAGGTTGAATAAAGCATGAATTTG
1 TGATAAGATACATACCCCATTTTCCTAAGCACGAATA-GATCAGGTTGAATAAAACATGAATTTC
*
1528547 TTTGAAAATCAGACAAATTTGATGTT
65 TTTGAAAATCAGACAAAGTTGATGTT
1528573 CTTTCAAGTC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 1 0.01
112 77 0.99
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (112 bp):
TGATAAGATACATACCCCATTTTCCTAAGCACGAATAGATCAGGTTGAATAAAACATGAATTTCT
TTGAAAATCAGACAAAGTTGATGTTGTTTGATCAAACATTTCACTAG
Found at i:1529153 original size:22 final size:22
Alignment explanation
Indices: 1529115--1529175 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1529105 CTTCATTTCC
*
1529115 TTTTTATTCTTTT-TTTTG-CAT
1 TTTTTATTTTTTTCTTTTGTC-T
1529136 TTTTTATTTTTTTCTTTTGTCT
1 TTTTTATTTTTTTCTTTTGTCT
* *
1529158 TTTTCATTTTTCTCTTTT
1 TTTTTATTTTTTTCTTTT
1529176 TTTGTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.34
22 22 0.63
23 1 0.03
ACGTcount: A:0.07, C:0.11, G:0.03, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTTTCTTTTGTCT
Found at i:1529160 original size:21 final size:20
Alignment explanation
Indices: 1529114--1529175 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1529104 TCTTCATTTC
*
1529114 CTTTTTATTCTTTT-TTTTG
1 CTTTTTATTTTTTTCTTTTG
1529133 CATTTTTTATTTTTTTCTTTTG
1 C--TTTTTATTTTTTTCTTTTG
*
1529155 TCTTTTTCATTTTTCTCTTTT
1 -CTTTTT-ATTTTTTTCTTTT
1529176 TTTGTTCTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.03
21 17 0.47
22 17 0.47
23 1 0.03
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (20 bp):
CTTTTTATTTTTTTCTTTTG
Found at i:1531563 original size:126 final size:126
Alignment explanation
Indices: 1531338--1531580 Score: 450
Period size: 126 Copynumber: 1.9 Consensus size: 126
1531328 CAGAACTTAG
1531338 AGCTATTTCACATCCTTTTAAGATCTTGGGTAACCCATGCCCCTTCCATATGCCTAGAAGAAAGT
1 AGCTATTTCACATCCTTTTAAGATCTTGGGTAACCCATGCCCCTTCCATATGCCTAGAAGAAAGT
*
1531403 CTAATGCATATGCATGTGCACAGCGTGTGCGGGAAATAAACAAACTTTTTATAAAACTCAA
66 CTAATGCATATGCATGTGCACAGCGTGTGCGGGAAATAAACAAACCTTTTATAAAACTCAA
* *
1531464 AGCTATTTCACCTCCTTTTAAGATCTTGGGTAACCTATGCCCCTTCCATATGCCTAGAAGAAAGT
1 AGCTATTTCACATCCTTTTAAGATCTTGGGTAACCCATGCCCCTTCCATATGCCTAGAAGAAAGT
*
1531529 CTAATGCATATGCATGTGCACAGCGTGTGCGGGAAATGAACAAACCTTTTAT
66 CTAATGCATATGCATGTGCACAGCGTGTGCGGGAAATAAACAAACCTTTTAT
1531581 GACTCCACTC
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (126 bp):
AGCTATTTCACATCCTTTTAAGATCTTGGGTAACCCATGCCCCTTCCATATGCCTAGAAGAAAGT
CTAATGCATATGCATGTGCACAGCGTGTGCGGGAAATAAACAAACCTTTTATAAAACTCAA
Found at i:1535975 original size:20 final size:21
Alignment explanation
Indices: 1535946--1535996 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1535936 TTTAGGCATG
1535946 TATCGATACATTCACT-TATT
1 TATCGATACATTCACTATATT
* * *
1535966 TATTGATACATTTACTATTTT
1 TATCGATACATTCACTATATT
1535987 TATCGATACA
1 TATCGATACA
1535997 AATTATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (21 bp):
TATCGATACATTCACTATATT
Found at i:1536705 original size:52 final size:53
Alignment explanation
Indices: 1536623--1537341 Score: 227
Period size: 52 Copynumber: 12.8 Consensus size: 53
1536613 TGTCTGTGAT
* * *
1536623 GTGCCAGTGTGCAGATTCAAGGCCTA-CGACACTAGACTTAAAGATAAGAAGA-
1 GTGCCAATGTGCTGATTCAAGG-CTAGCGACATTAGACTTAAAGATAAGAAGAG
* *
1536675 GTGCCAATGTGCTGATTCAAGGCGAGCGACATTGGACTTAAAGATGCAAAGAATGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGAT---AAGAA-G----AG
* * * * * * * *
1536736 GTGCCAATATGTTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGACAA-AT
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* *
1536788 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTTGACTTGAAGATGAGAAGAATGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTT-AA-A-GATAAGAA-G----AG
* * * * * * * * * *
1536849 GTGCTAATATGCTAATTCAAGGCTAGTGATATTAGGCTTACAGTTGACAA-AG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* * * * * * * *
1536901 GTGCCAATGTACTAATTTAAGGCCAGCAATATTTGACTTGAAGATAAGAAGAATGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGAT---AAGAA-G----AG
* * * * *
1536962 GTGCCAATATGCTGATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGAGAAGAATGATAA
1 GTGCC-A-ATG-T---GCTGATTCAAGGCTAGCGACATTAGACTT-AA-A-GATAAGAA-G----
1537027 AG
52 AG
* * * * * * * * *
1537029 ATGCTAATATGTTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGACAA-AG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* * *
1537081 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTTGACTTAAAGATGAGAAGAATGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGAT---AAGAA-G----AG
* * * * * *
1537142 GTGCCAATATGTTGATTCAAGGCTAGCGACATTGGGCTTAACGAT-ACAA-AG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* * * * * *
1537193 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGATAA-AT
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* * * * * * * * * * *
1537245 GCGCCATTATGCTGACTCAAGGCCAGTGATATTGGA-TTTAAGA-AAGAAAAA
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
* * * *
1537296 G-GCATCAATGTGCTGATTAAAGACTAACGACATTGGACTTAAAGAT
1 GTGC--CAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGAT
1537342 GATAAGGATA
Statistics
Matches: 503, Mismatches: 112, Indels: 102
0.70 0.16 0.14
Matches are distributed among these distances:
50 5 0.01
51 51 0.10
52 202 0.40
53 8 0.02
54 1 0.00
55 16 0.03
56 1 0.00
57 3 0.01
58 12 0.02
59 2 0.00
60 4 0.01
61 146 0.29
62 1 0.00
63 3 0.01
64 2 0.00
65 2 0.00
66 1 0.00
67 39 0.08
68 1 0.00
69 1 0.00
70 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (53 bp):
GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTAAAGATAAGAAGAG
Found at i:1536756 original size:61 final size:60
Alignment explanation
Indices: 1536675--1537239 Score: 363
Period size: 61 Copynumber: 9.8 Consensus size: 60
1536665 GATAAGAAGA
* * *
1536675 GTGCCAATGTGCTGATTCAAGGCGAGCGACATTGGACTTAAAGATGCAAAGAATGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAAGAATGATAAAG
* *
1536736 GTGCCAATATGTTGATTCAAGGCCAGCGATATTAGG-CTTAAAGATG--ACAA--AT----
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGAAAGAATGATAAAG
* * * * *
1536788 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTTGACTTGAAGATGAGAAGAATGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAGAATGATAAAG
* * * * * *
1536849 GTGCTAATATGCTAATTCAAGGCTAGTGATATTAGG-CTTACAG-T-------TGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGAAAGAATGATAAAG
* * * * * * * *
1536901 GTGCCAATGTACTAATTTAAGGCCAGCAATATTTGACTTGAAGATAAGAAGAATGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAGAATGATAAAG
* *
1536962 GTGCCAATATGCTGATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGAGAAGAATGATAA
1 GTGCC-A-A---T-ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAGAATGATAA
1537027 AG
59 AG
* * * * * *
1537029 ATGCTAATATGTTGATTCAAGGCTAGCGATATTGGGC-T-----T-AAAG-ATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAGAATGATAAAG
* * * *
1537081 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTTGACTTAAAGATGAGAAGAATGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAGAATGATAAAG
* * * * * *
1537142 GTGCCAATATGTTGATTCAAGGCTAGCGACATTGGGC-T-----T-AACG-AT-ACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAGAATGATAAAG
* * *
1537193 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA
1537240 TAAATGCGCC
Statistics
Matches: 392, Mismatches: 68, Indels: 91
0.71 0.12 0.17
Matches are distributed among these distances:
51 39 0.10
52 115 0.29
53 7 0.02
54 2 0.01
55 5 0.01
56 2 0.01
57 3 0.01
58 5 0.01
59 1 0.00
60 6 0.02
61 150 0.38
62 5 0.01
63 1 0.00
65 1 0.00
66 2 0.01
67 48 0.12
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (60 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAGAATGATAAAG
Found at i:1536826 original size:113 final size:112
Alignment explanation
Indices: 1536636--1537014 Score: 429
Period size: 113 Copynumber: 3.3 Consensus size: 112
1536626 CCAGTGTGCA
* * * * * *
1536636 GATTCAAGGCCTA-CGACACTAGACTTAAAGATAAGAAGAGTGCCAATGTGCTGATTCAAGGCGA
1 GATTCAAGGCC-AGCGATATTAGGCTTAAAGATGACAA-AGTGCCAATGTGCTGATTCAAGGCCA
* *
1536700 GCGACATTGGACTTAAAGATGCA-AAGAATGATAAAGGTGCCAATATGTT
64 GCGACATTTGACTTGAAGATG-AGAAGAATGATAAAGGTGCCAATATGTT
*
1536749 GATTCAAGGCCAGCGATATTAGGCTTAAAGATGACAAATGTGCCAATGTGCTGATTCAAGGCTAG
1 GATTCAAGGCCAGCGATATTAGGCTTAAAGATGACAAA-GTGCCAATGTGCTGATTCAAGGCCAG
* *
1536814 CGACATTTGACTTGAAGATGAGAAGAATGATAAAGGTGCTAATATGCT
65 CGACATTTGACTTGAAGATGAGAAGAATGATAAAGGTGCCAATATGTT
* * * * * * * *
1536862 AATTCAAGGCTAGTGATATTAGGCTTACAGTTGACAAAGGTGCCAATGTACTAATTTAAGGCCAG
1 GATTCAAGGCCAGCGATATTAGGCTTAAAGATGACAAA-GTGCCAATGTGCTGATTCAAGGCCAG
* * *
1536927 CAATATTTGACTTGAAGATAAGAAGAATGATAAAGGTGCCAATATGCTGATGCT
65 CGACATTTGACTTGAAGATGAGAAGAATGATAAAGGTGCCAATA---TG-T--T
* *
1536981 GATTCAAGGCCAGCGATATTGGGCTTGAAGATGA
1 GATTCAAGGCCAGCGATATTAGGCTTAAAGATGA
1537015 GAAGAATGAT
Statistics
Matches: 225, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
112 3 0.01
113 192 0.85
116 2 0.01
119 28 0.12
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (112 bp):
GATTCAAGGCCAGCGATATTAGGCTTAAAGATGACAAAGTGCCAATGTGCTGATTCAAGGCCAGC
GACATTTGACTTGAAGATGAGAAGAATGATAAAGGTGCCAATATGTT
Found at i:1537015 original size:180 final size:180
Alignment explanation
Indices: 1536797--1537157 Score: 542
Period size: 180 Copynumber: 2.0 Consensus size: 180
1536787 TGTGCCAATG
* * *
1536797 TGCTGATTCAAGGCTAGCGACATTTGACTTGAAGATGAGAAGAATGATAAAGGTGCTAATATGCT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAGATGCTAATATGCT
* * * *
1536862 AATTCAAGGCTAGTGATATTAGGCTTACAGTTGACAAAGGTGCCAATGTACTAATTTAAGGCCAG
66 AATTCAAGGCTAGCGATATTAGGCTTAAAGATGACAAAGGTGCCAATGTACTAATTCAAGGCCAG
* *
1536927 CAATATTTGACTTGAAGATAAGAAGAATGATAAAGGTGCCAATATGCTGA
131 CAACATTTGACTTAAAGATAAGAAGAATGATAAAGGTGCCAATATGCTGA
* * *
1536977 TGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGAGAAGAATGATAAAGATGCTAATATGTT
1 TGCTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAGATGCTAATATGCT
* * * *
1537042 GATTCAAGGCTAGCGATATTGGGCTTAAAGATGACAAAGGTGCCAATGTGCTGATTCAAGGCCAG
66 AATTCAAGGCTAGCGATATTAGGCTTAAAGATGACAAAGGTGCCAATGTACTAATTCAAGGCCAG
** * *
1537107 TGACATTTGACTTAAAGATGAGAAGAATGATAAAGGTGCCAATATGTTGA
131 CAACATTTGACTTAAAGATAAGAAGAATGATAAAGGTGCCAATATGCTGA
1537157 T
1 T
1537158 TCAAGGCTAG
Statistics
Matches: 161, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
180 161 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (180 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAGAATGATAAAGATGCTAATATGCT
AATTCAAGGCTAGCGATATTAGGCTTAAAGATGACAAAGGTGCCAATGTACTAATTCAAGGCCAG
CAACATTTGACTTAAAGATAAGAAGAATGATAAAGGTGCCAATATGCTGA
Found at i:1537162 original size:113 final size:112
Alignment explanation
Indices: 1536977--1537239 Score: 436
Period size: 113 Copynumber: 2.3 Consensus size: 112
1536967 AATATGCTGA
* * * * *
1536977 TGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGAGAAGAATGATAAAGATGCTAATATGTT
1 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAATATGTT
*
1537042 GATTCAAGGCTAGCGATATTGGGCTTAAAGATGACAAAGGTGCCAATG
66 GATTCAAGGCTAGCGACATTGGGCTTAAAGAT-ACAAAGGTGCCAATG
* *
1537090 TGCTGATTCAAGGCCAGTGACATTTGACTTAAAGATGAGAAGAATGATAAAGGTGCCAATATGTT
1 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAATATGTT
*
1537155 GATTCAAGGCTAGCGACATTGGGCTTAACGATACAAAGGTGCCAATG
66 GATTCAAGGCTAGCGACATTGGGCTTAAAGATACAAAGGTGCCAATG
1537202 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGA
1 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGA
1537240 TAAATGCGCC
Statistics
Matches: 140, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
112 52 0.37
113 88 0.63
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.25
Consensus pattern (112 bp):
TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAGAAGAATGATAAAGATGCCAATATGTT
GATTCAAGGCTAGCGACATTGGGCTTAAAGATACAAAGGTGCCAATG
Found at i:1537593 original size:32 final size:32
Alignment explanation
Indices: 1537510--1538272 Score: 744
Period size: 32 Copynumber: 23.8 Consensus size: 32
1537500 TTTGGCTTAA
* * *
1537510 AAGGGTTGCCACTGACTTGTGTAGGCTTTAGAA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAG
** ***
1537543 AAGGGTTGCCACTAACTTGTGTGGGCTCAAAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1537575 AAGGGTTACCACCGACTTGTGTGGGCTTTAAAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAG
* * * *
1537608 AAAGGCTGCCACCGACTTGTGTAGG-TTTTAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
1537639 AAGGGTTGCCATCGACTTGTTTGGGTTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
1537671 AAGGGTTACCATCGACTTATGTGGGCTTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGC-TTTGAG
* *
1537704 AAGAGTTGCCACCGACTTATGTGGGCTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
*
1537736 AAGGGTTGCCATCGACTTGTGTGGGCTTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGC-TTTGAG
*
1537769 AAGGGTTGCCACCGACTTCTGTGGGCTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1537801 AAGGGTTGCCACCTACTTGTGTGGGCTTCGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * * *
1537833 AAGGATTGCCACCGACTTATCTAGGCTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
1537865 AAGGGTTGCCACAGACTTGTGTGAGCTTTTGGG
1 AAGGGTTGCCACCGACTTGTGTGGGC-TTTGAG
* * * *
1537898 AAGGGTTGCCATCAACTTATGTGGGCTTCGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
1537930 AAGGGTTACCACCGACTTGTGTGAGCTTCGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * * *
1537962 AAGGATTGCTACCGACTTGTGTAGGC-TTCAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1537993 AAGGGGTGCCATCGACTTGTGTGGGCTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *** * * **
1538025 AAAGGTTGTCAATAACATGTATGTGTTTTTGAG
1 AAGGGTTGCCACCGACTTGTGTG-GGCTTTGAG
* * * * * *
1538058 AAGGGCTACCACCTACTTTTGTGAGCTTTAAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1538090 AAGGGTTACCACCGACTTATGTGGGCTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1538122 AAGGGTTGCCACCAACTTGTGTAGGCTTT-AG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
1538153 AAGGGTTGTCACCAACTTGTATGGGCTTT-AG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
1538184 AAGGGTTGTCACCGACTTGTGTGGACTTT-AG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * * * *
1538215 AAGGGTTACCACCAACTTGTGTGGGTTTTAAAA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAG
*
1538248 AAAGGTTGCCACCGACTTGTGTGGG
1 AAGGGTTGCCACCGACTTGTGTGGG
1538273 ATTAAATCCA
Statistics
Matches: 598, Mismatches: 123, Indels: 18
0.81 0.17 0.02
Matches are distributed among these distances:
31 128 0.21
32 293 0.49
33 177 0.30
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
Found at i:1537618 original size:65 final size:65
Alignment explanation
Indices: 1537510--1538272 Score: 653
Period size: 65 Copynumber: 11.9 Consensus size: 65
1537500 TTTGGCTTAA
* * * * ***
1537510 AAGGGTTGCCACTGACTTGTGTAGGCTTTAGAAAAGGGTTGCCACTAACTTGTGTGGGC-TCAAA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGA
1537574 G
65 G
* * * * * *
1537575 AAGGGTTACCACCGACTTGTGTGGGCTTTAAAGAAAGGCTGCCACCGACTTGTGTAGG-TTTT-A
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGA
1537638 G
65 G
* * * * *
1537639 AAGGGTTGCCATCGACTTGTTTGGGTTTTGAGAAGGGTTACCA-TCGACTTATGTGGGCTTTTGA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACT-GACTTGTGTGGGCTTTTGA
1537703 G
65 G
* *
1537704 AAGAGTTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCA-TCGACTTGTGTGGGCTTTTGA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACT-GACTTGTGTGGGCTTTTGA
1537768 G
65 G
* *
1537769 AAGGGTTGCCACCGACTTCTGTGGGCTTTGAGAAGGGTTGCCACCT-ACTTGTGTGGGC-TTCGA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCA-CTGACTTGTGTGGGCTTTTGA
1537832 G
65 G
* * * * * * *
1537833 AAGGATTGCCACCGACTTATCTAGGCTTTGAGAAGGGTTGCCACAGACTTGTGTGAGCTTTTGGG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAG
* * * * * * * *
1537898 AAGGGTTGCCATCAACTTATGTGGGCTTCGAGAAGGGTTACCACCGACTTGTGTGAGC-TTCGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAG
* * * * *
1537962 AAGGATTGCTACCGACTTGTGTAGGC-TTCAGAAGGGGTGCCA-TCGACTTGTGTGGGC-TTTGA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACT-GACTTGTGTGGGCTTTTGA
1538024 G
65 G
* * *** * * ** * * * * *
1538025 AAAGGTTGTCAATAACATGTATGTGTTTTTGAGAAGGGCTACCACCT-ACTTTTGTGAGC-TTTA
1 AAGGGTTGCCACCGACTTGTGTG-GGCTTTGAGAAGGGTTGCCA-CTGACTTGTGTGGGCTTTTG
1538088 AG
64 AG
* * ** *
1538090 AAGGGTTACCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCAACTTGTGTAGGC-TTT-AG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAG
* * * * * *
1538153 AAGGGTTGTCACCAACTTGTATGGGCTTT-AGAAGGGTTGTCACCGACTTGTGTGGAC-TTT-AG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAG
* * * * * * *
1538215 AAGGGTTACCACCAACTTGTGTGGGTTTTAAAAAAAGGTTGCCACCGACTTGTGTGGG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACTGACTTGTGTGGG
1538273 ATTAAATCCA
Statistics
Matches: 566, Mismatches: 116, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
62 54 0.10
63 90 0.16
64 162 0.29
65 258 0.46
67 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (65 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAG
Found at i:1537875 original size:129 final size:129
Alignment explanation
Indices: 1537510--1538272 Score: 727
Period size: 129 Copynumber: 5.9 Consensus size: 129
1537500 TTTGGCTTAA
** * * * ** *
1537510 AAGGGTTGCCACTGACTTGTGTAGGCTTTAGAAAAGGGTTGCCACTAACTTGTGTGGGC-TCAAA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTT-GAGAAGGGTTACCACCGACTTGTGTGGGCTTC-GA
* * * * * * *
1537574 GAAGGGTTACCACCGACTTGTGTGGGCTTTAAAGAAAGGCTGCCACCGACTTGTGTAGG-TTTT-
64 GAAGGATTGCCACCGACTTATGTGGGCTTT-GAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTG
1537637 AG
128 AG
* * * * * * *
1537639 AAGGGTTGCCATCGACTTGTTTGGGTTTTGAGAAGGGTTACCATCGACTTATGTGGGCTTTTGAG
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGC-TTCGAG
*
1537704 AA-GAGTTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCATCGACTTGTGTGGGCTTTTGA
65 AAGGA-TTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTGA
1537768 G
129 G
* * * *
1537769 AAGGGTTGCCACCGACTTCTGTGGGCTTTGAGAAGGGTTGCCACCTACTTGTGTGGGCTTCGAGA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGCTTCGAGA
* * * * *
1537834 AGGATTGCCACCGACTTATCTAGGCTTTGAGAAGGGTTGCCACAGACTTGTGTGAGCTTTTGGG
66 AGGATTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTGAG
* * * *
1537898 AAGGGTTGCCATCAACTTATGTGGGCTTCGAGAAGGGTTACCACCGACTTGTGTGAGCTTCGAGA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGCTTCGAGA
* * * * * *
1537963 AGGATTGCTACCGACTTGTGTAGGC-TTCAGAAGGGGTGCCATCGACTTGTGTGGGC-TTTGAG
66 AGGATTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTGAG
* * ** * * ** * * * * **
1538025 AAAGGTTGTCAATAACATGTATGTGTTTTTGAGAAGGGCTACCACCTACTTTTGTGAGCTTTAAG
1 AAGGGTTGCCACCAACTTGTGTG-GGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGCTTCGAG
* * * *
1538090 AAGGGTTACCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCAACTTGTGTAGGC-TTT-AG
65 AAGGATTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTGAG
* * ** * *
1538153 AAGGGTTGTCACCAACTTGTATGGGCTTT-AGAAGGGTTGTCACCGACTTGTGTGGACTT-TAGA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGCTTCGAGA
* * * * * * * *
1538216 AGGGTTACCACCAACTTGTGTGGGTTTTAAAAAAAGGTTGCCACCGACTTGTGTGGG
66 AGGATTGCCACCGACTTATGTGGGCTTT-GAGAAGGGTTGCCACCGACTTGTGTGGG
1538273 ATTAAATCCA
Statistics
Matches: 526, Mismatches: 99, Indels: 21
0.81 0.15 0.03
Matches are distributed among these distances:
125 28 0.05
126 46 0.09
127 25 0.05
128 148 0.28
129 224 0.43
130 55 0.10
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (129 bp):
AAGGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTACCACCGACTTGTGTGGGCTTCGAGA
AGGATTGCCACCGACTTATGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTTGAG
Found at i:1542202 original size:41 final size:41
Alignment explanation
Indices: 1542114--1542221 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
1542104 TTCTTCTCTC
** * * *
1542114 TTCCTCCTATCATCCCTCCGCTCTTTATTATCTCTCCTATCT
1 TTCCTCCTATCATCCCTCCTATC-TCACTATCTCTCATATCT
* *
1542156 CTCCTCTTATCATCCCTCCTATCTCACTATCTCTCATATCT
1 TTCCTCCTATCATCCCTCCTATCTCACTATCTCTCATATCT
*
1542197 TTCCTCCTACCATCCCTCCTATCTC
1 TTCCTCCTATCATCCCTCCTATCTC
1542222 TTCTTTCTCT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 37 0.66
42 19 0.34
ACGTcount: A:0.14, C:0.44, G:0.01, T:0.42
Consensus pattern (41 bp):
TTCCTCCTATCATCCCTCCTATCTCACTATCTCTCATATCT
Found at i:1546005 original size:14 final size:14
Alignment explanation
Indices: 1545981--1546013 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1545971 TTATATATTT
1545981 TAAATAATG-AAAA
1 TAAATAATGAAAAA
1545994 TAAATCAATGAAAAA
1 TAAAT-AATGAAAAA
1546009 TAAAT
1 TAAAT
1546014 TAATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 4 0.22
15 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
TAAATAATGAAAAA
Found at i:1546527 original size:19 final size:20
Alignment explanation
Indices: 1546505--1546542 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1546495 ATAGTTCAAA
1546505 TTAATTTTT-TAAAATCCAT
1 TTAATTTTTATAAAATCCAT
1546524 TTAATTTTTATAAAATCCA
1 TTAATTTTTATAAAATCCA
1546543 AAGCTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTTTTATAAAATCCAT
Found at i:1546532 original size:20 final size:19
Alignment explanation
Indices: 1546505--1546542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1546495 ATAGTTCAAA
*
1546505 TTAATTTTTTAAAATCCAT
1 TTAATTTTATAAAATCCAT
1546524 TTAATTTTTATAAAATCCA
1 TTAA-TTTTATAAAATCCA
1546543 AAGCTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTTTATAAAATCCAT
Found at i:1546728 original size:18 final size:16
Alignment explanation
Indices: 1546672--1546733 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
1546662 TATCCAAATC
1546672 TTTTTAATTTTTCTTTAT
1 TTTTTAA-TTTT-TTTAT
* *
1546690 TTTATCATTTTTGTTAAT
1 TTTTTAATTTTT-TT-AT
1546708 TTTTTAATTATTTTTAT
1 TTTTTAATT-TTTTTAT
*
1546725 TTTTAAATT
1 TTTTTAATT
1546734 CTTTAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 16 0.44
18 16 0.44
19 3 0.08
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTAATTTTTTTAT
Found at i:1550179 original size:11 final size:11
Alignment explanation
Indices: 1550165--1550199 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1550155 ATTCAATTTC
1550165 CTTCATTTGAA
1 CTTCATTTGAA
1550176 CTTC--TTGAA
1 CTTCATTTGAA
1550185 CTTCATTTGAA
1 CTTCATTTGAA
1550196 CTTC
1 CTTC
1550200 TTGAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (11 bp):
CTTCATTTGAA
Found at i:1550183 original size:9 final size:9
Alignment explanation
Indices: 1550171--1550204 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
1550161 TTTCCTTCAT
1550171 TTGAACTTC
1 TTGAACTTC
1550180 TTGAACTTC
1 TTGAACTTC
1550189 ATTTGAACTTC
1 --TTGAACTTC
1550200 TTGAA
1 TTGAA
1550205 TTTATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGAACTTC
Found at i:1550190 original size:20 final size:20
Alignment explanation
Indices: 1550165--1550204 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1550155 ATTCAATTTC
1550165 CTTCATTTGAACTTCTTGAA
1 CTTCATTTGAACTTCTTGAA
1550185 CTTCATTTGAACTTCTTGAA
1 CTTCATTTGAACTTCTTGAA
1550205 TTTATATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
CTTCATTTGAACTTCTTGAA
Found at i:1552109 original size:98 final size:98
Alignment explanation
Indices: 1551928--1552122 Score: 293
Period size: 98 Copynumber: 2.0 Consensus size: 98
1551918 GCATTTCTGG
* * *
1551928 ACCCAAAAGTTTCAAACAATTTCAGAATTTGGTGCCTTTACGGAATTCATAATCCTCCTCTTTTA
1 ACCCAAAAGCTTCAAACAATTTCAGAATTTGGTGCCTTTACAGAATTCATAATCCTCCTATTTTA
*
1551993 TAAAGTTTTATTGGTCAAAATACCAATGGGTTT
66 TAAAGTTTTATAGGTCAAAATACCAATGGGTTT
* * *
1552026 ACCCAAAAGCTT-AAACATTTTCAGAATTTGGTGCCTTTACAGAGTTCATAATTCCTCGTATTTT
1 ACCCAAAAGCTTCAAACAATTTCAGAATTTGGTGCCTTTACAGAATTCATAA-TCCTCCTATTTT
* *
1552090 ATAAAGTTTTGTAGGTCAAAATATCAATGGGTT
65 ATAAAGTTTTATAGGTCAAAATACCAATGGGTT
1552123 ATTGGATTCC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 36 0.41
98 51 0.59
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (98 bp):
ACCCAAAAGCTTCAAACAATTTCAGAATTTGGTGCCTTTACAGAATTCATAATCCTCCTATTTTA
TAAAGTTTTATAGGTCAAAATACCAATGGGTTT
Found at i:1555626 original size:3 final size:3
Alignment explanation
Indices: 1555618--1555649 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1555608 TCAAAGGAAA
*
1555618 AAT AAT AAT AAT AAT AAT AAG AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1555650 GAACTCATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1555650 original size:12 final size:12
Alignment explanation
Indices: 1555618--1555652 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1555608 TCAAAGGAAA
*
1555618 AATAATAATAAT
1 AATAATAAGAAT
1555630 AATAATAAGAAT
1 AATAATAAGAAT
1555642 AATAATAAGAA
1 AATAATAAGAA
1555653 CTCATAGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (12 bp):
AATAATAAGAAT
Found at i:1556193 original size:23 final size:23
Alignment explanation
Indices: 1556167--1556218 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1556157 TTAGATGATG
* *
1556167 TAAATTTCAA-ATTATTTTTATTT
1 TAAATTT-AATATTATTTTAAATT
1556190 TAAATTTAATATTATTTTAAATT
1 TAAATTTAATATTATTTTAAATT
1556213 TAAATT
1 TAAATT
1556219 AATTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAATTTAATATTATTTTAAATT
Found at i:1556206 original size:17 final size:17
Alignment explanation
Indices: 1556184--1556232 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1556174 CAAATTATTT
1556184 TTATTTTAAATTTAATA
1 TTATTTTAAATTTAATA
1556201 TTATTTTAAATTTAA-A
1 TTATTTTAAATTTAATA
*
1556217 TTA-ATTAAATTTAATA
1 TTATTTTAAATTTAATA
1556233 CTCTCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 10 0.33
16 5 0.17
17 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTTAAATTTAATA
Found at i:1556226 original size:15 final size:15
Alignment explanation
Indices: 1556189--1556260 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
1556179 TATTTTTATT
*
1556189 TTAAATTTAATATTATT
1 TTAAATTTAA-ATTA-A
1556206 TTAAATTTAAATTAA
1 TTAAATTTAAATTAA
*
1556221 TTAAATTT-AA-TAC
1 TTAAATTTAAATTAA
*
1556234 TCTCAAATTTAAAATAA
1 T-T-AAATTTAAATTAA
*
1556251 TAAAATTTAA
1 TTAAATTTAA
1556261 TACTTTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 22 0.47
16 6 0.13
17 13 0.28
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:1556244 original size:30 final size:30
Alignment explanation
Indices: 1556208--1556264 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1556198 ATATTATTTT
* *
1556208 AAATTTAAATTAATTAAATTTAATACTCTC
1 AAATTTAAAATAATAAAATTTAATACTCTC
1556238 AAATTTAAAATAATAAAATTTAATACT
1 AAATTTAAAATAATAAAATTTAATACT
1556265 TTAATTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (30 bp):
AAATTTAAAATAATAAAATTTAATACTCTC
Found at i:1556384 original size:19 final size:20
Alignment explanation
Indices: 1556347--1556401 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
1556337 TTTATTTTAA
*
1556347 ATTTAAAATTCAGATTTAAATT
1 ATTT-AAATTCA-AATTAAATT
1556369 ATTTAAATT-AAATTAAATT
1 ATTTAAATTCAAATTAAATT
*
1556388 TTTTAAATTCAAAT
1 ATTTAAATTCAAAT
1556402 GTTGACAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.53
20 5 0.17
21 5 0.17
22 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTTAAATTCAAATTAAATT
Found at i:1556672 original size:15 final size:15
Alignment explanation
Indices: 1556654--1556702 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1556644 TATTATTTAT
1556654 ATTAAATTTAAATAA
1 ATTAAATTTAAATAA
* *
1556669 ATTAATTTTAAATAT
1 ATTAAATTTAAATAA
1556684 ATTAATTATATTAAATAA
1 ATTAA--AT-TTAAATAA
1556702 A
1 A
1556703 ATATATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 18 0.67
17 1 0.04
18 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATTTAAATAA
Found at i:1556725 original size:39 final size:40
Alignment explanation
Indices: 1556633--1556742 Score: 93
Period size: 39 Copynumber: 2.8 Consensus size: 40
1556623 GTATAATATA
* *
1556633 AATTATAATAATATTATTTATATTAAATTTAAATAAATTAAT
1 AATTAT-AT-ATATTAATTATATTAAATTAAAATAAATTAAT
* * *
1556675 -TTTAAATATATTAATTATATTAAA-TAAAATATA-TAAT
1 AATTATATATATTAATTATATTAAATTAAAATAAATTAAT
* *
1556712 AATTATATCATATTTA-TATTTTAAAATTAAA
1 AATTATAT-ATATTAATTATATT-AAATTAAA
1556743 TATTTTTAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
37 4 0.07
38 17 0.31
39 25 0.45
40 6 0.11
41 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
AATTATATATATTAATTATATTAAATTAAAATAAATTAAT
Found at i:1562491 original size:21 final size:20
Alignment explanation
Indices: 1562453--1562491 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1562443 TTAATTTAAA
**
1562453 TAAAAATAATTTTTATTATT
1 TAAAAATAATTTAAATTATT
1562473 TAAATAATAATTTAAATTA
1 TAAA-AATAATTTAAATTA
1562492 AATCAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAAATAATTTAAATTATT
Found at i:1575201 original size:2 final size:2
Alignment explanation
Indices: 1575194--1575236 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1575184 AATGTATTTG
*
1575194 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1575236 A
1 A
1575237 CAAAACAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1577879 original size:21 final size:23
Alignment explanation
Indices: 1577833--1577905 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 23
1577823 ATAATTTCAT
*
1577833 ATATAATTAATATTTAGTAA-ATTA
1 ATATAATTAA-ATTTAATAATA-TA
1577857 AT-T-ATTAAATTTAATAATATAA
1 ATATAATTAAATTTAATAATAT-A
1577879 TTATATAATTAAATTTAATAATATA
1 --ATATAATTAAATTTAATAATATA
1577904 AT
1 AT
1577906 CATATTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
21 9 0.21
22 7 0.17
23 3 0.07
24 4 0.10
25 2 0.05
26 17 0.40
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
ATATAATTAAATTTAATAATATA
Found at i:1577880 original size:13 final size:13
Alignment explanation
Indices: 1577864--1577905 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1577854 TTAATTATTA
1577864 AATTTAATAATAT
1 AATTTAATAATAT
1577877 AA-TTATATAAT-T
1 AATTTA-ATAATAT
1577889 AAATTTAATAATAT
1 -AATTTAATAATAT
1577903 AAT
1 AAT
1577906 CATATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTAATAATAT
Found at i:1577891 original size:26 final size:26
Alignment explanation
Indices: 1577852--1577910 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1577842 ATATTTAGTA
*
1577852 AATTA-ATTATTAAATTTAATAATAT
1 AATTATATAATTAAATTTAATAATAT
1577877 AATTATATAATTAAATTTAATAATAT
1 AATTATATAATTAAATTTAATAATAT
*
1577903 AATCATAT
1 AATTATAT
1577911 TTTTATGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTATATAATTAAATTTAATAATAT
Found at i:1579079 original size:2 final size:2
Alignment explanation
Indices: 1579072--1579097 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1579062 TATTATGTAA
1579072 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1579098 GTGTGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1579575 original size:23 final size:23
Alignment explanation
Indices: 1579549--1579592 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1579539 TTCTAAACTA
1579549 TTAAAAAAATTTTATAATTTTGC
1 TTAAAAAAATTTTATAATTTTGC
** *
1579572 TTAAGTAAATTTTATATTTTT
1 TTAAAAAAATTTTATAATTTT
1579593 ATTATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TTAAAAAAATTTTATAATTTTGC
Found at i:1579696 original size:30 final size:30
Alignment explanation
Indices: 1579662--1579763 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
1579652 AAAAGATTAA
* *
1579662 TTTAAATATTTATTTAGGTATAAATTAAAG
1 TTTAAAGATTTATTTAGGTATAAAATAAAG
* *
1579692 TTTAAAGGTTTATTTA-GT-TAAAAAAAAG
1 TTTAAAGATTTATTTAGGTATAAAATAAAG
1579720 -TTAAAGATTTATTTAACGG-A-AAAATAAA-
1 TTTAAAGATTTATTT-A-GGTATAAAATAAAG
*
1579748 TGTTAAATATTTATTT
1 T-TTAAAGATTTATTT
1579764 GAGAGTAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
27 13 0.22
28 9 0.15
29 9 0.15
30 28 0.47
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (30 bp):
TTTAAAGATTTATTTAGGTATAAAATAAAG
Found at i:1579863 original size:19 final size:19
Alignment explanation
Indices: 1579823--1579863 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1579813 AAGATTTTTT
** *
1579823 TATTATTTTATTTTGTTTA
1 TATTATTTTATTTCCTTAA
1579842 TATTATTTTATTTCCTTAA
1 TATTATTTTATTTCCTTAA
1579861 TAT
1 TAT
1579864 CTTTCTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTATTTTATTTCCTTAA
Found at i:1580271 original size:20 final size:21
Alignment explanation
Indices: 1580246--1580292 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1580236 CTACAAAATT
* *
1580246 TTAAAAAATTAATAATTA-TC
1 TTAAAAAATAAAAAATTATTC
1580266 TTAAAAAATAAAAAATTATTC
1 TTAAAAAATAAAAAATTATTC
1580287 TTAAAA
1 TTAAAA
1580293 GTTTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAAATAAAAAATTATTC
Found at i:1587956 original size:6 final size:6
Alignment explanation
Indices: 1587947--1587972 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1587937 GTTGTAAGTT
1587947 GAAAAG GAAAAG GAAAAG GAAAAG GA
1 GAAAAG GAAAAG GAAAAG GAAAAG GA
1587973 TAAAAGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:1588108 original size:14 final size:16
Alignment explanation
Indices: 1588077--1588107 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1588067 TGATATTTTT
1588077 TTTAAAAAATTATATA
1 TTTAAAAAATTATATA
1588093 TTTAAAAAATTATAT
1 TTTAAAAAATTATAT
1588108 TATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAAAATTATATA
Found at i:1588403 original size:2 final size:2
Alignment explanation
Indices: 1588398--1588428 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1588388 AAAAAAATGA
1588398 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1588429 TCATGTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1588620 original size:18 final size:19
Alignment explanation
Indices: 1588570--1588621 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
1588560 TTTAAGTGAT
*
1588570 TTTTTAATGATAAAAATTA
1 TTTTTAATGATAAAAATAA
* *
1588589 GTATT-ATGAT-AAAA-AA
1 TTTTTAATGATAAAAATAA
1588605 TTTTTAATGATAAAAAT
1 TTTTTAATGATAAAAAT
1588622 TGAAGTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
16 4 0.16
17 9 0.36
18 9 0.36
19 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TTTTTAATGATAAAAATAA
Found at i:1588903 original size:29 final size:27
Alignment explanation
Indices: 1588847--1588913 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1588837 ACGTAATTAA
* *
1588847 TAAAGATTTATTATATTTTAAAAATAT
1 TAAATATTTATTATATTATAAAAATAT
** *
1588874 TTTATATTTATTTTATATATAAAAATTAT
1 TAAATATTTATTATAT-TATAAAAA-TAT
1588903 TAAATATTTAT
1 TAAATATTTAT
1588914 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
27 12 0.39
28 7 0.23
29 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TAAATATTTATTATATTATAAAAATAT
Found at i:1588928 original size:15 final size:17
Alignment explanation
Indices: 1588897--1588929 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1588887 TATATATAAA
1588897 AATTATTAAATATTTAT
1 AATTATTAAATATTTAT
1588914 AATT-TTAAA-ATTTAT
1 AATTATTAAATATTTAT
1588929 A
1 A
1588930 TTTACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTAAATATTTAT
Found at i:1589900 original size:11 final size:11
Alignment explanation
Indices: 1589884--1589929 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
1589874 AAAGTTTTAC
1589884 ATATTTAATAA
1 ATATTTAATAA
1589895 ATATTTAATATTA
1 ATATTTAATA--A
1589908 A-ATTTAATAA
1 ATATTTAATAA
1589918 ATATTTAATAA
1 ATATTTAATAA
1589929 A
1 A
1589930 AATATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.06
11 20 0.62
12 8 0.25
13 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTTAATAA
Found at i:1607371 original size:79 final size:78
Alignment explanation
Indices: 1607116--1607499 Score: 342
Period size: 79 Copynumber: 4.9 Consensus size: 78
1607106 TGGGGATAAC
* * * * * * *
1607116 AACGGGGCTAGAGTATCCTCGATTATGGAAAATCGATGTTCT-GGAATAAAATCGGGGTTGAAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAACT-GGGGTTGGAGT
*
1607180 ATCTCCTCGAAAAT
65 ATCCCCTCGAAAAT
** * * * * *
1607194 AATAGGGTTGGAGTATCCCTGATTATAGAAAATCGAGGTTTT-GAAAATAAAATCGGGGTTAGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTAG-AAATAAACT-GGGGTTGGAG
*** *
1607258 TATCATTTTGAAAAT
64 TATCCCCTCGAAAAT
* * * *
1607273 AACAGAGTTGGAGTATCCCCGATTATGGAAAATCGATGCTTTAGAAATAAGGCTGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAA-ACTGGGGTTGGAGT
*
1607338 ATCCCCGCGAAAAT
65 ATCCCCTCGAAAAT
* * * * **
1607352 AACGGGGTTGGAGTATCCCCAATTGT-GAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGGA-AAATCGATGTTTTAGAAATAAA-CTGGGGTTGGAG
* *
1607416 TATCCCTTCGGAAAT
64 TATCCCCTCGAAAAT
* * * * * *
1607431 AACGGGATTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAAT-AAACTGGGGTTGGAGT
1607496 ATCC
65 ATCC
1607500 TCGAGATGAA
Statistics
Matches: 246, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
78 36 0.15
79 204 0.83
80 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAACTGGGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:1607417 original size:158 final size:156
Alignment explanation
Indices: 1607124--1607499 Score: 382
Period size: 158 Copynumber: 2.4 Consensus size: 156
1607114 ACAACGGGGC
* * * * * *
1607124 TAGAGTATCCTCGATTATGGAAAATCGATGTTCT-GGAATAAAATCGGGGTTGAAGTATCTCCTC
1 TAGAGTATCCCCGATTATGGAAAATCGATGTT-TAGAAATAAACT-GGGGTTGGAGTATCCCCGC
* ** * * * *
1607188 GAAAATAATAGGGTTGGAGTATCCCTGATTATAGAAAATCGAGGTTTTGAAAATAAAATCGGGGT
64 GAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAAGATTTTGAAAATAAAACCAGGGT
* *
1607253 TAGAGTATCATTTTGAAAATAAC-AGAGT
129 TAGAGTATCACTTCGAAAATAACGAGA-T
* *
1607281 TGGAGTATCCCCGATTATGGAAAATCGATGCTTTAGAAATAAGGCTGGGGTTGGAGTATCCCCGC
1 TAGAGTATCCCCGATTATGGAAAATCGATG-TTTAGAAATAA-ACTGGGGTTGGAGTATCCCCGC
* * * *
1607346 GAAAATAACGGGGTTGGAGTATCCCCAATTGT-GAGAAATCAATATTTT-AGAAATAAAGCCAGG
64 GAAAATAACAGGGTTGGAGTATCCCCAATTATAGA-AAATCAAGATTTTGA-AAATAAAACCAGG
* * * *
1607409 GTTGGAGTATCCCTTCGGAAATAACGGGAT
127 GTTAGAGTATCACTTCGAAAATAACGAGAT
* * * *
1607439 TAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCC
1 TAGAGTATCCCCGATTATGGAAAATCGATG-TTTAGAAAT-AAACTGGGGTTGGAGTATCC
1607500 TCGAGATGAA
Statistics
Matches: 180, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
157 32 0.18
158 143 0.79
159 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (156 bp):
TAGAGTATCCCCGATTATGGAAAATCGATGTTTAGAAATAAACTGGGGTTGGAGTATCCCCGCGA
AAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAAGATTTTGAAAATAAAACCAGGGTTA
GAGTATCACTTCGAAAATAACGAGAT
Found at i:1610584 original size:61 final size:61
Alignment explanation
Indices: 1610498--1611013 Score: 696
Period size: 61 Copynumber: 8.4 Consensus size: 61
1610488 AATGAAATGG
* * * * *
1610498 GTCCTGCTCCTTGGGGACTAGAAGGTACCACCAACTTGTGTTGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
1610559 GTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
*
1610620 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
1610681 GTCCTGCTCCTTAAGGACCAAAAAGTGCCACCAACTTGTGTGGGCTTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TTTAAAAGGAAAAGGC
* * * * *
1610743 GTCCTGCTTTTTGAAGACTAGAAA-GTGCCACCAATTTATATGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
1610804 GTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAGCC
1 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * **
1610866 GTCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCGAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
*
1610926 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
1610987 ATCTTGCTCTTTGAGGACTGAAAGGTG
1 GTCCTGCTCTTTGAGGACTAAAAGGTG
1611014 AAAGGAGAGA
Statistics
Matches: 401, Mismatches: 48, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
60 72 0.18
61 208 0.52
62 118 0.29
63 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:1610806 original size:184 final size:184
Alignment explanation
Indices: 1610498--1611009 Score: 744
Period size: 184 Copynumber: 2.8 Consensus size: 184
1610488 AATGAAATGG
* * * *
1610498 GTCCTGCTCCTTGGGGACTAGAAGGTACCACCAACTTGTGTTGGCTTTAAAAGGAAAAGGCGTCC
1 GTCCTGCTCCTTGAGGACCAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * *
1610563 TACTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTCAAAGGAAAAGGCGTCCTGC
66 TGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTGC
* *
1610627 TCTTTGAGGACTAGAAAAGTGCCACCAACTTGTG-TGGCTTTAAAAGGAAAAGGC
130 TCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAGCC
* * *
1610681 GTCCTGCTCCTTAAGGACCAAAAAGTGCCACCAACTTGTGTGGGCTTTTAAAAGGAAAAGGCGTC
1 GTCCTGCTCCTTGAGGACCAGAAGGTGCCACCAACTTGTGTGGGC-TTTAAAAGGAAAAGGCGTC
* * * * *
1610746 CTGCTTTTTGAAGACTAGAAAGTGCCACCAATTTATATGGGCTTTAAAAGGAAAAGGCGTCTTGC
65 CTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTGC
1610811 TCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAGCC
130 TCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAGCC
* * * * * **
1610866 GTCCTACTCTTTGAGGA-CTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGCGAAGGCGTCC
1 GTCCTGCTCCTTGAGGACCAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
1610930 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCT
66 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTGCT
1610995 CTTTGAGGACT-GAAA
131 CTTTGAGGACTAGAAA
1611010 GGTGAAAGGA
Statistics
Matches: 292, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
182 4 0.01
183 124 0.42
184 129 0.44
185 35 0.12
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (184 bp):
GTCCTGCTCCTTGAGGACCAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTGCT
CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAGCC
Found at i:1611085 original size:100 final size:100
Alignment explanation
Indices: 1610924--1611121 Score: 353
Period size: 100 Copynumber: 2.0 Consensus size: 100
1610914 AAAGGCGAAG
*
1610924 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGCAT
* *
1610989 CTTGCTCTTTGAGGACTGAAAGGTGAAAGGAGAGA
66 CCTGCTCTTTGAGGACTGAAAAGTGAAAGGAGAGA
1611024 GCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGCA
1 GCGTCCTGCTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGCA
1611088 TCCTGCTCTTTGAGGACTGAAAAGTGAAAGGAGA
65 TCCTGCTCTTTGAGGACTGAAAAGTGAAAGGAGA
1611122 AAGTTTAGAT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
100 91 0.97
101 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (100 bp):
GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAGGCAT
CCTGCTCTTTGAGGACTGAAAAGTGAAAGGAGAGA
Found at i:1612102 original size:13 final size:12
Alignment explanation
Indices: 1612081--1612148 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
1612071 AAGAGGGTTC
*
1612081 TTTTCTTTTCTCT
1 TTTTTTTTTCT-T
1612094 TTTTTTTTTCTT
1 TTTTTTTTTCTT
* *
1612106 TTTTGTTTTGTT
1 TTTTTTTTTCTT
1612118 TTTTTTTTAT-TT
1 TTTTTTTT-TCTT
* * *
1612130 GTTTGTTTTGTT
1 TTTTTTTTTCTT
1612142 TTTTTTT
1 TTTTTTT
1612149 GTTTGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
11 1 0.02
12 33 0.73
13 11 0.24
ACGTcount: A:0.01, C:0.06, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:1612104 original size:18 final size:19
Alignment explanation
Indices: 1612081--1612125 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1612071 AAGAGGGTTC
1612081 TTTTCTTTTCTCTTTT-TT
1 TTTTCTTTTCTCTTTTGTT
* *
1612099 TTTTCTTTTTTGTTTTGTT
1 TTTTCTTTTCTCTTTTGTT
1612118 TTTT-TTTT
1 TTTTCTTTT
1612126 ATTTGTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTTGTT
Found at i:1612114 original size:5 final size:5
Alignment explanation
Indices: 1612106--1612152 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
1612096 TTTTTTTCTT
* *
1612106 TTTTG TTTTG TTTT- TTTTT TATTTG -TTTG TTTTG TTTTT TTTTG TTT
1 TTTTG TTTTG TTTTG TTTTG T-TTTG TTTTG TTTTG TTTTG TTTTG TTT
1612153 GTAAAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 8 0.22
5 25 0.69
6 3 0.08
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:1612119 original size:19 final size:19
Alignment explanation
Indices: 1612081--1612152 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1612071 AAGAGGGTTC
* *
1612081 TTTTCTTTTCTCTTTT-TT
1 TTTTCTTTTTTGTTTTGTT
1612099 TTTTCTTTTTTGTTTTGTT
1 TTTTCTTTTTTGTTTTGTT
*
1612118 TTTTTTTTATTTG-TTTGTT
1 TTTTCTTT-TTTGTTTTGTT
*
1612137 TTGTTTTTTTTTGTTT
1 TT-TTCTTTTTTGTTT
1612153 GTAAAAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.30
19 21 0.45
20 12 0.26
ACGTcount: A:0.01, C:0.06, G:0.08, T:0.85
Consensus pattern (19 bp):
TTTTCTTTTTTGTTTTGTT
Found at i:1612153 original size:19 final size:18
Alignment explanation
Indices: 1612096--1612154 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 18
1612086 TTTTCTCTTT
1612096 TTTTTTTCTTTTTTGTTTTG
1 TTTTTTT-TTTTTTG-TTTG
1612116 TTTTTTTTTTATTTGTTTG
1 TTTTTTTTTT-TTTGTTTG
1612135 TTTTGTTTTTTTTTGTTTG
1 TTTT-TTTTTTTTTGTTTG
1612154 T
1 T
1612155 AAAAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTTTGTTTG
Found at i:1612154 original size:23 final size:24
Alignment explanation
Indices: 1612093--1612148 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1612083 TTCTTTTCTC
*
1612093 TTTTTTTTTTCTTT-TTTGTTTTG
1 TTTTTTTTTTATTTGTTTGTTTTG
1612116 TTTTTTTTTTATTTGTTTGTTTTG
1 TTTTTTTTTTATTTGTTTGTTTTG
1612140 TTTTTTTTT
1 TTTTTTTTT
1612149 GTTTGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTATTTGTTTGTTTTG
Found at i:1619898 original size:79 final size:78
Alignment explanation
Indices: 1619803--1620180 Score: 382
Period size: 79 Copynumber: 4.8 Consensus size: 78
1619793 ACAACGGGGC
* *
1619803 TGGAGTATCCCCGATTATGGAAAATCGGTGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTATGGAAAATCGATGTT-TGAAAATAAAATCGGGGTTGGAGTATCCCCTC
**
1619868 GGAAATAACAAGGT
65 AAAAATAACAAGGT
** * * * *
1619882 TGGAGTATCCTTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTT
1 TGGAGTATCCCCGATTATGGAAAATCGATG-TTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
* *
1619947 GAAAATAACAAAGT
65 AAAAATAACAAGGT
* * *** * *
1619961 TGGAGTATCCCCGATTATGAAAAATTGATGCTTT-AGAAATAAGGCCGGGGTTTGAGTATCCCCG
1 TGGAGTATCCCCGATTATGGAAAATCGATG-TTTGA-AAATAAAATCGGGGTTGGAGTATCCCCT
*
1620025 CAAAAATAACGAGGT
64 CAAAAATAACAAGGT
* * * * * * *
1620040 TGGAGCATCCCCGATTGT-GAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAATATCCCCT
1 TGGAGTATCCCCGATTATGGA-AAATCGATGTTTGA-AAATAAAATCGGGGTTGGAGTATCCCCT
* *
1620104 CAAAAATAACGAGAT
64 CAAAAATAACAAGGT
* * * *
1620119 TGAAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCC
1 TGGAGTATCCCCGATTATGGAAAATCGATG-TTTGAAAATAAAATCGGGGTTGGAGTATCCC
1620181 TGAGATGAAA
Statistics
Matches: 247, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.02
79 236 0.96
80 6 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGGAAAATCGATGTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCA
AAAATAACAAGGT
Found at i:1622354 original size:13 final size:13
Alignment explanation
Indices: 1622336--1622365 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1622326 GCAAACCCAG
*
1622336 AATGTATCGATAC
1 AATGTATCAATAC
1622349 AATGTATCAATAC
1 AATGTATCAATAC
1622362 AATG
1 AATG
1622366 AAAAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:1622374 original size:20 final size:20
Alignment explanation
Indices: 1622349--1622403 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1622339 GTATCGATAC
*
1622349 AATGTATCAATACAATGAAA
1 AATGTATCGATACAATGAAA
*
1622369 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAA
1622389 AATGTATCGATACAA
1 AATGTATCGATACAA
1622404 ATTGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:1623495 original size:158 final size:157
Alignment explanation
Indices: 1623309--1623621 Score: 398
Period size: 158 Copynumber: 2.0 Consensus size: 157
1623299 GAAAAATTTA
*
1623309 ATATTTTGGATATAAAAAAGGAGTTAGAGTAT-CCCTAAAAAATAATAGAATT-AGAGTATCCTT
1 ATATTTTGGAAATAAAAAAGGAGTTAGAGTATCCCCTAAAAAATAATAGAATTGA-AGTATCCTT
* *
1623372 GATGATGAAAAATCGATATTTTAAAAATAAAATCGAGGCTGGAGTATCCCTTC-GAAAATAACAG
65 GATGATGAAAAATCAATATTTTAAAAATAAAAAC-AGGCTGGAGTATCCCTTCAG-AAATAACAG
*
1623436 GGTTAGAATATCCTCGATGATAAAAAATCG
128 GGTTAGAATATCCCCGATGATAAAAAATCG
* ** * **
1623466 ATATTTTGGAAATAAAAAATGGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGAAGTATCCTT
1 ATATTTTGGAAATAAAAAA-GGAGTTAGAGTATCCCCTAAAAAATAATAGAATTGAAGTATCCTT
* * ** *
1623531 GATGGTTAAAAATCAATATTTTGGAAATAAAAACAGGGTGGAGTATCCCTTCAGAAATAACAGGG
65 GATGATGAAAAATCAATATTTTAAAAATAAAAACAGGCTGGAGTATCCCTTCAGAAATAACAGGG
* * * *
1623596 TTGGAGTATCCCCGATGGTGAAAAAT
130 TTAGAATATCCCCGATGATAAAAAAT
1623622 TGATGGTGAA
Statistics
Matches: 133, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
157 18 0.14
158 61 0.46
159 53 0.40
160 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (157 bp):
ATATTTTGGAAATAAAAAAGGAGTTAGAGTATCCCCTAAAAAATAATAGAATTGAAGTATCCTTG
ATGATGAAAAATCAATATTTTAAAAATAAAAACAGGCTGGAGTATCCCTTCAGAAATAACAGGGT
TAGAATATCCCCGATGATAAAAAATCG
Found at i:1623528 original size:80 final size:80
Alignment explanation
Indices: 1623309--1623606 Score: 276
Period size: 80 Copynumber: 3.8 Consensus size: 80
1623299 GAAAAATTTA
* * ** **
1623309 ATATTTTGGATATAAAAAA-GGAGTTAGAGTAT-CCCTAAAAAATAATAGAATT-AGAGTATCCT
1 ATATTTTGGAAATAAAAAATGGGGTTAGAGTATCCCCTCGAAAATAATAGGGTTGA-AGTATCCT
*
1623371 TGATGATGAAAAATCG
65 TGATGATAAAAAATCG
* * * * *
1623387 ATATTTT--AAA-AATAAAATCGAGGCTGGAGTATCCCTTCGAAAATAACAGGGTTAGAA-TATC
1 ATATTTTGGAAATAA-AAAAT-GGGGTTAGAGTATCCCCTCGAAAATAATAGGGTT-GAAGTATC
*
1623448 CTCGATGATAAAAAATCG
63 CTTGATGATAAAAAATCG
*
1623466 ATATTTTGGAAATAAAAAATGGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGAAGTATCCTT
1 ATATTTTGGAAATAAAAAATGGGGTTAGAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCCTT
* * *
1623531 GATGGTTAAAAATCA
66 GATGATAAAAAATCG
* * * *
1623546 ATATTTTGGAAATAAAAACA--GGG-TGGAGTATCCCTTC-AGAAATAACAGGGTTGGAGTATCC
1 ATATTTTGGAAATAAAAA-ATGGGGTTAGAGTATCCCCTCGA-AAATAATAGGGTTGAAGTATCC
1623607 CCGATGGTGA
Statistics
Matches: 180, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
75 2 0.01
76 6 0.03
77 1 0.01
78 47 0.26
79 47 0.26
80 65 0.36
81 10 0.06
82 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (80 bp):
ATATTTTGGAAATAAAAAATGGGGTTAGAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCCTT
GATGATAAAAAATCG
Found at i:1623628 original size:14 final size:14
Alignment explanation
Indices: 1623609--1623635 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1623599 GAGTATCCCC
1623609 GATGGTGAAAAATT
1 GATGGTGAAAAATT
1623623 GATGGTGAAAAAT
1 GATGGTGAAAAAT
1623636 CGATATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (14 bp):
GATGGTGAAAAATT
Found at i:1623887 original size:77 final size:77
Alignment explanation
Indices: 1623675--1623918 Score: 314
Period size: 78 Copynumber: 3.1 Consensus size: 77
1623665 AATATCCCTA
* * * *
1623675 ATAGTG-AAAATCGATATTTTGGAAATAAAAATGGGATTAGAGTATCTCCTCGAAAAGAACGAGG
1 ATAGTGAAAAATCGATATTTTAGAAATAAAAACGGGGTTAGAGTATCTCCTCGAAAATAACG-GG
*
1623739 TTAGAGTATCTTG
65 TTAGAGTATCCTG
* * *
1623752 ATAGTGAAAAATCGATATTTTAGAAATAAAAACGGAGTTAGAGTATCCCCTTGAAAATAACAGGG
1 ATAGTGAAAAATCGATATTTTAGAAATAAAAACGGGGTTAGAGTATCTCCTCGAAAATAAC-GGG
1623817 TTAGAGTATCCTG
65 TTAGAGTATCCTG
* * *
1623830 ATGGTGAAAAATTGATATTTT-GAAATAAAAACGGGGTTAGAGTATCTTCTC-AGAAATAACGGG
1 ATAGTGAAAAATCGATATTTTAGAAATAAAAACGGGGTTAGAGTATCTCCTCGA-AAATAAC-GG
*
1623893 GTTGGAGTATCCTTG
64 GTTAGAGTATCC-TG
1623908 ATAGTGAAAAA
1 ATAGTGAAAAA
1623919 AATAATATTT
Statistics
Matches: 146, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
76 1 0.01
77 52 0.36
78 92 0.63
79 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.28
Consensus pattern (77 bp):
ATAGTGAAAAATCGATATTTTAGAAATAAAAACGGGGTTAGAGTATCTCCTCGAAAATAACGGGT
TAGAGTATCCTG
Found at i:1625806 original size:32 final size:32
Alignment explanation
Indices: 1625769--1625834 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1625759 AAATTGCCTG
1625769 CATGTATCGATAC-ATCGAAAAATGTATCGATA
1 CATGTATCGATACAAT-GAAAAATGTATCGATA
* * *
1625801 CATGTATTGATACAATTAAAAATGTATTGATA
1 CATGTATCGATACAATGAAAAATGTATCGATA
1625833 CA
1 CA
1625835 ATGAGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (32 bp):
CATGTATCGATACAATGAAAAATGTATCGATA
Found at i:1625827 original size:20 final size:20
Alignment explanation
Indices: 1625802--1625857 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1625792 GTATCGATAC
1625802 ATGTATTGATACAATTAAAA
1 ATGTATTGATACAATTAAAA
* *
1625822 ATGTATTGATACAATGAGAA
1 ATGTATTGATACAATTAAAA
*
1625842 ATGTATCGATACAATT
1 ATGTATTGATACAATT
1625858 GTAATCATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATTGATACAATTAAAA
Found at i:1629111 original size:7 final size:7
Alignment explanation
Indices: 1629099--1629160 Score: 70
Period size: 7 Copynumber: 8.3 Consensus size: 7
1629089 TGGAAAAGAG
1629099 AAGAAAA
1 AAGAAAA
1629106 AAGAAAA
1 AAGAAAA
1629113 AAGAAAGA
1 AAGAAA-A
*
1629121 AGGAAAA
1 AAGAAAA
*
1629128 CGAAAAAAA
1 --AAGAAAA
1629137 AAGAAAA
1 AAGAAAA
1629144 AAGAAAAA
1 AAG-AAAA
1629152 AAGAAAA
1 AAGAAAA
1629159 AA
1 AA
1629161 TGTGACCTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
7 29 0.62
8 13 0.28
9 5 0.11
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:1629113 original size:8 final size:8
Alignment explanation
Indices: 1629102--1629160 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
1629092 AAAAGAGAAG
1629102 AAAAAAG-
1 AAAAAAGA
1629109 AAAAAAGA
1 AAAAAAGA
* *
1629117 AAGAAGGA
1 AAAAAAGA
*
1629125 AAACGAA-A
1 AAA-AAAGA
1629133 AAAAAAG-
1 AAAAAAGA
1629140 AAAAAAGA
1 AAAAAAGA
1629148 AAAAAAGA
1 AAAAAAGA
1629156 AAAAA
1 AAAAA
1629161 TGTGACCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 16 0.38
8 25 0.60
9 1 0.02
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1629330 original size:42 final size:42
Alignment explanation
Indices: 1629266--1629353 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
1629256 TATATAAAAA
*
1629266 ATAAAATAAGTGGCATAGGTCACCTAAGTGAATAGGTCAATT
1 ATAAAATAAGTGGCATAAGTCACCTAAGTGAATAGGTCAATT
*
1629308 ATAAAATAAGTGGCATAAGTCACCTAAGTGAATGGGTCAATT
1 ATAAAATAAGTGGCATAAGTCACCTAAGTGAATAGGTCAATT
1629350 ATAA
1 ATAA
1629354 CCCATGCACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.26
Consensus pattern (42 bp):
ATAAAATAAGTGGCATAAGTCACCTAAGTGAATAGGTCAATT
Found at i:1632072 original size:20 final size:20
Alignment explanation
Indices: 1632049--1632096 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1632039 ACTATCCTTT
*
1632049 ATGAAAGATGCATTGGTTAG
1 ATGAAAAATGCATTGGTTAG
*
1632069 ATGAAAAAATGCATTTGTTAG
1 ATG-AAAAATGCATTGGTTAG
1632090 ATGAAAA
1 ATGAAAA
1632097 TATGTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (20 bp):
ATGAAAAATGCATTGGTTAG
Found at i:1632082 original size:21 final size:21
Alignment explanation
Indices: 1632056--1632096 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1632046 TTTATGAAAG
1632056 ATGCATTGGTTAGATGAAAAA
1 ATGCATTGGTTAGATGAAAAA
*
1632077 ATGCATTTGTTAGATGAAAA
1 ATGCATTGGTTAGATGAAAA
1632097 TATGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
ATGCATTGGTTAGATGAAAAA
Found at i:1636964 original size:20 final size:20
Alignment explanation
Indices: 1636939--1636980 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1636929 CAACAAAAGA
1636939 TATCTTCCTCATGAAAGAGT
1 TATCTTCCTCATGAAAGAGT
1636959 TATCTTCCTCATGAAAGAGT
1 TATCTTCCTCATGAAAGAGT
1636979 TA
1 TA
1636981 GATTCATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TATCTTCCTCATGAAAGAGT
Found at i:1639850 original size:28 final size:29
Alignment explanation
Indices: 1639796--1639855 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1639786 CATGTCTTTA
1639796 TTTAAATGTTATGTCTTTACATAACAA-T
1 TTTAAATGTTATGTCTTTACATAACAACT
*
1639824 TTTAAATGTTGTGTTCTTT-CA-ACACAACT
1 TTTAAATGTTATG-TCTTTACATA-ACAACT
1639853 TTT
1 TTT
1639856 TGATGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAAATGTTATGTCTTTACATAACAACT
Found at i:1641828 original size:18 final size:18
Alignment explanation
Indices: 1641785--1641828 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1641775 ATATTTAAGT
1641785 AATTTAA-AAATTTTAAA
1 AATTTAATAAATTTTAAA
**
1641802 AATAAAATAAATTTTAAA
1 AATTTAATAAATTTTAAA
*
1641820 TATTTAATA
1 AATTTAATA
1641829 TTATTTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAATAAATTTTAAA
Found at i:1641848 original size:12 final size:11
Alignment explanation
Indices: 1641821--1641874 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
1641811 AATTTTAAAT
*
1641821 ATTT-AATATT
1 ATTTAAATATA
1641831 ATTTAAATAATA
1 ATTTAAAT-ATA
1641843 ATTTAAAT-TA
1 ATTTAAATATA
*
1641853 ATTAAAATATAA
1 ATTTAAATAT-A
1641865 ATTT-AATATA
1 ATTTAAATATA
1641875 GAATAGGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 14 0.38
11 9 0.24
12 14 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTAAATATA
Found at i:1641864 original size:21 final size:23
Alignment explanation
Indices: 1641821--1641873 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1641811 AATTTTAAAT
*
1641821 ATTTAATATTATTTAAATAAT-A
1 ATTTAATATTATTAAAATAATAA
1641843 ATTTAA-ATTAATTAAAAT-ATAA
1 ATTTAATATT-ATTAAAATAATAA
1641865 ATTTAATAT
1 ATTTAATAT
1641874 AGAATAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 20 0.74
23 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATATTATTAAAATAATAA
Found at i:1644313 original size:21 final size:20
Alignment explanation
Indices: 1644288--1644337 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1644278 AAATTTTATT
1644288 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAA-ATA
*
1644309 TAAATATTTA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
*
1644329 -ATATTTAAT
1 TAAATTTAAT
1644338 ATTTTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 3 0.12
21 12 0.50
22 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:1644818 original size:27 final size:28
Alignment explanation
Indices: 1644788--1644853 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
1644778 ATTTAATTAT
*
1644788 AATTACTAAT-ATAAAA-ATATTTTTTAA
1 AATTACTAATAATAAAATA-AATTTTTAA
**
1644815 AATTTTTAATAATAAAATAAATTTTTAA
1 AATTACTAATAATAAAATAAATTTTTAA
*
1644843 ATTTATCTAAT
1 AATTA-CTAAT
1644854 TCAAATAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 8 0.27
28 17 0.57
29 5 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTACTAATAATAAAATAAATTTTTAA
Found at i:1645270 original size:22 final size:20
Alignment explanation
Indices: 1645236--1645283 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
1645226 CTATTTATAT
1645236 TATATTTTTTTTATTTTTAA
1 TATATTTTTTTTATTTTTAA
1645256 TATATTTTTAATTTAATTTTTAA
1 TATATTTTT--TTT-ATTTTTAA
1645279 T-TATT
1 TATATT
1645284 AAATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATATTTTTTTTATTTTTAA
Found at i:1645274 original size:12 final size:11
Alignment explanation
Indices: 1645245--1645280 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1645235 TTATATTTTT
1645245 TTTATTTTTAA
1 TTTATTTTTAA
*
1645256 TATATTTTTAA
1 TTTATTTTTAA
1645267 TTTAATTTTTAA
1 TTT-ATTTTTAA
1645279 TT
1 TT
1645281 ATTAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATTTTTAA
Found at i:1646560 original size:32 final size:32
Alignment explanation
Indices: 1646524--1646585 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1646514 AATAAAGAGT
* * *
1646524 TTTACAAGTTCTTAATTTCAATTTCTGAAGTG
1 TTTACAAGTTCTGAACTTCAATTTCAGAAGTG
1646556 TTTACAAGTTCTGAACTTCAATTTCAGAAG
1 TTTACAAGTTCTGAACTTCAATTTCAGAAG
1646586 AGTAGTGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (32 bp):
TTTACAAGTTCTGAACTTCAATTTCAGAAGTG
Found at i:1654194 original size:49 final size:45
Alignment explanation
Indices: 1654141--1654243 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
1654131 TCAAGGTCAA
*
1654141 CGACATCGGGCTAAGGGAAAAGTGGACCAATGTGCTGACTCAAAGCCAG
1 CGACATCGGGCTAA--GAAAAGT-G-CCAATATGCTGACTCAAAGCCAG
* * * * *
1654190 CGACATTGGGCTTAGAAAGGTGCCAATATGCTGATTCAAGGCCAG
1 CGACATCGGGCTAAGAAAAGTGCCAATATGCTGACTCAAAGCCAG
*
1654235 CGATATCGG
1 CGACATCGG
1654244 ACTTTAAGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
45 27 0.59
46 1 0.02
47 6 0.13
49 12 0.26
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.18
Consensus pattern (45 bp):
CGACATCGGGCTAAGAAAAGTGCCAATATGCTGACTCAAAGCCAG
Found at i:1654372 original size:64 final size:64
Alignment explanation
Indices: 1654278--1654718 Score: 549
Period size: 64 Copynumber: 7.0 Consensus size: 64
1654268 TTTGAAAAGG
* * * * ** *
1654278 GTTGCCACTGACTTGTGTGGGTTTTTAAAAGGGTTTCCACCGA-AAGTGTGGACTTTTGAAAGAA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC-TTTGAAAGAA
* * * * *
1654342 GTTCCCATCAACTTGTGTGGACTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-GAA
* * *
1654407 -TTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTACCACCGACTTGTGTGGGCTTTGAAATG-G
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-GAA
* * * *
1654470 GTTGCCATCGATTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAA
* *
1654534 GTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-TA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAA
* * *
1654597 G-TACCACCGACTTGTATGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATG-G
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-GAA
*
1654660 GTTGCCACCGACTTGTGTGGGCTTTGAAATA--G-TGCCACCGACTTATGTGGGCTTTGAAA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAA-AGGGTTGCCACCGACTTGTGTGGGCTTTGAAA
1654719 TGGTGCCACT
Statistics
Matches: 333, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
62 82 0.25
63 3 0.01
64 238 0.71
65 10 0.03
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (64 bp):
GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAGAA
Found at i:1654432 original size:96 final size:96
Alignment explanation
Indices: 1654268--1654764 Score: 597
Period size: 96 Copynumber: 5.3 Consensus size: 96
1654258 AAAATGGTGA
* * * * * * * ** *
1654268 TTTGAAAAGGGTTGCCACTGACTTGTGTGGGTTTTTAAAAGGGTTTCCACCGA-AAGTGTGGACT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGC-
* * * * *
1654332 TTTGAAAGAAGTTCCCATCAACTTGTGTGGAC
65 TTTGAAAGAGGTTGCCACCGACTTGTGTGGGC
*
1654364 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
*
1654429 TTGAAATG-GGTTACCACCGACTTGTGTGGGC
66 TTGAAA-GAGGTTGCCACCGACTTGTGTGGGC
* * * *
1654460 TTTGAAATGGGTTGCCATCGATTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
*
1654525 TTGAAATAGGTTGCCACCGACTTGTGTGGGC
66 TTGAAAGAGGTTGCCACCGACTTGTGTGGGC
* * *
1654556 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT--AGTACCACCGACTTGTATGGGCT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
1654619 TTGAAA-AGGGTTGCCACCGACTTGTGTGGGC
66 TTGAAAGA-GGTTGCCACCGACTTGTGTGGGC
* *
1654650 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT--AGTGCCACCGACTTATGTGGGCT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
* * *
1654713 TTGAAA-TGG-TGCCACTGAC-T-TGTGGTC
66 TTGAAAGAGGTTGCCACCGACTTGTGTGGGC
*
1654740 TTTGAAAT-GG-TGCCACTGACTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1654765 GGCTTAAAAA
Statistics
Matches: 362, Mismatches: 35, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
88 14 0.04
89 2 0.01
90 14 0.04
91 1 0.00
92 9 0.02
93 3 0.01
94 114 0.31
96 197 0.54
97 8 0.02
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (96 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGTGGGCT
TTGAAAGAGGTTGCCACCGACTTGTGTGGGC
Found at i:1654745 original size:28 final size:28
Alignment explanation
Indices: 1654705--1655406 Score: 1054
Period size: 28 Copynumber: 25.5 Consensus size: 28
1654695 CACCGACTTA
* * * * *
1654705 TGTGGGCTTTGAAATGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * *
1654733 TGTGGTCTTTGAAATGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
1654761 TGTGGGCTTAAAAAGGGTGCCATGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
1654789 TGTGAAC-TTAAAAGGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGG-TGCCACGGAGT
1654817 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
1654844 TGTGGACTTTAAAAGGGTGCCACAGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1654872 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1654900 TGTGGAC-TTAAAAGGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGG-TGCCACGGAGT
*
1654928 TGTGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
1654955 TGTGGAC-TTAAAAGGGTGCCATGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1654982 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
1655010 TGTGGAC-TTACAAGGGTGCCAGGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655037 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
1655064 TGTGGACTTAAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655092 TGTGGAC-TTAAAAGGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGG-TGCCACGGAGT
1655120 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655147 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655174 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655201 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655229 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655257 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
1655284 TGTGGAC-TTAAAAGGGTACCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655311 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655339 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
1655367 TGTGGAC-TTAAAAGGGTGCCATGGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
1655394 TGTGGACTTTAAA
1 TGTGGACTTTAAA
1655407 GAGGTCATGG
Statistics
Matches: 632, Mismatches: 33, Indels: 18
0.93 0.05 0.03
Matches are distributed among these distances:
27 284 0.45
28 348 0.55
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.25
Consensus pattern (28 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGT
Found at i:1654865 original size:55 final size:54
Alignment explanation
Indices: 1654720--1655407 Score: 1070
Period size: 55 Copynumber: 12.5 Consensus size: 54
1654710 GCTTTGAAAT
* * * * * * * *
1654720 GGTGCCACTGACTTGTGGTCTTTGAAATGGTGCCACTGACTTGTGGGCTTAAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAG
* * *
1654776 GGTGCCATGAAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAG
*
1654831 GGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
1654887 GGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAG
* *
1654942 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
* *
1654997 GGTGCCACGGAGTTGTGGACTTACAAGGGTGCCAGGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
*
1655051 GGTGCCACGGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1655106 GGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 GG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1655161 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
1655216 GGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
*
1655271 GGTGCCACGGAGTTGTGGACTTAAAAGGGTACCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
1655326 GGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* * *
1655381 GGTGCCATGGACTTGTGGACTTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAG
1655408 AGGTCATGGT
Statistics
Matches: 591, Mismatches: 30, Indels: 24
0.92 0.05 0.04
Matches are distributed among these distances:
54 123 0.21
55 311 0.53
56 157 0.27
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (54 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:1660343 original size:164 final size:164
Alignment explanation
Indices: 1660071--1660401 Score: 608
Period size: 164 Copynumber: 2.0 Consensus size: 164
1660061 CCTAAATAGG
* *
1660071 TATCCGAATCGTTCCTTTGTCCAGTAAGGGTAGTCGAGGCACCTCGATTCCAGGCCCATCGCGGG
1 TATCCGAATCGTTCCTTCGTCCAGTAAGGGCAGTCGAGGCACCTCGATTCCAGGCCCATCGCGGG
*
1660136 TTTGATGAATCGAGTTCGATCCGGTGGATGTATTTCCCTATGCAAATGCGGAGGGTTACTCACGA
66 TTTGATGAATCGAGTTCGATCCGGTGAATGTATTTCCCTATGCAAATGCGGAGGGTTACTCACGA
1660201 GAGCATAGGTAATTTACATCCTGAAAGTTATTGC
131 GAGCATAGGTAATTTACATCCTGAAAGTTATTGC
*
1660235 TATCCGAATCGTTCCTTCGTCCAGTAAGGGCAGTTGAGGCACCTCGATTCCAGGCCCATCGCGGG
1 TATCCGAATCGTTCCTTCGTCCAGTAAGGGCAGTCGAGGCACCTCGATTCCAGGCCCATCGCGGG
*
1660300 TTTGATGAATCGAGTTCGATCCGGTGAATGTATTTCTCTATGCAAATGCGGAGGGTTACTCACGA
66 TTTGATGAATCGAGTTCGATCCGGTGAATGTATTTCCCTATGCAAATGCGGAGGGTTACTCACGA
*
1660365 GAGCATAGGTAATTTACATCCTGGAAGTTATTGC
131 GAGCATAGGTAATTTACATCCTGAAAGTTATTGC
1660399 TAT
1 TAT
1660402 GCCTATGCGG
Statistics
Matches: 161, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 161 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (164 bp):
TATCCGAATCGTTCCTTCGTCCAGTAAGGGCAGTCGAGGCACCTCGATTCCAGGCCCATCGCGGG
TTTGATGAATCGAGTTCGATCCGGTGAATGTATTTCCCTATGCAAATGCGGAGGGTTACTCACGA
GAGCATAGGTAATTTACATCCTGAAAGTTATTGC
Found at i:1663358 original size:9 final size:9
Alignment explanation
Indices: 1663344--1663399 Score: 67
Period size: 10 Copynumber: 5.8 Consensus size: 9
1663334 CCATTTCATA
1663344 TTTTTTTCT
1 TTTTTTTCT
1663353 TTTTTTTCT
1 TTTTTTTCT
1663362 TTTTCTTTCT
1 TTTT-TTTCT
1663372 TTCTTTTTCAT
1 TT-TTTTTC-T
*
1663383 CTTTTTTCT
1 TTTTTTTCT
1663392 TTCTTTTT
1 TT-TTTTT
1663400 TACCTAACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 15 0.37
10 22 0.54
11 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1663374 original size:14 final size:15
Alignment explanation
Indices: 1663346--1663393 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
1663336 ATTTCATATT
*
1663346 TTTTTCTTTTTTTTC
1 TTTTTCTTTTCTTTC
1663361 TTTTTC-TTTCTTTC
1 TTTTTCTTTTCTTTC
1663375 TTTTTCATCTTT-TTTC
1 TTTTTC-T-TTTCTTTC
1663391 TTT
1 TTT
1663394 CTTTTTTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 7 0.24
17 3 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTCTTTC
Found at i:1663378 original size:20 final size:20
Alignment explanation
Indices: 1663337--1663399 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
1663327 GGCCACTCCA
1663337 TTTCATATTTTTTTCTTT-TT
1 TTTCAT-TTTTTTTCTTTCTT
1663357 TTTC-TTTTTCTTTCTTTCTT
1 TTTCATTTTT-TTTCTTTCTT
*
1663377 TTTCATCTTTTTTCTTTCTT
1 TTTCATTTTTTTTCTTTCTT
1663397 TTT
1 TTT
1663400 TACCTAACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
18 4 0.10
19 8 0.21
20 23 0.59
21 4 0.10
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCATTTTTTTTCTTTCTT
Found at i:1663388 original size:24 final size:23
Alignment explanation
Indices: 1663348--1663397 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1663338 TTCATATTTT
**
1663348 TTTCTTTTTTTTCTTTTTCTTTC
1 TTTCTTTTTCATCTTTTTCTTTC
1663371 TTTCTTTTTCATCTTTTTTCTTTC
1 TTTCTTTTTCATC-TTTTTCTTTC
1663395 TTT
1 TTT
1663398 TTTACCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTCATCTTTTTCTTTC
Found at i:1663410 original size:24 final size:24
Alignment explanation
Indices: 1663361--1663413 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1663351 CTTTTTTTTC
** *
1663361 TTTTTCTTTCTTTCTTTTTCATCT
1 TTTTTCTTTCTTTCTTTACCAACT
1663385 TTTTTCTTTCTTT-TTTACCTAACT
1 TTTTTCTTTCTTTCTTTACC-AACT
1663409 TTTTT
1 TTTTT
1663414 TTCAACCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTTCTTTCTTTCTTTACCAACT
Found at i:1666326 original size:42 final size:42
Alignment explanation
Indices: 1666206--1666315 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
1666196 TTTTTCTTTC
* * * ***
1666206 CTCCTCCTGTCATCCCTCTTCTCTCTATTATCTCTCCGATCT
1 CTCCTCCTATCATCCCTCTTATCTCTACTATCTCTTTTATCT
1666248 CTCCTCCTATCATCCCTCTTATCTCTACTATCTCTTTTATCT
1 CTCCTCCTATCATCCCTCTTATCTCTACTATCTCTTTTATCT
* * *
1666290 CTCCTCCTTTTATCCCTTTTATCTCT
1 CTCCTCCTATCATCCCTCTTATCTCT
1666316 TTTTTCTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.11, C:0.40, G:0.02, T:0.47
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCTTATCTCTACTATCTCTTTTATCT
Found at i:1670093 original size:19 final size:19
Alignment explanation
Indices: 1670069--1670107 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1670059 AATGTTAAAC
*
1670069 ATGTATTGG-ACATGTCAAA
1 ATGTA-TGGAACATGGCAAA
1670088 ATGTATGGAACATGGCAAA
1 ATGTATGGAACATGGCAAA
1670107 A
1 A
1670108 AAGTGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (19 bp):
ATGTATGGAACATGGCAAA
Found at i:1673432 original size:42 final size:42
Alignment explanation
Indices: 1673368--1673451 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1673358 GTATCATGAG
1673368 ACCAATTTCTAATTCACCAGGATATCAATCATACAATATATT
1 ACCAATTTCTAATTCACCAGGATATCAATCATACAATATATT
*
1673410 ACCAATTTCTAATTCACTAGGATATCAATCATACAATATATT
1 ACCAATTTCTAATTCACCAGGATATCAATCATACAATATATT
1673452 TGGGCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (42 bp):
ACCAATTTCTAATTCACCAGGATATCAATCATACAATATATT
Found at i:1681413 original size:20 final size:21
Alignment explanation
Indices: 1681390--1681428 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1681380 TTACAAAATT
1681390 ATTTA-ATTATTAT-TTTAAAA
1 ATTTATATT-TTATATTTAAAA
1681410 ATTTATATTTTATATTTAA
1 ATTTATATTTTATATTTAA
1681429 TATATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTATATTTTATATTTAAAA
Found at i:1682557 original size:2 final size:2
Alignment explanation
Indices: 1682496--1682538 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1682486 GAACTAGAGA
1682496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1682538 A
1 A
1682539 GAAATGCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1683306 original size:19 final size:19
Alignment explanation
Indices: 1683278--1683318 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1683268 TTAAATAAAT
*
1683278 TTTATTTTTTAAAGCTTAA
1 TTTATATTTTAAAGCTTAA
*
1683297 TTTATATTTTAAAGTTTAA
1 TTTATATTTTAAAGCTTAA
1683316 TTT
1 TTT
1683319 GTCAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATATTTTAAAGCTTAA
Found at i:1688940 original size:17 final size:17
Alignment explanation
Indices: 1688918--1688950 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1688908 TGTGGCTTGA
1688918 AGGTTGAGGTTTATATG
1 AGGTTGAGGTTTATATG
1688935 AGGTTGAGGTTTATAT
1 AGGTTGAGGTTTATAT
1688951 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (17 bp):
AGGTTGAGGTTTATATG
Found at i:1702439 original size:20 final size:20
Alignment explanation
Indices: 1702402--1702439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1702392 TTGAATAAAC
*
1702402 TTATCCATTTTCTTAAAAGA
1 TTATCCATTTTCTAAAAAGA
1702422 TTATCCAATTTT-TAAAAA
1 TTATCC-ATTTTCTAAAAA
1702440 TGTTACCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATCCATTTTCTAAAAAGA
Found at i:1703199 original size:19 final size:18
Alignment explanation
Indices: 1703175--1703210 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1703165 ATATAAAAGA
1703175 AAAAATCAAATTAAAATAG
1 AAAAAT-AAATTAAAATAG
*
1703194 AAAAATAAATTTAAATA
1 AAAAATAAATTAAAATA
1703211 AAACAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAAATAAATTAAAATAG
Found at i:1703647 original size:16 final size:15
Alignment explanation
Indices: 1703628--1703665 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1703618 TCAGGGTTTG
1703628 TGTTATTCTTAGATTA
1 TGTTATT-TTAGATTA
*
1703644 TGTTATTTTGGATTA
1 TGTTATTTTAGATTA
1703659 T-TTATTT
1 TGTTATTT
1703666 GGATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 8 0.38
16 7 0.33
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.63
Consensus pattern (15 bp):
TGTTATTTTAGATTA
Found at i:1703668 original size:13 final size:14
Alignment explanation
Indices: 1703639--1703674 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1703629 GTTATTCTTA
1703639 GATTATGTTATTTTG
1 GATTAT-TTATTTTG
1703654 GATTATTTA-TTTG
1 GATTATTTATTTTG
1703667 GATTATTT
1 GATTATTT
1703675 TAAGTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (14 bp):
GATTATTTATTTTG
Found at i:1703689 original size:16 final size:16
Alignment explanation
Indices: 1703668--1703699 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1703658 ATTTATTTGG
*
1703668 ATTATTTTAAGTTTAA
1 ATTATTTTAAATTTAA
1703684 ATTATTTTAAATTTAA
1 ATTATTTTAAATTTAA
1703700 GTCATTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:1703785 original size:23 final size:24
Alignment explanation
Indices: 1703754--1703802 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1703744 TATTCTTGAA
* * *
1703754 TTAGGTTATTTTAGTTT-AATTAT
1 TTAGATTATTTAAATTTAAATTAT
1703777 TTAGATTATTTAAATTTAAATTAT
1 TTAGATTATTTAAATTTAAATTAT
1703801 TT
1 TT
1703803 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (24 bp):
TTAGATTATTTAAATTTAAATTAT
Found at i:1703806 original size:16 final size:16
Alignment explanation
Indices: 1703775--1703816 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1703765 TAGTTTAATT
*
1703775 ATTTAGATTA-TTTAA
1 ATTTAAATTATTTTAA
1703790 ATTTAAATTATTTTAA
1 ATTTAAATTATTTTAA
1703806 ATTTAAATTAT
1 ATTTAAATTAT
1703817 GAAAAAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:1703870 original size:14 final size:13
Alignment explanation
Indices: 1703834--1703867 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1703824 TTGTCGATGA
1703834 TTTTTAATTGAAT
1 TTTTTAATTGAAT
*
1703847 TATATTAATTGAAT
1 T-TTTTAATTGAAT
1703861 TTTTTAA
1 TTTTTAA
1703868 ATTTAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
TTTTTAATTGAAT
Found at i:1704439 original size:19 final size:19
Alignment explanation
Indices: 1704408--1704452 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1704398 ACATATTTTT
*
1704408 AAAATTAAATTTTTA-TAA
1 AAAAATAAATTTTTATTAA
1704426 AAAAATAAATTTTTATTAA
1 AAAAATAAATTTTTATTAA
*
1704445 ATAAATAA
1 AAAAATAA
1704453 TAATTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATAAATTTTTATTAA
Found at i:1720587 original size:19 final size:19
Alignment explanation
Indices: 1720544--1720616 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1720534 TACACCCAGA
*
1720544 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1720564 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1720583 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1720603 TGTATCGATACATG
1 TGTATCGATACATG
1720617 AAATTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1720670 original size:20 final size:20
Alignment explanation
Indices: 1720645--1720710 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1720635 CTACCACTGT
1720645 TTGTATCGATACATAGGACA
1 TTGTATCGATACATAGGACA
1720665 TTGTATCGATAC-----A-A
1 TTGTATCGATACATAGGACA
*
1720679 -TGTACCGATACATAGGACA
1 TTGTATCGATACATAGGACA
1720698 TTGTATCGATACA
1 TTGTATCGATACA
1720711 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.62
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (20 bp):
TTGTATCGATACATAGGACA
Found at i:1720693 original size:33 final size:33
Alignment explanation
Indices: 1720646--1720743 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1720636 TACCACTGTT
1720646 TGTATCGATACATAGGACATTGTATCGATACAA
1 TGTATCGATACATAGGACATTGTATCGATACAA
*
1720679 TGTACCGATACATAGGACATTGTATCGATACAA
1 TGTATCGATACATAGGACATTGTATCGATACAA
1720712 TGTATCGATACATTATGG--ATTGTATCGATACA
1 TGTATCGATACA-TA-GGACATTGTATCGATACA
1720744 TTATAGATTG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 57 0.93
34 2 0.03
35 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGACATTGTATCGATACAA
Found at i:1720717 original size:13 final size:13
Alignment explanation
Indices: 1720699--1720723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1720689 CATAGGACAT
1720699 TGTATCGATACAA
1 TGTATCGATACAA
1720712 TGTATCGATACA
1 TGTATCGATACA
1720724 TTATGGATTG
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:1720737 original size:20 final size:20
Alignment explanation
Indices: 1720712--1720765 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1720702 ATCGATACAA
*
1720712 TGTATCGATACATTATGGAT
1 TGTATCGATACATTATAGAT
1720732 TGTATCGATACATTATAGAT
1 TGTATCGATACATTATAGAT
1720752 TGTATCGATACATT
1 TGTATCGATACATT
1720766 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTATAGAT
Found at i:1721163 original size:17 final size:17
Alignment explanation
Indices: 1721124--1721163 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1721114 TAAGAGGCAA
*
1721124 TCTTTGGTTGTACAAAT
1 TCTTTGTTTGTACAAAT
1721141 TC-TTGTTTGTACAAAT
1 TCTTTGTTTGTACAAAT
1721157 TCTTTGT
1 TCTTTGT
1721164 CTAGATAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (17 bp):
TCTTTGTTTGTACAAAT
Found at i:1723245 original size:6 final size:6
Alignment explanation
Indices: 1723234--1723285 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
1723224 TATATAAATT
* *
1723234 TATATC TATATC TATAT- TCATATC GATATC TATATC TATATC TATATA
1 TATATC TATATC TATATC T-ATATC TATATC TATATC TATATC TATATC
1723282 TATA
1 TATA
1723286 ATATAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 1 0.02
6 40 0.98
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (6 bp):
TATATC
Found at i:1723291 original size:5 final size:5
Alignment explanation
Indices: 1723276--1723310 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
1723266 TATCTATATC
1723276 TATATA TATAA TATAA TATAA TATAA TATAA TATA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATA
1723311 TAAGTGTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:1725128 original size:18 final size:18
Alignment explanation
Indices: 1725105--1725139 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1725095 TTTTTCAACA
1725105 TATTATTTTAGATAATTT
1 TATTATTTTAGATAATTT
1725123 TATTATTTTAGATAATT
1 TATTATTTTAGATAATT
1725140 CTTTTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TATTATTTTAGATAATTT
Found at i:1726192 original size:12 final size:12
Alignment explanation
Indices: 1726175--1726228 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
1726165 ATATTTTTTG
1726175 ATGTATCGATAC
1 ATGTATCGATAC
1726187 ATGTAT-G--A-
1 ATGTATCGATAC
1726195 ATGTATCGATAC
1 ATGTATCGATAC
1726207 ATGTAT-G--A-
1 ATGTATCGATAC
1726215 ATGTATCGATAC
1 ATGTATCGATAC
1726227 AT
1 AT
1726229 TTTGTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
11 4 0.12
12 14 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Done.