Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold149
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1065560
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 107426 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:912439 original size:2 final size:2
Alignment explanation
Indices: 912432--912466 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
912422 ACCCAAGATG
912432 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
912467 ATATTAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:914182 original size:36 final size:36
Alignment explanation
Indices: 914135--914313 Score: 313
Period size: 36 Copynumber: 4.9 Consensus size: 36
914125 ACTTACGCTG
*
914135 AGATCCTGTACACAACATCATTGAATGACATGTAAC
1 AGATCTTGTACACAACATCATTGAATGACATGTAAC
914171 AGATCTTGTACACAACATCATTGAATGACATGTAAC
1 AGATCTTGTACACAACATCATTGAATGACATGTAAC
914207 AGATCTTGTACACAACATCATTGAATGACATGTAAC
1 AGATCTTGTACACAACATCATTGAATGACATGTAAC
914243 AGATCTTGTACACAACATCATTGAATGACATGTAAC
1 AGATCTTGTACACAACATCATTGAATGACATGTAAC
* *
914279 AGATCTTGTACACAAAATCTTTGAACTGTACATGT
1 AGATCTTGTACACAACATCATTGAA-TG-ACATGT
914314 CATATAGATC
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
36 130 0.94
37 2 0.01
38 6 0.04
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (36 bp):
AGATCTTGTACACAACATCATTGAATGACATGTAAC
Found at i:915130 original size:22 final size:22
Alignment explanation
Indices: 915105--915236 Score: 192
Period size: 22 Copynumber: 5.7 Consensus size: 22
915095 CTTTACTGTG
*
915105 ACTATAACATGACTACAGCATT
1 ACTATAACATGACTACAACATT
*
915127 ACTACCGGTATAACATGACTACAGCATT
1 ACTA------TAACATGACTACAACATT
915155 ACTATAACATGACTACAACATT
1 ACTATAACATGACTACAACATT
915177 ACTATAACATGACTACAACATT
1 ACTATAACATGACTACAACATT
915199 ACTATAACATGACTACAACATT
1 ACTATAACATGACTACAACATT
915221 ACTATAACATGACTAC
1 ACTATAACATGACTAC
915237 CTACCCAGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 12
0.89 0.01 0.10
Matches are distributed among these distances:
22 81 0.79
28 22 0.21
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (22 bp):
ACTATAACATGACTACAACATT
Found at i:915169 original size:11 final size:11
Alignment explanation
Indices: 915135--915235 Score: 121
Period size: 11 Copynumber: 9.2 Consensus size: 11
915125 TTACTACCGG
915135 TATAACATGAC
1 TATAACATGAC
* * *
915146 TACAGCATTAC
1 TATAACATGAC
915157 TATAACATGAC
1 TATAACATGAC
* *
915168 TACAACATTAC
1 TATAACATGAC
915179 TATAACATGAC
1 TATAACATGAC
* *
915190 TACAACATTAC
1 TATAACATGAC
915201 TATAACATGAC
1 TATAACATGAC
* *
915212 TACAACATTAC
1 TATAACATGAC
915223 TATAACATGAC
1 TATAACATGAC
915234 TA
1 TA
915236 CCTACCCAGA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 72 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.28
Consensus pattern (11 bp):
TATAACATGAC
Found at i:916501 original size:2 final size:2
Alignment explanation
Indices: 916494--916556 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
916484 GTAAAACTCA
916494 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
916536 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
916557 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:917223 original size:36 final size:36
Alignment explanation
Indices: 917173--917280 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
917163 ACATGGACAG
*
917173 CTAG-TGTCATGTTGTAAATTTTGTATATACTGTCA
1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA
*
917208 CTAGTTGTCAAGTTGTAAATTTTGTATTTACTGTCA
1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA
917244 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA
1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA
917280 C
1 C
917281 CCGGTAAATT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 4 0.06
36 65 0.94
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (36 bp):
CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA
Found at i:917575 original size:4 final size:4
Alignment explanation
Indices: 917568--917644 Score: 77
Period size: 4 Copynumber: 19.8 Consensus size: 4
917558 CCTCCCTCTT
* * * *
917568 TAAA TAAA TAGA TAAA TAAA T-AA TAAA -AAA AAAA TGAA TGAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
917614 TAAA TAGA CAAA TAGA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
917645 CAAAGATTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 6 0.10
4 54 0.90
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:919353 original size:18 final size:18
Alignment explanation
Indices: 919330--919449 Score: 91
Period size: 18 Copynumber: 6.7 Consensus size: 18
919320 TTCATTATAT
*
919330 CACAGAATCATAAATTAC
1 CACAGAATCACAAATTAC
*
919348 CACAGAATCACCAATTAC
1 CACAGAATCACAAATTAC
*
919366 CACAGAATCAC-ACTGTAC
1 CACAGAATCACAAAT-TAC
* * * * *
919384 CATATAATTATACATTAC
1 CACAGAATCACAAATTAC
* * *
919402 AACATAATCACACATTAC
1 CACAGAATCACAAATTAC
* *
919420 CACATAATCACACATTAC
1 CACAGAATCACAAATTAC
919438 CAC-GAAATCACA
1 CACAG-AATCACA
919450 CTGTACCACT
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
17 2 0.02
18 81 0.96
19 1 0.01
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (18 bp):
CACAGAATCACAAATTAC
Found at i:919450 original size:18 final size:18
Alignment explanation
Indices: 919343--919495 Score: 152
Period size: 18 Copynumber: 8.5 Consensus size: 18
919333 AGAATCATAA
*
919343 ATTACCACAGAATCAC-C
1 ATTACCACATAATCACAC
*
919360 AATTACCACAGAATCACAC
1 -ATTACCACATAATCACAC
* * *
919379 -TGTACCATATAATTATAC
1 AT-TACCACATAATCACAC
*
919397 ATTACAACATAATCACAC
1 ATTACCACATAATCACAC
919415 ATTACCACATAATCACAC
1 ATTACCACATAATCACAC
919433 ATTACCACGA-AATCACAC
1 ATTACCAC-ATAATCACAC
* *
919451 -TGTACCACTTAATCATAC
1 AT-TACCACATAATCACAC
*
919469 ATTACAACATAATCACAC
1 ATTACCACATAATCACAC
*
919487 ATTATCACA
1 ATTACCACA
919496 CCGTACCACA
Statistics
Matches: 112, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
17 2 0.02
18 106 0.95
19 4 0.04
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (18 bp):
ATTACCACATAATCACAC
Found at i:919452 original size:72 final size:72
Alignment explanation
Indices: 919343--919495 Score: 231
Period size: 72 Copynumber: 2.1 Consensus size: 72
919333 AGAATCATAA
*
919343 ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCA-TATAATTATACATTACAACAT
1 ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCACT-TAATCATACATTACAACAT
919407 AATCACAC
65 AATCACAC
*
919415 ATTACCACATAATCA-CACATTACCAC-GAAATCACACTGTACCACTTAATCATACATTACAACA
1 ATTACCACAGAATCACCA-ATTACCACAG-AATCACACTGTACCACTTAATCATACATTACAACA
919478 TAATCACAC
64 TAATCACAC
*
919487 ATTATCACA
1 ATTACCACA
919496 CCGTACCACA
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
71 3 0.04
72 71 0.95
73 1 0.01
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (72 bp):
ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCACTTAATCATACATTACAACATA
ATCACAC
Found at i:919507 original size:28 final size:29
Alignment explanation
Indices: 919475--919550 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
919465 ATACATTACA
* *
919475 ACATAATCACACATTATCACACCGTA-C-C
1 ACATAAACACACATTA-CACACCGAATCAC
* *
919503 ACATAAAAACACATTGC-CACCGAATCAC
1 ACATAAACACACATTACACACCGAATCAC
*
919531 ACATAACCACACATTACACA
1 ACATAAACACACATTACACA
919551 TAATCTTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.16
27 2 0.05
28 28 0.74
29 2 0.05
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (29 bp):
ACATAAACACACATTACACACCGAATCAC
Found at i:919718 original size:18 final size:18
Alignment explanation
Indices: 919697--920121 Score: 294
Period size: 18 Copynumber: 24.1 Consensus size: 18
919687 TCATGATATT
919697 TTACCACATAATCACACA
1 TTACCACATAATCACACA
* *
919715 TTACCACAGAACCACACA
1 TTACCACATAATCACACA
* * * *
919733 TTGCAACAAAATCACAAA
1 TTACCACATAATCACACA
* *
919751 TTATCAGAT-AT-A-AC-
1 TTACCACATAATCACACA
*
919765 -TA-CA-AAAAT-ACACA
1 TTACCACATAATCACACA
* *
919779 TTACCACATTATCATACA
1 TTACCACATAATCACACA
* * * * *
919797 TCACAACATTATTACAAA
1 TTACCACATAATCACACA
* * *
919815 TAACTACAGAATCACACA
1 TTACCACATAATCACACA
*
919833 TTACCACATCATCACACA
1 TTACCACATAATCACACA
* *
919851 TTAACACAGAATCACACA
1 TTACCACATAATCACACA
* *
919869 TTACCATATTATCACACA
1 TTACCACATAATCACACA
* *
919887 TTACCATATTATCACACA
1 TTACCACATAATCACACA
* *
919905 -TATCTACAGAATCACACA
1 TTA-CCACATAATCACACA
* *
919923 TTAACACAGAATCACACA
1 TTACCACATAATCACACA
* * *
919941 TTTCCATATTATCACACA
1 TTACCACATAATCACACA
* * *
919959 TAACTACAGAATCACACA
1 TTACCACATAATCACACA
*
919977 TTACCACATCATCACACA
1 TTACCACATAATCACACA
* * *
919995 TTAACACAGAATCACATA
1 TTACCACATAATCACACA
* *
920013 TTACCATATTATCACACA
1 TTACCACATAATCACACA
* *
920031 TTACCATATTATCACACA
1 TTACCACATAATCACACA
* * * *
920049 TAACAACAGAATCACTCA
1 TTACCACATAATCACACA
*
920067 TTACCACAGAATCACACA
1 TTACCACATAATCACACA
* * *
920085 -TATCTACAGAATCATACA
1 TTA-CCACATAATCACACA
920103 TTACCACATAATCACACA
1 TTACCACATAATCACACA
920121 T
1 T
920122 ATCTACAGAA
Statistics
Matches: 313, Mismatches: 83, Indels: 22
0.75 0.20 0.05
Matches are distributed among these distances:
11 1 0.00
12 5 0.02
13 4 0.01
15 3 0.01
16 3 0.01
17 9 0.03
18 284 0.91
19 4 0.01
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (18 bp):
TTACCACATAATCACACA
Found at i:919840 original size:10 final size:9
Alignment explanation
Indices: 919827--920049 Score: 58
Period size: 8 Copynumber: 24.8 Consensus size: 9
919817 ACTACAGAAT
919827 CACACATTA
1 CACACATTA
*
919836 C-CACATCA
1 CACACATTA
919844 TCACACATTA
1 -CACACATTA
**
919854 -ACACAGAA
1 CACACATTA
919862 TCACACATTA
1 -CACACATTA
*
919872 C-CATATTA
1 CACACATTA
919880 TCACACATTA
1 -CACACATTA
*
919890 C-CATATTA
1 CACACATTA
919898 TCACACA-TA
1 -CACACATTA
* *
919907 TCTACAGAAT-
1 -C-ACACATTA
919917 CACACATTA
1 CACACATTA
**
919926 -ACACAGAA
1 CACACATTA
*
919934 TCACACATTT
1 -CACACATTA
*
919944 C-CATATTA
1 CACACATTA
*
919952 TCACACATAA
1 -CACACATTA
* *
919962 CTACAGAAT-
1 C-ACACATTA
919971 CACACATTA
1 CACACATTA
*
919980 C-CACATCA
1 CACACATTA
919988 TCACACATTA
1 -CACACATTA
**
919998 -ACACAGAA
1 CACACATTA
*
920006 TCACATATTA
1 -CACACATTA
*
920016 C-CATATTA
1 CACACATTA
920024 TCACACATTA
1 -CACACATTA
*
920034 C-CATATTA
1 CACACATTA
920042 TCACACAT
1 -CACACAT
920050 AACAACAGAA
Statistics
Matches: 152, Mismatches: 37, Indels: 49
0.64 0.16 0.21
Matches are distributed among these distances:
8 70 0.46
9 21 0.14
10 60 0.39
11 1 0.01
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.26
Consensus pattern (9 bp):
CACACATTA
Found at i:920168 original size:72 final size:72
Alignment explanation
Indices: 919824--920177 Score: 195
Period size: 72 Copynumber: 4.9 Consensus size: 72
919814 ATAACTACAG
* * ** * * * * * * **
919824 AATCACACATTACCACATCATCACACATTAACACAGAATCACACATTACCATATTATCACACATT
1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
*
919889 ACCATAT
66 ACCACAT
* * * * * * ** * * ** *
919896 TATCACACATATCTACAGAATCACACATTAACACAGAATCACACATTTCCATATTATCACACATA
1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
* *
919961 ACTACAG
66 ACCACAT
* * ** * * * * * * * **
919968 AATCACACATTACCACATCATCACACATTAACACAGAATCACATATTACCATATTATCACACATT
1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
*
920033 ACCATAT
66 ACCACAT
* * * * * * * *
920040 TATCACACATAACAACAGAATCACTCATTACCACAGAATCACACATATCTACAGAATCATACATT
1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
920105 ACCACAT
66 ACCACAT
* * * ** * *
920112 AATCACACATATCTACAGAATCACACACTATCACATCACCACATATAACGAAAGAATTACACATT
1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
920177 A
66 A
920178 ACGCATTGTC
Statistics
Matches: 228, Mismatches: 54, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 228 1.00
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (72 bp):
AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT
ACCACAT
Found at i:920370 original size:18 final size:18
Alignment explanation
Indices: 920344--920380 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
920334 TTGCCACATC
*
920344 GTATCACACATTACTTCA
1 GTATCACACATTACCTCA
*
920362 GTATTACACATTACCTCA
1 GTATCACACATTACCTCA
920380 G
1 G
920381 CATACAACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (18 bp):
GTATCACACATTACCTCA
Found at i:920430 original size:18 final size:18
Alignment explanation
Indices: 920404--920455 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
920394 AGCAAACATT
*
920404 ACCAAAGCAGTATACCTC
1 ACCACAGCAGTATACCTC
* *
920422 ACCACAGCA-TGATACTTT
1 ACCACAGCAGT-ATACCTC
920440 ACCACAGCAGTATACC
1 ACCACAGCAGTATACC
920456 CCATTACAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.19
Consensus pattern (18 bp):
ACCACAGCAGTATACCTC
Found at i:920449 original size:36 final size:36
Alignment explanation
Indices: 920402--920478 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
920392 ATAGCAAACA
*
920402 TTACCAAAGCAGTATACCTCACCACAGCATGATACT
1 TTACCAAAGCAGTATACCCCACCACAGCATGATACT
* **
920438 TTACCACAGCAGTATACCCCATTACAGCATGATACT
1 TTACCAAAGCAGTATACCCCACCACAGCATGATACT
920474 TTACC
1 TTACC
920479 TTAGACGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (36 bp):
TTACCAAAGCAGTATACCCCACCACAGCATGATACT
Found at i:921690 original size:47 final size:47
Alignment explanation
Indices: 921621--921714 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
921611 CGTACATACC
921621 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG
1 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG
*
921668 TACCCTTAAATGACAGATGGACGTGATTCCAGTGGGGCTCGGGTGTG
1 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG
921715 GGGTCTGTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (47 bp):
TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG
Found at i:923016 original size:20 final size:20
Alignment explanation
Indices: 922991--923031 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
922981 CGAGTCGCGA
922991 GTACTATAGTGTGGTACTGG
1 GTACTATAGTGTGGTACTGG
923011 GTACTATAGTGTGGTACTGG
1 GTACTATAGTGTGGTACTGG
923031 G
1 G
923032 AGAATCCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.37, T:0.34
Consensus pattern (20 bp):
GTACTATAGTGTGGTACTGG
Found at i:924533 original size:2 final size:2
Alignment explanation
Indices: 924526--924575 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
924516 CTTGCATAAA
*
924526 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
924567 CT CT CT CT C
1 CT CT CT CT C
924576 ATGCGAGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:925474 original size:20 final size:20
Alignment explanation
Indices: 925449--925488 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
925439 AGGAAATCAT
925449 CTGGCCCCACTGTCATTAAC
1 CTGGCCCCACTGTCATTAAC
*
925469 CTGGCCCCGCTGTCATTAAC
1 CTGGCCCCACTGTCATTAAC
925489 GTTTCTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.40, G:0.17, T:0.25
Consensus pattern (20 bp):
CTGGCCCCACTGTCATTAAC
Found at i:926053 original size:46 final size:46
Alignment explanation
Indices: 926003--927316 Score: 1577
Period size: 46 Copynumber: 28.8 Consensus size: 46
925993 TGAAACTGCT
* *
926003 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATCTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
** * *
926049 GTGTGGTTTTTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * *
926095 GTGTGGATTCCGTCGTAAGTTTTACCACTAGTCGATGTGAAACTGTC
1 GTGTGGTTTCCGT-GTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926142 --GTGCTTTCCGTTTAGGTTCTACCACTAGTCGATGTGTAACTGAC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926186 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* *
926232 GTGTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926278 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926324 GTGTTGTTTCTGTGTAGCTTCTACCACTAGTCGATCTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926370 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATGTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * * *
926416 GTGTTGTTTCTGTCTATGTTTTACCGCTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926462 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926508 GTGTTGTTTCTGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926554 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGAC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926600 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATGTATAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
*
926646 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTA
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * *
926692 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATCTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926736 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926782 GTGTTGTTTCTGTGTAGCTTCTACCACTAGTCGATCTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926828 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATGTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * * *
926874 GTGTTGTTTCTGTCTATGTTTTACCGCTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
926920 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
926966 GTGTTGTTTCTGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
927012 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGAC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * *
927058 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATGTATAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
*
927104 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTA
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * *
927150 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATCTGTAACTGCC
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * *
927194 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTA
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * * * * *
927240 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATGTGTAACTGTA
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
* * ** *
927284 ATATATTTTCCGTGT--GTTTTACCACTAGTCGAT
1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGAT
927317 ATGAACTTGG
Statistics
Matches: 1117, Mismatches: 144, Indels: 16
0.87 0.11 0.01
Matches are distributed among these distances:
44 164 0.15
45 9 0.01
46 915 0.82
47 29 0.03
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.40
Consensus pattern (46 bp):
GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC
Found at i:928310 original size:2 final size:2
Alignment explanation
Indices: 928303--928338 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
928293 GACCGGAATA
928303 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
928339 AGTAACCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:930062 original size:2 final size:2
Alignment explanation
Indices: 930055--930097 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
930045 NNNNNNNNNN
* * *
930055 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TC TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
930097 T
1 T
930098 GCTGTTGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:930489 original size:24 final size:24
Alignment explanation
Indices: 930461--930557 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 24
930451 AACGTTCTAC
*
930461 ATTTTTTGTTTTTGTTGTACG-AT
1 ATTTTTTTTTTTTGTTGTACGTAT
*
930484 ATTTTTATTTTTTTGTTGT-GGTAT
1 ATTTTT-TTTTTTTGTTGTACGTAT
*
930508 ATTTTTTTATTGTTGTTGTACAATGTTAT
1 ATTTTTTT-TTTTTGTTGTAC---G-TAT
930537 ATTTTTTTATTTTTTGTTGTA
1 A-TTTTTT-TTTTTTGTTGTA
930558 GATCTTCAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
23 9 0.15
24 28 0.47
28 1 0.02
29 4 0.07
30 16 0.27
31 1 0.02
ACGTcount: A:0.15, C:0.02, G:0.14, T:0.68
Consensus pattern (24 bp):
ATTTTTTTTTTTTGTTGTACGTAT
Found at i:931206 original size:21 final size:21
Alignment explanation
Indices: 931180--931596 Score: 200
Period size: 21 Copynumber: 18.7 Consensus size: 21
931170 AATACGCTGA
*
931180 TATACAATGTTACATGCAGTG
1 TATACAATGTTACATACAGTG
*
931201 TATACAATGTTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931222 TATACAATGTTACA-ACATGCAATT
1 TATACAATGTTACATACA-G---TG
* * *
931246 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931267 TATACAATTAATGTTACA-ACATGCAATC
1 TATAC----AATGTTACATACA-G---TG
* * *
931295 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931316 TATACAATGTTACA-ACATGCAATC
1 TATACAATGTTACATACA-G---TG
* * *
931340 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931361 TATACAATGTTACA-ACATGCAATC
1 TATACAATGTTACATACA-G---TG
* * *
931385 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931406 TATACAATGTTACATGCAGTG
1 TATACAATGTTACATACAGTG
*
931427 TATACAATGTTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931448 TATACAATGTTACA-ACATGCAATC
1 TATACAATGTTACATACA-G---TG
* * *
931472 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
* *
931493 TATACAGTGTTACA-ACAAGCAATC
1 TATACAATGTTACATAC-AG---TG
* * *
931517 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
*
931538 TATACAATGTTACA-ACAAGCAATC
1 TATACAATGTTACATAC-AG---TG
* * *
931562 TATACATTGGTACATATAGTG
1 TATACAATGTTACATACAGTG
931583 TATACAATGTTACA
1 TATACAATGTTACA
931597 ACATGCAATC
Statistics
Matches: 295, Mismatches: 62, Indels: 78
0.68 0.14 0.18
Matches are distributed among these distances:
20 10 0.03
21 163 0.55
24 96 0.33
25 20 0.07
28 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
TATACAATGTTACATACAGTG
Found at i:931260 original size:45 final size:45
Alignment explanation
Indices: 931180--931688 Score: 778
Period size: 45 Copynumber: 11.3 Consensus size: 45
931170 AATACGCTGA
* * * *
931180 TATACAATGTT---ACATGCAGTGTATACAATGTTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
*
931222 TATACAATGTTACAACATGCAATTTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
931267 TATACAATTAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
1 TATAC----AATGTTACAACATGCAATCTATACATTGGTACATATAGTG
931316 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
931361 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
* * * *
931406 TATACAATGTT---ACATGCAGTGTATACAATGTTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
931448 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
* *
931493 TATACAGTGTTACAACAAGCAATCTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
*
931538 TATACAATGTTACAACAAGCAATCTATACATTGGTACATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
*
931583 TATACAATGTTACAACATGCAATCTATACATTGGTGCATATAGTG
1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
*
931628 TATACAATTAATGTTACAACATGCAATCTATACATTAGTACATATAGTG
1 TATAC----AATGTTACAACATGCAATCTATACATTGGTACATATAGTG
931677 TATACAATGTTA
1 TATACAATGTTA
931689 TACCATGCGA
Statistics
Matches: 433, Mismatches: 20, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
42 49 0.11
45 297 0.69
49 87 0.20
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (45 bp):
TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG
Found at i:931809 original size:24 final size:24
Alignment explanation
Indices: 931675--931817 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
931665 GTACATATAG
* * * *
931675 TGTATACAATGTTATACCATGCGA
1 TGTATTCAATGTTACACAATGCAA
931699 TGTATTCATAATG--ACACAATGCAA
1 TGTATTC--AATGTTACACAATGCAA
931723 TGTATTCAATGTTACACAATGCAA
1 TGTATTCAATGTTACACAATGCAA
931747 TGTATTCAATGTTACACAATGCAA
1 TGTATTCAATGTTACACAATGCAA
931771 TGTATTCAATGTTACACAATGCAA
1 TGTATTCAATGTTACACAATGCAA
* *
931795 TGTATTCAATATTACACCATGCA
1 TGTATTCAATGTTACACAATGCA
931818 TTAAGGCACC
Statistics
Matches: 109, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
22 4 0.04
24 101 0.93
26 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (24 bp):
TGTATTCAATGTTACACAATGCAA
Found at i:938144 original size:4 final size:4
Alignment explanation
Indices: 938135--938187 Score: 79
Period size: 4 Copynumber: 13.2 Consensus size: 4
938125 TTAGAATCTA
* * *
938135 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TCTC TCTC TCTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
938183 TGTC T
1 TGTC T
938188 CTGTCTCTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.00, C:0.30, G:0.19, T:0.51
Consensus pattern (4 bp):
TGTC
Found at i:938176 original size:2 final size:2
Alignment explanation
Indices: 938169--938225 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
938159 TGTCTGTCTG
* *
938169 TC TC TC TC TC TC TC TG TC TC TG TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
938211 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
938226 GTTTCCTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.51
Consensus pattern (2 bp):
TC
Found at i:938188 original size:8 final size:8
Alignment explanation
Indices: 938135--938221 Score: 88
Period size: 8 Copynumber: 11.1 Consensus size: 8
938125 TTAGAATCTA
*
938135 TGTCTGTC
1 TGTCTCTC
*
938143 TGTCTGTC
1 TGTCTCTC
*
938151 TGTCTGTC
1 TGTCTCTC
*
938159 TGTCTGTC
1 TGTCTCTC
938167 TGTCTCTC
1 TGTCTCTC
*
938175 TCTCTCTC
1 TGTCTCTC
938183 TG--TCTC
1 TGTCTCTC
938189 TGTCTCTC
1 TGTCTCTC
*
938197 TCTCTCTC
1 TGTCTCTC
*
938205 TCTCTCTC
1 TGTCTCTC
*
938213 TCTCTCTC
1 TGTCTCTC
938221 T
1 T
938222 CTCTGTTTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
6 6 0.08
8 67 0.92
ACGTcount: A:0.00, C:0.37, G:0.13, T:0.51
Consensus pattern (8 bp):
TGTCTCTC
Found at i:938188 original size:12 final size:12
Alignment explanation
Indices: 938141--938227 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
938131 TCTATGTCTG
* *
938141 TCTGTCTGTCTG
1 TCTGTCTCTCTC
* *
938153 TCTGTCTGTCTG
1 TCTGTCTCTCTC
938165 TCTGTCTCTCTC
1 TCTGTCTCTCTC
*
938177 TC--TCTCTGTC
1 TCTGTCTCTCTC
938187 TCTGTCTCTCTC
1 TCTGTCTCTCTC
*
938199 TCTCTCTCTCTC
1 TCTGTCTCTCTC
*
938211 TCTCTCTCTCTC
1 TCTGTCTCTCTC
938223 TCTGT
1 TCTGT
938228 TTCCTGTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.13
12 58 0.87
ACGTcount: A:0.00, C:0.38, G:0.11, T:0.51
Consensus pattern (12 bp):
TCTGTCTCTCTC
Found at i:938576 original size:44 final size:44
Alignment explanation
Indices: 938513--938622 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
938503 CATAAGATCA
*
938513 TTAGGATCGTAGGACCTTGACGGAAGGATCATAGGCCAAAGACG
1 TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG
**** * * *
938557 TTAGGATCATAGGACCTTGATTTTAGGATTATAGGCCAATGCCG
1 TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG
938601 TTAGGATCATAGGACCTTGACG
1 TTAGGATCATAGGACCTTGACG
938623 TTGGAAGGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (44 bp):
TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG
Found at i:938582 original size:22 final size:22
Alignment explanation
Indices: 938513--938624 Score: 102
Period size: 22 Copynumber: 5.1 Consensus size: 22
938503 CATAAGATCA
*
938513 TTAGGATCGTAGGACCTTGACG
1 TTAGGATCATAGGACCTTGACG
** **
938535 GAAGGATCATAGG-CCAAAGACG
1 TTAGGATCATAGGACC-TTGACG
**
938557 TTAGGATCATAGGACCTTGATT
1 TTAGGATCATAGGACCTTGACG
* * *
938579 TTAGGATTATAGG-CCAATGCCG
1 TTAGGATCATAGGACC-TTGACG
938601 TTAGGATCATAGGACCTTGACG
1 TTAGGATCATAGGACCTTGACG
938623 TT
1 TT
938625 GGAAGGCTAG
Statistics
Matches: 67, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
21 4 0.06
22 59 0.88
23 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (22 bp):
TTAGGATCATAGGACCTTGACG
Found at i:939546 original size:2 final size:2
Alignment explanation
Indices: 939539--939596 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
939529 AATCAGGTAC
939539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
939581 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
939597 NATAATTCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:939790 original size:251 final size:250
Alignment explanation
Indices: 939347--939826 Score: 933
Period size: 251 Copynumber: 1.9 Consensus size: 250
939337 ATTTAATGAT
939347 ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC
1 ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC
939412 CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT
66 CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT
*
939477 ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTCAGAAAGAAATCAGGTACAGA
131 ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAGA
939542 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
196 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
939597 NATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATG
1 -ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATG
939662 CCAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTG
65 CCAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTG
*
939727 TACGCGCGAATCTTTGACACTGGACGTGTGTAGGAACATATACCTAAGAAAGAAATCAGGTACAG
130 TACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAG
939792 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
195 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
939827 ATATACCTAA
Statistics
Matches: 227, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
251 227 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.19
Consensus pattern (250 bp):
ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC
CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT
ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAGA
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
Found at i:939797 original size:2 final size:2
Alignment explanation
Indices: 939790--939826 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
939780 AATCAGGTAC
939790 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
939827 ATATACCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:940654 original size:20 final size:20
Alignment explanation
Indices: 940629--940693 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
940619 ACGTGCCCAT
940629 TCCTAGCGACATTCCCGACA
1 TCCTAGCGACATTCCCGACA
* * *
940649 TCCTAGAGTA-AGTTCTC-A-T
1 TCCTAGCG-ACA-TTCCCGACA
*
940668 TTCTAGCGACATTCCCGACA
1 TCCTAGCGACATTCCCGACA
940688 TCCTAG
1 TCCTAG
940694 AGTAAGTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 14 0.44
21 5 0.16
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (20 bp):
TCCTAGCGACATTCCCGACA
Found at i:940685 original size:39 final size:39
Alignment explanation
Indices: 940626--942045 Score: 1364
Period size: 39 Copynumber: 36.9 Consensus size: 39
940616 AGAACGTGCC
* *
940626 CATTCCTAGCGACATTCCCGACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
*
940665 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTTT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* ** * * *
940704 CATTCCTAGC-ATTTTTCCCAACATCCTAGAGTTAGTTAC
1 CATTTCTAGCGA-CATTCCCGACATCCTAGAGTAAGTTAT
* * *
940743 CATTTCTATCGACATTCCCGACATCTTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
940782 CATTCCTACCGACATTCCCGACATCTTAGAGTAAGTTTT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * *
940821 CA-TTCTAAGCGACACTCCTGAAATCCTAGAGTAAGTTAT
1 CATTTCT-AGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
940860 CATTTCTAGCGATATTCCTGACATCCTAGAGTTAGATAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * ** * *
940899 CATTTTTAGCCACACCCCCGA-ATTCTTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACA-TCCTAGAGTAAGTTAT
* * * *
940938 CATTCCTATCGACATTCCCGACATCTTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * * *
940977 CATTCCTATCGACATTCTCGACATCTTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * **
941016 CA-TTCTTAGAGAAACTCTTGACATCCTAGAGTAAGTTAT
1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * *
941055 CATTTCTGGCGACATTCCCGACATCCTAGAATAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941094 CATTCCAAGCGACATTCCCGATATCCTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * * *
941133 CATTCCTATCGACATTCCCGACATCTTAGAGTAATTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
941172 CATTCCAAGCGACATTCCCGACATCCTAGAGTAAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * *
941211 -A-AT-T-----C-TTACCGACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941241 CATTCCAAGCGACATTCCCGATATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
*
941280 CATTCCTAG-GAACATTCCCGACATCCTAGAGTAAGTTAT
1 CATTTCTAGCG-ACATTCCCGACATCCTAGAGTAAGTTAT
*
941319 CA-TTCTTAACGACATTCCCGACATCCTAGAGTAAGTTAT
1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
941358 CA-TTCTTAACGACATTCCCGACATCCTAGAGTAAGTTTT
1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * * *
941397 CATTCCTAGC-ATTATTCCCAACATCTTAGAGTTAGTTAT
1 CATTTCTAGCGA-CATTCCCGACATCCTAGAGTAAGTTAT
* *
941436 CA--T-T--C--C--TACCGACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941466 CATTCCAAGCGACATTCCCGATATCCTAGAGTAAGTAAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
941505 -A-AT-T-----C-TTGCCGACATCCTAGAGTAAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * ***
941535 CATTCCTACCAACATTCTTAACATCCTAGAGTAAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
941574 CATTTCTAGCGACATTCCTGACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
** *
941613 CATTTCTAGCGACATTCCTAACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
941652 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
*
941691 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTCT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941730 CATTTCTAGCGATATTCCTGACATCTTAAAGTAAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* ** *
941769 CA-TTCTTAGCGACACTCCTTACATCCTAAAGTAAGTTAT
1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941808 CATTTCTAGCGATATTCTCGACATCCTAGAGTTAGATAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * *
941847 CATTTCTAGCGATATTCCCGACATCTTAGAGTTAGTTAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* * * *
941886 CATTTCTAGCGATATTCTCGACATCCTAGAGTTAGATAT
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
941925 CATTTCTAGCGATATTCCCGACATCCTAGCCGGAGTAAATTAT
1 CATTTCTAGCGACATTCCCGACATCCTA----GAGTAAGTTAT
* * * * *
941968 TATTCCCAGCGACATTCCTGACATCCTAGAGTAAGTTAC
1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
* *
942007 CATCTCTAGCGACAAATTCCCGACATCCTAGAGTCAGTT
1 CATTTCTAGCGAC--ATTCCCGACATCCTAGAGTAAGTT
942046 CCTTGCGACA
Statistics
Matches: 1152, Mismatches: 181, Indels: 94
0.81 0.13 0.07
Matches are distributed among these distances:
30 66 0.06
31 4 0.00
33 1 0.00
34 1 0.00
35 1 0.00
36 1 0.00
37 1 0.00
38 18 0.02
39 991 0.86
40 15 0.01
41 22 0.02
43 31 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (39 bp):
CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT
Found at i:941254 original size:30 final size:30
Alignment explanation
Indices: 941189--941255 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
941179 AGCGACATTC
**
941189 CCGACATCCTAGAGTAAGTTATAATTCTTA
1 CCGACATCCTAGAGTAAGTTATAATTCCAA
* *
941219 CCGACATCCTAGAGTAAGTTCTCATTCCAA
1 CCGACATCCTAGAGTAAGTTATAATTCCAA
*
941249 GCGACAT
1 CCGACAT
941256 TCCCGATATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (30 bp):
CCGACATCCTAGAGTAAGTTATAATTCCAA
Found at i:941288 original size:19 final size:19
Alignment explanation
Indices: 941225--941288 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
941215 CTTACCGACA
941225 TCCTAGAGTAAGTTCTCAT
1 TCCTAGAGTAAGTTCTCAT
* * *
941244 TCCAAGCG-ACA-TTCCCGAT
1 TCCTAGAGTA-AGTTCTC-AT
941263 ATCCTAGAGTAAGTTCTCAT
1 -TCCTAGAGTAAGTTCTCAT
941283 TCCTAG
1 TCCTAG
941289 GAACATTCCC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 5 0.15
19 15 0.44
20 9 0.26
21 5 0.15
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (19 bp):
TCCTAGAGTAAGTTCTCAT
Found at i:941451 original size:30 final size:30
Alignment explanation
Indices: 941417--941480 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
941407 ATTATTCCCA
* * *
941417 ACATCTTAGAGTTAGTTATCATTCCTACCG
1 ACATCCTAGAGTAAGTTATCATTCCAACCG
* *
941447 ACATCCTAGAGTAAGTTCTCATTCCAAGCG
1 ACATCCTAGAGTAAGTTATCATTCCAACCG
941477 ACAT
1 ACAT
941481 TCCCGATATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (30 bp):
ACATCCTAGAGTAAGTTATCATTCCAACCG
Found at i:950701 original size:10 final size:10
Alignment explanation
Indices: 950686--950723 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
950676 TTCCGCTTGA
950686 ATTTGGGTCC
1 ATTTGGGTCC
*
950696 ATTTGGGTTC
1 ATTTGGGTCC
950706 ATTTGGGTCC
1 ATTTGGGTCC
950716 ATTTGGGT
1 ATTTGGGT
950724 AAATCGACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45
Consensus pattern (10 bp):
ATTTGGGTCC
Found at i:950711 original size:20 final size:20
Alignment explanation
Indices: 950686--950723 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
950676 TTCCGCTTGA
950686 ATTTGGGTCCATTTGGGTTC
1 ATTTGGGTCCATTTGGGTTC
950706 ATTTGGGTCCATTTGGGT
1 ATTTGGGTCCATTTGGGT
950724 AAATCGACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45
Consensus pattern (20 bp):
ATTTGGGTCCATTTGGGTTC
Found at i:952138 original size:10 final size:10
Alignment explanation
Indices: 952123--952160 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
952113 TTCCGCTTGA
952123 ATTTGGGTCC
1 ATTTGGGTCC
*
952133 ATTTGGGTTC
1 ATTTGGGTCC
952143 ATTTGGGTCC
1 ATTTGGGTCC
952153 ATTTGGGT
1 ATTTGGGT
952161 AAATCGACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45
Consensus pattern (10 bp):
ATTTGGGTCC
Found at i:952148 original size:20 final size:20
Alignment explanation
Indices: 952123--952160 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
952113 TTCCGCTTGA
952123 ATTTGGGTCCATTTGGGTTC
1 ATTTGGGTCCATTTGGGTTC
952143 ATTTGGGTCCATTTGGGT
1 ATTTGGGTCCATTTGGGT
952161 AAATCGACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45
Consensus pattern (20 bp):
ATTTGGGTCCATTTGGGTTC
Found at i:964360 original size:33 final size:33
Alignment explanation
Indices: 964311--965071 Score: 370
Period size: 33 Copynumber: 21.6 Consensus size: 33
964301 GAGTCAATTA
* *
964311 ACATAGTGGTAAGTGTTGTGGAGTCTTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
* * * *
964344 ACAAAGCGGTAGGTGTTGTTAAGT-TCTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG
* * ** *
964377 ACATAACGGTAAGTGATGAAGAGTCTTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
** *
964410 ACATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAG-TCT---TT--GGTTG
*
964449 A-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTTGGTTG
1 ACA-T--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG
* ** *
964488 ACATGGAAGTAAGTGTTGTGGAGTCTTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
*
964521 ACATAGCGGTAGGTGTTGTTGAGT-TCTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG
*** * *
964554 ACATAGAAATAAGTGTTGTAGAGTCTTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
* ** * *
964587 ATATAGTAGTAGGTGTTGTTGAGT-TCTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG
* *
964620 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG
1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG
** *
964659 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
*
964692 ACATAGCGGT-AGCTGTTGTTGAGT-TCTCGGTTG
1 ACATAGCGGTAAG-TGTTGTTGAGTCT-TTGGTTG
* **
964725 ACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTG
1 ACAT--AG---CG-GTAAGTGTTGTTGAGTCTTTGGTTG
* ** *
964764 ATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAG-TCT---TT--GGTTG
* *
964803 A-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG
1 ACA-T--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG
** *
964842 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
* * *
964875 ACATAGCGGTAGGTGTTGTTAAGT-TCTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG
* *
964908 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG
1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG
* ** * *
964947 ATATAGTAGTAGGTGTTGTTGAGT-TCTCGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG
* *
964980 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG
1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG
** *
965019 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG
1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
*
965052 ACATAGCGGTAGGTGTTGTT
1 ACATAGCGGTAAGTGTTGTT
965072 NNNNNNNNNN
Statistics
Matches: 555, Mismatches: 107, Indels: 132
0.70 0.13 0.17
Matches are distributed among these distances:
32 8 0.01
33 344 0.62
34 8 0.01
35 5 0.01
36 8 0.01
37 7 0.01
38 6 0.01
39 122 0.22
40 8 0.01
41 5 0.01
42 2 0.00
44 6 0.01
45 26 0.05
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35
Consensus pattern (33 bp):
ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG
Found at i:964615 original size:177 final size:174
Alignment explanation
Indices: 964319--965071 Score: 1128
Period size: 177 Copynumber: 4.3 Consensus size: 174
964309 TAACATAGTG
*
964319 GTAAGTGTTGTGGAGTCTTTGGTTGACAAAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACAT--A
1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
* * *
964382 -ACGGTAAGTGAT-GAAGAGTCTTCGGTTGACATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG-C
66 GACAGTAAGTG-TCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGAC
* *
964444 GGTTGAAGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTTGGTTGACATGGAA
130 ------A-TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
* *
964496 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTGAGTTCTTGGTTGACATAGA
1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
*
964561 -A-A-TAAGTGTTGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA
66 GACAGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA
964623 TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
131 TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
* *
964667 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGCTGTTGTTGAGTTCTCGGTTGACATAGA
1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
* *
964732 GATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG
66 G--AC-AGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG
964797 -CGGTTGAAGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
128 AC------A-TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
964850 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
*
964915 GGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG
66 -G-AC-AGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG
964980 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
128 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
965027 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTT
1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTT
965072 NNNNNNNNNN
Statistics
Matches: 541, Mismatches: 16, Indels: 38
0.91 0.03 0.06
Matches are distributed among these distances:
171 105 0.19
172 1 0.00
174 1 0.00
176 3 0.01
177 255 0.47
178 2 0.00
179 2 0.00
182 1 0.00
183 169 0.31
184 2 0.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35
Consensus pattern (174 bp):
GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA
GACAGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA
TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA
Found at i:964683 original size:105 final size:105
Alignment explanation
Indices: 964462--965062 Score: 392
Period size: 105 Copynumber: 5.7 Consensus size: 105
964452 TAGAGGTACG
* * * * * *
964462 AGTAAGTGTCGTTGAGTCTTTGGTTGACATGGAAGTAAGTGTTGTGGAG-TCTTTGGTTGACATA
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTC-TCGGTTGACATA
*
964526 GCGGTA-G-GT--GT-T-GTTGAGTTCTT-GGTTGACATAGA
65 GAGGTACGAGTAAGTGTCGTTGAG-TCTTCGGTTGACATAGA
* * * *
964561 AATAAGTGTTGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG
964626 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA
66 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA
* * ** *
964666 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGCTGTTGTTGAGTTCTCGGTTGACATAG
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG
* * * *
964731 AGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGT
66 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA
* *
964771 AGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTGA-AGTAGAGGTACGAGTAAGTGTCGTTGAG-TC
1 AGTAAGTGTTGTTGAG---TC--TT-CGGTTGACA-TAGAAGTA-G-GT--GT-T-GTTGAGTTC
* * * *
964834 TTCGGTTGACAT--A-G-A--AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGC
53 -TCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA
* * * *
964882 GGTAGGTGTTGTTAAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAG-TCTTCGGT
1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAAGTA-G-GT--GT-T-GTTGAGTTC-TCGGT
*
964945 TGATATAGTA-GTA-G-GT--GT-T-GTTGAGT-TCTCGGTTGACATAGAGGTA
58 TGACATAG-AGGTACGAGTAAGTGTCGTTGAGTCT-TCGGTTGACAT--A-G-A
* * * *
964991 CGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAAGTAAGTGTTGTGGAG-TCTTTGGTTGACA
1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTC-TCGGTTGACA
*
965055 TAGCGGTA
63 TAGAGGTA
965063 GGTGTTGTTN
Statistics
Matches: 414, Mismatches: 50, Indels: 70
0.78 0.09 0.13
Matches are distributed among these distances:
99 56 0.14
100 3 0.01
101 2 0.00
103 2 0.00
104 6 0.01
105 211 0.51
106 4 0.01
107 5 0.01
108 6 0.01
109 5 0.01
110 3 0.01
111 84 0.20
112 2 0.00
113 2 0.00
115 3 0.01
116 3 0.01
117 17 0.04
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.35
Consensus pattern (105 bp):
AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG
AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA
Found at i:964691 original size:72 final size:71
Alignment explanation
Indices: 964462--965063 Score: 422
Period size: 72 Copynumber: 8.5 Consensus size: 71
964452 TAGAGGTACG
* * * * *
964462 AGTAAGTGTCGTTGAGTCTTTGGTTGACAT---GG-A-AGTAAGTGTTGTGGAGTCTTTGGTTGA
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTGA
*
964522 CATAGC
66 CATAGA
* * * *
964528 GGTAGGTGTTGTTGAGTTCTT-GGTTGACATAGA---A-A-TAAGTGTTGTAGAGTCTTCGGTTG
1 AGTAAGTGTTGTTGAG-TCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTG
* *
964587 ATATAGT
65 ACATAGA
*
964594 AGTAGGTGTTGTTGAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT
1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT
964658 GACATAGA
64 GACATAGA
* * * *
964666 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAG-CT--GT-T-GTTGAGT-TCTCGGTTG
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCT-TCGGTTG
964725 ACATAGAGATA
65 ACAT--AG--A
* * *
964736 CGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTA-GTAG-GT--GT-T-GTTGAGTTCTCGGT
1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAG-AGGTAGAGTAAGTGTCGTTGAG---TC--T
964795 TGCGGTTGA-AGTAGAGGTA
58 T-CGGTTGACA-T--A-G-A
* * * *
964814 CGAGTAAGTGTCGTTGAGTCTTCGGTTGACAT--A-G-A-AGTAAGTGTTGTGGAGTCTTTGGTT
1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTT
*
964874 GACATAGC
64 GACATAGA
* * *
964882 GGTAGGTGTTGTTAAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT
1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT
* *
964946 GATATAGT
64 GACATAGA
*
964954 AGTAGGTGTTGTTGAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT
1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT
965018 GACATAGA
64 GACATAGA
* * *
965026 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAG
1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAG
965064 GTGTTGTTNN
Statistics
Matches: 446, Mismatches: 46, Indels: 83
0.78 0.08 0.14
Matches are distributed among these distances:
64 1 0.00
65 4 0.01
66 118 0.26
67 7 0.02
68 5 0.01
69 3 0.01
70 4 0.01
71 3 0.01
72 233 0.52
73 5 0.01
74 3 0.01
75 5 0.01
76 2 0.00
77 3 0.01
78 49 0.11
79 1 0.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35
Consensus pattern (71 bp):
AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTGA
CATAGA
Found at i:964874 original size:78 final size:78
Alignment explanation
Indices: 964719--964865 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 78
964709 GTTGAGTTCT
* * * *
964719 CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTAGTAGGTGTTGTT
1 CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGTG
964784 GAGTTCTCGGTTG
66 GAGTTCTCGGTTG
* *
964797 CGGTTGA-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAAGTAAGTGTTGT
1 CGGTTGACA-TAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGT
964861 GGAGT
65 GGAGT
964866 CTTTGGTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
77 1 0.02
78 61 0.98
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33
Consensus pattern (78 bp):
CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGTG
GAGTTCTCGGTTG
Found at i:973662 original size:112 final size:112
Alignment explanation
Indices: 973465--973745 Score: 544
Period size: 112 Copynumber: 2.5 Consensus size: 112
973455 NNNNNNNNNN
*
973465 GAACTAACACAGAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCATGTTTGTG
1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG
973530 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG
66 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG
*
973577 GAACTAACACAGAATATACAAGATAAACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG
1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG
973642 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG
66 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG
973689 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
973746 CGTCAGGGTT
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 166 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (112 bp):
GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG
TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG
Found at i:974625 original size:11 final size:11
Alignment explanation
Indices: 974609--974662 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
974599 ATTTTTTTAA
974609 TGGCTTAAAGG
1 TGGCTTAAAGG
974620 TGGCTTAAAGG
1 TGGCTTAAAGG
*
974631 TAGCTTAAAGG
1 TGGCTTAAAGG
974642 TGGCTTAAAGG
1 TGGCTTAAAGG
974653 TGGCTTAAAG
1 TGGCTTAAAG
974663 AAGTTTAGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:974710 original size:11 final size:11
Alignment explanation
Indices: 974694--974722 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
974684 ATAAGTTGTC
974694 CTTAAAGGTGG
1 CTTAAAGGTGG
974705 CTTAAAGGTGG
1 CTTAAAGGTGG
974716 CTTAAAG
1 CTTAAAG
974723 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:974804 original size:11 final size:11
Alignment explanation
Indices: 974788--974819 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
974778 GCAATACATA
974788 TAGCTTAAAGG
1 TAGCTTAAAGG
974799 TAGCTTAAAGG
1 TAGCTTAAAGG
*
974810 TGGCTTAAAG
1 TAGCTTAAAG
974820 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:974841 original size:11 final size:11
Alignment explanation
Indices: 974825--974863 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
974815 TAAAGATCGT
974825 CTTTAAGCTAC
1 CTTTAAGCTAC
*
974836 CTTTAAAC-AC
1 CTTTAAGCTAC
*
974846 CTTTAAGCTAT
1 CTTTAAGCTAC
974857 CTTTAAG
1 CTTTAAG
974864 GAGAAGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:978566 original size:2 final size:2
Alignment explanation
Indices: 978561--978590 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
978551 TATATATATT
*
978561 TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
978591 GAGATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:981210 original size:9 final size:9
Alignment explanation
Indices: 981192--981223 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
981182 AAAATTGCGG
*
981192 GGTGATTTT
1 GGTGAGTTT
981201 GGTGAGTTT
1 GGTGAGTTT
981210 GGTGAGTTT
1 GGTGAGTTT
981219 GGTGA
1 GGTGA
981224 AGTAGGTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (9 bp):
GGTGAGTTT
Found at i:983428 original size:98 final size:98
Alignment explanation
Indices: 983255--983438 Score: 271
Period size: 98 Copynumber: 1.9 Consensus size: 98
983245 TCATGATCAA
* * * *
983255 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAGCACAATTAAAGTTGATCTGACAGAAG
1 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAAG
*
983320 GCACGCTTCTGCCAAAAGTATATGTGTACTGTT
66 GCAAGCTTCTGCCAAAAGTATATGTGTACTGTT
** *
983353 AGGCTAATTGCTGCTGCTTATACAAACAGTGTTATTGAACATAATAAAAGATGATCTGA-AAAAG
1 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAA-
*
983417 GGCAAGGTTCTGCCAAAAGTAT
65 GGCAAGCTTCTGCCAAAAGTAT
983439 TTGAATACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
97 3 0.04
98 73 0.96
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (98 bp):
AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAAG
GCAAGCTTCTGCCAAAAGTATATGTGTACTGTT
Found at i:983616 original size:22 final size:24
Alignment explanation
Indices: 983586--983631 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
983576 AATATTTGCC
983586 CTTACATACTAGT-A-TACAATAT
1 CTTACATACTAGTAATTACAATAT
*
983608 CTTATATACTAGTAATTACAATAT
1 CTTACATACTAGTAATTACAATAT
983632 AATTTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 1 0.05
24 8 0.38
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (24 bp):
CTTACATACTAGTAATTACAATAT
Found at i:996939 original size:12 final size:12
Alignment explanation
Indices: 996922--996946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
996912 ACAAATTATA
996922 TATAATAATAAT
1 TATAATAATAAT
996934 TATAATAATAAT
1 TATAATAATAAT
996946 T
1 T
996947 GCAAGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATAATAAT
Found at i:998726 original size:18 final size:18
Alignment explanation
Indices: 998703--998738 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
998693 CAGACTTGTC
*
998703 TTTGAGTTTTTTCTCAAA
1 TTTGAGATTTTTCTCAAA
998721 TTTGAGATTTTTCTCAAA
1 TTTGAGATTTTTCTCAAA
998739 CGTGCGTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTGAGATTTTTCTCAAA
Found at i:999831 original size:21 final size:21
Alignment explanation
Indices: 999745--1000016 Score: 203
Period size: 21 Copynumber: 13.0 Consensus size: 21
999735 AATTATGATC
*
999745 TTTTCCATTTGTATTATATAAA
1 TTTTCCATTTGTATTGTAT-AA
* **
999767 TATTT--ATTTGTAATGTACCA
1 T-TTTCCATTTGTATTGTATAA
* * *
999787 TTTTCTATTTGTAATGTATCA
1 TTTTCCATTTGTATTGTATAA
* *
999808 TTTTCTATTTGTATTCTATAA
1 TTTTCCATTTGTATTGTATAA
*
999829 TTTTCCATTTGCATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
999850 ATTTCCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
* *
999871 TTTTCTATTTGTTTTGTATAA
1 TTTTCCATTTGTATTGTATAA
* *
999892 TTTTCCATTTGTATTCTTTAA
1 TTTTCCATTTGTATTGTATAA
*
999913 TTGTCCATTTGTATTG-AGTAA
1 TTTTCCATTTGTATTGTA-TAA
* * * **
999934 TATTCTATTTGCATTGTACGA
1 TTTTCCATTTGTATTGTATAA
* ** *
999955 GTTT-CATAAGTATTCTATAAA
1 TTTTCCATTTGTATTGTAT-AA
* * * *
999976 TTTT-TATTTATATTCTCTAA
1 TTTTCCATTTGTATTGTATAA
*
999996 TTTTCCATTTGTATTCTATAA
1 TTTTCCATTTGTATTGTATAA
1000017 GAAGATGGGT
Statistics
Matches: 196, Mismatches: 47, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.02
20 16 0.08
21 172 0.88
22 2 0.01
23 3 0.02
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (21 bp):
TTTTCCATTTGTATTGTATAA
Found at i:1000815 original size:21 final size:21
Alignment explanation
Indices: 1000791--1001049 Score: 194
Period size: 21 Copynumber: 12.4 Consensus size: 21
1000781 TATAGAACAA
*
1000791 AAATTGAAAATTATACAATAC
1 AAATGGAAAATTATACAATAC
*
1000812 AAATGGAAAATGATACAATAC
1 AAATGGAAAATTATACAATAC
* * **
1000833 AAATAGCAAATGGTACAATAC
1 AAATGGAAAATTATACAATAC
1000854 AAAT--AAATATT-TACAAAATAC
1 AAATGGAAA-ATTATAC--AATAC
*
1000875 AAATGGAAAATTATAGAATAC
1 AAATGGAAAATTATACAATAC
*
1000896 AAATGGAAAATTATAGAATAC
1 AAATGGAAAATTATACAATAC
* * * * *
1000917 AATTTGACATTTATATAATAC
1 AAATGGAAAATTATACAATAC
*
1000938 AAGTGGAAAATTATACAATAC
1 AAATGGAAAATTATACAATAC
* * *
1000959 AAA-AG-AAATTCATATAATGC
1 AAATGGAAAATT-ATACAATAC
*
1000979 AAATGGAAAATTATAGAATAC
1 AAATGGAAAATTATACAATAC
* * *
1001000 AAAT-AAAAAGTTAAACAATGC
1 AAATGGAAAA-TTATACAATAC
1001021 -AAT--AAATATTTATACAATAC
1 AAATGGAAA-A-TTATACAATAC
*
1001041 CAATGGAAA
1 AAATGGAAA
1001050 TGATTGAGTA
Statistics
Matches: 192, Mismatches: 32, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
19 13 0.07
20 30 0.16
21 133 0.69
22 8 0.04
23 8 0.04
ACGTcount: A:0.56, C:0.09, G:0.10, T:0.25
Consensus pattern (21 bp):
AAATGGAAAATTATACAATAC
Found at i:1010397 original size:12 final size:13
Alignment explanation
Indices: 1010371--1010401 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1010361 CAGAAATTTA
1010371 AGATTTGAGGCTG
1 AGATTTGAGGCTG
1010384 AGATTTGA-GCTG
1 AGATTTGAGGCTG
1010396 AGATTT
1 AGATTT
1010402 TTATATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (13 bp):
AGATTTGAGGCTG
Found at i:1012670 original size:25 final size:25
Alignment explanation
Indices: 1012640--1012720 Score: 135
Period size: 25 Copynumber: 3.2 Consensus size: 25
1012630 AGTCTCACAG
*
1012640 GCATCTTATAATATTCATTCCATAT
1 GCATCTTATCATATTCATTCCATAT
* *
1012665 ACATCTTATCATATTCATACCATAT
1 GCATCTTATCATATTCATTCCATAT
1012690 GCATCTTATCATATTCATTCCATAT
1 GCATCTTATCATATTCATTCCATAT
1012715 GCATCT
1 GCATCT
1012721 CATTATGTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (25 bp):
GCATCTTATCATATTCATTCCATAT
Found at i:1020696 original size:2 final size:2
Alignment explanation
Indices: 1020689--1020760 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
1020679 AATTGAAATT
* * *
1020689 TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC CC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1020731 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1020761 ATACCAACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.01, C:0.50, G:0.01, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1027197 original size:2 final size:2
Alignment explanation
Indices: 1027190--1027240 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1027180 CTTTATCATT
1027190 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1027232 GA GA GA GA G
1 GA GA GA GA G
1027241 TGTGTGTGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1028018 original size:2 final size:2
Alignment explanation
Indices: 1028011--1028071 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1028001 AATTTTTGAT
*
1028011 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1028053 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1028072 ATGTTTCTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1028638 original size:40 final size:40
Alignment explanation
Indices: 1028528--1028627 Score: 191
Period size: 40 Copynumber: 2.5 Consensus size: 40
1028518 TATTTCTATA
1028528 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
1028568 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
*
1028608 TTTAGAAAGTACAGCTCAAT
1 TTTAGAAAGTACAGGTCAAT
1028628 TTGCATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (40 bp):
TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
Found at i:1035852 original size:4 final size:4
Alignment explanation
Indices: 1035843--1035893 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
1035833 ACTAAAGTGG
* * * * *
1035843 GACA GACA GACA GACA GACA GACA GACG GACG GTCG GACG GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1035891 GAC
1 GAC
1035894 TGACGCAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.39, C:0.25, G:0.33, T:0.02
Consensus pattern (4 bp):
GACA
Found at i:1042386 original size:21 final size:21
Alignment explanation
Indices: 1042362--1042453 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
1042352 ATCTGACACC
1042362 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
1042383 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
*
1042404 ACCTGTCAGATAATTATGTTC-
1 ACTTGTCAGATAATTATG-TCG
* ** *
1042425 ACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCG
1042446 ACTTGTCA
1 ACTTGTCA
1042454 CTTATTCACG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.07
21 51 0.86
22 4 0.07
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:1042412 original size:42 final size:42
Alignment explanation
Indices: 1042365--1042453 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
1042355 TGACACCACT
*
1042365 TGTCAGATAATTATG-TCGACTTGTCAGATCTTGATGTCGACC
1 TGTCAGATAATTATGTTC-ACTTGTCAGATCTTGAAGTCGACC
* * *
1042407 TGTCAGATAATTATGTTCACTTGTCAGTTCTTTAAGTCGACT
1 TGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCGACC
1042449 TGTCA
1 TGTCA
1042454 CTTATTCACG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (42 bp):
TGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCGACC
Found at i:1042556 original size:21 final size:21
Alignment explanation
Indices: 1042530--1042689 Score: 196
Period size: 21 Copynumber: 7.7 Consensus size: 21
1042520 AATAATATTT
* *
1042530 TCTGACAAGTCGACATTATGA
1 TCTGACAAGTCGACATAATTA
*
1042551 TCTGACAAGTCGACATAATCA
1 TCTGACAAGTCGACATAATTA
***
1042572 TCTTTTAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
*
1042593 TTTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
1042614 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
1042635 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAATTA
* * *
1042655 TCTGACAAGACAACATCATTA
1 TCTGACAAGTCGACATAATTA
1042676 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
1042690 TTACAATATG
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
20 16 0.14
21 102 0.86
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:1042804 original size:42 final size:42
Alignment explanation
Indices: 1042743--1042825 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1042733 ATTCTTTCGG
* *
1042743 TCAGATAATTATGTTAACTTCTCAGATCTTTATGTCGACTTT
1 TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTTT
* *
1042785 TCAGATGATTATGTAAACTTGTCAGATATTTATGTCGACTT
1 TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTT
1042826 ATATGGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (42 bp):
TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTTT
Found at i:1042825 original size:21 final size:21
Alignment explanation
Indices: 1042742--1042825 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
1042732 TATTCTTTCG
* *
1042742 GTCAGATAATTATGTTAACTT
1 GTCAGATATTTATGTCAACTT
* * *
1042763 CTCAGATCTTTATGTCGACTT
1 GTCAGATATTTATGTCAACTT
* *
1042784 TTCAGATGA-TTATGTAAACTT
1 GTCAGAT-ATTTATGTCAACTT
*
1042805 GTCAGATATTTATGTCGACTT
1 GTCAGATATTTATGTCAACTT
1042826 ATATGGTATT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.43
Consensus pattern (21 bp):
GTCAGATATTTATGTCAACTT
Found at i:1042944 original size:21 final size:21
Alignment explanation
Indices: 1042919--1043012 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
1042909 ATGGTTATTT
*
1042919 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCAACATAAATA
**
1042940 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAATA
* * *
1042961 TATGACAAGTCGACAT-TATCA
1 TCTGACAAGTCAACATAAAT-A
* * * *
1042982 TATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAATA
1043003 TCTGACAAGT
1 TCTGACAAGT
1043013 GGTGGCAGAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.95
22 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAATA
Found at i:1044770 original size:21 final size:21
Alignment explanation
Indices: 1044722--1044770 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1044712 TACAAGATAA
* * * *
1044722 ACGATAAGATATGATTCATGC
1 ACGATAGGATAGGATTAACGC
1044743 ACGATAGGATAGGATTAACGC
1 ACGATAGGATAGGATTAACGC
1044764 ACGATAG
1 ACGATAG
1044771 AACAGTATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (21 bp):
ACGATAGGATAGGATTAACGC
Found at i:1049484 original size:21 final size:21
Alignment explanation
Indices: 1049460--1049593 Score: 83
Period size: 21 Copynumber: 6.4 Consensus size: 21
1049450 CGATAAACCT
1049460 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* *
1049481 GATAGGAATAACACACGATAG
1 GATAGGATTAACGCACGATAG
* * * ***
1049502 AAAAGTAAGCACGCACGATAG
1 GATAGGATTAACGCACGATAG
* *
1049523 GATAGGATAAACGCATGATAG
1 GATAGGATTAACGCACGATAG
* * * *
1049544 AACAGTA-TACACGCACGATAC
1 GATAGGATTA-ACGCACGATAG
* * *
1049565 GATAGAATTGAA-ACACAATAG
1 GATAGGATT-AACGCACGATAG
1049586 GATAGGAT
1 GATAGGAT
1049594 AGGATTGTAA
Statistics
Matches: 82, Mismatches: 28, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
20 1 0.01
21 78 0.95
22 2 0.02
23 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:1049517 original size:42 final size:42
Alignment explanation
Indices: 1049470--1049569 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
1049460 GATAGGATTA
1049470 ACGCACGATAGGATAGGA-ATAACACACGATAGAAAAGTA-AGC
1 ACGCACGATAGGATAGGATA-AACACACGATAGAAAAGTATA-C
* * *
1049512 ACGCACGATAGGATAGGATAAACGCATGATAGAACAGTATAC
1 ACGCACGATAGGATAGGATAAACACACGATAGAAAAGTATAC
*
1049554 ACGCACGATACGATAG
1 ACGCACGATAGGATAG
1049570 AATTGAAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
42 50 0.96
43 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (42 bp):
ACGCACGATAGGATAGGATAAACACACGATAGAAAAGTATAC
Found at i:1053999 original size:8 final size:8
Alignment explanation
Indices: 1053988--1054035 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
1053978 TGAAAAGTTC
1053988 ACAGACGG
1 ACAGACGG
*
1053996 ACAGACAG
1 ACAGACGG
1054004 ACAGACGG
1 ACAGACGG
* *
1054012 ACGGACAG
1 ACAGACGG
*
1054020 ACGGACGG
1 ACAGACGG
1054028 AC-GACGG
1 ACAGACGG
1054035 A
1 A
1054036 TAAACTGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
7 6 0.17
8 29 0.83
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:1054005 original size:12 final size:12
Alignment explanation
Indices: 1053988--1054035 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1053978 TGAAAAGTTC
* *
1053988 ACAGACGGACAG
1 ACAGACAGACGG
1054000 ACAGACAGACGG
1 ACAGACAGACGG
*
1054012 ACGGACAGACGG
1 ACAGACAGACGG
*
1054024 ACGGAC-GACGG
1 ACAGACAGACGG
1054035 A
1 A
1054036 TAAACTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 6 0.18
12 27 0.82
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Done.