Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 199 of 255
Found at i:66344820 original size:16 final size:17
Alignment explanation
Indices: 66344785--66344839 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
66344775 AAACTTCACT
66344785 AAATGCAAGACATAAATTA
1 AAATGCAA-ACAT-AATTA
66344804 AAATGCAAAC-TAATTA
1 AAATGCAAACATAATTA
* * *
66344820 AACTGAAAACTTAATTA
1 AAATGCAAACATAATTA
66344837 AAA
1 AAA
66344840 GTCCTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 13 0.41
17 9 0.28
18 2 0.06
19 8 0.25
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATGCAAACATAATTA
Found at i:66352338 original size:20 final size:19
Alignment explanation
Indices: 66352294--66352339 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
66352284 AACAATAAAG
*
66352294 ATTTTAGCCTTAGCATGTC
1 ATTTTAGCCTTAGCATGTA
66352313 ATTTTAGCCTTAGCATGTTA
1 ATTTTAGCCTTAGCATG-TA
66352333 ATTTTAG
1 ATTTTAG
66352340 AGTTGTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTTTAGCCTTAGCATGTA
Found at i:66352438 original size:24 final size:24
Alignment explanation
Indices: 66352417--66352472 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
66352407 AAGATTTAGT
*
66352417 ATTTATTAATATAATATATTTAAC
1 ATTTATTAACATAATATATTTAAC
* *
66352441 ATTTATTAGCATAATATATTTGAC
1 ATTTATTAACATAATATATTTAAC
*
66352465 ATTGATTA
1 ATTTATTA
66352473 GAATTAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTTATTAACATAATATATTTAAC
Found at i:66354409 original size:3 final size:3
Alignment explanation
Indices: 66354401--66354442 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
66354391 AGGAATATGT
66354401 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
66354443 TATTTAGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:66354516 original size:20 final size:20
Alignment explanation
Indices: 66354491--66354529 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66354481 CAAATAAGAA
66354491 AAATATAATAATATAAAAAG
1 AAATATAATAATATAAAAAG
* *
66354511 AAATATTATATTATAAAAA
1 AAATATAATAATATAAAAA
66354530 TTAAATTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATATAATAATATAAAAAG
Found at i:66366544 original size:93 final size:93
Alignment explanation
Indices: 66366432--66366603 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
66366422 GCCCATAAGT
* *
66366432 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
66366496 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
66366525 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
66366590 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
66366604 CAAACATCCT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:66366594 original size:46 final size:46
Alignment explanation
Indices: 66366424--66366599 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
66366414 TGTAACCCGC
* * *
66366424 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * *
66366470 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
66366520 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
66366563 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
66366600 TGCCCAAACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
45 1 0.01
46 62 0.57
47 28 0.26
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:66368965 original size:58 final size:58
Alignment explanation
Indices: 66368821--66368966 Score: 152
Period size: 57 Copynumber: 2.5 Consensus size: 58
66368811 GCCTCATAAA
* * * ** * *
66368821 TATAACAGGATTACCAGTCCAGGCCAAATCATTTTTGTAATATATGCTCAGAAGAGCT
1 TATATCAGGATTACCAGTCCAGGCAAAATCCTAATTGTAACATATGCTCAGAAGAGAT
* * * * *
66368879 CA-ATTAGGATTACCAGTTCAGGCTAAATCCTAATTGTAACATATGCTCA-AGAGGGAT
1 TATATCAGGATTACCAGTCCAGGCAAAATCCTAATTGTAACATATGCTCAGA-AGAGAT
*
66368936 TATATCAGGACTACCAGTCCAGGCAAAATCC
1 TATATCAGGATTACCAGTCCAGGCAAAATCC
66368967 CGTCAGCAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
56 1 0.01
57 44 0.63
58 25 0.36
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (58 bp):
TATATCAGGATTACCAGTCCAGGCAAAATCCTAATTGTAACATATGCTCAGAAGAGAT
Found at i:66370309 original size:25 final size:25
Alignment explanation
Indices: 66370281--66370369 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
66370271 ATAATTCGCT
* *
66370281 ACAAAAGTTTTCCAAATGGTACACC
1 ACAAAAGCTTTCCAAATGATACACC
* * * *
66370306 ACAAAGGCTTTCTAAA-GAATTCGCC
1 ACAAAAGCTTTCCAAATG-ATACACC
66370331 ACAAAAGCTTTCCAAATGATACACC
1 ACAAAAGCTTTCCAAATGATACACC
66370356 AC-AAAGACTTTCCA
1 ACAAAAG-CTTTCCA
66370370 GGGAATTTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
24 5 0.10
25 45 0.88
26 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (25 bp):
ACAAAAGCTTTCCAAATGATACACC
Found at i:66370343 original size:50 final size:50
Alignment explanation
Indices: 66370256--66370385 Score: 170
Period size: 50 Copynumber: 2.6 Consensus size: 50
66370246 ACAACTCACT
* * * * *
66370256 ACAATGACTTTCTAGATAATTCGCTACAAAAGTTTTCCAAATGGTACACC
1 ACAAAGACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACC
* *
66370306 ACAAAGGCTTTCTAAAGAATTCGCCACAAAAGCTTTCCAAATGATACACC
1 ACAAAGACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACC
* * *
66370356 ACAAAGACTTTCCAGGGAATTTGCCACAAA
1 ACAAAGACTTTCTAGAGAATTCGCCACAAA
66370386 GATTTTCTAG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (50 bp):
ACAAAGACTTTCTAGAGAATTCGCCACAAAAGCTTTCCAAATGATACACC
Found at i:66370382 original size:25 final size:25
Alignment explanation
Indices: 66370354--66370401 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
66370344 AAATGATACA
*
66370354 CCACAAAGACTTTCCAGGGAATTTG
1 CCACAAAGACTTTCCAGAGAATTTG
* *
66370379 CCACAAAGATTTTCTAGAGAATT
1 CCACAAAGACTTTCCAGAGAATT
66370402 CTCGAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (25 bp):
CCACAAAGACTTTCCAGAGAATTTG
Found at i:66373854 original size:49 final size:49
Alignment explanation
Indices: 66373795--66374014 Score: 186
Period size: 49 Copynumber: 4.6 Consensus size: 49
66373785 CATCAAAGTT
66373795 GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGCC
1 GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGCC
* * ** * ** *
66373844 GATGCCATGTCCCAGATAGGTCTTACACTGGCTCTCATCCATCG-GTGTC
1 GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAG-GCC
* * * * * *
66373893 GATGCCATGTCCTAGACAAGTCTTACACTGAC--ACAGA-A-C-AAGCT
1 GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGCC
** * * *
66373937 GGCGCCATGTCCCAGACAGGTCTTACACTAGCTTGT-ATATCTCGAGGCC
1 GATGCCATGTCCCAGACAAGTCTTACACTAACTT-TCATATATCGAGGCC
*
66373986 GATG-CATGTCCCAGACATGTCTTACACTA
1 GATGCCATGTCCCAGACAAGTCTTACACTA
66374015 GCTCTCGTCT
Statistics
Matches: 131, Mismatches: 32, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
44 27 0.21
45 1 0.01
46 3 0.02
47 2 0.02
48 26 0.20
49 72 0.55
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (49 bp):
GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGCC
Found at i:66374086 original size:46 final size:48
Alignment explanation
Indices: 66373795--66374105 Score: 185
Period size: 49 Copynumber: 6.6 Consensus size: 48
66373785 CATCAAAGTT
* ** * *
66373795 GATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGCC
1 GATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATATATCGTGGCC
* * ** *
66373844 GATGCCATGTCCCAGATAGGTCTTACACTGGCTCTCATCCATCG-GTGTC
1 GATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATATATCGTG-GCC
* * * * ** * *
66373893 GATGCCATGTCCTAGACAAGTCTTACACTGACACAGA-ACA-AGCTGG-C
1 GATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATATATCG-TGGCC
* * * * * *
66373940 G--CCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATATATCGTGGCC
* * * ** **
66373986 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCT-TAAT-ATC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATATCGTGGCC
*
66374032 GATACATGTCCCAGACATGTCTTACACTGGCTCTCATA-AT-GTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATATCGTGGCC
**
66374078 GATGCATGTCTTAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
66374106 AGTACACATA
Statistics
Matches: 201, Mismatches: 49, Indels: 27
0.73 0.18 0.10
Matches are distributed among these distances:
44 24 0.12
45 4 0.02
46 65 0.32
47 4 0.02
48 33 0.16
49 71 0.35
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATATCGTGGCC
Found at i:66394596 original size:2 final size:2
Alignment explanation
Indices: 66394591--66394619 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66394581 ATATATACAT
66394591 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 A
66394620 ACCATACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66397533 original size:20 final size:22
Alignment explanation
Indices: 66397489--66397533 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
66397479 CATATAATTT
*
66397489 TTTATAATATAATATTTCAGGA
1 TTTATAATATAATATTTCAGAA
66397511 TTTATAATATAAT-TTT-AGAA
1 TTTATAATATAATATTTCAGAA
66397531 TTT
1 TTT
66397534 TTAGTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 3 0.14
22 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTATAATATAATATTTCAGAA
Found at i:66399421 original size:17 final size:17
Alignment explanation
Indices: 66399370--66399427 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
66399360 ATATATACTT
66399370 AAAAATATAAAAATAACA
1 AAAAATATAAAAATAA-A
* *
66399388 ATATAATATAAACATAAA
1 A-AAAATATAAAAATAAA
*
66399406 AAAAATAAAAAAATAAA
1 AAAAATATAAAAATAAA
66399423 AAAAA
1 AAAAA
66399428 AATATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 18 0.53
18 3 0.09
19 13 0.38
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAATATAAAAATAAA
Found at i:66399425 original size:8 final size:8
Alignment explanation
Indices: 66399370--66399426 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
66399360 ATATATACTT
*
66399370 AAAAATAT
1 AAAAATAA
66399378 AAAAATAA
1 AAAAATAA
*
66399386 CAATATAATAT
1 -AA-A-AATAA
*
66399397 AAACATAAA
1 AAAAAT-AA
66399406 AAAAATAA
1 AAAAATAA
66399414 AAAAATAA
1 AAAAATAA
66399422 AAAAA
1 AAAAA
66399427 AAATATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 24 0.60
9 9 0.22
10 3 0.08
11 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:66399555 original size:11 final size:11
Alignment explanation
Indices: 66399539--66399573 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
66399529 TCCTTCCCCC
66399539 CTCCCTTCTCT
1 CTCCCTTCTCT
66399550 CTCCCTTCTCT
1 CTCCCTTCTCT
66399561 CTTCCC-TCTCT
1 C-TCCCTTCTCT
66399572 CT
1 CT
66399574 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:66400063 original size:3 final size:3
Alignment explanation
Indices: 66400039--66400106 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
66400029 AATATCCTTG
* * * *
66400039 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA GTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
66400087 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
66400107 GTACGTGTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:66400116 original size:23 final size:23
Alignment explanation
Indices: 66400046--66400117 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
66400036 TTGTTATTTT
* *
66400046 TATATTATTAGTAT-TATTAGTA
1 TATATTATTATTATGTAGTAGTA
*
66400068 TTAGTATTATTATTATGTATTAGTA
1 -TA-TATTATTATTATGTAGTAGTA
*
66400093 TATATTTTTATTATGTACGT-GTA
1 TATATTATTATTATGTA-GTAGTA
66400116 TA
1 TA
66400118 CATATACATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 21 0.49
24 14 0.33
25 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (23 bp):
TATATTATTATTATGTAGTAGTA
Found at i:66400173 original size:13 final size:13
Alignment explanation
Indices: 66400125--66400174 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
66400115 ATACATATAC
66400125 ATATTTTCATATCTA
1 ATATTTT-AT-TCTA
*
66400140 ATATTTTTATT-TC
1 ATA-TTTTATTCTA
66400153 AT-TTTTATTCTA
1 ATATTTTATTCTA
66400165 ATATTTTATT
1 ATATTTTATT
66400175 AATCTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 10 0.33
14 1 0.03
15 5 0.17
16 4 0.13
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTTTATTCTA
Found at i:66400220 original size:3 final size:3
Alignment explanation
Indices: 66400207--66400242 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
66400197 TATTCCAATG
* *
66400207 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
66400243 GTTTATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66400546 original size:19 final size:20
Alignment explanation
Indices: 66400509--66400570 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
66400499 ATTATCATTG
*
66400509 TATATATTTTATTATTATTA
1 TATATATTTTATCATTATTA
66400529 GT-TATATTTTA-CATTATTA
1 -TATATATTTTATCATTATTA
*
66400548 TATATATTTT-TCTAATATTA
1 TATATATTTTATC-ATTATTA
66400568 TAT
1 TAT
66400571 TGTATATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.44
20 18 0.50
21 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
TATATATTTTATCATTATTA
Found at i:66400983 original size:18 final size:19
Alignment explanation
Indices: 66400924--66401019 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 19
66400914 ATATACGTAC
*
66400924 TTATACATACTTAAATATAT
1 TTAT-CATACTTACATATAT
* * *
66400944 TTTTCAT-CTTTCATAATTT
1 TTATCATACTTACAT-ATAT
66400963 TTAT-ATACTTACATATAT
1 TTATCATACTTACATATAT
*
66400981 TTATGCATATTTTACATCATA-
1 TTAT-CATA-CTTACAT-ATAT
*
66401002 -TA-CATACTTATATATAT
1 TTATCATACTTACATATAT
66401019 T
1 T
66401020 CTTTATATTC
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
16 3 0.05
17 5 0.09
18 18 0.31
19 15 0.26
20 8 0.14
21 6 0.10
22 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATCATACTTACATATAT
Found at i:66402649 original size:13 final size:13
Alignment explanation
Indices: 66402631--66402668 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
66402621 TCACAATCCT
66402631 AGTCATCGTCATA
1 AGTCATCGTCATA
66402644 AGTCATCGTCATA
1 AGTCATCGTCATA
66402657 AGTCATCGTCAT
1 AGTCATCGTCAT
66402669 CTATAGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (13 bp):
AGTCATCGTCATA
Found at i:66409236 original size:19 final size:18
Alignment explanation
Indices: 66409207--66409251 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
66409197 GGTATAGCAG
66409207 ATTTT-GTTTATTATTTT
1 ATTTTAGTTTATTATTTT
*
66409224 ATTTCTAGTTTATTTTTTT
1 ATTT-TAGTTTATTATTTT
66409243 ATTTTAGTT
1 ATTTTAGTT
66409252 GGGGGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 15 0.60
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (18 bp):
ATTTTAGTTTATTATTTT
Found at i:66412012 original size:18 final size:18
Alignment explanation
Indices: 66411972--66412016 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
66411962 AGTATAGTAG
66411972 ATTTT-GTTTATTATTTT
1 ATTTTAGTTTATTATTTT
66411989 ATTTTTAGTTTATTATTTT
1 A-TTTTAGTTTATTATTTT
66412008 ATTTTAGTT
1 ATTTTAGTT
66412017 AGAGGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 13 0.50
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (18 bp):
ATTTTAGTTTATTATTTT
Found at i:66412094 original size:37 final size:37
Alignment explanation
Indices: 66412044--66412118 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
66412034 AGGAGGGGAA
* *
66412044 CCCAAATTGTTTTACAGATTCCCACATTTCTCTGTTT
1 CCCAAATTGTTTTACACATTCCCACAGTTCTCTGTTT
66412081 CCCAAATTGTTTTACACATTCCCACAGTTCTCTGTTT
1 CCCAAATTGTTTTACACATTCCCACAGTTCTCTGTTT
66412118 C
1 C
66412119 TTTTTCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.41
Consensus pattern (37 bp):
CCCAAATTGTTTTACACATTCCCACAGTTCTCTGTTT
Found at i:66412814 original size:20 final size:22
Alignment explanation
Indices: 66412768--66412823 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
66412758 TGTCCCTAGG
66412768 CCACATGGGCGTGTGCCTCCTT
1 CCACATGGGCGTGTGCCTCCTT
*
66412790 CCACACGGGCGTGTGCC-CC-T
1 CCACATGGGCGTGTGCCTCCTT
66412810 CCACATGGGCGTGT
1 CCACATGGGCGTGT
66412824 TGACCCCCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 16 0.50
ACGTcount: A:0.11, C:0.38, G:0.30, T:0.21
Consensus pattern (22 bp):
CCACATGGGCGTGTGCCTCCTT
Found at i:66412833 original size:20 final size:20
Alignment explanation
Indices: 66412768--66412837 Score: 88
Period size: 20 Copynumber: 3.4 Consensus size: 20
66412758 TGTCCCTAGG
66412768 CCACATGGGCGTGTGCCTCCTT
1 CCACATGGGCGTGTGCC-CC-T
*
66412790 CCACACGGGCGTGTGCCCCT
1 CCACATGGGCGTGTGCCCCT
*
66412810 CCACATGGGCGTGTTGACCC-
1 CCACATGGGCGTG-TGCCCCT
66412830 CCACATGG
1 CCACATGG
66412838 CCTAGGCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 21 0.48
21 7 0.16
22 16 0.36
ACGTcount: A:0.13, C:0.39, G:0.29, T:0.20
Consensus pattern (20 bp):
CCACATGGGCGTGTGCCCCT
Found at i:66414757 original size:7 final size:7
Alignment explanation
Indices: 66414742--66414773 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
66414732 AGAGATAGAG
*
66414742 AGAATAA
1 AGAACAA
66414749 AGAACAA
1 AGAACAA
66414756 AGAACAA
1 AGAACAA
66414763 AGAACAA
1 AGAACAA
66414770 AGAA
1 AGAA
66414774 AATATGGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.03
Consensus pattern (7 bp):
AGAACAA
Found at i:66415257 original size:19 final size:20
Alignment explanation
Indices: 66415219--66415298 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 20
66415209 TATTTAAAAC
66415219 TAAAAATTATTA-AAATATTA
1 TAAAAATT-TTAGAAATATTA
66415239 TAAAAATTTTAGAAA-ATTA
1 TAAAAATTTTAGAAATATTA
* * * *
66415258 GAAATATTATAGAAATACTA
1 TAAAAATTTTAGAAATATTA
66415278 TAAAAA---TAGAAATATTA
1 TAAAAATTTTAGAAATATTA
66415295 TAAA
1 TAAA
66415299 TATTATTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.27
19 19 0.37
20 18 0.35
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAAATTTTAGAAATATTA
Found at i:66415262 original size:28 final size:28
Alignment explanation
Indices: 66415227--66415298 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
66415217 ACTAAAAATT
**
66415227 ATTA-AAATATTATAAAAATTTTAGAAA
1 ATTAGAAATATTATAAAAATACTAGAAA
* *
66415254 ATTAGAAATATTATAGAAATACTATAAA
1 ATTAGAAATATTATAAAAATACTAGAAA
*
66415282 AATAGAAATATTATAAA
1 ATTAGAAATATTATAAA
66415299 TATTATTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 4 0.11
28 34 0.89
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (28 bp):
ATTAGAAATATTATAAAAATACTAGAAA
Found at i:66415288 original size:17 final size:17
Alignment explanation
Indices: 66415266--66415298 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
66415256 TAGAAATATT
66415266 ATAGAAATACTATAAAA
1 ATAGAAATACTATAAAA
*
66415283 ATAGAAATATTATAAA
1 ATAGAAATACTATAAA
66415299 TATTATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
ATAGAAATACTATAAAA
Found at i:66415301 original size:9 final size:9
Alignment explanation
Indices: 66415226--66415304 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
66415216 AACTAAAAAT
66415226 TATTA-AAA
1 TATTATAAA
66415234 TATTATAAA
1 TATTATAAA
* *
66415243 AATTTTAGAA
1 TATTATA-AA
* *
66415253 AATTAGAAA
1 TATTATAAA
66415262 TATTATAGAAA
1 TATTAT--AAA
*
66415273 TACTATAAA
1 TATTATAAA
* *
66415282 -AATAGAAA
1 TATTATAAA
66415290 TATTATAAA
1 TATTATAAA
66415299 TATTAT
1 TATTAT
66415305 TTCAATATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
8 11 0.20
9 29 0.53
10 7 0.13
11 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (9 bp):
TATTATAAA
Found at i:66415361 original size:31 final size:29
Alignment explanation
Indices: 66415321--66415379 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
66415311 ATAATTAATA
*
66415321 TATTATGAAAATT-TTGAAAATTTATAAAAC
1 TATTATG-AAATTATAGAAAA-TTATAAAAC
66415351 TATTATTGAAATTATAGAAAATTATAAAA
1 TATTA-TGAAATTATAGAAAATTATAAAA
66415380 AAATAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (29 bp):
TATTATGAAATTATAGAAAATTATAAAAC
Found at i:66415506 original size:9 final size:9
Alignment explanation
Indices: 66415457--66415529 Score: 58
Period size: 9 Copynumber: 7.6 Consensus size: 9
66415447 GGAATTTTAG
66415457 AAATTATAGA
1 AAATTATA-A
*
66415467 AAAATA-AA
1 AAATTATAA
66415475 AAAGTTATAGA
1 AAA-TTATA-A
66415486 AAACTATATAA
1 AAA-T-TATAA
66415497 AAATTATAA
1 AAATTATAA
*
66415506 AAACTTGTAA
1 AAA-TTATAA
*
66415516 AACTTATAA
1 AAATTATAA
66415525 AAATT
1 AAATT
66415530 TTGTTAACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 4 0.08
9 20 0.39
10 14 0.27
11 9 0.18
12 4 0.08
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (9 bp):
AAATTATAA
Found at i:66415507 original size:19 final size:19
Alignment explanation
Indices: 66415473--66415527 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
66415463 TAGAAAAATA
66415473 AAAAAGTTATAGAAAACTATAT
1 AAAAA-TTATA-AAAACT-TAT
*
66415495 AAAAATTATAAAAACTTGT
1 AAAAATTATAAAAACTTAT
*
66415514 AAAACTTATAAAAA
1 AAAAATTATAAAAA
66415528 TTTTGTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 15 0.48
20 6 0.19
21 5 0.16
22 5 0.16
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAAAACTTAT
Found at i:66415527 original size:10 final size:10
Alignment explanation
Indices: 66415473--66415527 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
66415463 TAGAAAAATA
*
66415473 AAAAAGTTAT
1 AAAAACTTAT
66415483 AGAAAACTATAT
1 A-AAAACT-TAT
66415495 AAAAA-TTAT
1 AAAAACTTAT
*
66415504 AAAAACTTGT
1 AAAAACTTAT
66415514 -AAAACTTAT
1 AAAAACTTAT
66415523 AAAAA
1 AAAAA
66415528 TTTTGTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 16 0.42
10 9 0.24
11 9 0.24
12 4 0.11
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:66416993 original size:22 final size:21
Alignment explanation
Indices: 66416963--66417003 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
66416953 AACAATTGAT
*
66416963 GAAAAAATATATCAACAAAGTA
1 GAAAAAATAT-TAAACAAAGTA
*
66416985 GAAATAATATTAAACAAAG
1 GAAAAAATATTAAACAAAG
66417004 AATTGAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (21 bp):
GAAAAAATATTAAACAAAGTA
Found at i:66418796 original size:23 final size:23
Alignment explanation
Indices: 66418753--66418808 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
66418743 AATTAATAAA
* *
66418753 ATATTTTTAAATTTTTATTTTTT
1 ATATTTTTAAATATTTATTTTCT
*
66418776 ATGTTTTTAAATAATTT-TTTTCT
1 ATATTTTTAAAT-ATTTATTTTCT
66418799 ATATTTTTAA
1 ATATTTTTAA
66418809 CTTGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
ATATTTTTAAATATTTATTTTCT
Found at i:66419906 original size:19 final size:19
Alignment explanation
Indices: 66419878--66419916 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
66419868 TTGGGGTAAA
66419878 TGGTGAAAAATAAAA-GTT
1 TGGTGAAAAATAAAACGTT
66419896 TGGTGGAAAAATAAAACGTT
1 TGGT-GAAAAATAAAACGTT
66419916 T
1 T
66419917 TGAGGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (19 bp):
TGGTGAAAAATAAAACGTT
Found at i:66432615 original size:5 final size:5
Alignment explanation
Indices: 66432605--66432636 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
66432595 AATTTGTGAA
66432605 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
66432637 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:66432630 original size:9 final size:9
Alignment explanation
Indices: 66432606--66432636 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
66432596 ATTTGTGAAA
66432606 AAATAAAAT
1 AAATAAAAT
66432615 AAAATAAAAT
1 -AAATAAAAT
66432625 AAATAAAAT
1 AAATAAAAT
66432634 AAA
1 AAA
66432637 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:66435087 original size:14 final size:14
Alignment explanation
Indices: 66435047--66435093 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
66435037 CCAAACCCAG
*
66435047 CAAAGCCAAATAAC
1 CAAAACCAAATAAC
*
66435061 CAAAAAC-AATAAC
1 CAAAACCAAATAAC
66435074 CAAAACCAAATAACC
1 CAAAACCAAATAA-C
66435089 CAAAA
1 CAAAA
66435094 TCAGTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.43
14 10 0.36
15 6 0.21
ACGTcount: A:0.64, C:0.28, G:0.02, T:0.06
Consensus pattern (14 bp):
CAAAACCAAATAAC
Found at i:66435506 original size:12 final size:12
Alignment explanation
Indices: 66435489--66435514 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
66435479 CGGGAAAAGG
66435489 AAAATGGAAAAA
1 AAAATGGAAAAA
66435501 AAAATGGAAAAA
1 AAAATGGAAAAA
66435513 AA
1 AA
66435515 TGGATATAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAATGGAAAAA
Found at i:66436861 original size:3 final size:3
Alignment explanation
Indices: 66436853--66436881 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
66436843 GTCTTGAACC
66436853 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
66436882 ACCCTTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:66443962 original size:28 final size:29
Alignment explanation
Indices: 66443913--66443968 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
66443903 ATGTTGCCAT
*
66443913 TGATGAATCTTTGTGATTTTAGATGTTAAA
1 TGATGAA-CTTTGTGATATTAGATGTTAAA
* *
66443943 TGATGAA-TTTGTGGTATTAGTTGTTA
1 TGATGAACTTTGTGATATTAGATGTTA
66443969 TTTATAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
30 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (29 bp):
TGATGAACTTTGTGATATTAGATGTTAAA
Found at i:66452546 original size:29 final size:29
Alignment explanation
Indices: 66452446--66452547 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
66452436 TACCTGTATC
* * * *
66452446 TGGCCCATTAAG-CCTAATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * *
66452474 TGGCCCATTAGGTCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
66452503 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
**
66452532 TGGCCTGTTAGGCCCA
1 TGGCCCATTAGGCCCA
66452548 GTCACACTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 11 0.18
29 51 0.82
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:66452835 original size:8 final size:8
Alignment explanation
Indices: 66452807--66452837 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
66452797 CATTTCAACT
*
66452807 TTTCAGCA
1 TTTCGGCA
66452815 TTTCGGCA
1 TTTCGGCA
66452823 TTTCGGCA
1 TTTCGGCA
66452831 TTTCGGC
1 TTTCGGC
66452838 TTTTATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.39
Consensus pattern (8 bp):
TTTCGGCA
Found at i:66454370 original size:20 final size:20
Alignment explanation
Indices: 66454345--66454392 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
66454335 AAGCTTATGC
66454345 TAAGTAAAT-GAAATGGAAAG
1 TAAGTAAATAG-AATGGAAAG
*
66454365 TAAGTAAATAGATTGGAAAG
1 TAAGTAAATAGAATGGAAAG
66454385 TAAAGTAA
1 T-AAGTAA
66454393 GTAAATGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (20 bp):
TAAGTAAATAGAATGGAAAG
Found at i:66454658 original size:81 final size:81
Alignment explanation
Indices: 66454518--66454692 Score: 332
Period size: 81 Copynumber: 2.1 Consensus size: 81
66454508 GTGAGTTGAT
*
66454518 GGTTATAAAGTTTTACAAATCTTATGGTATTGGCATAAGTTTATATTTATCCTATAAAGTTCGTT
1 GGTT-TAAAGTTTTACAAATCTTATGGTATTGGCATAAGTTTATATTTATCCTATAAAGTTCATT
66454583 ATTGAAATGGAATGTTA
65 ATTGAAATGGAATGTTA
66454600 GGTTTAAAGTTTTACAAATCTTATGGTATTGGCATAAGTTTATATTTATCCTATAAAGTTCATTA
1 GGTTTAAAGTTTTACAAATCTTATGGTATTGGCATAAGTTTATATTTATCCTATAAAGTTCATTA
66454665 TTGAAATGGAATGTTA
66 TTGAAATGGAATGTTA
66454681 GGTTTAAAGTTT
1 GGTTTAAAGTTT
66454693 ATATGAGCTT
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 88 0.96
82 4 0.04
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (81 bp):
GGTTTAAAGTTTTACAAATCTTATGGTATTGGCATAAGTTTATATTTATCCTATAAAGTTCATTA
TTGAAATGGAATGTTA
Found at i:66455649 original size:20 final size:20
Alignment explanation
Indices: 66455620--66455659 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
66455610 CCCCTACAGT
* * *
66455620 TTAATTTTTCCAATTTTTCC
1 TTAATGTTTCAAATGTTTCC
66455640 TTAATGTTTCAAATGTTTCC
1 TTAATGTTTCAAATGTTTCC
66455660 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (20 bp):
TTAATGTTTCAAATGTTTCC
Found at i:66462828 original size:80 final size:80
Alignment explanation
Indices: 66462687--66462839 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
66462677 GTATTGGTAG
* * *
66462687 TTTATCTGCAATACTGGCAGTGTTTTTGCACTACTGGCAATTTATCTGTATTACTGATGGCTTGA
1 TTTATCTGCAATACTGGCAGTGTGTTTGCACTACTGACAATTTATCTGCATTACTGATGGCTTGA
66462752 CCACATTACTGGAAA
66 CCACATTACTGGAAA
* * * * * *
66462767 TTTATCTGCAATATTGGGAGCT-TGTTTGCACTACTGACAGTTTATTTGCATTATTGGTGGCTTG
1 TTTATCTGCAATACTGGCAG-TGTGTTTGCACTACTGACAATTTATCTGCATTACTGATGGCTTG
66462831 ACCACATTA
65 ACCACATTA
66462840 TTGGCAGCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 62 0.98
81 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.39
Consensus pattern (80 bp):
TTTATCTGCAATACTGGCAGTGTGTTTGCACTACTGACAATTTATCTGCATTACTGATGGCTTGA
CCACATTACTGGAAA
Found at i:66464130 original size:19 final size:19
Alignment explanation
Indices: 66464106--66464146 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
66464096 ACCTTAGGAA
66464106 ATAGTCAACCCAAATGAAC
1 ATAGTCAACCCAAATGAAC
66464125 ATAGTCAACCCAAATGAAC
1 ATAGTCAACCCAAATGAAC
66464144 ATA
1 ATA
66464147 TTGTTTGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.17
Consensus pattern (19 bp):
ATAGTCAACCCAAATGAAC
Found at i:66468279 original size:32 final size:32
Alignment explanation
Indices: 66468241--66468305 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
66468231 AAACATACCT
66468241 AAACATGTGCATATTTAACCATTTATCAACTA
1 AAACATGTGCATATTTAACCATTTATCAACTA
66468273 AAACATGTGCATATTTAACCATTTATCAACTA
1 AAACATGTGCATATTTAACCATTTATCAACTA
66468305 A
1 A
66468306 CTTGTTTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (32 bp):
AAACATGTGCATATTTAACCATTTATCAACTA
Found at i:66472734 original size:55 final size:56
Alignment explanation
Indices: 66472669--66472773 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 56
66472659 AGCATGGCTG
* *
66472669 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCAGTGCCA
* * *
66472725 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCA
66472774 TAGCCATCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
55 21 0.49
56 22 0.51
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCAGTGCCA
Found at i:66472746 original size:27 final size:27
Alignment explanation
Indices: 66472694--66472773 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
66472684 GTGACAGAGT
*
66472694 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGGGC
*
66472723 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGGGC
66472750 CACCAGAACAGATAATTTGTGGCA
1 CACCAGAACAGAT-ATTTGTGGCA
66472774 TAGCCATCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.51
28 16 0.34
29 7 0.15
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGGGC
Found at i:66472936 original size:28 final size:28
Alignment explanation
Indices: 66472889--66472952 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
66472879 AAATTAACCC
*
66472889 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
66472917 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
66472945 TAGGGGTA
1 TAGGGGTA
66472953 CTCTAGTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:66473216 original size:8 final size:8
Alignment explanation
Indices: 66473200--66473231 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
66473190 CCCAAAATTC
66473200 CGGCTTTT
1 CGGCTTTT
*
66473208 CGGCATTT
1 CGGCTTTT
66473216 CGGCTTTT
1 CGGCTTTT
66473224 CGGCTTTT
1 CGGCTTTT
66473232 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:66475759 original size:20 final size:21
Alignment explanation
Indices: 66475722--66475760 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66475712 TTACCCTCGG
66475722 TGTTGCGACACATGGCTCTTA
1 TGTTGCGACACATGGCTCTTA
*
66475743 TGTTGTGACAC-TGGCTCT
1 TGTTGCGACACATGGCTCT
66475761 GTTTTTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (21 bp):
TGTTGCGACACATGGCTCTTA
Found at i:66478455 original size:45 final size:45
Alignment explanation
Indices: 66478394--66478483 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
66478384 GATTAGTAAC
66478394 AATAAAGAAAATAAAATCATATGTATCACCTAAAAATTTCTTAAT
1 AATAAAGAAAATAAAATCATATGTATCACCTAAAAATTTCTTAAT
*
66478439 AATAAAGAAAATAAAATCTTATGTATCACCTAAAAATTTCTTAAT
1 AATAAAGAAAATAAAATCATATGTATCACCTAAAAATTTCTTAAT
66478484 TATTCTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.32
Consensus pattern (45 bp):
AATAAAGAAAATAAAATCATATGTATCACCTAAAAATTTCTTAAT
Found at i:66483006 original size:30 final size:30
Alignment explanation
Indices: 66482970--66483026 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
66482960 TATAAAATCG
66482970 ATAAATTCAGCTCGATGTCATGACACAACA
1 ATAAATTCAGCTCGATGTCATGACACAACA
*
66483000 ATAAATTTAGCTCGATGTCATGACACA
1 ATAAATTCAGCTCGATGTCATGACACA
66483027 GCACCTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (30 bp):
ATAAATTCAGCTCGATGTCATGACACAACA
Found at i:66484300 original size:22 final size:22
Alignment explanation
Indices: 66484272--66484324 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
66484262 GACTAATGTT
66484272 GTGACACCGTAGTGCTTGTGTC
1 GTGACACCGTAGTGCTTGTGTC
66484294 GTGACACCGTAGTGCTTGTGTC
1 GTGACACCGTAGTGCTTGTGTC
66484316 GTGACACCG
1 GTGACACCG
66484325 AAGGCAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (22 bp):
GTGACACCGTAGTGCTTGTGTC
Found at i:66491129 original size:12 final size:12
Alignment explanation
Indices: 66491112--66491139 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
66491102 AAAATTATTT
66491112 CAAATCATTTTA
1 CAAATCATTTTA
66491124 CAAATCATTTTA
1 CAAATCATTTTA
66491136 CAAA
1 CAAA
66491140 AACCAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (12 bp):
CAAATCATTTTA
Found at i:66491910 original size:40 final size:40
Alignment explanation
Indices: 66491853--66491929 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
66491843 ACAAACCATG
**
66491853 TGGGGATAAAATCAACCCACCCAGGCCTACACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
* *
66491893 TGGGGATAAAATTAACCCATCCAACCCTACACACCAA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAA
66491930 ATGGTACTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.39, C:0.32, G:0.14, T:0.14
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:66501304 original size:42 final size:42
Alignment explanation
Indices: 66501223--66501324 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 42
66501213 TCTTACATGT
* *
66501223 AATCAAATATCGATGCCACTGTCAGATAAGGTCTTACACG-A
1 AATCAAATATCGATGCCACTGTCAGATAAGATCTCACACGTA
*
66501264 AATCAAATA-CGATGCCGA-TGTCCTAGATATGATCTCACACGTA
1 AATCAAATATCGATGCC-ACTGT-C-AGATAAGATCTCACACGTA
*
66501307 AATCATAA-GTCGATGCCA
1 AATCA-AATATCGATGCCA
66501325 ACGTCCCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
40 10 0.20
41 11 0.22
42 14 0.27
43 7 0.14
44 9 0.18
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (42 bp):
AATCAAATATCGATGCCACTGTCAGATAAGATCTCACACGTA
Found at i:66501348 original size:44 final size:42
Alignment explanation
Indices: 66501192--66501348 Score: 126
Period size: 44 Copynumber: 3.7 Consensus size: 42
66501182 AGCTCGTACA
* * *
66501192 ATGCCAACGTCCTAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATC-AA-ATCG
* *
66501235 ATGCC-ACTGT--CAGATAAGGTCTTACACG-AAATCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAATCAAAT-CG
* * * * * *
66501275 ATGCCGATGTCCTAGATATGATCTCACACGTAAATCATAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCA-AA-TCG
66501319 ATGCCAACGTCCCAGACATGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
66501349 ATAACACATA
Statistics
Matches: 89, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
39 2 0.02
40 11 0.12
41 18 0.20
42 16 0.18
43 13 0.15
44 28 0.31
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATCG
Found at i:66516445 original size:42 final size:43
Alignment explanation
Indices: 66516386--66516546 Score: 263
Period size: 43 Copynumber: 3.8 Consensus size: 43
66516376 TTTTTAAGGT
*
66516386 CTTTAGCGGCGC-TTTCCCACAAACACCGCTAAAGATCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCACGAC
* *
66516428 CTTTAGTGGCGC-TTTCCCACAAACGCCGTTAAAGATCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCACGAC
66516470 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCACGAC
* *
66516513 CTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
66516547 AGTCATGAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 50 0.45
43 61 0.55
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCACGAC
Found at i:66520460 original size:40 final size:40
Alignment explanation
Indices: 66520382--66520562 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
66520372 ACCCAAGTAT
* *
66520382 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
66520421 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66520461 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
66520501 CATCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66520541 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
66520563 CATTCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 11 0.09
40 117 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:66527294 original size:22 final size:22
Alignment explanation
Indices: 66527269--66527312 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
66527259 AATTATTTAC
*
66527269 GACTAAA-GTATAGTGTTCATAT
1 GACTAAATGAATAGT-TTCATAT
66527291 GACTAAATGAATAGTTTCATAT
1 GACTAAATGAATAGTTTCATAT
66527313 ATGCACATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
GACTAAATGAATAGTTTCATAT
Found at i:66527624 original size:40 final size:40
Alignment explanation
Indices: 66527540--66527720 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
66527530 GCCCAAGTAT
* * *
66527540 CTTCGGGATTTAG-CCGGATAAAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * **
66527579 CTTCGGGTCTTAGCCCCGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66527619 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66527659 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
66527699 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
66527721 CATTCAGATA
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 11 0.09
40 117 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:66530557 original size:22 final size:23
Alignment explanation
Indices: 66530506--66530557 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
66530496 TGAATTTTAT
** *
66530506 TATTTTTTAATTTAATTTTTTTT
1 TATTTTTTAACATAATTTTTTTC
66530529 TA-TTTTTAACAT-ATTTTTTTC
1 TATTTTTTAACATAATTTTTTTC
66530550 TATTTTTT
1 TATTTTTT
66530558 TCTTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.40
22 13 0.52
23 2 0.08
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (23 bp):
TATTTTTTAACATAATTTTTTTC
Found at i:66530902 original size:14 final size:14
Alignment explanation
Indices: 66530882--66530926 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
66530872 CACTAAAAAT
66530882 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
66530896 TACACCCTAAACTA
1 TAAACCCTAAACCA
*
66530910 TAAACCCTAAACTA
1 TAAACCCTAAACCA
66530924 TAA
1 TAA
66530927 TGATAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:66530955 original size:19 final size:21
Alignment explanation
Indices: 66530931--66530970 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
66530921 CTATAATGAT
66530931 AATTAAT-TCAATATT-TTAA
1 AATTAATATCAATATTATTAA
*
66530950 AATTAATATTAATATTATTAA
1 AATTAATATCAATATTATTAA
66530971 TATAATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTAATATCAATATTATTAA
Found at i:66531490 original size:18 final size:19
Alignment explanation
Indices: 66531467--66531510 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
66531457 CCGTATATCT
66531467 TAAACCATAG-TT-AACTC
1 TAAACCATAGTTTAAACTC
66531484 ATAAACC-T-GTTTAAACTC
1 -TAAACCATAGTTTAAACTC
66531502 TAAACCATA
1 TAAACCATA
66531511 TATCTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 12 0.55
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAACCATAGTTTAAACTC
Found at i:66531760 original size:41 final size:41
Alignment explanation
Indices: 66531698--66531957 Score: 362
Period size: 41 Copynumber: 6.3 Consensus size: 41
66531688 TTATATAACT
* *
66531698 TTTAGCGGCGTTTTACTAAAAGCACCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
66531739 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
*
66531780 TTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * *
66531821 TTTAGCGGCGTTTTACCAAAGGCGCCTCTAATGCTCTTGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* **
66531862 TTTAGCGGCATTTTACCAATGGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * ** *
66531903 TTTAGCGGCGTTTTTTACTAAAA-CGACGCTGTTGCTCT-GTT
1 TTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTGGTC
66531944 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
66531958 TTGTAAAACG
Statistics
Matches: 198, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
39 4 0.02
41 174 0.88
42 12 0.06
43 8 0.04
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:66531959 original size:42 final size:40
Alignment explanation
Indices: 66531697--66531988 Score: 153
Period size: 41 Copynumber: 7.1 Consensus size: 40
66531687 GTTATATAAC
* *
66531697 TTTTAGCGGCG-TTTTACTAAAA-GCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTTCTAAAACG-A-CGCTATTGCTCT-GT
* * * * *
66531738 CTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTTCTAAAA-CGACGCTATTGCTCT-GT
* ** * * *
66531779 CTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTTCTAAAACGACGCTATTGCTCT-GT
* * * * * * *
66531820 CTTTAGCGGCG-TTTTACCAAAGGCGCCTCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTTTCTAAA-ACGACGCTATTGCTC-TGT
* * * * ** * *
66531861 CTTTAGCGGC-ATTTTACCAATGGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTTCTAA-AACGACGCTATTGCTCT-GT
* *
66531902 CTTTAGCGGCGTTTTTTACTAAAACGACGCTGTTGCTCTGT
1 TTTTAGCGGCGTTTTTT-CTAAAACGACGCTATTGCTCTGT
* *
66531943 TTTTAGCGGCGTTTTTTGTAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTTTCTAAAACGACGCTATTGCTCTGT
66531983 ATTTTA
1 -TTTTA
66531989 AAATTTTTGT
Statistics
Matches: 215, Mismatches: 25, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
40 28 0.13
41 159 0.74
42 24 0.11
43 4 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTTTCTAAAACGACGCTATTGCTCTGT
Found at i:66532027 original size:12 final size:12
Alignment explanation
Indices: 66532012--66532037 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
66532002 ATTTTTTGAT
66532012 AAAACGCCGCTA
1 AAAACGCCGCTA
66532024 AAAACGCCGCTA
1 AAAACGCCGCTA
66532036 AA
1 AA
66532038 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:66534355 original size:27 final size:28
Alignment explanation
Indices: 66534323--66534407 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 28
66534313 AGGAAGCGTC
* *
66534323 CTGGTGGTTATGCTACAATTATCTGT-T
1 CTGGTGGCTATGCCACAATTATCTGTAT
* *
66534350 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTGTAT
* * *
66534378 CTGGTGACTCTGTCAC-ATTATCTGT-T
1 CTGGTGGCTATGCCACAATTATCTGTAT
66534404 CTGG
1 CTGG
66534408 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.10
27 31 0.61
28 15 0.29
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (28 bp):
CTGGTGGCTATGCCACAATTATCTGTAT
Found at i:66534388 original size:28 final size:26
Alignment explanation
Indices: 66534340--66534407 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
66534330 TTATGCTACA
*
66534340 ATTATCTGTTCTGGTGGCTCTGCCAC
1 ATTATCTGTTCTGGTGACTCTGCCAC
*
66534366 GATTATCTGTATCTGGTGACTCTGTCAC
1 -ATTATCTGT-TCTGGTGACTCTGCCAC
66534394 ATTATCTGTTCTGG
1 ATTATCTGTTCTGG
66534408 CAGCCATGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 5 0.13
27 18 0.47
28 15 0.39
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (26 bp):
ATTATCTGTTCTGGTGACTCTGCCAC
Found at i:66542756 original size:6 final size:6
Alignment explanation
Indices: 66542738--66542819 Score: 71
Period size: 6 Copynumber: 13.3 Consensus size: 6
66542728 AAGAAACATT
*
66542738 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAAGTA A-CAGA ATTAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATC-AG-A ATCAGA ATCAGA
* *
66542787 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
66542820 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
5 5 0.08
6 47 0.76
7 7 0.11
8 3 0.05
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:66542787 original size:25 final size:25
Alignment explanation
Indices: 66542752--66542819 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
66542742 GAACTAGAAT
66542752 CAGAATCAGAATCAGAATCAAGTAA
1 CAGAATCAGAATCAGAATCAAGTAA
* * *
66542777 CAGAATTAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAAGTAA
*
66542802 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
66542820 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAAGTAA
Found at i:66543082 original size:27 final size:26
Alignment explanation
Indices: 66543035--66543085 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
66543025 CGAGGCTGCC
*
66543035 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
66543061 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
66543086 TTATAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:66543094 original size:67 final size:68
Alignment explanation
Indices: 66542965--66543104 Score: 201
Period size: 67 Copynumber: 2.1 Consensus size: 68
66542955 TCACCAAATA
* * *
66542965 CAGATATTGTGGCTAAGCCACCAGAACAGATATATATGTGGCGAAGCCACCAGATTGCAGCGAGG
1 CAGATATTGTGACGAAGCCACCAGAACAGA-ATATATGTGGCGAAGCCACCAGATTACAGCGAGG
66543030 CTGC
65 CTGC
* * * *
66543034 CAGATATTGTGACGAAGTCACCAGAATAG-ATATATGTGGCGAGGCCACCAGATTATAGCGAGGC
1 CAGATATTGTGACGAAGCCACCAGAACAGAATATATGTGGCGAAGCCACCAGATTACAGCGAGGC
66543098 TGC
66 TGC
66543101 CAGA
1 CAGA
66543105 ATGCTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
67 39 0.61
69 25 0.39
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (68 bp):
CAGATATTGTGACGAAGCCACCAGAACAGAATATATGTGGCGAAGCCACCAGATTACAGCGAGGC
TGC
Found at i:66543768 original size:27 final size:27
Alignment explanation
Indices: 66543330--66543760 Score: 524
Period size: 27 Copynumber: 16.0 Consensus size: 27
66543320 GGGGTAAAAT
* * *
66543330 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
66543357 GGTAATTCTACCCTACAGGGGTTTTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
66543384 AGTAATTCTACCCTACAAGTGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543411 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * ** *
66543438 TGTAATTCTATCCTACTGGGGTATTCC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543465 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
66543492 GGTATTTCTACCCTACAAGGGTATATA
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
66543519 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543546 AGTAATTCTACCCTAC-AGGAGTATTTC
1 GGTAATTCTACCCTACAAGG-GTATTTC
* * *
66543573 AGCAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543600 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
66543627 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
66543654 GGTAATTCTACCCTATAGGGGTA-TTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543680 TAGTAATTCTACCCTACAAGGGTATTTC
1 -GGTAATTCTACCCTACAAGGGTATTTC
* *
66543708 GGTATTTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
66543735 GGTAATTCTACCCTATAAGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
66543761 TAGTAATTTT
Statistics
Matches: 351, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.01
27 341 0.97
28 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:66543784 original size:27 final size:27
Alignment explanation
Indices: 66543751--66543937 Score: 202
Period size: 27 Copynumber: 7.0 Consensus size: 27
66543741 TCTACCCTAT
*
66543751 AAGGGTATTTTAGTAATTTTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAACC
* *
66543778 -GGAGGTATTTT-GATAATTTTATAAA-C
1 AAG-GGTATTTTAG-TAATTTTGTAAACC
**
66543804 AATGGGTATTTTAGTAATTTTACAAACC
1 AA-GGGTATTTTAGTAATTTTGTAAACC
*
66543832 -AGGGTATTTTGGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAACC
* * *
66543858 AAGGGTATTTTGGTAATTTTATAAAAC
1 AAGGGTATTTTAGTAATTTTGTAAACC
* *
66543885 AGGGGTATTTTGGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAACC
* *
66543912 AAGGGTATTTTAATAATTTGGTAAAC
1 AAGGGTATTTTAGTAATTTTGTAAAC
66543938 TAAAGTATTC
Statistics
Matches: 137, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
26 25 0.18
27 109 0.80
28 3 0.02
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAACC
Found at i:66543811 original size:54 final size:53
Alignment explanation
Indices: 66543751--66543930 Score: 245
Period size: 54 Copynumber: 3.4 Consensus size: 53
66543741 TCTACCCTAT
* * * *
66543751 AAGGGTATTTTAGTAATTTTGTAAATCGGAGGTATTTTGATAATTTTATAAA-C
1 AAGGGTATTTTAGTAATTTTATAAAACGG-GGTATTTTGGTAATTTTGTAAACC
* * *
66543804 AATGGGTATTTTAGTAATTTTACAAACCAGGGTATTTTGGTAATTTTGTAAACC
1 AA-GGGTATTTTAGTAATTTTATAAAACGGGGTATTTTGGTAATTTTGTAAACC
*
66543858 AAGGGTATTTTGGTAATTTTATAAAACAGGGGTATTTTGGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTATAAAAC-GGGGTATTTTGGTAATTTTGTAAACC
*
66543912 AAGGGTATTTTAATAATTT
1 AAGGGTATTTTAGTAATTT
66543931 GGTAAACTAA
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
53 44 0.39
54 68 0.61
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (53 bp):
AAGGGTATTTTAGTAATTTTATAAAACGGGGTATTTTGGTAATTTTGTAAACC
Found at i:66543865 original size:80 final size:81
Alignment explanation
Indices: 66543751--66543937 Score: 245
Period size: 80 Copynumber: 2.3 Consensus size: 81
66543741 TCTACCCTAT
* * *
66543751 AAGGGTATTTTAGTAATTTTGTAAATCGGAGGTATTTTGATAATTTTAT-AAACAATGGGTATTT
1 AAGGGTATTTTAGTAATTTTGTAAACCAGAGGTATTTTGATAATTTTATAAAAC-AGGGGTATTT
66543815 TAGTAATTTTACAAACC
65 TAGTAATTTTACAAACC
* *
66543832 -AGGGTATTTTGGTAATTTTGTAAACCA-AGGGTATTTTGGTAATTTTATAAAACAGGGGTATTT
1 AAGGGTATTTTAGTAATTTTGTAAACCAGA-GGTATTTTGATAATTTTATAAAACAGGGGTATTT
* **
66543895 TGGTAATTTTGTAAACC
65 TAGTAATTTTACAAACC
* *
66543912 AAGGGTATTTTAATAATTTGGTAAAC
1 AAGGGTATTTTAGTAATTTTGTAAAC
66543938 TAAAGTATTC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 65 0.71
81 26 0.28
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (81 bp):
AAGGGTATTTTAGTAATTTTGTAAACCAGAGGTATTTTGATAATTTTATAAAACAGGGGTATTTT
AGTAATTTTACAAACC
Found at i:66561539 original size:43 final size:44
Alignment explanation
Indices: 66561490--66561642 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 44
66561480 GATTACCGAG
*
66561490 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
*
66561534 -TGTGATTA-A-GT----CCATGTCTGGGACATTGGCATTGT-T
1 ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
* * * * * * *
66561570 ATATGATTTCGTATAAGACCCTATCTGGGACAGTGGCATCG-AT
1 ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
*
66561613 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACATGTAAGACCATATCTGGGA
66561643 TATAACATTG
Statistics
Matches: 87, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
36 1 0.01
37 30 0.34
39 1 0.01
41 2 0.02
42 1 0.01
43 52 0.60
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
Found at i:66561577 original size:37 final size:37
Alignment explanation
Indices: 66561503--66561577 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
66561493 TGATTACATG
*
66561503 TAAGACCATGTCTGGGACATTGGCATTGTATTGTGAT
1 TAAGACCATGTCTGGGACATTGGCATTGTATTATGAT
*
66561540 TAAGTCCATGTCTGGGACATTGGCATTGT-TATATGAT
1 TAAGACCATGTCTGGGACATTGGCATTGTAT-TATGAT
66561577 T
1 T
66561578 TCGTATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (37 bp):
TAAGACCATGTCTGGGACATTGGCATTGTATTATGAT
Found at i:66561657 original size:34 final size:34
Alignment explanation
Indices: 66561619--66561688 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
66561609 CGATATGTGA
66561619 TAACATGTAAGACCATATCTGGGATATAACATTG
1 TAACATGTAAGACCATATCTGGGATATAACATTG
**
66561653 TAACATGTAAGACCATATCTGGGATATGGCATTG
1 TAACATGTAAGACCATATCTGGGATATAACATTG
66561687 TA
1 TA
66561689 TGAGCTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (34 bp):
TAACATGTAAGACCATATCTGGGATATAACATTG
Found at i:66563446 original size:81 final size:81
Alignment explanation
Indices: 66563306--66563471 Score: 296
Period size: 81 Copynumber: 2.0 Consensus size: 81
66563296 CAGGATTGTT
*
66563306 TTATGAACTACTTAGTGGGCACCACCAGAACCCTTGCTCTATTGCATAAGGCCACCACTATGTGG
1 TTATGAACTACTTAGTGGACACCACCAGAACCCTTGCTCTATTGCATAAGGCCACCACTATGTGG
66563371 GGATACCAAGATTTTG
66 GGATACCAAGATTTTG
* * *
66563387 TTATGAACTTCTTAGTGGACACCACCAGAACCCTTGCTCTGTTGCATAAGGCCATCACTATGTGG
1 TTATGAACTACTTAGTGGACACCACCAGAACCCTTGCTCTATTGCATAAGGCCACCACTATGTGG
66563452 GGATACCAAGATTTTG
66 GGATACCAAGATTTTG
66563468 TTAT
1 TTAT
66563472 AAAATTCAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (81 bp):
TTATGAACTACTTAGTGGACACCACCAGAACCCTTGCTCTATTGCATAAGGCCACCACTATGTGG
GGATACCAAGATTTTG
Found at i:66570628 original size:42 final size:42
Alignment explanation
Indices: 66570582--66570664 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
66570572 TCGATGCTGC
66570582 ATCCCAGACACGGTCTTACACGAAATCTCATACCGAAGCCAT
1 ATCCCAGACACGGTCTTACACGAAATCTCATACCGAAGCCAT
* * * * *
66570624 ATCCCAGAGATGGTCTTACACGTAATCTCATATCGATGCCA
1 ATCCCAGACACGGTCTTACACGAAATCTCATACCGAAGCCA
66570665 ATACTATATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (42 bp):
ATCCCAGACACGGTCTTACACGAAATCTCATACCGAAGCCAT
Found at i:66570637 original size:84 final size:84
Alignment explanation
Indices: 66570509--66570662 Score: 193
Period size: 84 Copynumber: 1.8 Consensus size: 84
66570499 ATCCAACTAT
* * * * * * *
66570509 GGTCTTACACAAAGTCTCACATCTATGCCATCTCCTAGAAATGGTCTTATACGAAATCACTTATC
1 GGTCTTACACAAAGTCTCACACCGAAGCCATATCCCAGAAATGGTCTTACACGAAATCACATATC
66570574 GATGCTGCATCCCAGACAC
66 GATGCTGCATCCCAGACAC
* * * *
66570593 GGTCTTACACGAAA-TCTCATACCGAAGCCATATCCCAGAGATGGTCTTACACGTAATCTCATAT
1 GGTCTTACAC-AAAGTCTCACACCGAAGCCATATCCCAGAAATGGTCTTACACGAAATCACATAT
66570657 CGATGC
65 CGATGC
66570663 CAATACTATA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 55 0.95
85 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (84 bp):
GGTCTTACACAAAGTCTCACACCGAAGCCATATCCCAGAAATGGTCTTACACGAAATCACATATC
GATGCTGCATCCCAGACAC
Found at i:66570792 original size:37 final size:37
Alignment explanation
Indices: 66570705--66570846 Score: 184
Period size: 37 Copynumber: 3.9 Consensus size: 37
66570695 GATCTCATAT
*
66570705 CGATGCCAT-GTCCCAGAC-ATGGTCTTACACCT-ATCA
1 CGATGCCATAG-CCCAG-CTATGGTCTTACACGTCATCA
* *
66570741 CAATGCCATAGCCCAGCTATGGTCTTACATGTCATCA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTCATCA
* *
66570778 CGATGCCATGGCCCAGCTATGGTCTTACACG-CTATTA
1 CGATGCCATAGCCCAGCTATGGTCTTACACGTC-ATCA
66570815 CGATGCCATAGCCCAGCTATGGTCTTACACGT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGT
66570847 ACTCACATGT
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
35 1 0.01
36 26 0.28
37 66 0.71
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (37 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGTCATCA
Found at i:66570800 original size:73 final size:74
Alignment explanation
Indices: 66570705--66570843 Score: 228
Period size: 74 Copynumber: 1.9 Consensus size: 74
66570695 GATCTCATAT
*
66570705 CGATGCCATGTCCCAGACATGGTCTTACAC-CTATCACAATGCCATAGCCCAGCTATGGTCTTAC
1 CGATGCCATGGCCCAGACATGGTCTTACACGCTATCACAATGCCATAGCCCAGCTATGGTCTTAC
66570769 ATGTCATCA
66 ATGTCATCA
* *
66570778 CGATGCCATGGCCCAG-CTATGGTCTTACACGCTATTACGATGCCATAGCCCAGCTATGGTCTTA
1 CGATGCCATGGCCCAGAC-ATGGTCTTACACGCTATCACAATGCCATAGCCCAGCTATGGTCTTA
66570842 CA
65 CA
66570844 CGTACTCACA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
72 1 0.02
73 27 0.44
74 33 0.54
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (74 bp):
CGATGCCATGGCCCAGACATGGTCTTACACGCTATCACAATGCCATAGCCCAGCTATGGTCTTAC
ATGTCATCA
Found at i:66571740 original size:12 final size:12
Alignment explanation
Indices: 66571723--66571764 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
66571713 TCCAAAACTT
66571723 GGAAAACTTTTG
1 GGAAAACTTTTG
66571735 GGAAAAC--TT-
1 GGAAAACTTTTG
66571744 GGAAAACTTTTG
1 GGAAAACTTTTG
66571756 GGAAAACTT
1 GGAAAACTT
66571765 AAAAAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 2 0.07
12 16 0.59
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (12 bp):
GGAAAACTTTTG
Found at i:66571770 original size:21 final size:21
Alignment explanation
Indices: 66571716--66571764 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
66571706 GATTAAATCC
66571716 AAAACTTGGAAAACTTTTGGG
1 AAAACTTGGAAAACTTTTGGG
66571737 AAAACTTGGAAAACTTTTGGG
1 AAAACTTGGAAAACTTTTGGG
66571758 AAAACTT
1 AAAACTT
66571765 AAAAAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AAAACTTGGAAAACTTTTGGG
Found at i:66573578 original size:28 final size:28
Alignment explanation
Indices: 66573536--66573610 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
66573526 ATCTTCGATG
* * *
66573536 TCTCGAACACTAAGTGTCATACTCAATA
1 TCTCGCACACTAAGTGCCATACTAAATA
* *
66573564 TCTCGCACACCAAGTGCCATTCTAAATA
1 TCTCGCACACTAAGTGCCATACTAAATA
*
66573592 TTTCGCACACTAAGTGCCA
1 TCTCGCACACTAAGTGCCA
66573611 CATATATATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACTAAATA
Found at i:66579739 original size:19 final size:19
Alignment explanation
Indices: 66579715--66579753 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
66579705 ACTTAAATAG
66579715 GAAGAAGTAGAGTGATGGA
1 GAAGAAGTAGAGTGATGGA
66579734 GAAGAAGTAGAGTGATGGA
1 GAAGAAGTAGAGTGATGGA
66579753 G
1 G
66579754 TAATTACAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (19 bp):
GAAGAAGTAGAGTGATGGA
Found at i:66581659 original size:13 final size:13
Alignment explanation
Indices: 66581643--66581675 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
66581633 TTTAATTAAA
*
66581643 TTAGTTAATTAGT
1 TTAGATAATTAGT
66581656 TTAGATAATTAGT
1 TTAGATAATTAGT
66581669 TTA-ATAA
1 TTAGATAA
66581676 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:66585109 original size:21 final size:20
Alignment explanation
Indices: 66585077--66585121 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
66585067 ACCATTCAGC
* *
66585077 CGTGTACAATAATACATGGG
1 CGTGTACAATAAAACACGGG
*
66585097 CGTGCTACCATAAAACACGGG
1 CGTG-TACAATAAAACACGGG
66585118 CGTG
1 CGTG
66585122 GGAGAAGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (20 bp):
CGTGTACAATAAAACACGGG
Found at i:66587055 original size:16 final size:15
Alignment explanation
Indices: 66587034--66587090 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 15
66587024 CCTCCTATTT
66587034 TTTTTATTTATTCTTA
1 TTTTTATTTATT-TTA
66587050 TTTTTATTTTATTTTA
1 TTTTTA-TTTATTTTA
66587066 TTTATT-TTTATTTTTA
1 TTT-TTATTTA-TTTTA
*
66587082 TTTTAATTT
1 TTTTTATTT
66587091 TTATTTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 5 0.14
16 23 0.64
17 8 0.22
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:66587056 original size:6 final size:6
Alignment explanation
Indices: 66587029--66587102 Score: 76
Period size: 6 Copynumber: 11.8 Consensus size: 6
66587019 TGAATCCTCC
* * *
66587029 TATTTT TTTTATT TATTCT TATTTT TATTTT ATTTTATT TATTTT TATTTT
1 TATTTT TATT-TT TATTTT TATTTT TATTTT -TATT-TT TATTTT TATTTT
* *
66587080 TATTTT AATTTT TATTTT CATTT
1 TATTTT TATTTT TATTTT TATTT
66587103 CAATTTTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
6 43 0.77
7 11 0.20
8 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:66587057 original size:12 final size:11
Alignment explanation
Indices: 66587034--66587122 Score: 76
Period size: 12 Copynumber: 7.9 Consensus size: 11
66587024 CCTCCTATTT
66587034 TTTTTA-TTTA
1 TTTTTATTTTA
*
66587044 TTCTTATTTT-
1 TTTTTATTTTA
66587054 TATTTTATTTTA
1 T-TTTTATTTTA
*
66587066 TTTAT-TTTTA
1 TTTTTATTTTA
66587076 TTTTTATTTTAA
1 TTTTTATTTT-A
66587088 TTTTTATTTTCA
1 TTTTTATTTT-A
**
66587100 TTTCAATTTTA
1 TTTTTATTTTA
66587111 TTATTTTATTTT
1 -T-TTTTATTTT
66587123 GAAAGACATA
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
10 15 0.24
11 19 0.30
12 22 0.35
13 7 0.11
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:66587061 original size:5 final size:5
Alignment explanation
Indices: 66587029--66587122 Score: 72
Period size: 5 Copynumber: 18.2 Consensus size: 5
66587019 TGAATCCTCC
66587029 TATTT T-TTT TA-TT TATTCT TATTTT TATTT TATTT TA-TT TATTTT
1 TATTT TATTT TATTT TATT-T TA-TTT TATTT TATTT TATTT TA-TTT
*
66587074 TATTTT TATTT TAATTTT TATTT TCATTT CAATTT TA--T TATTT TATTT
1 TA-TTT TATTT T-A-TTT TATTT T-ATTT -TATTT TATTT TATTT TATTT
66587122 T
1 T
66587123 GAAAGACATA
Statistics
Matches: 75, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
3 3 0.04
4 12 0.16
5 28 0.37
6 26 0.35
7 6 0.08
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:66587066 original size:26 final size:26
Alignment explanation
Indices: 66587029--66587096 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
66587019 TGAATCCTCC
66587029 TATTTT-TTTTATTTATTCTTATTTT
1 TATTTTATTTTATTTATTCTTATTTT
*
66587054 TATTTTATTTTATTTATTTTTATTTT
1 TATTTTATTTTATTTATTCTTATTTT
66587080 TATTTTAATTTTTATTT
1 TATTTT-A-TTTTATTT
66587097 TCATTTCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 6 0.15
26 24 0.62
27 1 0.03
28 8 0.21
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (26 bp):
TATTTTATTTTATTTATTCTTATTTT
Found at i:66588960 original size:10 final size:10
Alignment explanation
Indices: 66588940--66588983 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
66588930 ACCAAGAGTC
66588940 AAAAGGAACCA
1 AAAAGG-ACCA
*
66588951 AAAACGACCA
1 AAAAGGACCA
*
66588961 AAAAGGAGACA
1 AAAAGGA-CCA
66588972 AAAAGGACCA
1 AAAAGGACCA
66588982 AA
1 AA
66588984 TCGAGAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.64, C:0.18, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAGGACCA
Found at i:66588964 original size:21 final size:21
Alignment explanation
Indices: 66588940--66588983 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66588930 ACCAAGAGTC
66588940 AAAAGGA-ACCAAAAACGACCA
1 AAAAGGAGA-CAAAAACGACCA
*
66588961 AAAAGGAGACAAAAAGGACCA
1 AAAAGGAGACAAAAACGACCA
66588982 AA
1 AA
66588984 TCGAGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.64, C:0.18, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAGGAGACAAAAACGACCA
Found at i:66590698 original size:27 final size:27
Alignment explanation
Indices: 66590665--66590871 Score: 297
Period size: 27 Copynumber: 7.6 Consensus size: 27
66590655 TAAATTGTGC
*
66590665 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
66590692 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
66590720 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
66590747 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
66590775 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
66590802 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * * *
66590830 AGCACTAAATGTGAGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
66590857 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
66590872 GACTTAATAT
Statistics
Matches: 164, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
27 89 0.54
28 75 0.46
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:66590729 original size:55 final size:55
Alignment explanation
Indices: 66590665--66590871 Score: 342
Period size: 55 Copynumber: 3.8 Consensus size: 55
66590655 TAAATTGTGC
66590665 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
66590720 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
66590775 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * * * *
66590830 AGCACTAAATGTGAGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
66590872 GACTTAATAT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 145 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:66598761 original size:27 final size:28
Alignment explanation
Indices: 66598705--66598884 Score: 285
Period size: 27 Copynumber: 6.5 Consensus size: 28
66598695 TAAATTGTGC
66598705 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
66598733 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
66598760 AGCACTAGGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
66598788 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
66598815 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
66598843 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
66598870 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
66598885 GACTTAATAT
Statistics
Matches: 143, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
27 75 0.52
28 68 0.48
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:66598772 original size:55 final size:55
Alignment explanation
Indices: 66598705--66598884 Score: 306
Period size: 55 Copynumber: 3.3 Consensus size: 55
66598695 TAAATTGTGC
*
66598705 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
66598760 AGCACTAGGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
* * *
66598815 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
66598870 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
66598885 GACTTAATAT
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 118 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
Found at i:66601898 original size:34 final size:35
Alignment explanation
Indices: 66601827--66601910 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 35
66601817 GTTCCAGTTA
* *
66601827 GGGCCTTAGCCCCTTTTACAGTAACAGTATCAATCT
1 GGGCCTTAGCCCATTTTA-AGTAACAGTAGCAATCT
* * *
66601863 GGGCCTGAGCCCATTTT-AGTAACAGTGGCAGTCT
1 GGGCCTTAGCCCATTTTAAGTAACAGTAGCAATCT
66601897 GGGCCTTAGCCCAT
1 GGGCCTTAGCCCAT
66601911 ATCAATACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 27 0.64
36 15 0.36
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (35 bp):
GGGCCTTAGCCCATTTTAAGTAACAGTAGCAATCT
Found at i:66610102 original size:19 final size:17
Alignment explanation
Indices: 66610063--66610102 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
66610053 TTTTGTGTGG
*
66610063 GGCCCACAAGCCCATTG
1 GGCCCACAAGCCCATTC
66610080 GGCCCACACAGCCCAATTC
1 GGCCCACA-AGCCC-ATTC
66610099 GGCC
1 GGCC
66610103 TAACGTGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.10
Consensus pattern (17 bp):
GGCCCACAAGCCCATTC
Found at i:66613043 original size:43 final size:42
Alignment explanation
Indices: 66612985--66613077 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
66612975 GACGTTGATA
* * * *
66612985 GTCTTATATGTAATCAAATATCGATGCC-ACTGTCTCAGACATG
1 GTCTTACATGAAATCAAATAT-GATACCGA-TGTCCCAGACATG
*
66613028 GTCTTACATGAAATCATATATGATACCGATGTCCCAGACATG
1 GTCTTACATGAAATCAAATATGATACCGATGTCCCAGACATG
66613070 GTCTTACA
1 GTCTTACA
66613078 CGTAAATCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
GTCTTACATGAAATCAAATATGATACCGATGTCCCAGACATG
Found at i:66614237 original size:13 final size:13
Alignment explanation
Indices: 66614219--66614245 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
66614209 CAGAAACGAT
66614219 AAAATTTTCACAC
1 AAAATTTTCACAC
66614232 AAAATTTTCACAC
1 AAAATTTTCACAC
66614245 A
1 A
66614246 TTACATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:66619316 original size:55 final size:53
Alignment explanation
Indices: 66619229--66619483 Score: 252
Period size: 55 Copynumber: 4.8 Consensus size: 53
66619219 ATTAGGGTTT
* *
66619229 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATCGGTACGATTTCTAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT-GGTAAG-TTTCTAAGGA
* * * * *
66619284 AAGGATACCATGTAGGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT--TCTAAGG-A
* * * * *
66619340 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTC-TAAGGA
* * *
66619392 AAGGATACCATGTAAGGCCATGTCGAGACATGGCAATGGTAAGTTTC--A--A
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTCTAAGGA
* * *
66619441 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG
66619484 GTCCGTGTAT
Statistics
Matches: 166, Mismatches: 28, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
49 38 0.23
51 1 0.01
52 5 0.03
53 38 0.23
54 8 0.05
55 71 0.43
56 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTCTAAGGA
Found at i:66619435 original size:108 final size:109
Alignment explanation
Indices: 66619236--66619436 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 109
66619226 TTTAAGGATA
*
66619236 CCATGTAAGACCATGCCAAGGCATGGCAATCGGTACGATTTCTAAGGAAAGGATACCATGTAGGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATCGGTA-GAGTTCTAAGGAAAGGATACCATGTAGGA
*
66619301 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
65 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
66619346 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGT-GAGTTCATAAGGCAAGGATACCATGTAAGG
1 CCATGTAAGACCATGCCAAGGCATGGCAATCGGTAGAGTTC-TAAGGAAAGGATACCATGT-AGG
* *
66619409 -CCATGTCGAGACATGGCAATGGTAAGTT
64 ACCATGTCAAGACATGGCAATGATAAGTT
66619437 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
107 5 0.06
108 43 0.52
109 8 0.10
110 27 0.33
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (109 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATCGGTAGAGTTCTAAGGAAAGGATACCATGTAGGAC
CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Done.