Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 174 of 216
Found at i:54413669 original size:21 final size:22
Alignment explanation
Indices: 54413639--54413689 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
54413629 AATAAAATAA
*
54413639 AAATAAAAATAAA-AAATATTT
1 AAATATAAATAAACAAATATTT
*
54413660 AAATATAAATAAACACATATTT
1 AAATATAAATAAACAAATATTT
*
54413682 ATATATAA
1 AAATATAA
54413690 TGTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAAATAAACAAATATTT
Found at i:54414077 original size:70 final size:70
Alignment explanation
Indices: 54413964--54414104 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
54413954 CATCGGAACA
*
54413964 TTTGAAAAATACGGAGAGGAAAAGAAGAGTTTTGAGAGCAACAGAAATTCAGTGTAAGAGATTAT
1 TTTGAAAAATACGAAGAGGAAAAGAAGAGTTTTGAGAGCAACAGAAATTCAGTGTAAGAGATTAT
54414029 AAGAG
66 AAGAG
54414034 TTTGAAAAATACGAAGAGGAAAAGAAGAGTTTTGAGAGCAACAGAAATTCAGTGTAAGAGATTAT
1 TTTGAAAAATACGAAGAGGAAAAGAAGAGTTTTGAGAGCAACAGAAATTCAGTGTAAGAGATTAT
54414099 AAGAG
66 AAGAG
54414104 T
1 T
54414105 GTATAAAATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.22
Consensus pattern (70 bp):
TTTGAAAAATACGAAGAGGAAAAGAAGAGTTTTGAGAGCAACAGAAATTCAGTGTAAGAGATTAT
AAGAG
Found at i:54415720 original size:10 final size:10
Alignment explanation
Indices: 54415705--54415739 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
54415695 TAAAAAATAA
54415705 AAAAGTATTT
1 AAAAGTATTT
54415715 AAAAGTATTT
1 AAAAGTATTT
*
54415725 AAAAATATTTT
1 AAAAGTA-TTT
54415736 AAAA
1 AAAA
54415740 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (10 bp):
AAAAGTATTT
Found at i:54417743 original size:21 final size:21
Alignment explanation
Indices: 54417717--54417768 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
54417707 CTATCATCGG
* *
54417717 AGGAGAATAGTCGGCAAATTC
1 AGGAGAAGAGTCAGCAAATTC
54417738 AGGAGAAGAGTCAGCAAATTC
1 AGGAGAAGAGTCAGCAAATTC
* *
54417759 ATGTGAAGAG
1 AGGAGAAGAG
54417769 GTCACGTCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.31, T:0.17
Consensus pattern (21 bp):
AGGAGAAGAGTCAGCAAATTC
Found at i:54422548 original size:53 final size:53
Alignment explanation
Indices: 54422468--54422575 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
54422458 AAGGAGTGTC
54422468 CATTTCAATTATTCATACATATTTATTTAGGTTTCATATTTACAATTTGTTAA
1 CATTTCAATTATTCATACATATTTATTTAGGTTTCATATTTACAATTTGTTAA
*
54422521 CATTTCAATTATTCATACATATTTATTTTGGTTTCATATTTACAATTTGTTAA
1 CATTTCAATTATTCATACATATTTATTTAGGTTTCATATTTACAATTTGTTAA
54422574 CA
1 CA
54422576 AGAGAATGCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (53 bp):
CATTTCAATTATTCATACATATTTATTTAGGTTTCATATTTACAATTTGTTAA
Found at i:54424479 original size:49 final size:49
Alignment explanation
Indices: 54424390--54424486 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
54424380 TGTGAATATT
** *** *
54424390 GCGATACCATTGAAGGGTGGTCTCCAATCTTGGGTTTGTTGGAGGTATA
1 GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTATA
*
54424439 GCGATACCATTGAAGGGTGGTCTTCAATCTCAGAACTGTTGGACGTAT
1 GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTAT
54424487 TGTGATTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (49 bp):
GCGATACCATTGAAGGGTGGTCTCCAATCTCAGAACTGTTGGACGTATA
Found at i:54426179 original size:19 final size:18
Alignment explanation
Indices: 54426125--54426179 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
54426115 AAAAATTTGA
54426125 AAATAAACACATAAAAAT
1 AAATAAACACATAAAAAT
*
54426143 AACATGAAACA-AGAAAAAAT
1 AA-AT-AAACACA-TAAAAAT
54426163 AAATAAAACACATAAAA
1 AAAT-AAACACATAAAA
54426180 CTATGTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (18 bp):
AAATAAACACATAAAAAT
Found at i:54426179 original size:20 final size:19
Alignment explanation
Indices: 54426125--54426179 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
54426115 AAAAATTTGA
54426125 AAATAAACACAT-AAAAAT
1 AAATAAACACATAAAAAAT
*
54426143 AACATGAAACA-AGAAAAAAT
1 AA-AT-AAACACATAAAAAAT
54426163 AAATAAAACACATAAAA
1 AAAT-AAACACATAAAA
54426180 CTATGTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.07
19 10 0.33
20 18 0.60
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (19 bp):
AAATAAACACATAAAAAAT
Found at i:54431680 original size:60 final size:60
Alignment explanation
Indices: 54431608--54431726 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
54431598 GATTTACCAT
54431608 GTTACAGAGTTTCGAGCATTCTAGAGCTAAAATTCCTATAATACCCTTAAAACTCTTAGA
1 GTTACAGAGTTTCGAGCATTCTAGAGCTAAAATTCCTATAATACCCTTAAAACTCTTAGA
54431668 GTTACAGAGTTTCGAGCATTCTAGAGCTAAAATTCCTATAATACCCTTAAAACTCTTAG
1 GTTACAGAGTTTCGAGCATTCTAGAGCTAAAATTCCTATAATACCCTTAAAACTCTTAG
54431727 GCCTTATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (60 bp):
GTTACAGAGTTTCGAGCATTCTAGAGCTAAAATTCCTATAATACCCTTAAAACTCTTAGA
Found at i:54448370 original size:28 final size:29
Alignment explanation
Indices: 54448311--54448371 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
54448301 GTAAGTTACG
*
54448311 ACATTCAGGGACCAAATCAAAAAAATCGAA
1 ACATTCAGGGA-CAAATCAAAAAAATCAAA
54448341 ACATTCAGGGA-AAAT-AAAAAAATTCAAA
1 ACATTCAGGGACAAATCAAAAAAA-TCAAA
54448369 ACA
1 ACA
54448372 AGGGTCACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.24
28 11 0.38
30 11 0.38
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.15
Consensus pattern (29 bp):
ACATTCAGGGACAAATCAAAAAAATCAAA
Found at i:54449454 original size:39 final size:39
Alignment explanation
Indices: 54449385--54449589 Score: 259
Period size: 39 Copynumber: 5.3 Consensus size: 39
54449375 TAATGGTCAT
* * *
54449385 TTGAGCA-ACTCTCAGTAGAATCAGTGGGTATGGCTCGA
1 TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
* *
54449423 TTGAGCATACTTTTAGTAGAACCAGTAGGTATGGATCGA
1 TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
* * *
54449462 TTGAGTATACTTTTATTAGAATCAGTAGGTATGGCTCGT
1 TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
* * *
54449501 TTGAGCATACTTTTAGTAGAATTAGTGGGTATGGCTTGA
1 TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
* * * *
54449540 TTGAGCATACTTTCAGTGGAATCAGTAGGTATAGCTTGA
1 TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
*
54449579 TTGCGCATACT
1 TTGAGCATACT
54449590 ATCATACATT
Statistics
Matches: 144, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 7 0.05
39 137 0.95
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (39 bp):
TTGAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGA
Found at i:54458067 original size:184 final size:184
Alignment explanation
Indices: 54457756--54458124 Score: 569
Period size: 184 Copynumber: 2.0 Consensus size: 184
54457746 GAATGCGAAA
* *
54457756 ATGATTGTGTATTTATGATTTGGTATATTTATATTAATCTGTAGCTAACATCGACCTGGATTCCT
1 ATGATTGTGTATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
* * * * *
54457821 CCAAATGGAAAGGAAAAGATATAGTCATCGACAAATAGCTCTGAGTTTATGGTTTTTATTTCTAT
66 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
* *
54457886 AACCTAAACCTTTTAATTTGTTGCATTACGAAA-TGTGTTGCATGGTAATAACAT
131 AACCTAAACCTTTTAATTTGCTGCATTAC-AAATTGCGTTGCATGGTAATAACAT
* * * *
54457940 ATGATTGTGTTTTTATGATTTTGTATATTTATGTTAATCCGTAGCTAATATCGACATGGATTCCT
1 ATGATTGTGTATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
54458005 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
66 CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
* * * *
54458070 AACTTGAACCTTTTCATTTGCTGCATTACAAATTGCGTTTCATGGTAATAACAT
131 AACCTAAACCTTTTAATTTGCTGCATTACAAATTGCGTTGCATGGTAATAACAT
54458124 A
1 A
54458125 AGGTAAGCTG
Statistics
Matches: 167, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
183 3 0.02
184 164 0.98
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (184 bp):
ATGATTGTGTATTTATGATTTGGTATATTTATATTAATCCGTAGCTAACATCGACATGGATTCCT
CAAAATGGAAAGGAAAAGATAAAGTCATCGACAAATAGCTCGGAGTTTATGATTTGTATTTCTAT
AACCTAAACCTTTTAATTTGCTGCATTACAAATTGCGTTGCATGGTAATAACAT
Found at i:54459054 original size:22 final size:25
Alignment explanation
Indices: 54459019--54459067 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
54459009 TAAGTGATAG
54459019 TGAATGTGATATTTA-ATGTT-TAA
1 TGAATGTGATATTTAGATGTTCTAA
*
54459042 TGAAT-TGGTATTTAGATGTTCTAA
1 TGAATGTGATATTTAGATGTTCTAA
54459066 TG
1 TG
54459068 GTTGTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 10 0.43
24 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (25 bp):
TGAATGTGATATTTAGATGTTCTAA
Found at i:54471408 original size:20 final size:20
Alignment explanation
Indices: 54471383--54471423 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54471373 GGCTTTTCTT
54471383 AAACATTATTCTCTTGATTC
1 AAACATTATTCTCTTGATTC
54471403 AAACATTATTCTCTTGATTC
1 AAACATTATTCTCTTGATTC
54471423 A
1 A
54471424 TTATTCATGT
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:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (20 bp):
AAACATTATTCTCTTGATTC
Found at i:54471427 original size:16 final size:17
Alignment explanation
Indices: 54471385--54471429 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
54471375 CTTTTCTTAA
54471385 ACATTATTCTCTTGATT
1 ACATTATTCTCTTGATT
54471402 CAAACATTATTCTCTTGATT
1 ---ACATTATTCTCTTGATT
54471422 -CATTATTC
1 ACATTATTC
54471430 ATGTCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
20 17 0.68
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (17 bp):
ACATTATTCTCTTGATT
Found at i:54478731 original size:39 final size:41
Alignment explanation
Indices: 54478643--54478738 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 41
54478633 ACGAGATTTT
*
54478643 CACTTCGGTG-CCTATGTATACACTTTAGTGTCCCTGTTCA
1 CACTTCGGTGCCCTATGTATACACATTAGTGTCCCTGTTCA
* * * *
54478683 CACTACGGTGCCCT-TGTTTGCACATTCGTG-CCCTG-TCA
1 CACTTCGGTGCCCTATGTATACACATTAGTGTCCCTGTTCA
54478721 GCACTTCGGTGCTCCTAT
1 -CACTTCGGTGC-CCTAT
54478739 TATGCATCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.07
39 15 0.33
40 24 0.52
41 4 0.09
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (41 bp):
CACTTCGGTGCCCTATGTATACACATTAGTGTCCCTGTTCA
Found at i:54478732 original size:19 final size:19
Alignment explanation
Indices: 54478674--54478732 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
54478664 ACTTTAGTGT
*
54478674 CCCTGTTCA-CACTACGGTG
1 CCCTG-TCAGCACTTCGGTG
**
54478693 CCCTTGTTTGCACATTC-GTG
1 CCC-TGTCAGCAC-TTCGGTG
54478713 CCCTGTCAGCACTTCGGTG
1 CCCTGTCAGCACTTCGGTG
54478732 C
1 C
54478733 TCCTATTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 3 0.10
19 15 0.48
20 11 0.35
21 2 0.06
ACGTcount: A:0.12, C:0.36, G:0.22, T:0.31
Consensus pattern (19 bp):
CCCTGTCAGCACTTCGGTG
Found at i:54479037 original size:52 final size:52
Alignment explanation
Indices: 54478981--54479084 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
54478971 GATGAGTTTG
54478981 GATTGAATTATTATCGTAGAGGAAACATACAATGAACCATTTTCAGTAGTAA
1 GATTGAATTATTATCGTAGAGGAAACATACAATGAACCATTTTCAGTAGTAA
54479033 GATTGAATTATTATCGTAGAGGAAACATACAATGAACCATTTTCAGTAGTAA
1 GATTGAATTATTATCGTAGAGGAAACATACAATGAACCATTTTCAGTAGTAA
54479085 TCCTATAAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (52 bp):
GATTGAATTATTATCGTAGAGGAAACATACAATGAACCATTTTCAGTAGTAA
Found at i:54480190 original size:25 final size:25
Alignment explanation
Indices: 54480155--54480209 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
54480145 AAGTTAATGA
54480155 GTTACACGGCCTGACACACGGGCAT
1 GTTACACGGCCTGACACACGGGCAT
*
54480180 GTTACATGGCCTGACACACGGGCAT
1 GTTACACGGCCTGACACACGGGCAT
54480205 GTTAC
1 GTTAC
54480210 GTGACCGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (25 bp):
GTTACACGGCCTGACACACGGGCAT
Found at i:54482184 original size:30 final size:30
Alignment explanation
Indices: 54482150--54482206 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54482140 AAACCTTTTT
* *
54482150 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTTCCC
54482180 ACTTTCCCCCCAAAACTTTTACTCCTT
1 ACTTTCCCCCCAAAACTTTTACTCCTT
54482207 TCTCCTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.40, G:0.00, T:0.39
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCTTCCC
Found at i:54482369 original size:30 final size:31
Alignment explanation
Indices: 54482315--54482374 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
54482305 AAACCTTTTA
*
54482315 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
54482345 TTTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
54482375 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:54485597 original size:41 final size:41
Alignment explanation
Indices: 54485540--54485677 Score: 183
Period size: 41 Copynumber: 3.4 Consensus size: 41
54485530 CTTTTAGGGC
*
54485540 TTTAGCGACGTTTTTGAGAAAGCGCCGCTAATGCTCGAACT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAACT
54485581 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT--AAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAA--CT
* * **
54485622 TTTAGCGGCGTTTTTTCA-AAAACGCCGCTAATGCTCGGTCT
1 TTTAGCGGCG-TTTTTGAGAAAGCGCCGCTAATGCTCGAACT
54485663 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
54485678 TCAAAAAGCG
Statistics
Matches: 87, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.02
40 5 0.06
41 74 0.85
42 6 0.07
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAACT
Found at i:54486207 original size:74 final size:75
Alignment explanation
Indices: 54486110--54486251 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
54486100 TTCGGTGTCA
* *
54486110 GGTTAGGGTTTAGGGTTTAGATTAATTAGTGAGTTTTAATTT-T-TATGAAATAAGGTTTAAGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAAT-AGTTTTAATTTATATATGAAATAAGGTTTAAGGG
54486173 TTAGGGATTCG
65 TTAGGGATTCG
* * *
54486184 GGTTAGGATTTAGGGGTTT-GATTAATTAATATTTTTAATTTATATATTAAATAAGGTTTAGGGG
1 GGTTAGGATTTA-GGGTTTAGATTAATTAATAGTTTTAATTTATATATGAAATAAGGTTTAAGGG
54486248 TTAG
65 TTAG
54486252 TAGTTAGGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
73 10 0.17
74 22 0.37
75 28 0.47
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.44
Consensus pattern (75 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATAGTTTTAATTTATATATGAAATAAGGTTTAAGGGT
TAGGGATTCG
Found at i:54486264 original size:7 final size:7
Alignment explanation
Indices: 54486241--54486293 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
54486231 TAAATAAGGT
54486241 TTAGGGG
1 TTAGGGG
**
54486248 TTAGTAG
1 TTAGGGG
54486255 TTAGGGG
1 TTAGGGG
*
54486262 TTAGTGG
1 TTAGGGG
*
54486269 TTTGGGG
1 TTAGGGG
*
54486276 TTTGGGG
1 TTAGGGG
*
54486283 TTAAGGG
1 TTAGGGG
54486290 TTAG
1 TTAG
54486294 AAGTTAAGAG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (7 bp):
TTAGGGG
Found at i:54486265 original size:21 final size:21
Alignment explanation
Indices: 54486241--54486299 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
54486231 TAAATAAGGT
*
54486241 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGAAGTTAGGGG
* * ** *
54486262 TTAGTGGTTTGGGGTTTGGGG
1 TTAGGGGTTAGAAGTTAGGGG
*
54486283 TTAAGGGTTAGAAGTTA
1 TTAGGGGTTAGAAGTTA
54486300 AGAGTTAGTG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (21 bp):
TTAGGGGTTAGAAGTTAGGGG
Found at i:54488322 original size:30 final size:30
Alignment explanation
Indices: 54488286--54488460 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
54488276 ACTTTTCTCA
*
54488286 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
54488316 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
54488346 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
54488376 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
54488406 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
54488436 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
54488461 CTTGTACCTA
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:54488351 original size:60 final size:60
Alignment explanation
Indices: 54488286--54488460 Score: 332
Period size: 60 Copynumber: 2.9 Consensus size: 60
54488276 ACTTTTCTCA
*
54488286 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
54488346 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
*
54488406 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
54488461 CTTGTACCTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:54488604 original size:27 final size:26
Alignment explanation
Indices: 54488546--54488619 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
54488536 TATATGGGCG
54488546 GGGATTTTTTTGGAGAGTTTTAGGCA
1 GGGATTTTTTTGGAGAGTTTTAGGCA
* **
54488572 GGGATTTTTTTGGAAAGTTTTAGGGG
1 GGGATTTTTTTGGAGAGTTTTAGGCA
54488598 GGAGATTTTTTTGGAGAGTTTT
1 GG-GATTTTTTTGGAGAGTTTT
54488620 TGGGAGAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 25 0.58
27 18 0.42
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (26 bp):
GGGATTTTTTTGGAGAGTTTTAGGCA
Found at i:54488628 original size:26 final size:26
Alignment explanation
Indices: 54488548--54488628 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
54488538 TATGGGCGGG
* *
54488548 GATTTTTTTGGAGAGTTTTAGGCAGG
1 GATTTTTTTGGAGAGTTTTAGGGAGA
* *
54488574 GATTTTTTTGGAAAGTTTTAGGGGGGA
1 GATTTTTTTGGAGAGTTTTA-GGGAGA
*
54488601 GATTTTTTTGGAGAGTTTTTGGGAGA
1 GATTTTTTTGGAGAGTTTTAGGGAGA
54488627 GA
1 GA
54488629 AAGTTATTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 26 0.55
27 21 0.45
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.42
Consensus pattern (26 bp):
GATTTTTTTGGAGAGTTTTAGGGAGA
Found at i:54489161 original size:30 final size:30
Alignment explanation
Indices: 54489127--54489209 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
54489117 TACGTATATA
* *
54489127 TAATATTAT-TCTATTTTATGTATATATCTT
1 TAATATTATAT-TATTATATATATATATCTT
*
54489157 TAATATTATATTATTATATATATATATTTT
1 TAATATTATATTATTATATATATATATCTT
* *
54489187 TACATGTTATCTTATGTATATAT
1 TA-ATATTATATTAT-TATATAT
54489210 CTTAACTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 27 0.60
31 11 0.24
32 7 0.16
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (30 bp):
TAATATTATATTATTATATATATATATCTT
Found at i:54489260 original size:25 final size:23
Alignment explanation
Indices: 54489198--54489260 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
54489188 ACATGTTATC
*
54489198 TTATGTATATATCTT-A-ACTATA
1 TTATGTATAT-TTTTAACACTATA
54489220 TTATGTATATTTTTAACACTATA
1 TTATGTATATTTTTAACACTATA
54489243 TTATGTACATATTTTTAA
1 TTATGT--ATATTTTTAA
54489261 TATTATCACG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 3 0.08
22 11 0.31
23 12 0.33
25 10 0.28
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (23 bp):
TTATGTATATTTTTAACACTATA
Found at i:54489441 original size:16 final size:15
Alignment explanation
Indices: 54489417--54489464 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
54489407 TAATTATTAT
* *
54489417 TATTCTAATGTTTTGA
1 TATTTTAATATTTT-A
54489433 TATTTTAATATTTTA
1 TATTTTAATATTTTA
54489448 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
54489464 T
1 T
54489465 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:54489452 original size:7 final size:8
Alignment explanation
Indices: 54489417--54489468 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
54489407 TAATTATTAT
*
54489417 TATTCTAA
1 TATTTTAA
* *
54489425 TGTTTTGA
1 TATTTTAA
54489433 TATTTTAA
1 TATTTTAA
54489441 TATTTT-A
1 TATTTTAA
54489448 TATTTTATA
1 TATTTTA-A
*
54489457 TATTTTAT
1 TATTTTAA
54489465 TATT
1 TATT
54489469 CACATCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
9 8 0.22
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:54497940 original size:68 final size:70
Alignment explanation
Indices: 54497774--54497948 Score: 219
Period size: 71 Copynumber: 2.5 Consensus size: 70
54497764 CTTTCCAAGG
* ** *
54497774 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
54497839 TTTTT
66 GTTTT
* * * *
54497844 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
54497908 TGTTTT
65 TGTTTT
** *
54497914 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
54497949 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
68 31 0.34
70 25 0.27
71 35 0.38
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:54498219 original size:147 final size:146
Alignment explanation
Indices: 54497952--54498296 Score: 478
Period size: 147 Copynumber: 2.3 Consensus size: 146
54497942 TAAGCCTTTT
* * *
54497952 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
54498017 TAATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-
65 TAATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGT
54498081 ACACGCTGAGGTAATTTC
129 ACACGCTGAGGTAATTTC
* ** *
54498099 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
* * **
54498164 TATTTTCAATTTCTGTT-TTCAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGT
65 TAATTTCAATTTCTGTTGTT-AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGG-
* *
54498228 TCACATGCTGAGGTATTTTC
128 T-ACACGCTGAGGTAATTTC
*
54498248 AATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AATTTCTGTTTT--CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
54498297 TTCAGATTAC
Statistics
Matches: 174, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
146 13 0.07
147 102 0.59
149 28 0.16
150 27 0.16
151 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (146 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT
AATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGTAC
ACGCTGAGGTAATTTC
Found at i:54498321 original size:75 final size:74
Alignment explanation
Indices: 54497966--54498301 Score: 464
Period size: 75 Copynumber: 4.5 Consensus size: 74
54497956 TTTGTTTTTC
* *
54497966 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
54498031 GTTGTTAAAA
66 GTT-TTAAAA
** *
54498041 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
54498106 GTTTT--CA
66 GTTTTAAAA
* * ** * *
54498113 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
54498178 GTTTTCAAAA
66 GTTTT-AAAA
* *
54498188 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
54498252 TCTGTTTT-AAA
63 TCTGTTTTAAAA
*
54498263 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
54498302 ATTACACACT
Statistics
Matches: 236, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
72 66 0.28
74 3 0.01
75 138 0.58
76 1 0.00
77 28 0.12
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTAAAA
Found at i:54498537 original size:72 final size:72
Alignment explanation
Indices: 54498456--54498596 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
54498446 TCAAAATCAG
* * *
54498456 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTGTTTTA
54498521 ATTTCAA
66 ATTTCAA
* *
54498528 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTTA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTGTTTTA
54498593 ATTT
66 ATTT
54498597 ATGTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (72 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTGTTTTA
ATTTCAA
Found at i:54498624 original size:160 final size:157
Alignment explanation
Indices: 54498448--54499381 Score: 844
Period size: 160 Copynumber: 5.9 Consensus size: 157
54498438 CTACTTTTTC
* * * * *
54498448 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* **
54498513 GTGTT-TTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
66 GTGTTATAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
54498577 CAATTTCTGTTTTTTAATTTATGTTTCAAAA
131 CAATTTCTGTTTTTT-ATTT-TGTTTC--AA
*
54498608 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* *
54498672 GCTCAATTTTATTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC---ACAT
66 G-----------TG-TTAT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
54498734 GCTGAGGT-TTTTCAATTTCTG---------TT-TTTCAA
118 GCTGAGGTATTTTCAATTTCTGTTTTTTATTTTGTTTCAA
*
54498763 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCACACGCTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTCAATTTC
* ** * *
54498827 TGT-TTGTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACGCTGAGGTAA
65 TGTGTTAT--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAT
*
54498889 TTTCAA-------TTTTT-TGTTG--TC-A
128 TTTCAATTTCTGTTTTTTATTTTGTTTCAA
* *
54498908 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTT-AATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* * * * *
54498972 CT-TCATCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACACACTGAGGTA
66 GTGTTAT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTA
*
54499035 TTTTCAATTTCTGTTTTCTATTTCTGTTTTTC-A
127 TTTTCAATTTCTGTTTTTTATTT-TG--TTTCAA
* * *
54499068 AAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* * *
54499133 GT-TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTC
66 GTGTTAT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTA
* ***
54499196 TTTTCAATTTCTGTTCTTCAATTTCTATTTGTAAAAA
127 TTTTCAATTTCTG-T-TT---TTTAT-TTTGTTTCAA
* * * *
54499233 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
54499298 GTTGTTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
66 G-TGTT---ATAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
* *
54499363 TTTTTAAATTTCTATTTTT
127 -TTTTCAATTTCTGTTTTT
54499382 CAAAAATCAA
Statistics
Matches: 650, Mismatches: 62, Indels: 121
0.78 0.07 0.15
Matches are distributed among these distances:
143 37 0.06
144 45 0.07
145 65 0.10
146 10 0.02
147 19 0.03
154 6 0.01
155 42 0.06
156 24 0.04
157 4 0.01
158 1 0.00
159 22 0.03
160 94 0.14
161 74 0.11
162 1 0.00
163 4 0.01
164 1 0.00
165 62 0.10
166 8 0.01
167 16 0.02
168 11 0.02
169 51 0.08
170 15 0.02
171 2 0.00
172 1 0.00
173 35 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (157 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTGTTATAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
CAATTTCTGTTTTTTATTTTGTTTCAA
Found at i:54498692 original size:88 final size:84
Alignment explanation
Indices: 54498524--54499375 Score: 527
Period size: 88 Copynumber: 10.7 Consensus size: 84
54498514 TGTTTTAATT
*
54498524 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTATTTTCAATTTCTGTAT
54498589 TTTAATTTATGTTTCAAAAAAAA
65 TTTAATTTATGTTTC---AAAAA
*
54498612 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGTTGAGGTATTTTCAATTTCTGCTCA
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTATTTTCAATTTCTG-T--
54498677 ATTTT-ATTGT-T-TTTCAAAAA
63 ATTTTAATT-TATGTTTCAAAAA
* *
54498697 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-CA-TGCTGAGGT-TTTTCAATTTCTG---T
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTATTTTCAATTTCTGTATT
*
54498756 TT--TTCA------AAAAA
66 TTAATTTATGTTTCAAAAA
*
54498767 TCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCACACGCTGAGGTATTTTCAATTTCTG--
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-AC-CGCTGAGGTATTTTCAATTTCTGTA
54498829 -------TT-TG--TCAAAAAA
64 TTTTAATTTATGTTTC-AAAAA
** * *
54498841 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA-CGCTGAGGTAATTTCAA------T-TT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTATTTTCAATTTCTGTATT
*
54498898 TT--TGT-TG--TCAAAAA
66 TTAATTTATGTTTCAAAAA
*
54498912 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTT-AA--T-T-TA-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTATTTTCAATTTCTGTAT
* *
54498971 --T-CTTCA----TCAAAAA
65 TTTAATTTATGTTTCAAAAA
* * *
54498984 TCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACACACTGAGGTATTTTCAATTTCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---AC-CGCTGAGGTATTTTCAATTTCTG
*
54499048 T-TTTCT-ATTTCTGTTTTTCAAAAA
62 TATTT-TAATTTATG--TTTCAAAAA
* * *
54499072 TCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTG---
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTATTTTCAATTTCTGTAT
54499134 ------TT-TG--TCAAAAA
65 TTTAATTTATGTTTCAAAAA
* *
54499145 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATTTCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---AC-CGCTGAGGTATTTTCAATTTCTG
* *
54499209 T-TCTTCAATTTCTAT-TTGTAAAAAAAAA
62 TAT-TTTAA-TT-TATGTT-T---CAAAAA
* * * *
54499237 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTCAATTTCTGT-T
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTATTTTCAATTTCTGTAT
* **
54499301 GTTAA---A----AAAAAAA
65 TTTAATTTATGTTTCAAAAA
*
54499314 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC-CGCTGAGGTA-TTTTCAATTTCT
54499376 ATTTTTCAAA
Statistics
Matches: 642, Mismatches: 51, Indels: 152
0.76 0.06 0.18
Matches are distributed among these distances:
70 38 0.06
71 41 0.06
72 64 0.10
73 61 0.10
74 66 0.10
75 28 0.04
76 3 0.00
77 55 0.09
78 13 0.02
79 1 0.00
82 16 0.02
83 7 0.01
84 2 0.00
85 40 0.06
86 25 0.04
87 23 0.04
88 80 0.12
89 10 0.02
90 31 0.05
92 37 0.06
93 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (84 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACCGCTGAGGTATTTTCAATTTCTGTATT
TTAATTTATGTTTCAAAAA
Found at i:54499003 original size:72 final size:72
Alignment explanation
Indices: 54498684--54499050 Score: 467
Period size: 72 Copynumber: 5.1 Consensus size: 72
54498674 TCAATTTTAT
* * *
54498684 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-T-CACATGCTGAGGT-TTTT
1 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACACGCTGAGGTATTTT
54498746 CAATTTC
66 CAATTTC
*
54498753 TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCACACGCTGAGGTATT
1 TGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-ACACGCTGAGGTATT
54498818 TTCAATTTC
64 TTCAATTTC
** ** * *
54498827 TGTTTGTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCC-TCAAGACGCTGAGGTAATT
1 TGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACACGCTGAGGTATTT
54498891 TCAATTT-
65 TCAATTTC
*
54498898 TTTGTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATT
1 TGT-TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGACACGCTGAGGTATT
*
54498963 TT-AATTTA
64 TTCAATTTC
* ** * *
54498971 TCTTCATCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACACTGAGGTAT
1 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG---ACACGCTGAGGTAT
54499036 TTTCAATTTC
63 TTTCAATTTC
54499046 TGTTT
1 TGTTT
54499051 TCTATTTCTG
Statistics
Matches: 261, Mismatches: 24, Indels: 20
0.86 0.08 0.07
Matches are distributed among these distances:
69 8 0.03
70 36 0.14
71 39 0.15
72 72 0.28
73 29 0.11
74 69 0.26
75 8 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (72 bp):
TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACACGCTGAGGTATTTT
CAATTTC
Found at i:54499057 original size:13 final size:13
Alignment explanation
Indices: 54499035--54499064 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54499025 CACTGAGGTA
54499035 TTTTCAATTTCTG
1 TTTTCAATTTCTG
*
54499048 TTTTCTATTTCTG
1 TTTTCAATTTCTG
54499061 TTTT
1 TTTT
54499065 TCAAAAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:54499173 original size:73 final size:74
Alignment explanation
Indices: 54499049--54499210 Score: 245
Period size: 73 Copynumber: 2.2 Consensus size: 74
54499039 CAATTTCTGT
* * * *
54499049 TTTCTATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
54499113 CTGAGGTAA
66 CTGAGGTAA
*
54499122 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACAC
**
54499187 GCTGAGGTCT
65 GCTGAGGTAA
54499197 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
54499211 CTTCAATTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 55 0.69
75 25 0.31
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
CTGAGGTAA
Found at i:54499194 original size:161 final size:163
Alignment explanation
Indices: 54498905--54499380 Score: 615
Period size: 161 Copynumber: 2.9 Consensus size: 163
54498895 TTTTTTGTTG
* *
54498905 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGT-ATTTTAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* * ** * * *
54498969 TATCTTCATCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACACTGAGGT
66 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGT
* *
54499034 ATTTTCAATTTCTGTTTTCTATTTCTGTTT-T-
131 ATTTTCAATTTCTGTTTTCAATTTCTATTTGTA
* *
54499065 TCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
54499130 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGT
66 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGT
*
54499195 CTTTTCAATTTCTGTTCTTCAATTTCTATTTGTAA
131 ATTTTCAATTTCTGTT-TTCAATTTCTATTTGT-A
** * * *
54499230 AAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
54499295 TCTG-TTGTTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGC
66 TCTGTTTG-T----CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACACGC
* *
54499356 TGAGGTATTTTTAAATTTCTATTTT
125 TGAGGTA-TTTTCAATTTCTGTTTT
54499381 TCAAAAATCA
Statistics
Matches: 277, Mismatches: 27, Indels: 17
0.86 0.08 0.05
Matches are distributed among these distances:
160 52 0.19
161 80 0.29
162 12 0.04
163 1 0.00
164 3 0.01
165 63 0.23
167 13 0.05
168 13 0.05
169 38 0.14
170 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (163 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGT
ATTTTCAATTTCTGTTTTCAATTTCTATTTGTA
Found at i:54499338 original size:77 final size:76
Alignment explanation
Indices: 54499212--54499419 Score: 278
Period size: 77 Copynumber: 2.7 Consensus size: 76
54499202 ATTTCTGTTC
* *
54499212 TTCAATTTCTATTTGTAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAAGACAT
1 TTCAATTTCTATTT-TAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
54499277 GCTGAGGTA-AT
65 GCTGAGGTATAT
* *
54499288 TTCAATTTCTGTTGTTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTCAATTTCTATT-TT-AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
54499353 CGCTGAGGTATTT
64 CGCTGAGGTATAT
* ** * *
54499366 TTAAATTTCTATTTT--TCAAAAATCAACTCATATTGCGATATGTGAGTTGAGCCT
1 TTCAATTTCTATTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
54499420 TGGGTTCACA
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
74 35 0.30
76 13 0.11
77 58 0.49
78 12 0.10
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (76 bp):
TTCAATTTCTATTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
CTGAGGTATAT
Found at i:54500167 original size:30 final size:30
Alignment explanation
Indices: 54500131--54500305 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
54500121 ACTTTTCTCA
*
54500131 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
54500161 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
54500191 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
54500221 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
54500251 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
54500281 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
54500306 CTTGTACCTA
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:54500196 original size:60 final size:60
Alignment explanation
Indices: 54500131--54500305 Score: 332
Period size: 60 Copynumber: 2.9 Consensus size: 60
54500121 ACTTTTCTCA
*
54500131 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
54500191 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
*
54500251 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
54500306 CTTGTACCTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:54500449 original size:27 final size:26
Alignment explanation
Indices: 54500387--54500464 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
54500377 TTTGTATATG
54500387 GGCGGGGATTTTTTTGGAGAGTTTTA
1 GGCGGGGATTTTTTTGGAGAGTTTTA
54500413 GGCGGGGATTTTTTTGGAGAGTTTTA
1 GGCGGGGATTTTTTTGGAGAGTTTTA
*
54500439 GGGGGGAGATTTTTTTGGAGAGTTTT
1 GGCGGG-GATTTTTTTGGAGAGTTTT
54500465 TGGGAGAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 31 0.62
27 19 0.38
ACGTcount: A:0.15, C:0.03, G:0.40, T:0.42
Consensus pattern (26 bp):
GGCGGGGATTTTTTTGGAGAGTTTTA
Found at i:54500473 original size:26 final size:25
Alignment explanation
Indices: 54500393--54500473 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 25
54500383 TATGGGCGGG
*
54500393 GATTTTTTTGGAGAGTTTTAGGCGGG
1 GATTTTTTTGGAGAGTTTTAGG-GGA
54500419 GATTTTTTTGGAGAGTTTTAGGGGGGA
1 GATTTTTTTGGAGAGTTTTA--GGGGA
*
54500446 GATTTTTTTGGAGAGTTTTTGGGAGA
1 GATTTTTTTGGAGAGTTTTAGGG-GA
54500472 GA
1 GA
54500474 AAGTTATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
25 3 0.06
26 24 0.48
27 21 0.42
28 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.38, T:0.42
Consensus pattern (25 bp):
GATTTTTTTGGAGAGTTTTAGGGGA
Found at i:54500947 original size:25 final size:25
Alignment explanation
Indices: 54500858--54501057 Score: 82
Period size: 23 Copynumber: 8.2 Consensus size: 25
54500848 ATTATATTTC
* * *
54500858 TTAATATTATATTATATATAT-TCT
1 TTAATACTATATTATGTATATATAT
* *
54500882 TT--TAGTATATTAGGTATAT-T-T
1 TTAATACTATATTATGTATATATAT
* * * *
54500903 TAAATTCTAGATTACGTATATATA-
1 TTAATACTATATTATGTATATATAT
* *
54500927 TT-ATACTATTTTATGTATATATCT
1 TTAATACTATATTATGTATATATAT
* *
54500951 TTAATATTATATTATTTATATATATTTTTT
1 TTAATACTATATTATGTATATATA-----T
** * *
54500981 TTACATGTTATCTTATGTATATAT-C
1 TTA-ATACTATATTATGTATATATAT
54501006 TT-A-ACTATATTATGTATAT-T-T
1 TTAATACTATATTATGTATATATAT
* * *
54501027 TTAACACTATATTATGTACATATTT
1 TTAATACTATATTATGTATATATAT
54501052 TTAATA
1 TTAATA
54501058 TTATCACGTA
Statistics
Matches: 132, Mismatches: 28, Indels: 31
0.69 0.15 0.16
Matches are distributed among these distances:
21 5 0.04
22 29 0.22
23 45 0.34
24 7 0.05
25 25 0.19
30 4 0.03
31 17 0.13
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:54501232 original size:16 final size:15
Alignment explanation
Indices: 54501208--54501255 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
54501198 TAATTATTAT
* *
54501208 TATTCTAATGTTTTGA
1 TATTTTAATATTTT-A
54501224 TATTTTAATATTTTA
1 TATTTTAATATTTTA
54501239 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
54501255 T
1 T
54501256 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:54501243 original size:7 final size:8
Alignment explanation
Indices: 54501208--54501259 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
54501198 TAATTATTAT
*
54501208 TATTCTAA
1 TATTTTAA
* *
54501216 TGTTTTGA
1 TATTTTAA
54501224 TATTTTAA
1 TATTTTAA
54501232 TATTTT-A
1 TATTTTAA
54501239 TATTTTATA
1 TATTTTA-A
*
54501248 TATTTTAT
1 TATTTTAA
54501256 TATT
1 TATT
54501260 CACATCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
9 8 0.22
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:54503952 original size:43 final size:43
Alignment explanation
Indices: 54503892--54503982 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
54503882 CTTTGAGTTC
* *
54503892 ATTA-CAAGATTTCCTTGATTAAGT-AAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAA-TAAAATGCATTATATCTTTT
* *
54503934 ATTACCAAGATTTACTTGATTAATAAAATGCATTCTATGTTTT
1 ATTACCAAGATTTACTTGATTAATAAAATGCATTATATCTTTT
54503977 ATTACC
1 ATTACC
54503983 TTGCATATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAATAAAATGCATTATATCTTTT
Found at i:54504360 original size:43 final size:43
Alignment explanation
Indices: 54504250--54504562 Score: 380
Period size: 43 Copynumber: 7.3 Consensus size: 43
54504240 AAGATATGTT
* *
54504250 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTT-TGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
** * * *
54504292 AATAGCAGCGTTTGTAGGAAAAGCGCCGCTAAAGGTTATGGAC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
* * *
54504335 TTTAGCGGCGTTTGTGGGAAAAGCGCCTCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
* * *
54504378 TTTAGCGGCGTTTATGGAAAAAGCGACGCTAAAGGTCT-TGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TATGGTC
* * * * *
54504421 TTTAGCGGCGTTTGTGGGAAAAGTGCCACTAAAGATCATTGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
* *
54504464 TTTAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCT-TGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TATGGTC
* **
54504507 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
54504550 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
54504563 ATTTCTGAAA
Statistics
Matches: 227, Mismatches: 39, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
42 32 0.14
43 195 0.86
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGGTC
Found at i:54504434 original size:86 final size:86
Alignment explanation
Indices: 54504250--54504564 Score: 420
Period size: 86 Copynumber: 3.7 Consensus size: 86
54504240 AAGATATGTT
* * * * ** * *
54504250 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGT-TTGTTCAATAGCAGCGTTTGTAGG-AAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTAT-GGAAAA
*
54504313 AGCGCCGCTAAAGGT-TATGGAC
65 AGCGCCGCTAAAGGTCT-TGGTC
*
54504335 TTTAGCGGCGTTTGTGGGAAAAGCGCCTCTAAAGATCATGGTCTTTAGCGGCGTTTATGGAAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGGAAAAA
*
54504400 GCGACGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCTTGGTC
* * * *
54504421 TTTAGCGGCGTTTGTGGGAAAAGTGCCACTAAAGATCATTGTCTTTAGCGGCGTTTGTGGAAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGGAAAAA
*
54504486 GTGCCGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCTTGGTC
* **
54504507 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTAT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTAT
54504565 TTCTGAAAAC
Statistics
Matches: 203, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
85 35 0.17
86 167 0.82
87 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTATGGAAAAA
GCGCCGCTAAAGGTCTTGGTC
Found at i:54504669 original size:13 final size:13
Alignment explanation
Indices: 54504648--54504694 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
54504638 AAACACTTTT
*
54504648 AGCGACGCTAAAA
1 AGCGCCGCTAAAA
54504661 AGCGCCGCT--AA
1 AGCGCCGCTAAAA
54504672 AG-G-C-CTAAAA
1 AGCGCCGCTAAAA
54504682 AGCGCCGCTAAAA
1 AGCGCCGCTAAAA
54504695 GCCTGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
8 2 0.07
9 1 0.04
10 5 0.18
11 5 0.18
12 1 0.04
13 14 0.50
ACGTcount: A:0.40, C:0.28, G:0.23, T:0.09
Consensus pattern (13 bp):
AGCGCCGCTAAAA
Found at i:54504681 original size:21 final size:21
Alignment explanation
Indices: 54504655--54504698 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
54504645 TTTAGCGACG
*
54504655 CTAAAAAGCGCCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
54504676 CTAAAAAGCGCCGCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
54504697 CT
1 CT
54504699 GTTTTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:54517881 original size:13 final size:13
Alignment explanation
Indices: 54517863--54517887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54517853 TTTTTTCTAA
54517863 ATATTATCACTAT
1 ATATTATCACTAT
54517876 ATATTATCACTA
1 ATATTATCACTA
54517888 AATAATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTATCACTAT
Found at i:54519751 original size:13 final size:13
Alignment explanation
Indices: 54519733--54519758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54519723 AAGTTGGTTG
54519733 ATATTTAAATGTT
1 ATATTTAAATGTT
54519746 ATATTTAAATGTT
1 ATATTTAAATGTT
54519759 TTTGGTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTAAATGTT
Found at i:54521589 original size:23 final size:23
Alignment explanation
Indices: 54521563--54521714 Score: 133
Period size: 23 Copynumber: 6.6 Consensus size: 23
54521553 AGATAACATG
***
54521563 AAGCACTGAAGTGTTGTAACACA
1 AAGCACTGAAGTGCAATAACACA
** * **
54521586 AAGCACAAAAGTGCAATATCATG
1 AAGCACTGAAGTGCAATAACACA
**
54521609 AAGCACTGAAGTGTTATAACACA
1 AAGCACTGAAGTGCAATAACACA
* *
54521632 AAGCACCGAAGTGCAATAACACG
1 AAGCACTGAAGTGCAATAACACA
* ***
54521655 AAGCACCGAAGTGTTGTAACACA
1 AAGCACTGAAGTGCAATAACACA
** *
54521678 AAGCACAAAAGTGCAATAACACG
1 AAGCACTGAAGTGCAATAACACA
54521701 AAGCACTGAAGTGC
1 AAGCACTGAAGTGC
54521715 TAAATTCACG
Statistics
Matches: 98, Mismatches: 31, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 98 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (23 bp):
AAGCACTGAAGTGCAATAACACA
Found at i:54521629 original size:46 final size:46
Alignment explanation
Indices: 54521555--54521713 Score: 255
Period size: 46 Copynumber: 3.5 Consensus size: 46
54521545 AACATATCAG
*
54521555 ATAACATGAAGCACTGAAGTGTTGTAACACAAAGCACAAAAGTGCA
1 ATAACACGAAGCACTGAAGTGTTGTAACACAAAGCACAAAAGTGCA
* * * **
54521601 ATATCATGAAGCACTGAAGTGTTATAACACAAAGCACCGAAGTGCA
1 ATAACACGAAGCACTGAAGTGTTGTAACACAAAGCACAAAAGTGCA
*
54521647 ATAACACGAAGCACCGAAGTGTTGTAACACAAAGCACAAAAGTGCA
1 ATAACACGAAGCACTGAAGTGTTGTAACACAAAGCACAAAAGTGCA
54521693 ATAACACGAAGCACTGAAGTG
1 ATAACACGAAGCACTGAAGTG
54521714 CTAAATTCAC
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 102 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.16
Consensus pattern (46 bp):
ATAACACGAAGCACTGAAGTGTTGTAACACAAAGCACAAAAGTGCA
Found at i:54523350 original size:50 final size:50
Alignment explanation
Indices: 54523233--54523523 Score: 359
Period size: 50 Copynumber: 5.8 Consensus size: 50
54523223 GAATATAACA
* * * ** * * * *
54523233 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * * * ** *
54523282 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
** *
54523332 TGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * *
54523382 TGCCAACGCCATGCCCCAGACATGGTCTTACGTGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
*
54523432 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
54523482 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54523524 TTACCCAAAT
Statistics
Matches: 212, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
49 36 0.17
50 176 0.83
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:54530241 original size:50 final size:50
Alignment explanation
Indices: 54530186--54530604 Score: 493
Period size: 50 Copynumber: 8.6 Consensus size: 50
54530176 CAATGTCACA
* * ** * **
54530186 TCCCAGATATGGTCTTACATGAGAGTTCTCATATAAGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
**
54530236 TCCCAGACATGGTCTTACGGGGGACAC-CTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGAC-CTCTCATCTTGGTGCCAACGCCATG
* * **
54530286 T-CC---CA--G----ACATGGGACCTCTCATCTCGGTGCCAATGCTGTG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* * ** *
54530326 TCCTAGACATGGTCTTACATGGAACCTCTCATCGCGGTGCCAACGTCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* *
54530376 TCCCAAACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* * *
54530426 TCCCAGGCATGATCTTATATGGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* *
54530476 TCCCAGACATGGTCTTACATGGGTCCTCTCATCTTGGTGGCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* *
54530526 TCCCAGACATGGTCTTACATGGGACCTC-CTATCTCGGTTCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTC-ATCTTGGTGCCAACGCCATG
54530576 TCCCAGACATGGTCTTACATGGGACCTCT
1 TCCCAGACATGGTCTTACATGGGACCTCT
54530605 TTACCCAAAT
Statistics
Matches: 312, Mismatches: 43, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.00
40 27 0.09
41 1 0.00
44 3 0.01
46 3 0.01
49 3 0.01
50 274 0.88
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
Found at i:54534054 original size:37 final size:37
Alignment explanation
Indices: 54534013--54534086 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
54534003 TTTATGAGAA
54534013 AACACATTCATTTCCAAATGTGACCCATTTATCTAAC
1 AACACATTCATTTCCAAATGTGACCCATTTATCTAAC
54534050 AACACATTCATTTCCAAATGTGACCCATTTATCTAAC
1 AACACATTCATTTCCAAATGTGACCCATTTATCTAAC
54534087 TTTATCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (37 bp):
AACACATTCATTTCCAAATGTGACCCATTTATCTAAC
Found at i:54534497 original size:25 final size:26
Alignment explanation
Indices: 54534449--54534498 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
54534439 CCTTCATAGA
54534449 AAGTCATTTACTATCAAACAAAAATC
1 AAGTCATTTACTATCAAACAAAAATC
* * *
54534475 AAGTCGTTTATTA-CAAAGAAAAAT
1 AAGTCATTTACTATCAAACAAAAAT
54534499 GACCTGTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (26 bp):
AAGTCATTTACTATCAAACAAAAATC
Found at i:54542097 original size:41 final size:41
Alignment explanation
Indices: 54542035--54542142 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
54542025 AATTATACCA
* * * **
54542035 TGAATTGCACATACATCCCCCTTTTTGTACTTCGGTACCTT
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
54542076 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
54542117 TGAATAGCACATACGTGCCCCTGTTT
1 TGAATTGCACATACGTGCCCCTGTTT
54542143 ACACTCCGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:54543661 original size:14 final size:13
Alignment explanation
Indices: 54543642--54543680 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
54543632 TAGTAATTTT
54543642 AAAGAAAGAAATAA
1 AAAGAAAGAAAT-A
54543656 AAAGAATA-AAATA
1 AAAGAA-AGAAATA
54543669 AAAGAAAGAAAT
1 AAAGAAAGAAAT
54543681 GCTCATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 11 0.48
14 10 0.43
15 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAGAAAGAAATA
Found at i:54552219 original size:3 final size:3
Alignment explanation
Indices: 54552211--54552237 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54552201 TTTAGAAAAG
54552211 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
54552238 TGACTGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54555388 original size:30 final size:30
Alignment explanation
Indices: 54555352--54555419 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
54555342 AAAGAGACCT
*
54555352 AGACTGATAACACC-CAGTTGAAGAAGGTCCA
1 AGACTGATAACACCTAAG-TGAAGAAGGT-CA
54555383 A-ACTGATAACACCTAAGTGAAGAAGGTCA
1 AGACTGATAACACCTAAGTGAAGAAGGTCA
54555412 AGACTGAT
1 AGACTGAT
54555420 CAAACCCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.09
30 28 0.82
31 3 0.09
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (30 bp):
AGACTGATAACACCTAAGTGAAGAAGGTCA
Found at i:54566650 original size:202 final size:201
Alignment explanation
Indices: 54566304--54566706 Score: 761
Period size: 202 Copynumber: 2.0 Consensus size: 201
54566294 CATATAACTT
54566304 CTCTTGCTTCAATTATAAATTTTACAAAGTTTACAATTTAATCCTTAGCATCGTGAAAATTCATT
1 CTCTTGCTTCAATTATAAATTTTACAAAGTTTACAATTTAATCCTTAGCATCGTGAAAATTCATT
*
54566369 ATTTACTATAATTTCACCTTAATATCACTTTGTAATCAATACATTACTTATCATAAATCTTAAAT
66 ATTTACTATAATTTCACCTTAATATCACTTTGTAATAAATACATTACTTATCATAAATCTTAAAT
*
54566434 GTATATGTTTTTTTCATTGAAAAAAATTTTTATGAAATATTTTCAGGAAAATTGCCAAACAATAG
131 GTATATGTTTTTTTCACTGAAAAAAA-TTTTATGAAATATTTTCAGGAAAATTGCCAAACAATAG
54566499 AAAATAC
195 AAAATAC
*
54566506 CTCTTGCTTCTATTATAAATTTTACAAAGTTTACAATTTAATCCTTAGCATCGTGAAAATTCATT
1 CTCTTGCTTCAATTATAAATTTTACAAAGTTTACAATTTAATCCTTAGCATCGTGAAAATTCATT
*
54566571 ATTTACTATAATTTCACCTTAATATCACTTTGTAATAAATTCATTACTTATCATAAATCTTAAAT
66 ATTTACTATAATTTCACCTTAATATCACTTTGTAATAAATACATTACTTATCATAAATCTTAAAT
54566636 GTATATGTTTTTTTCACTGAAAAAAATTTTATGAAATATTTTCAGGAAAATTGCCAAACAATAGA
131 GTATATGTTTTTTTCACTGAAAAAAATTTTATGAAATATTTTCAGGAAAATTGCCAAACAATAGA
54566701 AAATAC
196 AAATAC
54566707 TTTACATAGA
Statistics
Matches: 197, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
201 45 0.23
202 152 0.77
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (201 bp):
CTCTTGCTTCAATTATAAATTTTACAAAGTTTACAATTTAATCCTTAGCATCGTGAAAATTCATT
ATTTACTATAATTTCACCTTAATATCACTTTGTAATAAATACATTACTTATCATAAATCTTAAAT
GTATATGTTTTTTTCACTGAAAAAAATTTTATGAAATATTTTCAGGAAAATTGCCAAACAATAGA
AAATAC
Found at i:54570439 original size:426 final size:426
Alignment explanation
Indices: 54569646--54570494 Score: 1565
Period size: 426 Copynumber: 2.0 Consensus size: 426
54569636 GCATAACTTT
* * *
54569646 TGATTCTTAGCTTCGGATTAAAATTTGATTTCAAATACTCTCATTAGGGACCTTATACTTTCTAT
1 TGATTCTTAGCTTCAGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTCTAT
*
54569711 TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTTGGTCCCTAATGTTACAAAACTAA
66 TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACTAA
*
54569776 CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATCTAAACTCAATATCTATCAATT
131 CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATATAAACTCAATATCTATCAATT
*
54569841 TCAAGATTAATTAATCAATTAATCAACATGGAAACTTGCTAAAATTTTAAAAATTGATCAAATTG
196 TCAAGATTAATTAATCAATTAATCAACATGAAAACTTGCTAAAATTTTAAAAATTGATCAAATTG
54569906 GTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATGACATGAAAAAGGGT
261 GTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATGACATGAAAAAGGGT
54569971 TTGTTTACCTTGAATTTTGCTTGTTGGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAA
326 TTGTTTACCTTGAATTTTGCTTGTTGGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAA
54570036 CTATGATGGATGGTTAAAAGATAGAGAAGAAGAAGA
391 CTATGATGGATGGTTAAAAGATAGAGAAGAAGAAGA
54570072 TGATTCTTAGCTTCAGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTCTAT
1 TGATTCTTAGCTTCAGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTCTAT
*
54570137 TTCTAGCATAATTTCATGACAAAA-TTTATATTTATTCAATTGGGTCCCTAATGTTACAAAACTA
66 TTCTAGCATAATTTCATGA-AAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACTA
*
54570201 ACAAACAAGCTTAACTAACTTTACAATTTAGTTATTTTCACAATATAAACTCAATATCTATCAAT
130 ACAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATATAAACTCAATATCTATCAAT
*
54570266 TTCAAGATTAATTAATCAATTAATCAACATGAAAACTTGCTAAAATTTTAACAATTGATCAAATT
195 TTCAAGATTAATTAATCAATTAATCAACATGAAAACTTGCTAAAATTTTAAAAATTGATCAAATT
*
54570331 GGTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATTACATGAAAAAGGG
260 GGTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATGACATGAAAAAGGG
54570396 TTTGTTTACCTTGAATTTTGCTTGTTGGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCA
325 TTTGTTTACCTTGAATTTTGCTTGTTGGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCA
* * *
54570461 ACTATGGTGTATGGTTAAAAGATGGAGAAGAAGA
390 ACTATGATGGATGGTTAAAAGATAGAGAAGAAGA
54570495 TGATAAATTA
Statistics
Matches: 409, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
426 405 0.99
427 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (426 bp):
TGATTCTTAGCTTCAGATTAAAAATTGATTTCAAATACTCTCATTAGGGACCTTATAATTTCTAT
TTCTAGCATAATTTCATGAAAAATTTTACATTTATTCAATTGGGTCCCTAATGTTACAAAACTAA
CAAACAAGCTTAACTAACTTTACAATTTAGTCATTTTCACAATATAAACTCAATATCTATCAATT
TCAAGATTAATTAATCAATTAATCAACATGAAAACTTGCTAAAATTTTAAAAATTGATCAAATTG
GTACATGGGCTAGCTAAATCAAGCTCCCATAATCCAAAATCTATAAAAATGACATGAAAAAGGGT
TTGTTTACCTTGAATTTTGCTTGTTGGAATGTTATGAAAGCTTTGAAGTTTTCTTTGGTTTTCAA
CTATGATGGATGGTTAAAAGATAGAGAAGAAGAAGA
Found at i:54579329 original size:22 final size:22
Alignment explanation
Indices: 54579268--54579329 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
54579258 AATATTAGTA
*
54579268 TATTTAGTATTATTAATCTTATG
1 TATTTA-TATTATTAATTTTATG
54579291 TATTTATATTATTAATTTTATG
1 TATTTATATTATTAATTTTATG
*
54579313 T-GTTATTATTATTAATT
1 TATTTA-TATTATTAATT
54579330 AGTTTCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 3 0.08
22 27 0.75
23 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (22 bp):
TATTTATATTATTAATTTTATG
Found at i:54582567 original size:41 final size:41
Alignment explanation
Indices: 54582522--54582660 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
54582512 GACCCAACAA
* ** * *
54582522 GCTTCGTGCCGGTGTATTGTGTCAAGCCTTGAGCCTAGCAG
1 GCTTCGTGCCGGTGAATTGAATTAGGCCTTGAGCCTAGCAG
* *
54582563 GCTTCATGCCGGTGCATTGAATTAGGCCTTGAGCCTAGC-G
1 GCTTCGTGCCGGTGAATTGAATTAGGCCTTGAGCCTAGCAG
* * **
54582603 AGCTTCGAGCCGGTGAATTGAATTAGGTCTTGAGCCTATAAG
1 -GCTTCGTGCCGGTGAATTGAATTAGGCCTTGAGCCTAGCAG
54582645 GCTTCGTGCCGGTGAA
1 GCTTCGTGCCGGTGAA
54582661 CTATATTAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 81 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (41 bp):
GCTTCGTGCCGGTGAATTGAATTAGGCCTTGAGCCTAGCAG
Found at i:54596466 original size:41 final size:41
Alignment explanation
Indices: 54596380--54596479 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 41
54596370 CTATCTGATT
* * *
54596380 AGCACTAAGTGTGCG-AACTAAATGATGAGGTTGAATATCG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
*
54596420 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
* *
54596461 GGCACTAAGTGTGTGAAAC
1 AGCACTAAGTGTGCGAAAC
54596480 CGAGATCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
Found at i:54604331 original size:41 final size:41
Alignment explanation
Indices: 54604245--54604344 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 41
54604235 CTATCTGATT
* * *
54604245 AGCACTAAGTGTGCG-AACTAAATGATGAGGTTGAATATCG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
*
54604285 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
* *
54604326 GGCACTAAGTGTGTGAAAC
1 AGCACTAAGTGTGCGAAAC
54604345 CGAGATCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
Found at i:54614500 original size:34 final size:38
Alignment explanation
Indices: 54614438--54614507 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 38
54614428 TTAATTCTTT
54614438 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
1 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
*
54614476 TTCTTTTA-TTTC-TTT-AGTTT-CCTTTTCTTTTT
1 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTT
54614508 GTTTTCTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 12 0.39
35 4 0.13
36 3 0.10
37 4 0.13
38 8 0.26
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (38 bp):
TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
Found at i:54619362 original size:18 final size:19
Alignment explanation
Indices: 54619341--54619386 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
54619331 ATATAATTTT
*
54619341 AAAAATATAT-AATACATC
1 AAAAATATATAAAAACATC
54619359 AAAAATAT-TAAAAACATC
1 AAAAATATATAAAAACATC
*
54619377 AAAAAAATAT
1 AAAAATATAT
54619387 TTCCCAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATATATAAAAACATC
Found at i:54619505 original size:30 final size:30
Alignment explanation
Indices: 54619461--54619553 Score: 168
Period size: 30 Copynumber: 3.1 Consensus size: 30
54619451 ACTTAACAAG
* *
54619461 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
54619491 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
54619521 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
54619551 CAA
1 CAA
54619554 TAAAATAAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAACAAAATTAA
Found at i:54620131 original size:18 final size:18
Alignment explanation
Indices: 54620097--54620131 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54620087 GACATAGTTT
*
54620097 AAAATGAAAATTTTAAAG
1 AAAATGAAAATTGTAAAG
*
54620115 AAAATGAATATTGTAAA
1 AAAATGAAAATTGTAAA
54620132 TATGGATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAATGAAAATTGTAAAG
Found at i:54626337 original size:28 final size:28
Alignment explanation
Indices: 54626282--54626362 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
54626272 GAACATGCCA
* * *
54626282 AAGAAAAAGGAAGCCTCTATAGAAATCT
1 AAGAAAAAGGAAGCCTTTATGGCAATCT
* *
54626310 AAGAAAAAGGAAGCCTTTGTGGCGATCT
1 AAGAAAAAGGAAGCCTTTATGGCAATCT
* *
54626338 AAGAAAATGGAAACCTTTATGGCAA
1 AAGAAAAAGGAAGCCTTTATGGCAA
54626363 ATCTTGTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (28 bp):
AAGAAAAAGGAAGCCTTTATGGCAATCT
Found at i:54630773 original size:23 final size:23
Alignment explanation
Indices: 54630741--54630784 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54630731 AATATTCGGT
* * *
54630741 ATATGTATTTGATAAGTATATAC
1 ATATGCATTTGAAAAGAATATAC
54630764 ATATGCATTTGAAAAGAATAT
1 ATATGCATTTGAAAAGAATAT
54630785 GCCTCTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (23 bp):
ATATGCATTTGAAAAGAATATAC
Found at i:54642629 original size:15 final size:14
Alignment explanation
Indices: 54642605--54642647 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
54642595 GATTTCTTAT
*
54642605 TTTTCATTTATTTAC
1 TTTTCTTTTATTT-C
54642620 TTTTCTTTTATTTC
1 TTTTCTTTTATTTC
*
54642634 CTTTCTTATTATTT
1 TTTTCTT-TTATTT
54642648 TTAGTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTTATTTC
Found at i:54642632 original size:19 final size:19
Alignment explanation
Indices: 54642589--54642648 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
54642579 AAATATTTGA
54642589 TTATTTGATTTCTTATTTT
1 TTATTTGATTTCTTATTTT
*
54642608 TCATTT-ATTTACTT-TTCTT
1 TTATTTGATTT-CTTATT-TT
**
54642627 TTATTTCCTTTCTTATTATT
1 TTATTTGATTTCTTATT-TT
54642647 TT
1 TT
54642649 TAGTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 6 0.18
19 18 0.55
20 9 0.27
ACGTcount: A:0.15, C:0.12, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTTGATTTCTTATTTT
Found at i:54656774 original size:36 final size:35
Alignment explanation
Indices: 54656705--54656774 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
54656695 GGATTTTTAT
*
54656705 TTAATTTAATATTAATATAATTATATTTTTTATTA
1 TTAATTTAATATTAATATAATTATATTTATTATTA
54656740 TTAATGTTAATATTAATATAA--A-ATTTATTATTA
1 TTAAT-TTAATATTAATATAATTATATTTATTATTA
54656773 TT
1 TT
54656775 TAAAGTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 12 0.36
34 1 0.03
35 5 0.15
36 15 0.45
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
TTAATTTAATATTAATATAATTATATTTATTATTA
Found at i:54659257 original size:30 final size:29
Alignment explanation
Indices: 54659221--54659281 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
54659211 TAATCGACCC
*
54659221 AACCAATCTAATCTGGTTAATCGGTTAGTT
1 AACCAATCTAATCTGGTTAA-AGGTTAGTT
* * *
54659251 AACCAATTTAGTTTGGTTAAAGGTTAGTT
1 AACCAATCTAATCTGGTTAAAGGTTAGTT
54659280 AA
1 AA
54659282 AAGTTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (29 bp):
AACCAATCTAATCTGGTTAAAGGTTAGTT
Found at i:54665903 original size:21 final size:22
Alignment explanation
Indices: 54665862--54665903 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
54665852 TATTCGTTAA
*
54665862 AAAAGAATAAATATGTACATAAG
1 AAAACAATAAATA-GTACATAAG
54665885 AAAACAATAAATA-TACATA
1 AAAACAATAAATAGTACATA
54665904 TATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAACAATAAATAGTACATAAG
Found at i:54665924 original size:17 final size:16
Alignment explanation
Indices: 54665904--54665935 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54665894 AATATACATA
54665904 TATATAAAATAATTACG
1 TATATAAAA-AATTACG
54665921 TATATAAAAAATTAC
1 TATATAAAAAATTAC
54665936 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (16 bp):
TATATAAAAAATTACG
Found at i:54667232 original size:3 final size:3
Alignment explanation
Indices: 54667226--54667260 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54667216 AACACTGGAC
54667226 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54667261 TTTGCTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54667749 original size:45 final size:45
Alignment explanation
Indices: 54667654--54667942 Score: 208
Period size: 45 Copynumber: 6.6 Consensus size: 45
54667644 CTCTAATTCA
* * * * *
54667654 CTCCACTACAACTTTAGGGAGATAGGATTTG-TTTATTTAGTCTG
1 CTCCACTACAACTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTG
* *
54667698 CCCCACTACAATTTCATGGG-GATAAGACTTGCTTTCTTGAGTCTG
1 CTCCACTACAACTTCA-GGGAGATAAGACTTGCTTTCTTGAGTCTG
* * *
54667743 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTG
1 CTCCACTACAACTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTG
* * * *
54667788 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC--GA-TCTG
1 CTCCACTACAACTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTG
* * * * *
54667829 CT-CTCTGCAACTTCAGAGAGATAAGATCTGTG-ATT-TT-AATCTG
1 CTCCACTACAACTTCAGGGAGATAAGA-CT-TGCTTTCTTGAGTCTG
* * * * * * *
54667872 CTCCTCTGCAACTTCAGGGAGATAGGA-TT-ATTGGCTTTAATCTG
1 CTCCACTACAACTTCAGGGAGATAAGACTTGCTT-TCTTGAGTCTG
54667916 CTCCACTGA-AACTTCAGGGAGATAAGA
1 CTCCACT-ACAACTTCAGGGAGATAAGA
54667943 TTCGCCATTT
Statistics
Matches: 204, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
40 22 0.11
41 10 0.05
42 6 0.03
43 8 0.04
44 78 0.38
45 80 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (45 bp):
CTCCACTACAACTTCAGGGAGATAAGACTTGCTTTCTTGAGTCTG
Found at i:54667884 original size:44 final size:42
Alignment explanation
Indices: 54667739--54667943 Score: 189
Period size: 44 Copynumber: 4.8 Consensus size: 42
54667729 CTTTCTTGAG
** ***
54667739 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T--CTTGATTTAA
* ***
54667784 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGATTTAA
* *
54667825 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-TGA-TTTAA
* * * *
54667868 TCTGCTCCTCTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TCTT-GATTTAA
*
54667912 TCTGCTCCACTGAAACTTCAGGGAGATAAGAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT
54667944 TCGCCATTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
40 22 0.16
41 12 0.09
42 2 0.01
43 9 0.07
44 56 0.41
45 34 0.25
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (42 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGATTTAA
Found at i:54668410 original size:45 final size:45
Alignment explanation
Indices: 54668361--54668498 Score: 145
Period size: 45 Copynumber: 3.1 Consensus size: 45
54668351 CAATTTGCTT
* * *
54668361 CACTGCCAGCACAGGAAGGCGAGATCTGCTATCTTCAACCTACTC
1 CACTGCCAGTACAGGAAGACAAGATCTGCTATCTTCAACCTACTC
* * * * * * * *
54668406 CACTG-CTGTTCAGGGAGACAAG-GCTGGTATCTTCGATCTACTT
1 CACTGCCAGTACAGGAAGACAAGATCTGCTATCTTCAACCTACTC
* *
54668449 CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
1 CACTGCCAGTACAGGAAGACAAGATCTGCTATCTTCAACCTACTC
54668494 CACTG
1 CACTG
54668499 TTGCTCAGGG
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
43 21 0.30
44 24 0.34
45 25 0.36
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (45 bp):
CACTGCCAGTACAGGAAGACAAGATCTGCTATCTTCAACCTACTC
Found at i:54668447 original size:43 final size:43
Alignment explanation
Indices: 54668386--54668519 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 43
54668376 AAGGCGAGAT
54668386 CTGCTATCTTCAACCTACTCCACTGCTGTTCAGGGAGACAAGG
1 CTGCTATCTTCAACCTACTCCACTGCTGTTCAGGGAGACAAGG
* * * * ** * * *
54668429 CTGGTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGAT
1 CTGCTATCTTCAACCTACTCCACTG-CTGTTCAGGGAGACAAG-G
* * * *
54668474 CTGCTATTTTCAACCTACTCCACTGTTGCTCAGGGAGATAAGG
1 CTGCTATCTTCAACCTACTCCACTGCTGTTCAGGGAGACAAGG
54668517 CTG
1 CTG
54668520 AAGTTTCACC
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
43 24 0.36
44 23 0.34
45 20 0.30
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (43 bp):
CTGCTATCTTCAACCTACTCCACTGCTGTTCAGGGAGACAAGG
Found at i:54668496 original size:88 final size:88
Alignment explanation
Indices: 54668358--54668519 Score: 252
Period size: 88 Copynumber: 1.8 Consensus size: 88
54668348 CTTCAATTTG
* * * *
54668358 CTTCACTGCCAGCACAGGAAGGCGAGATCTGCTATCTTCAACCTACTCCACTGCTGTTCAGGGAG
1 CTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAG
54668423 ACAAGGCTGGTATCTTCGATCTA
66 ACAAGGCTGGTATCTTCGATCTA
* * *
54668446 CTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGTTGCTCAGGGAG
1 CTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAG
*
54668511 ATAAGGCTG
66 ACAAGGCTG
54668520 AAGTTTCACC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 66 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (88 bp):
CTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAG
ACAAGGCTGGTATCTTCGATCTA
Found at i:54680639 original size:23 final size:23
Alignment explanation
Indices: 54680606--54680654 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
54680596 AATATTCGTT
* *
54680606 AAAAAAGAATAAATATGTACATA
1 AAAAAACAATAAATATATACATA
*
54680629 AAAAAACAATAAATATATATATA
1 AAAAAACAATAAATATATACATA
54680652 AAA
1 AAA
54680655 TAATTACGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAAACAATAAATATATACATA
Found at i:54680666 original size:17 final size:16
Alignment explanation
Indices: 54680646--54680677 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54680636 AATAAATATA
54680646 TATATAAAATAATTACG
1 TATATAAAA-AATTACG
54680663 TATATAAAAAATTAC
1 TATATAAAAAATTAC
54680678 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (16 bp):
TATATAAAAAATTACG
Found at i:54682044 original size:9 final size:10
Alignment explanation
Indices: 54682013--54682044 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
54682003 AGGTATTACA
54682013 AAAATCATAC
1 AAAATCATAC
54682023 AAAATCATA-
1 AAAATCATAC
54682032 AAAAT-ATAC
1 AAAATCATAC
54682041 AAAA
1 AAAA
54682045 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 9 0.43
10 9 0.43
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATCATAC
Found at i:54682122 original size:28 final size:26
Alignment explanation
Indices: 54682072--54682157 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 26
54682062 AATAAATATA
* * *
54682072 AAAATATAGAAAAGTGCACAAATTTAT
1 AAAATATA-AAAATTACAAAAATTTAT
*
54682099 AAAATTATTAAAAATTACAAAAATATTTT
1 AAAA-TA-TAAAAATTACAAAAAT-TTAT
* *
54682128 AATAATATATAAATTACAAATATTTAT
1 AA-AATATAAAAATTACAAAAATTTAT
54682155 AAA
1 AAA
54682158 TTACAAAAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.02
27 9 0.19
28 27 0.56
29 9 0.19
30 2 0.04
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (26 bp):
AAAATATAAAAATTACAAAAATTTAT
Found at i:54684164 original size:20 final size:20
Alignment explanation
Indices: 54684127--54684167 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54684117 GTTTCCATTG
* *
54684127 ATGTTAATTGAAGTTTTTGA
1 ATGTTAATGGAAGATTTTGA
*
54684147 ATGTTAATGGTAGATTTTGA
1 ATGTTAATGGAAGATTTTGA
54684167 A
1 A
54684168 GCTTAGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (20 bp):
ATGTTAATGGAAGATTTTGA
Found at i:54693372 original size:21 final size:22
Alignment explanation
Indices: 54693346--54693402 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
54693336 AACAATGGTG
*
54693346 GTGGTGAGATTAG-TTACTGTA
1 GTGGTGAGATTAGAATACTGTA
54693367 GTGGTGAGATT-GAATACTGTA
1 GTGGTGAGATTAGAATACTGTA
*
54693388 GCGGTGAGATTAGAA
1 GTGGTGAGATTAGAA
54693403 ATAGCGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.32
Consensus pattern (22 bp):
GTGGTGAGATTAGAATACTGTA
Found at i:54699968 original size:2 final size:2
Alignment explanation
Indices: 54699963--54699987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54699953 AATATATATA
54699963 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
54699988 AAACACGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:54702148 original size:17 final size:18
Alignment explanation
Indices: 54702123--54702159 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
54702113 GTTTTATTGA
*
54702123 TTTCATTGTTTGTTTATT
1 TTTCATTGTTTATTTATT
54702141 TTTC-TTGTTTATTTATT
1 TTTCATTGTTTATTTATT
54702158 TT
1 TT
54702160 CGTTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTCATTGTTTATTTATT
Found at i:54702587 original size:19 final size:18
Alignment explanation
Indices: 54702555--54702590 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
54702545 TTTATTTTTA
54702555 TTTTTATTTTTTAATTTC
1 TTTTTATTTTTTAATTTC
54702573 TTTTTAATTTTTTAATTT
1 TTTTT-ATTTTTTAATTT
54702591 GTTTATGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTTTAATTTC
Found at i:54705277 original size:28 final size:28
Alignment explanation
Indices: 54705246--54705300 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
54705236 TTATGAGACA
54705246 TGTTGATTGAGAAAACT-CAATTGATTGT
1 TGTTGATTGAGAAAA-TGCAATTGATTGT
* *
54705274 TGTTGATTGTGAATATGCAATTGATTG
1 TGTTGATTGAGAAAATGCAATTGATTG
54705301 ATTGAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (28 bp):
TGTTGATTGAGAAAATGCAATTGATTGT
Found at i:54708562 original size:13 final size:13
Alignment explanation
Indices: 54708534--54708568 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54708524 AATATTGGAC
*
54708534 TTTTATTATATTTA
1 TTTTA-TATATATA
54708548 TTTTATATATATA
1 TTTTATATATATA
54708561 TTTTATAT
1 TTTTATAT
54708569 TTGGGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATATATATA
Found at i:54708953 original size:50 final size:51
Alignment explanation
Indices: 54708820--54708965 Score: 136
Period size: 50 Copynumber: 2.9 Consensus size: 51
54708810 GTAACTCGTA
* *
54708820 ACTGTAATGTCAGGGAAGCAAGGTTCACCATTGTAGCTTTAATCTGTTCCG
1 ACTGTAATGTCAGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCG
* * * * * * * * *
54708871 -CTGCATTATCTGGGAAGTAATATTTGCTATTGTAGCTTTAATC--TTCTTG
1 ACTGTAATGTCAGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTC-CG
* * *
54708920 ACTGTAATGTCGGGGACGCAAGATTCGCCATTGTGGCTTTAATCTG
1 ACTGTAATGTCAGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTG
54708966 CTCCACTACA
Statistics
Matches: 70, Mismatches: 21, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
48 3 0.04
49 1 0.01
50 66 0.94
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (51 bp):
ACTGTAATGTCAGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCG
Found at i:54709252 original size:87 final size:87
Alignment explanation
Indices: 54709008--54709429 Score: 308
Period size: 87 Copynumber: 4.9 Consensus size: 87
54708998 AATTATTCGG
* * * *
54709008 TCTATTCCACTGTAATCTCAGGGAGATAATACCTGATACGATATGCTCTACTGT-ATCTTC--AG
1 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATC-TCAGAG
* *
54709070 AGATAAGATCCT-TTA-T-TTTAA
65 AGATAAGAT-CTGTAATTCTTTGA
* * * * * * * * * * **
54709091 TCCACTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATTTGCTCCGCTGTAATCTCAG
1 TCTATTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAATCTCAG
* *
54709156 GGAGATAAGATCTGAAATTCTTTGA
63 AGAGATAAGATCTGTAATTCTTTGA
* *
54709181 TCTATTCCATTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA-CTTCAGAG
1 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATC-TCAGAG
* *
54709245 AGATAAGATCCT-TTA-T-TTTAA
65 AGATAAGAT-CTGTAATTCTTTGA
** * * * ** * * * * **
54709266 TCCGTTCCACTATAATCTCAGGGAAATATGATTAGTGGCTTCAATCTGCTCCGCTGTAATCTCAG
1 TCTATTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAATCTCAG
* * *
54709331 GGAGATAAGATCTGTAATTCTTCGG
63 AGAGATAAGATCTGTAATTCTTTGA
54709356 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAA-CTTCAGAG
1 TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATC-TCAGAG
54709420 AGATAAGATC
65 AGATAAGATC
54709430 CTTTATTTCG
Statistics
Matches: 252, Mismatches: 68, Indels: 34
0.71 0.19 0.10
Matches are distributed among these distances:
83 26 0.10
85 30 0.12
86 19 0.08
87 69 0.27
88 48 0.19
89 3 0.01
90 57 0.23
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (87 bp):
TCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATCTCAGAGA
GATAAGATCTGTAATTCTTTGA
Found at i:54709337 original size:175 final size:175
Alignment explanation
Indices: 54708982--54709437 Score: 700
Period size: 175 Copynumber: 2.6 Consensus size: 175
54708972 TACATTATCT
** * * *
54708982 GGGAGATAAGGGCTGAAATTATTCGGTCTATTCCACTGTAATCTCAGGGAGATAATACCTGATAC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* * * *
54709047 GATATGCTCTACTGTATCTTC--AGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
66 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
* *
54709110 AAGGAGATAGGATTACTAGCTTCAATTTGCTCCGCTGTAATCTCA
131 AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
* * * *
54709155 GGGAGATAAGATCTGAAATTCTTTGATCTATTCCATTGTAATCTTAGGGAGATAAGACCTGATGC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
**
54709220 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTC
66 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
* * * *
54709285 AGGGAAATATGATTAGTGGCTTCAATCTGCTCCGCTGTAATCTCA
131 AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
*
54709330 GGGAGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
54709395 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
66 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
54709438 CGCTGTCGAT
Statistics
Matches: 255, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
173 74 0.29
175 181 0.71
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (175 bp):
GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
Found at i:54709376 original size:46 final size:45
Alignment explanation
Indices: 54709144--54709386 Score: 171
Period size: 46 Copynumber: 5.5 Consensus size: 45
54709134 ATTTGCTCCG
* *
54709144 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCTG-TATTCTTCGATCTATTCCA
* * * * * *
54709190 TTGTAATCTTAGGGAGATAAGACCTG-A---TGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATCTGTATTCTTCGATCTATTCCA
* * * **
54709231 CTGTAA-CTTCAGAGAGATAAGATCCTTTATT-TT-AATCCGTTCCA
1 CTGTAATC-TCAGGGAGATAAGAT-CTGTATTCTTCGATCTATTCCA
* * * ** * ** *
54709275 CTATAATCTCAGGGAAATATGAT-TAGT-GGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCT-GTATTCTTCGATCTATTCCA
*
54709319 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCTGT-ATTCTTCGATCTATTCCA
54709365 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
54709387 CCTGATGCGA
Statistics
Matches: 147, Mismatches: 38, Indels: 24
0.70 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 27 0.18
42 3 0.02
43 4 0.03
44 54 0.37
45 3 0.02
46 55 0.37
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (45 bp):
CTGTAATCTCAGGGAGATAAGATCTGTATTCTTCGATCTATTCCA
Found at i:54729910 original size:22 final size:19
Alignment explanation
Indices: 54729867--54729910 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
54729857 AATTTATTAC
*
54729867 AATTTAAACTATAATAATA
1 AATTTAAACTATAAAAATA
54729886 AATTTAAACACTATTAAAAATA
1 AATTT-AA-ACTA-TAAAAATA
54729908 AAT
1 AAT
54729911 ATTACAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 4 0.19
22 10 0.48
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTTAAACTATAAAAATA
Found at i:54735094 original size:16 final size:16
Alignment explanation
Indices: 54735073--54735106 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54735063 CCAATATCCA
* *
54735073 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
54735089 ATTATCACATTTACAC
1 ATTATCACATTTACAC
54735105 AT
1 AT
54735107 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:54735183 original size:20 final size:19
Alignment explanation
Indices: 54735153--54735193 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
54735143 TAATATATAT
54735153 ATCAATTTAA-TCCATTTCA
1 ATCAATTTAATTCCA-TTCA
54735172 ATCAACTTTAATTCCATTCA
1 ATCAA-TTTAATTCCATTCA
54735192 AT
1 AT
54735194 ATTAAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (19 bp):
ATCAATTTAATTCCATTCA
Found at i:54740222 original size:15 final size:15
Alignment explanation
Indices: 54740199--54740228 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54740189 AAAAAATTTA
54740199 ATTTAATTTTGTTTT
1 ATTTAATTTTGTTTT
*
54740214 ATTTTATTTTGTTTT
1 ATTTAATTTTGTTTT
54740229 TAGTAGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
ATTTAATTTTGTTTT
Found at i:54747050 original size:30 final size:30
Alignment explanation
Indices: 54747016--54747078 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
54747006 TAAAAACACC
*
54747016 TTAGAAACATTTGGAAAGTCGAAGAAAACG
1 TTAGAAAAATTTGGAAAGTCGAAGAAAACG
*
54747046 TTAGAAAAATTTGGAAAGTTGAAGAAAACG
1 TTAGAAAAATTTGGAAAGTCGAAGAAAACG
54747076 TTA
1 TTA
54747079 CAACTCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (30 bp):
TTAGAAAAATTTGGAAAGTCGAAGAAAACG
Found at i:54751264 original size:39 final size:39
Alignment explanation
Indices: 54751219--54751296 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
54751209 ACCATTTTTC
*
54751219 AACATACTTCTTTTTAAACTCGGTCTGAACGAAACCCTA
1 AACATACTTCTTTTTAAACTCAGTCTGAACGAAACCCTA
54751258 AACATACTTCTTTTTAAACTCAGTCTGAACGAAACCCTA
1 AACATACTTCTTTTTAAACTCAGTCTGAACGAAACCCTA
54751297 GGAAACTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.31
Consensus pattern (39 bp):
AACATACTTCTTTTTAAACTCAGTCTGAACGAAACCCTA
Found at i:54753201 original size:35 final size:35
Alignment explanation
Indices: 54753144--54753295 Score: 160
Period size: 35 Copynumber: 4.3 Consensus size: 35
54753134 AATCTAACCA
*
54753144 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
1 AAACACACCA-ATGCTCATAAGAGCCAATCCATCCG
* ** ** *
54753180 AAACACACTAATGCTTGTAAGAGTTAATCCCTCCG
1 AAACACACCAATGCTCATAAGAGCCAATCCATCCG
* * * *
54753215 AAACACACCAATGCTCATTAGAGCTAATCCGTCCA
1 AAACACACCAATGCTCATAAGAGCCAATCCATCCG
* * * *
54753250 AAACACACCAATGCTCATAAGAGCTAGTCTAACCG
1 AAACACACCAATGCTCATAAGAGCCAATCCATCCG
54753285 AAACACACCAA
1 AAACACACCAA
54753296 AACAGAGAGT
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 87 0.91
36 9 0.09
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.18
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCCAATCCATCCG
Found at i:54753271 original size:70 final size:70
Alignment explanation
Indices: 54753134--54753295 Score: 180
Period size: 70 Copynumber: 2.3 Consensus size: 70
54753124 AGTACTCAAC
* * ** * **
54753134 AATCTAACCAAAACACACCAGATGCTCATAAGAGCCAATCCATCTGAAACACACTAATGCTTGTA
1 AATCCAACCGAAACACACCA-ATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATA
*
54753199 AGAGTT
65 AGAGCT
** * * *
54753205 AATCCCTCCGAAACACACCAATGCTCATTAGAGCTAATCCGTCCAAAACACACCAATGCTCATAA
1 AATCCAACCGAAACACACCAATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATAA
54753270 GAGCT
66 GAGCT
* *
54753275 AGTCTAACCGAAACACACCAA
1 AATCCAACCGAAACACACCAA
54753296 AACAGAGAGT
Statistics
Matches: 74, Mismatches: 17, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
70 58 0.78
71 16 0.22
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.19
Consensus pattern (70 bp):
AATCCAACCGAAACACACCAATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATAA
GAGCT
Found at i:54758558 original size:23 final size:20
Alignment explanation
Indices: 54758530--54758578 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
54758520 AAAAATAAAG
54758530 AAATAAATTAAAATAATTAATT
1 AAATAAA-TAAAATAA-TAATT
54758552 AAGAT-AA-AAAATAATAATT
1 AA-ATAAATAAAATAATAATT
54758571 AAATAAAT
1 AAATAAAT
54758579 CAAAGATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 7 0.29
22 4 0.17
23 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAAATAAAATAATAATT
Found at i:54758561 original size:19 final size:18
Alignment explanation
Indices: 54758511--54758577 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
54758501 ATCCAAGTCA
* *
54758511 AATTAAAAAAAAAATAAAG
1 AATTAAATAAAAAAT-AAT
* *
54758530 AAATAAAT-TAAAATAATT
1 AATTAAATAAAAAATAA-T
54758548 AATTAAGATAAAAAATAAT
1 AATTAA-ATAAAAAATAAT
54758567 AATTAAATAAA
1 AATTAAATAAA
54758578 TCAAAGATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 2 0.05
18 15 0.38
19 15 0.38
20 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AATTAAATAAAAAATAAT
Found at i:54761207 original size:29 final size:29
Alignment explanation
Indices: 54761148--54761208 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
54761138 GTTTTAATTC
* *
54761148 TTTTCATAATTTTATGTTTTTAAATATAA
1 TTTTCATAATTTTATGTTTTCAAATAAAA
* * **
54761177 TTTTTATATTTTTATGTTTTCATTTAAAA
1 TTTTCATAATTTTATGTTTTCAAATAAAA
54761206 TTT
1 TTT
54761209 AACATTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTCATAATTTTATGTTTTCAAATAAAA
Found at i:54764294 original size:15 final size:16
Alignment explanation
Indices: 54764274--54764306 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
54764264 TAAAAAACTA
54764274 ATAAAATAAAT-TTTT
1 ATAAAATAAATATTTT
*
54764289 ATAAAATCAATATTTT
1 ATAAAATAAATATTTT
54764305 AT
1 AT
54764307 TGGTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAAATAAATATTTT
Found at i:54769269 original size:42 final size:42
Alignment explanation
Indices: 54769175--54769269 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
54769165 GCTAGGCTCA
*
54769175 AGCCTGATAAAAATTCACCGGCACTACGCCTGCTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACGCCTGCTAGGCTTTT
* *
54769217 AGTCTGATATAAATTCACCTGCACTACGCCTGCTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACGCCTGCTAGGCTTTT
* *
54769259 GGCCTCATATA
1 AGCCTGATATA
54769270 TCACACTAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (42 bp):
AGCCTGATATAAATTCACCGGCACTACGCCTGCTAGGCTTTT
Done.