Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 59 of 168
Found at i:16919110 original size:28 final size:28
Alignment explanation
Indices: 16919078--16919131 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16919068 ATCAGTACAC
*
16919078 TGTGGGCCTTAGCCCATTACAGTAATAG
1 TGTGGGCCTTAGCCCAATACAGTAATAG
16919106 TGTGGGCCTTAGCCCAATACAGTAAT
1 TGTGGGCCTTAGCCCAATACAGTAAT
16919132 CAGTACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAATAG
Found at i:16919277 original size:26 final size:26
Alignment explanation
Indices: 16919242--16919311 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
16919232 CACCAATATT
16919242 GCAGC-AAGCTGCCAGTAATAATGAA-
1 GCAGCAAAGCTGCCAGTAATAAT-AAC
* *
16919267 GTAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAATAAC
*
16919293 GCAGCAAGGCTGCCAGTAA
1 GCAGCAAAGCTGCCAGTAA
16919312 CAGTATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 6 0.15
26 33 0.85
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAATAAC
Found at i:16919522 original size:27 final size:27
Alignment explanation
Indices: 16919492--16919768 Score: 261
Period size: 27 Copynumber: 10.3 Consensus size: 27
16919482 AGTATAACAA
16919492 TCATTTTACCCTAT-GGGGGTATTTCGG
1 TCATTTTACCCT-TCGGGGGTATTTCGG
* * * * *
16919519 TCATTTCACCCTTTGAGGGCATTTCGA
1 TCATTTTACCCTTCGGGGGTATTTCGG
** * ** **
16919546 TGGTTTTACCTTTCAAGGGTATTTTAG
1 TCATTTTACCCTTCGGGGGTATTTCGG
* *
16919573 TCAATTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGGGGGTATTTCGG
* *
16919600 TTATTTTACCCTTCGGGGGGTATTTCGA
1 TCATTTTACCCTTC-GGGGGTATTTCGG
*
16919628 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
* * * *
16919655 TCATTTTATCCTTTGAGGGTATTTCAG
1 TCATTTTACCCTTCGGGGGTATTTCGG
**
16919682 TTTTTTTACCCTTCGGGGGTA-TTCGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
* * *
16919708 TCCTTTTACCCTTCGCGGGTATTTCGA
1 TCATTTTACCCTTCGGGGGTATTTCGG
* *
16919735 TCATTTTATCCTTCAGGGGTATTTCGG
1 TCATTTTACCCTTCGGGGGTATTTCGG
*
16919762 TTATTTT
1 TCATTTT
16919769 GCCATCGAAT
Statistics
Matches: 200, Mismatches: 47, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
26 23 0.12
27 151 0.75
28 26 0.13
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTTCGGGGGTATTTCGG
Found at i:16919690 original size:109 final size:107
Alignment explanation
Indices: 16919491--16919768 Score: 328
Period size: 109 Copynumber: 2.6 Consensus size: 107
16919481 GAGTATAACA
* * * * * **
16919491 ATCATTTTACCCTAT-GGGGGTATTTCGGTCATTTCACCCTTTGAGGGCATTTCGATGGTTTTAC
1 ATCATTTTACCCT-TCGGGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTAC
*
16919555 CTTTCAAGGGTATTTTAGTCAATTTACCCTTCGGGGGTATTTCG
65 CTTTCAAGGGTATTTCAGTCAATTTACCCTTCGGGGGTA-TTCG
*
16919599 ATTATTTTACCCTTCGGGGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTAT
1 ATCATTTTACCCTTC-GGGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA-
* ***
16919664 CCTTT-GAGGGTATTTCAGTTTTTTTACCCTTCGGGGGTATTCG
64 CCTTTCAAGGGTATTTCAGTCAATTTACCCTTCGGGGGTATTCG
* * * * *
16919707 GTCCTTTTACCCTTCGCGGGTATTTCGATCATTTTATCCTTC-AGGGGTATTTCGGTTATTTT
1 ATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTCGA-GGGTATTTCGGTCATTTT
16919769 GCCATCGAAT
Statistics
Matches: 147, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
106 1 0.01
107 43 0.29
108 28 0.19
109 70 0.48
110 5 0.03
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (107 bp):
ATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
TTTCAAGGGTATTTCAGTCAATTTACCCTTCGGGGGTATTCG
Found at i:16919739 original size:80 final size:82
Alignment explanation
Indices: 16919491--16919768 Score: 262
Period size: 82 Copynumber: 3.4 Consensus size: 82
16919481 GAGTATAACA
* * * * * * * * * **
16919491 ATCATTTTACCCTATGGGGGTATTTCGGTCATTTCACCCTT-TGAGGGCATTTCGATGGTTTTAC
1 ATCATTTTATCCTTTGAGGGTATTTCGATTATTTTACCCTTCGGGGGGTATTTCGATCATTTTAC
* * *
16919555 CTTTCAAGGGTATTT-T
66 CCTTCGAGGGTATTTCG
* * * *
16919571 AGTCAATTTACCCTTCGGGGGTATTTCGATTATTTTACCCTTCGGGGGGTATTTCGATCATTTTA
1 A-TCATTTTATCCTTTGAGGGTATTTCGATTATTTTACCCTTCGGGGGGTATTTCGATCATTTTA
16919636 CCCTTCGAGGGTATTTCG
65 CCCTTCGAGGGTATTTCG
* * * *
16919654 GTCATTTTATCCTTTGAGGGTATTTC-AGTTTTTTTACCCTTC-GGGGGTA-TTCGGTCCTTTTA
1 ATCATTTTATCCTTTGAGGGTATTTCGA-TTATTTTACCCTTCGGGGGGTATTTCGATCATTTTA
*
16919716 CCCTTCGCGGGTATTTCG
65 CCCTTCGAGGGTATTTCG
* *
16919734 ATCATTTTATCC-TTCAGGGGTATTTCGGTTATTTT
1 ATCATTTTATCCTTTGA-GGGTATTTCGATTATTTT
16919769 GCCATCGAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
79 3 0.02
80 55 0.33
81 42 0.25
82 65 0.39
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (82 bp):
ATCATTTTATCCTTTGAGGGTATTTCGATTATTTTACCCTTCGGGGGGTATTTCGATCATTTTAC
CCTTCGAGGGTATTTCG
Found at i:16926379 original size:25 final size:25
Alignment explanation
Indices: 16926330--16926379 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16926320 TATTTTTTTA
* * *
16926330 CTTAGTTTTTAACCCTTTTTTAACC
1 CTTAGTTTTTAACCATCTTTAAACC
*
16926355 CTTAGTTTTTAATCATCTTTAAACC
1 CTTAGTTTTTAACCATCTTTAAACC
16926380 AAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.50
Consensus pattern (25 bp):
CTTAGTTTTTAACCATCTTTAAACC
Found at i:16933313 original size:61 final size:61
Alignment explanation
Indices: 16933239--16933433 Score: 237
Period size: 61 Copynumber: 3.2 Consensus size: 61
16933229 AAAATTCCAT
* * * *
16933239 AAAGGATTTCCTGTCCAGAGTATTGCCACAAAAGTTGTCCTTTACGTTCAGTACTCGCCAC
1 AAAGGTTTTCCTGTCCAAAGTATTGCCACAAAGGTTGTCCTTTACATTCAGTACTCGCCAC
* * * * *
16933300 AAAGGTTTTCCTGTCCAAAGTAATGCCACAAAGGCTGTCATTTACATTTAGTACTCACCAC
1 AAAGGTTTTCCTGTCCAAAGTATTGCCACAAAGGTTGTCCTTTACATTCAGTACTCGCCAC
** * * * * *
16933361 AAAGGTTTTATTATCTACAGTATAGCCACAAAGGTTGTCCTTTTCATTCAGTACTCGCCAC
1 AAAGGTTTTCCTGTCCAAAGTATTGCCACAAAGGTTGTCCTTTACATTCAGTACTCGCCAC
*
16933422 AAAGGCTTTCCT
1 AAAGGTTTTCCT
16933434 TCTCTTGGTG
Statistics
Matches: 110, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 110 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (61 bp):
AAAGGTTTTCCTGTCCAAAGTATTGCCACAAAGGTTGTCCTTTACATTCAGTACTCGCCAC
Found at i:16933425 original size:32 final size:32
Alignment explanation
Indices: 16933263--16933434 Score: 128
Period size: 32 Copynumber: 5.6 Consensus size: 32
16933253 CCAGAGTATT
* *
16933263 GCCACAAAAGTTGTCCTTTACGTTCAGTACTC
1 GCCACAAAGGTTGTCCTTTACATTCAGTACTC
* * * * *
16933295 GCCACAAAGGTTTTCCTGTCCA--AAGTAAT-
1 GCCACAAAGGTTGTCCTTTACATTCAGTACTC
* * *
16933324 GCCACAAAGGCTGTCATTTACATTTAGTACTC
1 GCCACAAAGGTTGTCCTTTACATTCAGTACTC
* * *
16933356 ACCACAAAGGTT-T--TATTATC-TACAGTA-TA
1 GCCACAAAGGTTGTCCT-TTA-CATTCAGTACTC
*
16933385 GCCACAAAGGTTGTCCTTTTCATTCAGTACTC
1 GCCACAAAGGTTGTCCTTTACATTCAGTACTC
16933417 GCCACAAAGGCTT-TCCTT
1 GCCACAAAGG-TTGTCCTT
16933435 CTCTTGGTGA
Statistics
Matches: 106, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
29 30 0.28
30 15 0.14
31 15 0.14
32 44 0.42
33 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (32 bp):
GCCACAAAGGTTGTCCTTTACATTCAGTACTC
Found at i:16937484 original size:20 final size:20
Alignment explanation
Indices: 16937449--16937487 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16937439 TCAGCTCAAC
16937449 TTTAGCTCAATGAGCTCATT
1 TTTAGCTCAATGAGCTCATT
* *
16937469 TTTAGCTCATTTAGCTCAT
1 TTTAGCTCAATGAGCTCAT
16937488 CTTAAGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTAGCTCAATGAGCTCATT
Found at i:16937495 original size:20 final size:20
Alignment explanation
Indices: 16937431--16937500 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
16937421 ACTCTACTTC
* * *
16937431 AAGCTCACTCAGCTCAACTT
1 AAGCTCATTTAGCTCATCTT
* * * *
16937451 TAGCTCAATGAGCTCATTTT
1 AAGCTCATTTAGCTCATCTT
*
16937471 TAGCTCATTTAGCTCATCTT
1 AAGCTCATTTAGCTCATCTT
*
16937491 AAGCTTATTT
1 AAGCTCATTT
16937501 TAGTTTGCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (20 bp):
AAGCTCATTTAGCTCATCTT
Found at i:16952682 original size:40 final size:40
Alignment explanation
Indices: 16952638--16952778 Score: 210
Period size: 40 Copynumber: 3.5 Consensus size: 40
16952628 GGTTCTGTGC
16952638 CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
*
16952678 CTAGCAGGCTTAATGCCGATGAATTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
* * * ** *
16952718 CTAGCAAGCTTGATGCCAGTGACCTTTACAGACTTAATGT
1 CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
*
16952758 CTAGCAGGCTTAATGTCGGTG
1 CTAGCAGGCTTAATGCCGGTG
16952779 TTCTGAGTCT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
Found at i:16952994 original size:2 final size:2
Alignment explanation
Indices: 16952987--16953027 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16952977 GTTTTGGGTG
16952987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16953028 CACCTTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16954213 original size:41 final size:41
Alignment explanation
Indices: 16954156--16954293 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 41
16954146 GTTACAACCG
*
16954156 AAGTACAAACAAGGGCACATATGTGCAATTCAGGGGTACCA
1 AAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCA
* * *
16954197 AAGTACAAACAGGGGCACGTATATGCAATTCAGGGGTACCG
1 AAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCA
* *
16954238 AAGTACAAACAGAGGCA-AGTATGTGCAATTCAGGGCTA-CA
1 AAGTACAAACAGGGGCACA-TATGTGCAATTCAGGGGTACCA
*
16954278 GAAGTACAAATAGGGG
1 -AAGTACAAACAGGGG
16954294 ATAATTCAGT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.01
41 83 0.99
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (41 bp):
AAGTACAAACAGGGGCACATATGTGCAATTCAGGGGTACCA
Found at i:16955206 original size:20 final size:20
Alignment explanation
Indices: 16955181--16955219 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16955171 AAGTCCTTTG
16955181 AATGGTCTATTTACTATCTC
1 AATGGTCTATTTACTATCTC
16955201 AATGGTCTATTTACTATCT
1 AATGGTCTATTTACTATCT
16955220 AAGTCCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (20 bp):
AATGGTCTATTTACTATCTC
Found at i:16957385 original size:29 final size:30
Alignment explanation
Indices: 16957345--16957412 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
16957335 ATTGATAGTT
* *
16957345 CAAGTACTACATTAG-ATATTT-TCAAAGTA
1 CAAGTACCACATTAGCAT-TTTATAAAAGTA
*
16957374 CATGTACCACATTAGCATTTTATAAAAGTA
1 CAAGTACCACATTAGCATTTTATAAAAGTA
16957404 CAAGTACCA
1 CAAGTACCA
16957413 TCACAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (30 bp):
CAAGTACCACATTAGCATTTTATAAAAGTA
Found at i:16957493 original size:91 final size:90
Alignment explanation
Indices: 16957326--16957496 Score: 236
Period size: 91 Copynumber: 1.9 Consensus size: 90
16957316 CATAATAATA
* *
16957326 AAAAAACATATTGATAGTTCAAGTACTACATTAGATATTTTCAAAGTACATGTACCACATTAGCA
1 AAAAAACATATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTA-ATGTACCACATTAGCA
*
16957391 TTTTATAAAAGTACAAGTACCATCAC
65 TATTATAAAAGTACAAGTACCATCAC
* * * *
16957417 AAAACACATATTGATAGTTCAAGTACCATATTAGACATTTTCAAAGT-ATGATACCTCATTGGAC
1 AAAAAACATATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTAATG-TACCACATTAG-C
*
16957481 ATATTATGAAAGTACA
64 ATATTATAAAAGTACA
16957497 TGTATTAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
89 3 0.04
90 9 0.13
91 58 0.83
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (90 bp):
AAAAAACATATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTAATGTACCACATTAGCAT
ATTATAAAAGTACAAGTACCATCAC
Found at i:16966300 original size:16 final size:15
Alignment explanation
Indices: 16966273--16966302 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16966263 TGATAAAGTA
16966273 AATAAAAAAGTAAAT
1 AATAAAAAAGTAAAT
16966288 AATAAATAAAGTAAA
1 AATAAA-AAAGTAAA
16966303 CTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AATAAAAAAGTAAAT
Found at i:16967132 original size:14 final size:15
Alignment explanation
Indices: 16967103--16967135 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16967093 AAATATTGAC
*
16967103 ATTTTTTTTCTTAAT
1 ATTTATTTTCTTAAT
16967118 ATTTATTTT-TTAAT
1 ATTTATTTTCTTAAT
16967132 ATTT
1 ATTT
16967136 TAATATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTTTCTTAAT
Found at i:16969304 original size:50 final size:48
Alignment explanation
Indices: 16969250--16969371 Score: 115
Period size: 50 Copynumber: 2.5 Consensus size: 48
16969240 CAAAAGTTAA
* * *
16969250 TTTATTTTAATTTTTGTAAGTTTTAAAAACTT-TTACTATAT-TTTTTATTT
1 TTTATTTTAATTTTTATAA-TTTT-AAAA-TTATTA-TATATACTTTTAATT
* *
16969300 TTTATTTATAAAATTTTATTATTTTAAAATTATTATATATACTTTTAATT
1 TTTATTT-T-AATTTTTATAATTTTAAAATTATTATATATACTTTTAATT
16969350 TTTATTTTATATTTTTA-AATTT
1 TTTATTTTA-ATTTTTATAATTT
16969372 AATATATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
48 5 0.08
49 14 0.23
50 28 0.47
51 5 0.08
52 8 0.13
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (48 bp):
TTTATTTTAATTTTTATAATTTTAAAATTATTATATATACTTTTAATT
Found at i:16969327 original size:16 final size:17
Alignment explanation
Indices: 16969296--16969335 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
16969286 TATATTTTTT
16969296 ATTTT-TTATTTATAAA
1 ATTTTATTATTTATAAA
16969312 ATTTTATTATTT-TAAA
1 ATTTTATTATTTATAAA
16969328 ATTATTAT
1 ATT-TTAT
16969336 ATATACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATTATTTATAAA
Found at i:16969382 original size:36 final size:41
Alignment explanation
Indices: 16969312--16969388 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 41
16969302 TATTTATAAA
16969312 ATTTTATTATTTTAAAATTATTATATATACTTTTAATTTTT
1 ATTTTATTATTTTAAAATTATTATATATACTTTTAATTTTT
*
16969353 ATTTTA-TATTTTTAAA-T-TTA-ATATA-TTTTAATTTTT
1 ATTTTATTATTTTAAAATTATTATATATACTTTTAATTTTT
16969389 TTTAAATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 5 0.14
38 3 0.09
39 1 0.03
40 9 0.26
41 6 0.17
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (41 bp):
ATTTTATTATTTTAAAATTATTATATATACTTTTAATTTTT
Found at i:16969413 original size:26 final size:26
Alignment explanation
Indices: 16969361--16969413 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
16969351 TTATTTTATA
* * *
16969361 TTTTTAAATTTAATATATTTTAATTT
1 TTTTTAAATTGAACATATGTTAATTT
* *
16969387 TTTTTAAATTGAACGTATGTTAGTTT
1 TTTTTAAATTGAACATATGTTAATTT
16969413 T
1 T
16969414 GCCACATGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (26 bp):
TTTTTAAATTGAACATATGTTAATTT
Found at i:16970343 original size:41 final size:42
Alignment explanation
Indices: 16970240--16970544 Score: 174
Period size: 42 Copynumber: 7.0 Consensus size: 42
16970230 CGCTTACAGA
*
16970240 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAGG
* * * *
16970282 AAAAAACGTCGCTAATGATCAAGTTCTTTAGCGGCGCTT-GG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAGG
*
16970323 GAAAAACGCCGCTAAAGATCATGTTCTTTAGCATGATCTTTAGCGGCACTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTT---A-G--C---AGC-G--CTTAGG
* * * **
16970377 AAAAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTAAT
1 AAAA-AACGCCGCTAAAGA-TCATGTTCTTTAGCAGCGCTTAGG
* * * *
16970420 AAAAAACGCTGCTAAA-AGTAATGTTCTATAGCGGCGCTT-GG
1 AAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCAGCGCTTAGG
* * * **
16970461 TAGAAAACGCCGCTAAA-AGTAATGTTCTTTAGCGGCGCTTCATC
1 -AAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCAGCGCTT-AGG
* * *
16970505 TACAAACGCCGCTAAA-AGT-AGTGTTCTTTCGCAGCGCTTA
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCAGCGCTTA
16970545 TTTCACAAAC
Statistics
Matches: 215, Mismatches: 29, Indels: 38
0.76 0.10 0.13
Matches are distributed among these distances:
41 27 0.13
42 106 0.49
43 40 0.19
44 1 0.00
45 2 0.01
46 2 0.01
47 1 0.00
49 1 0.00
50 2 0.01
51 2 0.01
52 1 0.00
53 3 0.01
54 6 0.03
55 21 0.10
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAGG
Found at i:16970402 original size:55 final size:53
Alignment explanation
Indices: 16970306--16970409 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 53
16970296 ATGATCAAGT
* * * *
16970306 TCTTTAGCGGCGCTTGGGAAAAACGCCGCTAAAGATCATGTTCTTTAGCATGA
1 TCTTTAGCGGCACTTGGAAAAAACGCCGCTAAAGATAATGTTCTATAGCATGA
16970359 TCTTTAGCGGCACTTAGGAAAAAAACGCCGCTAAA-AGTAATGTTCTATAGC
1 TCTTTAGCGGCACTT-GG-AAAAAACGCCGCTAAAGA-TAATGTTCTATAGC
16970410 GGCGCTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 14 0.32
54 3 0.07
55 27 0.61
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (53 bp):
TCTTTAGCGGCACTTGGAAAAAACGCCGCTAAAGATAATGTTCTATAGCATGA
Found at i:16970403 original size:138 final size:139
Alignment explanation
Indices: 16970238--16970493 Score: 351
Period size: 138 Copynumber: 1.8 Consensus size: 139
16970228 GGCGCTTACA
* * * * *
16970238 GAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTTAGGAAAAAACG-TCGCT-AATGAT
1 GAAAAAAACGCCGCTAAAAGTAATGTTCTATAGCAGCGCTTAAGAAAAAACGCT-GCTAAAAG-T
* *
16970301 CAA-GTTCTTTAGCGGCGCTTGGGA-AAAACGCCGCT-AAAGATCATGTTCTTTAGCATGATCTT
64 -AATGTTCTATAGCGGCGCTTGGGAGAAAACGCCGCTAAAAG-TAATGTTCTTTAGCATGATCTT
16970363 TAGCGGCACTTAG
127 TAGCGGCACTTAG
* *
16970376 GAAAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAATAAAAAACGCTGCTAAAAGTAA
1 GAAAAAAACGCCGCTAAAAGTAATGTTCTATAGCAGCGCTTAAGAAAAAACGCTGCTAAAAGTAA
*
16970441 TGTTCTATAGCGGCGCTTGGTAGAAAACGCCGCTAAAAGTAATGTTCTTTAGC
66 TGTTCTATAGCGGCGCTTGGGAGAAAACGCCGCTAAAAGTAATGTTCTTTAGC
16970494 GGCGCTTCAT
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
137 2 0.02
138 69 0.67
139 28 0.27
140 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (139 bp):
GAAAAAAACGCCGCTAAAAGTAATGTTCTATAGCAGCGCTTAAGAAAAAACGCTGCTAAAAGTAA
TGTTCTATAGCGGCGCTTGGGAGAAAACGCCGCTAAAAGTAATGTTCTTTAGCATGATCTTTAGC
GGCACTTAG
Found at i:16970434 original size:42 final size:42
Alignment explanation
Indices: 16970378--16970531 Score: 218
Period size: 42 Copynumber: 3.6 Consensus size: 42
16970368 GCACTTAGGA
16970378 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* **
16970420 AAAAAACGCTGCTAAAAGTAATGTTCTATAGCGGCGCTTGGT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* * *
16970462 AGAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTCAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* * *
16970504 CTACAAACGCCGCTAAAAGTAGTGTTCT
1 -AAAAAACGCCGCTAAAAGTAATGTTCT
16970532 TTCGCAGCGC
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 76 0.77
43 23 0.23
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
Found at i:16970553 original size:43 final size:42
Alignment explanation
Indices: 16970381--16970555 Score: 199
Period size: 42 Copynumber: 4.1 Consensus size: 42
16970371 CTTAGGAAAA
* * *
16970381 AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAATAAA
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTATTTAC
* ** *
16970423 AAACGCTGCTAAAAGTAATGTTCTATAGCGGCGCTT-GGTAGA
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTATTTA-C
* *
16970465 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTT-ATTTAC
* * * *
16970508 AAACGCCGCTAAAAGTAGTGTTCTTTCGCAGCGCTTATTTCAC
1 AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTATTT-AC
16970551 AAACG
1 AAACG
16970556 GCACTAAATG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 73 0.63
43 40 0.34
44 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTATTTAC
Found at i:16970996 original size:12 final size:12
Alignment explanation
Indices: 16970979--16971006 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16970969 TTTTGAACCT
16970979 CTGCTTCTCTCG
1 CTGCTTCTCTCG
16970991 CTGCTTCTCTCG
1 CTGCTTCTCTCG
16971003 CTGC
1 CTGC
16971007 AGCCTCTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.18, T:0.39
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:16971015 original size:21 final size:21
Alignment explanation
Indices: 16970991--16971035 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16970981 GCTTCTCTCG
*
16970991 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
*
16971012 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCAGCCT
16971033 CTG
1 CTG
16971036 TTTTAAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.47, G:0.20, T:0.31
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:16972613 original size:27 final size:27
Alignment explanation
Indices: 16972575--16972805 Score: 272
Period size: 27 Copynumber: 8.6 Consensus size: 27
16972565 TCGAAGATCT
* * *
16972575 AGTTACGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
16972602 AGTTATGTAAGTTACT-TAATTTATGTA
1 AGTTATGTAAGTTA-TGTAAGTTATGTA
16972629 AGTTATGTAAGTTATGTAAGTTACT-TA
1 AGTTATGTAAGTTATGTAAGTTA-TGTA
* *
16972656 ATTTATGTAAGTTATGTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
16972683 ATTTATGTAAGTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16972710 AGGTTCT-TAATTTATGTAAGTTATGTA
1 A-GTTATGTAAGTTATGTAAGTTATGTA
* *
16972737 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
16972764 AGTTATTTAATTTTTGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
16972791 A-TTAATGTAAGTTAT
1 AGTT-ATGTAAGTTAT
16972806 TTAATTTGTG
Statistics
Matches: 185, Mismatches: 12, Indels: 14
0.88 0.06 0.07
Matches are distributed among these distances:
26 8 0.04
27 172 0.93
28 5 0.03
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (27 bp):
AGTTATGTAAGTTATGTAAGTTATGTA
Found at i:16972635 original size:36 final size:36
Alignment explanation
Indices: 16972575--16972805 Score: 252
Period size: 36 Copynumber: 6.7 Consensus size: 36
16972565 TCGAAGATCT
* * * *
16972575 AGTTACGTAAGTTATTTAATTTATGTAAGTTATGTA
1 AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
16972611 AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
1 AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
16972647 AGTTACTTAATTTATGTAAGTTATGTAAG---T-T-
1 AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
16972678 A--T--TTAATTTATGTAAGTTATGTAAGTTATGTA
1 AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
*
16972710 AGGTT-CTTAATTTATGTAAGTTATGTAAGTTATTTA
1 A-GTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
* * * * *
16972746 ATTTA-TGTAAGTTATGTAAGTTATTTAATTTTTGTA
1 AGTTACT-TAATTTATGTAAGTTATGTAAGTTATGTA
*
16972782 AGTTA-TGTAATTAATGTAAGTTAT
1 AGTTACT-TAATTTATGTAAGTTAT
16972806 TTAATTTGTG
Statistics
Matches: 170, Mismatches: 14, Indels: 22
0.83 0.07 0.11
Matches are distributed among these distances:
27 23 0.14
29 1 0.01
30 1 0.01
31 2 0.01
32 2 0.01
33 1 0.01
35 4 0.02
36 136 0.80
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (36 bp):
AGTTACTTAATTTATGTAAGTTATGTAAGTTATGTA
Found at i:16972674 original size:63 final size:63
Alignment explanation
Indices: 16972575--16972812 Score: 365
Period size: 63 Copynumber: 3.8 Consensus size: 63
16972565 TCGAAGATCT
* * *
16972575 AGTTACGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
16972638 AGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
16972701 AGTTATGTAAGGTT-CTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAA-GTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
* ** *
16972764 AGTTATTTAA-TTTTTGTAAGTTATGTAA-TTAATGTAAGTTATTTAATTT
1 AGTTATGTAAGTTACT-TAATTTATGTAAGTT-ATGTAAGTTATTTAATTT
16972813 GTGATACCTA
Statistics
Matches: 165, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
61 2 0.01
62 3 0.02
63 157 0.95
64 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (63 bp):
AGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTA
Found at i:16974064 original size:2 final size:2
Alignment explanation
Indices: 16974057--16974082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16974047 TATTAAACAA
16974057 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16974083 TATTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16976667 original size:113 final size:111
Alignment explanation
Indices: 16976485--16976832 Score: 412
Period size: 113 Copynumber: 3.1 Consensus size: 111
16976475 TCCCACAACG
* * * *
16976485 CGCCGCTAATAATATGTTTTAGCGGCGTTTTACCATAAGCGCCACAACTGCTAGTATACATCAAG
1 CGCCGCTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACAA-TGCTAATATACATCAAG
*
16976550 ACCAAAGCGTTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAAA
64 ACCAAAGCGTTGCGTTTTGGTTAATATTTTGCGGCGCTTTTCAATAAA
* * *
16976598 CGCCGCTAATACTATGCTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAG
1 CGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCAC-AATGCTAATATACATCAAG
* * * **
16976663 ACCAAA-C-TCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTTTCAGTACT
64 ACCAAAGCGT-TGCGTTTTGGTT-A-ATATTTTGCGGCGCTTTTCAATAAA
* * * *
16976712 CGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGGCACAATGATACTATACATCAAGA
1 CGCCGCTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACAATGCTAATATACATCAAGA
* * * *
16976777 CCAAAGCGCTGCGTTTTGGTTAATCTTTTGCGGCGTTTTTCAATAAG
65 CCAAAGCGTTGCGTTTTGGTTAATATTTTGCGGCGCTTTTCAATAAA
*
16976824 CGCCACTAA
1 CGCCGCTAA
16976833 GCCTAATATA
Statistics
Matches: 198, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.01
112 39 0.20
113 83 0.42
114 75 0.38
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
CGCCGCTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACAATGCTAATATACATCAAGAC
CAAAGCGTTGCGTTTTGGTTAATATTTTGCGGCGCTTTTCAATAAA
Found at i:16977155 original size:114 final size:113
Alignment explanation
Indices: 16976801--16977287 Score: 536
Period size: 114 Copynumber: 4.3 Consensus size: 113
16976791 TTTGGTTAAT
* * *
16976801 CTTTTGCGGCGTTTTTCAATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGCGTT
1 CTTTAGCGGCGTTTTT-GATAAGCGCCACTAATG-CTAATATACCTCAAGACCAAACTCTGCGTT
* * *
16976865 TTGGTTAAGAAATCTTGCGGTGCTTTTCACTACTTGCCGCTAATACTATG
64 TTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
* * * * * * *
16976915 ATTTAGCGGCGTTTTAATG-TAAGCACCAGTACTGCTAGTATACATCAAGACCAAAGCGCTGCGT
1 CTTTAGCGGCGTTTT--TGATAAGCGCCACTAATGCTAATATACCTCAAGACCAAA-CTCTGCGT
* * * * * **
16976979 TTTGGCT-A-ATATTTTGCGGCGCTTTACAATAAGCGCCGCTAATACTATG
63 TTTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
*
16977028 CTTTAGCGGCGTTTTTCGATAAGCGCCAGTAAT-CATAATATACCTCAAGACCAAACTCTGCGTT
1 CTTTAGCGGCGTTTTT-GATAAGCGCCACTAATGC-TAATATACCTCAAGACCAAACTCTGCGTT
* *
16977092 TTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCTCCGCTAATACTATT
64 TTGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
* * * *
16977142 CTTTAGCGGCGTTTTTGTATAAGTGCCACTAATGCTAGTGTACCTCATGACCAAACTCTGCGTTT
1 CTTTAGCGGCGTTTTTG-ATAAGCGCCACTAATGCTAATATACCTCAAGACCAAACTCTGCGTTT
** *** *
16977207 TGGTTAAGATGTATTGCGGCGCTTTT-TGGACTCGCCGCTAATTCTATG
65 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
**
16977255 CTTTAGCGGCGATTTTAAATAAGCGCCACTAAT
1 CTTTAGCGGCG-TTTTTGATAAGCGCCACTAAT
16977288 ACTTTCTTTA
Statistics
Matches: 311, Mismatches: 50, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
111 1 0.00
112 15 0.05
113 120 0.39
114 159 0.51
115 15 0.05
116 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (113 bp):
CTTTAGCGGCGTTTTTGATAAGCGCCACTAATGCTAATATACCTCAAGACCAAACTCTGCGTTTT
GGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATG
Found at i:16977245 original size:227 final size:227
Alignment explanation
Indices: 16976801--16977287 Score: 638
Period size: 227 Copynumber: 2.1 Consensus size: 227
16976791 TTTGGTTAAT
* * *
16976801 CTTTTGCGGCGTTTTTCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCGTTTTTCAATAAGCGCCACTAATCATAATATACCGCAAGACCAAACTCTGCGTTT
* *
16976866 TGGTTAAGAAATCTTGCGGTGCTTTTCACTACTTGCCGCTAATACTATGATTTAGCGGCGTTTTA
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTTGCCGCTAATACTATGATTTAGCGGCGTTTTA
* * * *
16976931 ATGTAAGCACCAGTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGCTAATATTTTGC
131 ATATAAGCACCACTAATGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGCTAAGATTTTGC
*
16976996 GGCGCTTTACAATAAGCGCCGCTAATACTATG
196 GGCGCTTTACAAGAAGCGCCGCTAATACTATG
* * *
16977028 CTTTAGCGGCGTTTTTCGATAAGCGCCAGTAATCATAATATACCTCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCGTTTTTCAATAAGCGCCACTAATCATAATATACCGCAAGACCAAACTCTGCGTTT
**
16977093 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCT-CCGCTAATACTATTCTTTAGCGGCGTTTT
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACT-TGCCGCTAATACTATGATTTAGCGGCGTTTT
** ** * * * * *
16977157 TGTATAAGTGCCACTAATGCTAGTGTACCTCATGACCAAA-CTCTGCGTTTTGGTTAAGATGTAT
130 AATATAAGCACCACTAATGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGCTAAGAT-T-T
*** ** *
16977221 TGCGGCGCTTT-TTGGACTCGCCGCTAATTCTATG
193 TGCGGCGCTTTACAAGAAGCGCCGCTAATACTATG
* *
16977255 CTTTAGCGGCGATTTTAAATAAGCGCCACTAAT
1 CTTTAGCGGCGTTTTTCAATAAGCGCCACTAAT
16977288 ACTTTCTTTA
Statistics
Matches: 223, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
226 17 0.08
227 193 0.87
228 13 0.06
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (227 bp):
CTTTAGCGGCGTTTTTCAATAAGCGCCACTAATCATAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTGCGGCGCTTTTCACTACTTGCCGCTAATACTATGATTTAGCGGCGTTTTA
ATATAAGCACCACTAATGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGCTAAGATTTTGC
GGCGCTTTACAAGAAGCGCCGCTAATACTATG
Found at i:16977985 original size:24 final size:24
Alignment explanation
Indices: 16977958--16978019 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
16977948 CCGCAAAGTT
* * **
16977958 CACTATCACTATCATCATAGTTTG
1 CACTATTACTATCATCATAGCTCA
16977982 CACTATTACTATCATCATAGCTCA
1 CACTATTACTATCATCATAGCTCA
16978006 CACTATTACTATCA
1 CACTATTACTATCA
16978020 ACTTCTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (24 bp):
CACTATTACTATCATCATAGCTCA
Found at i:16979721 original size:43 final size:43
Alignment explanation
Indices: 16979658--16979881 Score: 326
Period size: 43 Copynumber: 5.2 Consensus size: 43
16979648 GTGAAAAAAT
* * **
16979658 GCCGCTAAAGAACATTACCTTTAGTGGCGCTTTACAAACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
16979701 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
**
16979744 GCCGCTAAAGAACA-GAACCTTTAGCAACGCTTTACCCACAAAC
1 GCCGCTAAAGAACATG-ACCTTTAGCGGCGCTTTACCCACAAAC
* *
16979787 GCCACTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
* *
16979830 GCCGCTGAAGAACATGATCTTTAGCGGCGCTTTA-CCAGCAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCA-CAAAC
16979873 GCCGCTAAA
1 GCCGCTAAA
16979882 AGTACGATTC
Statistics
Matches: 165, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 4 0.02
43 160 0.97
44 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
Found at i:16981819 original size:10 final size:11
Alignment explanation
Indices: 16981793--16981818 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16981783 AAAATCAGTC
16981793 AAAAATAGGAT
1 AAAAATAGGAT
16981804 AAAAATAGGAT
1 AAAAATAGGAT
16981815 AAAA
1 AAAA
16981819 TTCCTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATAGGAT
Found at i:16982768 original size:9 final size:9
Alignment explanation
Indices: 16982754--16982784 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16982744 GTTAAACGAA
16982754 TCGAGTTAT
1 TCGAGTTAT
*
16982763 TCGAGTTAA
1 TCGAGTTAT
16982772 TCGAGTTAT
1 TCGAGTTAT
16982781 TCGA
1 TCGA
16982785 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16986678 original size:14 final size:14
Alignment explanation
Indices: 16986659--16986772 Score: 83
Period size: 14 Copynumber: 8.1 Consensus size: 14
16986649 ATCCCTGAAT
16986659 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
16986673 CCCTAAACCCTT-AA
1 CCCTAAA-CCTTAAA
*
16986687 CCTCT-AACCTCTAAC
1 CC-CTAAACCT-TAAA
*
16986702 CCCTAACCCTTAAA
1 CCCTAAACCTTAAA
* * *
16986716 CCTTAAATC-TCAA
1 CCCTAAACCTTAAA
* * *
16986729 CCCTAACCCCTAAC
1 CCCTAAACCTTAAA
16986743 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
*
16986757 TCCC-AACCCTTAAA
1 -CCCTAAACCTTAAA
16986771 CC
1 CC
16986773 ATAATCCCTA
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
13 14 0.18
14 47 0.61
15 16 0.21
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAAACCTTAAA
Found at i:16986683 original size:21 final size:21
Alignment explanation
Indices: 16986659--16986784 Score: 89
Period size: 21 Copynumber: 6.0 Consensus size: 21
16986649 ATCCCTGAAT
16986659 CCCTAAACCTTAAACCCTAAA
1 CCCTAAACCTTAAACCCTAAA
* *
16986680 CCCTTAACCTCT-AACCTCTAAC
1 CCCTAAACCT-TAAACC-CTAAA
* *
16986702 CCCTAACCCTTAAACCTTAAA
1 CCCTAAACCTTAAACCCTAAA
* * * * *
16986723 -TCTCAACCCTAACCCCTAAC
1 CCCTAAACCTTAAACCCTAAA
16986743 CCCTAAACCTTAAATCCC--AA
1 CCCTAAACCTTAAA-CCCTAAA
* *
16986763 CCCTTAAACCATAATCCCTAAA
1 CCC-TAAACCTTAAACCCTAAA
16986785 TCCATACTCC
Statistics
Matches: 77, Mismatches: 20, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
20 20 0.26
21 35 0.45
22 22 0.29
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAAACCTTAAACCCTAAA
Found at i:16986740 original size:34 final size:33
Alignment explanation
Indices: 16986671--16986784 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 33
16986661 CTAAACCTTA
*
16986671 AACCCTAAACCCTT-AACCTCTAACCTCTAACCCCT
1 AACCCTAAA-CCTTAAATCTC-AACC-CTAACCCCT
16986706 AACCCTTAAACCTTAAATCTCAACCCTAACCCCT
1 AACCC-TAAACCTTAAATCTCAACCCTAACCCCT
* * *
16986740 AACCCCTAAACCTTAAATCCCAACCCTTAAACCAT
1 AA-CCCTAAACCTTAAATCTCAACCC-TAACCCCT
16986775 AATCCCTAAA
1 AA-CCCTAAA
16986785 TCCATACTCC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
34 30 0.43
35 31 0.44
36 9 0.13
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (33 bp):
AACCCTAAACCTTAAATCTCAACCCTAACCCCT
Found at i:16986789 original size:15 final size:14
Alignment explanation
Indices: 16986767--16986801 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
16986757 TCCCAACCCT
16986767 TAAACCATAATCCC
1 TAAACCATAATCCC
*
16986781 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
16986796 TAAACC
1 TAAACC
16986802 TTACACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:16987243 original size:41 final size:41
Alignment explanation
Indices: 16987184--16987460 Score: 360
Period size: 41 Copynumber: 6.8 Consensus size: 41
16987174 AAATGTTTTT
*
16987184 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTA
*** * *
16987225 GCGGCGCTCCCT-AGAAAACGCCGCTAAAACACCGAGCATTA
1 GCGGCGCTTTTTCA-AAAACGCCGCTAAAACCCCAAGCATTA
* *
16987266 GCAGCGCTTTCTCAAAAACGCCGCTAAAACCCCAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTA
* *
16987307 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCTCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTA
* * *
16987348 GCGGTGCTTTTTAAAAAACGCCGCTAAAACCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTA
* * *
16987389 GCGGCACTTCTTCAAAAACGCCGCTAAAAGCCCGAA-CATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAA-CCCCAAGCATTA
* *
16987430 GCGGCGCTTTTACAAAAATGCCGCTAAAACC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACC
16987461 ACGAAAGGTC
Statistics
Matches: 205, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
40 3 0.01
41 197 0.96
42 5 0.02
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCATTA
Found at i:16987559 original size:39 final size:40
Alignment explanation
Indices: 16987516--16987648 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
16987506 GTTTTTTAAA
* * *
16987516 AAAACGCCGTTAATGCT-TATTTTTAGCGGCGCTTTCCT-T
1 AAAACGCCGCTAATGCTCGATTTTTAGCGGCG-TTTCATGT
* * *
16987555 AAAACACCGCTAATGCTCGATCTTTAGCGGCGTTTTATGT
1 AAAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTCATGT
* **
16987595 AAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTTTTGT
1 AAAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTCATGT
*
16987635 CCAAACGCCGCTAA
1 -AAAACGCCGCTAA
16987649 AAATGCCGCT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 19 0.24
40 49 0.62
41 11 0.14
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (40 bp):
AAAACGCCGCTAATGCTCGATTTTTAGCGGCGTTTCATGT
Found at i:16990071 original size:21 final size:22
Alignment explanation
Indices: 16990046--16990094 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
16990036 GAAATAGTTA
*
16990046 AATTTTGC-T-TTGTTATACTTT
1 AATTTTGCATCTTGTCATA-TTT
16990067 AA-TTTGCATCTTGTCATATTT
1 AATTTTGCATCTTGTCATATTT
16990088 AATTTTG
1 AATTTTG
16990095 TAACGGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.57
Consensus pattern (22 bp):
AATTTTGCATCTTGTCATATTT
Found at i:16992466 original size:44 final size:45
Alignment explanation
Indices: 16992367--16992467 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
16992357 TTGAAGGAAA
* * *
16992367 TGAATAATACCATAGTTGAAAGACACTATGGCACTATACCAGAAC
1 TGAATAAGACCATAGTTGAAAGAAACTATGGCACTATACCAAAAC
*
16992412 TGAATAAGACCATAGTTGAATGAAACTAT-GCA-TCATACCGAAAAC
1 TGAATAAGACCATAGTTGAAAGAAACTATGGCACT-ATACC-AAAAC
*
16992457 -GAGTAAGACCA
1 TGAATAAGACCA
16992468 AAGCTAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 18 0.37
45 30 0.61
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
TGAATAAGACCATAGTTGAAAGAAACTATGGCACTATACCAAAAC
Found at i:16995224 original size:25 final size:25
Alignment explanation
Indices: 16995196--16995244 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
16995186 CTGTTTTGGA
* *
16995196 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
*
16995221 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTGAAACTACTATAG
16995245 ATAGACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:17004944 original size:25 final size:25
Alignment explanation
Indices: 17004916--17005038 Score: 169
Period size: 25 Copynumber: 4.9 Consensus size: 25
17004906 AGACACACCA
*
17004916 CAGCTCGTGTGAGCTTACCGATTTG
1 CAGCTCGTGAGAGCTTACCGATTTG
17004941 CAGCTCGTGAGAGCTTACCGATTTG
1 CAGCTCGTGAGAGCTTACCGATTTG
17004966 CAGCTCGTGAGAGCTTACCGATTCT-
1 CAGCTCGTGAGAGCTTACCGATT-TG
*
17004991 CAGCTCGT-ATGAGCTTACCGATTTT
1 CAGCTCGTGA-GAGCTTACCGATTTG
* * *
17005016 TAGCTCGAGAGAGCATACCGATT
1 CAGCTCGTGAGAGCTTACCGATT
17005039 CATAGCTTGT
Statistics
Matches: 90, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.02
25 86 0.96
26 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (25 bp):
CAGCTCGTGAGAGCTTACCGATTTG
Found at i:17005051 original size:50 final size:50
Alignment explanation
Indices: 17004916--17005053 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 50
17004906 AGACACACCA
* * *
17004916 CAGCTCGTGTGAGCTTACCGATT-TGCAGCTCGTGA-GAGCTTACCGATTTG
1 CAGCTCGAGAGAGCATACCGATTCT-CAGCTCGT-ATGAGCTTACCGATTTG
* * *
17004966 CAGCTCGTGAGAGCTTACCGATTCTCAGCTCGTATGAGCTTACCGATTTT
1 CAGCTCGAGAGAGCATACCGATTCTCAGCTCGTATGAGCTTACCGATTTG
* *
17005016 TAGCTCGAGAGAGCATACCGATTCAT-AGCTTGTATGAG
1 CAGCTCGAGAGAGCATACCGATTC-TCAGCTCGTATGAG
17005054 AATACATGTA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
49 1 0.01
50 76 0.96
51 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (50 bp):
CAGCTCGAGAGAGCATACCGATTCTCAGCTCGTATGAGCTTACCGATTTG
Found at i:17008203 original size:9 final size:9
Alignment explanation
Indices: 17008189--17008225 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17008179 TATAGTTTGA
17008189 TATTCGAAT
1 TATTCGAAT
17008198 TATTCGAAT
1 TATTCGAAT
*
17008207 TATTCGAGT
1 TATTCGAAT
*
17008216 TATTTGAAT
1 TATTCGAAT
17008225 T
1 T
17008226 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17008516 original size:21 final size:24
Alignment explanation
Indices: 17008463--17008517 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
17008453 TTAATTGGGA
17008463 ATAAATAAATAAAATATATATTTTT
1 ATAAATAAATAAAATATATA-TTTT
**
17008488 ATCGATAAAT-AAA-ATATA-TTT
1 ATAAATAAATAAAATATATATTTT
17008509 ATAAATAAA
1 ATAAATAAA
17008518 ATATAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 10 0.38
23 5 0.19
24 3 0.12
25 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATAAATAAATAAAATATATATTTT
Found at i:17011068 original size:3 final size:3
Alignment explanation
Indices: 17011012--17011057 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
17011002 ATTATTATGA
17011012 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17011058 CAAGAATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17017542 original size:23 final size:23
Alignment explanation
Indices: 17017496--17017578 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
17017486 CGAAACACCC
17017496 CAATTT-CAGCAAC-TAAACAA-TT
1 CAATTTGCAGC-ACTTAAA-AACTT
*
17017518 CAATTTGCAGTACTTAAAAACTT
1 CAATTTGCAGCACTTAAAAACTT
* * * *
17017541 CAATTTACAACATTTAAACACTT
1 CAATTTGCAGCACTTAAAAACTT
17017564 CAATTTGCAGCACTT
1 CAATTTGCAGCACTT
17017579 TAACATCTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 10 0.20
23 39 0.80
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.33
Consensus pattern (23 bp):
CAATTTGCAGCACTTAAAAACTT
Found at i:17017560 original size:46 final size:47
Alignment explanation
Indices: 17017509--17017706 Score: 167
Period size: 46 Copynumber: 4.3 Consensus size: 47
17017499 TTTCAGCAAC
*
17017509 TAAACAATTCAATTTGCAGTACTTAAAAACT-TCAATTTACAACATT
1 TAAACACTTCAATTTGCAGTACTTAAAAACTCTCAATTTACAACATT
* * * * *
17017555 TAAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAAAAACATT
1 TAAACACTTCAATTTGCAGTACTTAAAAACTCTCAATTTACAACATT
* * * * * * **
17017601 TATACACCTCAA-TTACAG--C-GATAAAACATCTCAATTTCCACCAAC
1 TAAACACTTCAATTTGCAGTACTTA-AAAAC-TCTCAATTTACAACATT
* * **
17017646 TAAACACTTCAATTTGTAGTACTTAAACACT-TTGATTTACAACATT
1 TAAACACTTCAATTTGCAGTACTTAAAAACTCTCAATTTACAACATT
17017692 TAAACACTTCAATTT
1 TAAACACTTCAATTT
17017707 ACAAATCCAC
Statistics
Matches: 114, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
43 4 0.04
45 27 0.24
46 76 0.67
47 1 0.01
48 5 0.04
49 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (47 bp):
TAAACACTTCAATTTGCAGTACTTAAAAACTCTCAATTTACAACATT
Found at i:17017583 original size:23 final size:23
Alignment explanation
Indices: 17017511--17017591 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
17017501 TCAGCAACTA
* * *
17017511 AACAATTCAATTTGCAGTACTTA
1 AACACTTCAATTTGCAGCACTTT
* * *
17017534 AAAACTTCAATTTACAACA-TTT
1 AACACTTCAATTTGCAGCACTTT
17017556 AAACACTTCAATTTGCAGCACTTT
1 -AACACTTCAATTTGCAGCACTTT
17017580 AACA-TCTCAATT
1 AACACT-TCAATT
17017592 AAAAACATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 3 0.07
23 40 0.87
24 3 0.07
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
AACACTTCAATTTGCAGCACTTT
Found at i:17018621 original size:7 final size:7
Alignment explanation
Indices: 17018609--17018785 Score: 85
Period size: 7 Copynumber: 24.9 Consensus size: 7
17018599 CCCTATCCCC
17018609 TAAACCA
1 TAAACCA
*
17018616 TGAACCA
1 TAAACCA
*
17018623 TAAAACA
1 TAAACCA
17018630 TAAACCA
1 TAAACCA
*
17018637 TAAACCC
1 TAAACCA
* *
17018644 TAATCCCC
1 TAA-ACCA
*
17018652 T-AACCTT
1 TAAACC-A
* *
17018659 TAACCCC
1 TAAACCA
*
17018666 TAAACCT
1 TAAACCA
17018673 TAAACC-
1 TAAACCA
* *
17018679 TCAACCCT
1 T-AAACCA
17018687 TAAACCA
1 TAAACCA
17018694 TAAACCA
1 TAAACCA
*
17018701 TAATCCA
1 TAAACCA
17018708 TAAACCCA
1 TAAA-CCA
*
17018716 TAATCCA
1 TAAACCA
*
17018723 TAAACCT
1 TAAACCA
17018730 TAAA--A
1 TAAACCA
*
17018735 TAGTAACTCC
1 TA--AAC-CA
*
17018745 TAAACCT
1 TAAACCA
17018752 TAAATCC-
1 TAAA-CCA
17018759 TAAACCA
1 TAAACCA
* *
17018766 TATACCC
1 TAAACCA
17018773 TAAACCA
1 TAAACCA
17018780 TAAACC
1 TAAACC
17018786 CTAGACTATA
Statistics
Matches: 130, Mismatches: 27, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
5 2 0.02
6 5 0.04
7 102 0.78
8 19 0.15
10 2 0.02
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:17018716 original size:15 final size:15
Alignment explanation
Indices: 17018681--17018728 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
17018671 CTTAAACCTC
* *
17018681 AACCCTTAAACCATA
1 AACCCATAATCCATA
17018696 AA-CCATAATCCATA
1 AACCCATAATCCATA
17018710 AACCCATAATCCATA
1 AACCCATAATCCATA
17018725 AACC
1 AACC
17018729 TTAAAATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:17018733 original size:22 final size:21
Alignment explanation
Indices: 17018609--17018785 Score: 94
Period size: 21 Copynumber: 8.3 Consensus size: 21
17018599 CCCTATCCCC
* * *
17018609 TAAACCATGAACCATAAAACA
1 TAAACCATAAACCTTAAACCA
* * *
17018630 TAAACCATAAACCCTAATCCCC
1 TAAACCATAAACCTTAA-ACCA
* * * *
17018652 T-AACCTTTAACCCCTAAACCT
1 TAAACC-ATAAACCTTAAACCA
*
17018673 TAAACC-TCAACCCTTAAACCA
1 TAAACCAT-AAACCTTAAACCA
* *
17018694 TAAACCATAATCCATAAACCCA
1 TAAACCATAAACCTTAAA-CCA
*
17018716 TAATCCATAAACCTTAAA--A
1 TAAACCATAAACCTTAAACCA
*
17018735 TAGTAACTCCTAAACCTTAAATCC-
1 TA--AAC-CATAAACCTTAAA-CCA
* *
17018759 TAAACCATATACCCTAAACCA
1 TAAACCATAAACCTTAAACCA
17018780 TAAACC
1 TAAACC
17018786 CTAGACTATA
Statistics
Matches: 122, Mismatches: 21, Indels: 26
0.72 0.12 0.15
Matches are distributed among these distances:
19 3 0.02
20 3 0.02
21 65 0.53
22 49 0.40
24 2 0.02
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.21
Consensus pattern (21 bp):
TAAACCATAAACCTTAAACCA
Found at i:17018796 original size:14 final size:14
Alignment explanation
Indices: 17018586--17018788 Score: 108
Period size: 14 Copynumber: 14.2 Consensus size: 14
17018576 ACTAATTAAT
*
17018586 CTAAACCTTAAACCC
1 CTAAACCATAAA-CC
** *
17018601 CTATCCCCTAAACC
1 CTAAACCATAAACC
* * *
17018615 ATGAACCATAAAAC
1 CTAAACCATAAACC
*
17018629 ATAAACCATAAACC
1 CTAAACCATAAACC
* *
17018643 CTAATCCCCT-AACC
1 CTAA-ACCATAAACC
* * *
17018657 TTTAACCCCTAAACC
1 -CTAAACCATAAACC
* *
17018672 TTAAACC-TCAACC
1 CTAAACCATAAACC
17018685 CTTAAACCATAAACC
1 C-TAAACCATAAACC
* *
17018700 ATAATCCATAAACC
1 CTAAACCATAAACC
*
17018714 CATAATCCATAAACC
1 C-TAAACCATAAACC
*
17018729 TTAAA--ATAGTAACTC
1 CTAAACCATA--AAC-C
* *
17018744 CTAAACCTTAAATC
1 CTAAACCATAAACC
*
17018758 CTAAACCATATACC
1 CTAAACCATAAACC
17018772 CTAAACCATAAACC
1 CTAAACCATAAACC
17018786 CTA
1 CTA
17018789 GACTATAATG
Statistics
Matches: 146, Mismatches: 31, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
12 3 0.02
13 5 0.03
14 92 0.63
15 44 0.30
17 2 0.01
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.22
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:17019231 original size:40 final size:40
Alignment explanation
Indices: 17019169--17019293 Score: 135
Period size: 40 Copynumber: 3.1 Consensus size: 40
17019159 TTTTGCGGCA
* *
17019169 TTTTTCAAAAAGCGCCATTAATGGC-CGACCTATGGCAGCG
1 TTTTTCAAAAAGCGCAACTAAT-GCTCGACCTATGGCAGCG
* * *
17019209 TTTTTCAAAAAGTGCAACTAATGCTCGATCTATTGCAGCG
1 TTTTTCAAAAAGCGCAACTAATGCTCGACCTATGGCAGCG
* * * * * *
17019249 TTTTTCAAAAAGCACCACTAATACTCGATCTATAGCTGCG
1 TTTTTCAAAAAGCGCAACTAATGCTCGACCTATGGCAGCG
17019289 TTTTT
1 TTTTT
17019294 TATCCAAACG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 2 0.03
40 71 0.97
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCAACTAATGCTCGACCTATGGCAGCG
Found at i:17022237 original size:3 final size:3
Alignment explanation
Indices: 17022229--17022277 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
17022219 CGTATTATGA
17022229 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17022277 A
1 A
17022278 CAAAGAACAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17025330 original size:19 final size:19
Alignment explanation
Indices: 17025286--17025379 Score: 107
Period size: 19 Copynumber: 4.9 Consensus size: 19
17025276 TATGCATATT
* **
17025286 GTGTGCTAGGATATACTTC
1 GTGTGCCAGGATGCACTTC
* ** *
17025305 GTCTGCCAGGATGTGCTTT
1 GTGTGCCAGGATGCACTTC
17025324 GTGTGCCAGGATGCACTTC
1 GTGTGCCAGGATGCACTTC
17025343 GTGTGCCAGGATGCACTTC
1 GTGTGCCAGGATGCACTTC
* *
17025362 GTGTGCCAAGATTCACTT
1 GTGTGCCAGGATGCACTT
17025380 TGTACGCCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (19 bp):
GTGTGCCAGGATGCACTTC
Found at i:17027441 original size:44 final size:44
Alignment explanation
Indices: 17027388--17027473 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
17027378 TTGAAATAAA
* *
17027388 AATAAAAGTTGTGATAATTATACATTTAAAAATAATTGTAATTT
1 AATAAAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
* *
17027432 AATAGAAGTTGTGGTAATTACACATTTAAAAATAATTATAAT
1 AATAAAAGTTGTGATAATTACACATTTAAAAATAATTATAAT
17027474 CTAAATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (44 bp):
AATAAAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
Found at i:17027486 original size:6 final size:6
Alignment explanation
Indices: 17027463--17027506 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
17027453 ACATTTAAAA
17027463 ATAATT ATAATCT A-AATT ATAATT ATAATT ATAATT ATTAATT A
1 ATAATT ATAAT-T ATAATT ATAATT ATAATT ATAATT A-TAATT A
17027507 AAAAATTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.06
6 25 0.71
7 8 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:17027725 original size:25 final size:25
Alignment explanation
Indices: 17027697--17027764 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
17027687 ATTATAATTA
17027697 TTACTTAATTAATATTAGAGTTAAC
1 TTACTTAATTAATATTAGAGTTAAC
17027722 TTACTTAATTAATATTAGAGTTAAC
1 TTACTTAATTAATATTAGAGTTAAC
*
17027747 -TATGTTAATTAATTATTA
1 TTA-CTTAATTAA-TATTA
17027765 TTTTGAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 2 0.05
25 33 0.82
26 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (25 bp):
TTACTTAATTAATATTAGAGTTAAC
Found at i:17028183 original size:44 final size:44
Alignment explanation
Indices: 17028133--17028221 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
17028123 GTTGAAGTAA
* * *
17028133 AATAGAAGTTGTGATAATTATACATTTAAAAATATTTATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
*
17028177 AATAGAAATTGTGATGATTACACATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
17028221 A
1 A
17028222 TATTTATTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.40
Consensus pattern (44 bp):
AATAGAAATTGTGATAATTACACATTTAAAAATAATTATAATTT
Found at i:17029214 original size:55 final size:55
Alignment explanation
Indices: 17029130--17029239 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
17029120 GTATCCATTG
*
17029130 GATGATAAATCATCACTTTTAAATTGAATAGTGCTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAAATTGAATAGTGCTCATGAATAATTAATTTGCAA
*
17029185 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAAATTGAATAGTGCTCATGAATAATTAATTTGCAA
17029240 TATATAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAAATTGAATAGTGCTCATGAATAATTAATTTGCAA
Found at i:17033752 original size:55 final size:55
Alignment explanation
Indices: 17033668--17033773 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
17033658 GTATCCATTG
* * *
17033668 GATGATAAATCATCACTTTTAATTTGAATAGTGGTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGATCATAAATAATTAATTTGCAA
17033723 GATGATAAATCATCACTTTTAATTTGAATAGTGATCATAAATAATTAATTT
1 GATGATAAATCATCACTTTTAATTTGAATAGTGATCATAAATAATTAATTT
17033774 ACAATCTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGATCATAAATAATTAATTTGCAA
Found at i:17033757 original size:29 final size:29
Alignment explanation
Indices: 17033670--17033757 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
17033660 ATCCATTGGA
17033670 TGATAAATCATCACTTTTAATTTGAATAG
1 TGATAAATCATCACTTTTAATTTGAATAG
* * * * *
17033699 TGGT---T-ATGAATAATTAATTTGCA-AG
1 TGATAAATCATCACT-TTTAATTTGAATAG
17033724 ATGATAAATCATCACTTTTAATTTGAATAG
1 -TGATAAATCATCACTTTTAATTTGAATAG
17033754 TGAT
1 TGAT
17033758 CATAAATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 6 0.14
26 13 0.31
29 17 0.40
30 6 0.14
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (29 bp):
TGATAAATCATCACTTTTAATTTGAATAG
Found at i:17040657 original size:29 final size:29
Alignment explanation
Indices: 17040624--17040714 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
17040614 TGAACCTATT
17040624 AAAGGATAATCTTTGTGGCAGAACTCTGG
1 AAAGGATAATCTTTGTGGCAGAACTCTGG
* *
17040653 AAAGG-TAAGTCTTTGTGG-TGAAC-CTGTT
1 AAAGGATAA-TCTTTGTGGCAGAACTCTG-G
*** *
17040681 AAAGGATTGCCTTTGTGGCAAAACTCTGG
1 AAAGGATAATCTTTGTGGCAGAACTCTGG
17040710 AAAGG
1 AAAGG
17040715 TAAGGTTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.06
28 20 0.41
29 23 0.47
30 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAGGATAATCTTTGTGGCAGAACTCTGG
Found at i:17040685 original size:28 final size:28
Alignment explanation
Indices: 17040596--17040685 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
17040586 AAAACTCTAG
* * *
17040596 AAAGGTAAGTTTTTATGGTGAACCTATT
1 AAAGGTAAGTCTTTGTGGTGAACCTGTT
* *
17040624 AAAGGATAA-TCTTTGTGGCAGAACTCTG-G
1 AAAGG-TAAGTCTTTGTGG-TGAAC-CTGTT
17040653 AAAGGTAAGTCTTTGTGGTGAACCTGTT
1 AAAGGTAAGTCTTTGTGGTGAACCTGTT
17040681 AAAGG
1 AAAGG
17040686 ATTGCCTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.06
28 24 0.48
29 21 0.42
30 2 0.04
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAGGTAAGTCTTTGTGGTGAACCTGTT
Found at i:17040742 original size:57 final size:57
Alignment explanation
Indices: 17040577--17040755 Score: 218
Period size: 57 Copynumber: 3.1 Consensus size: 57
17040567 TTAAGGACGT
* * * * **
17040577 CTTTGTGGCAAAACTCTAGAAAGGTAAGTTTTTATGGTGAACCTATTAAAGGATAAT
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGGTTTTGTGGTGAACCTGTTAAAGGATAGC
* *
17040634 CTTTGTGGCAGAACTCTGGAAAGGTAA-GTCTTTGTGGTGAACCTGTTAAAGGATTGC
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGGT-TTTGTGGTGAACCTGTTAAAGGATAGC
* ** *
17040691 CTTTGTGGCAAAACTCTGGAAAGGTAAGGTTTTGTGGTAAATTTGTGAAAGGA-AGGC
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGGTTTTGTGGTGAACCTGTTAAAGGATA-GC
17040748 CTTTGTGG
1 CTTTGTGG
17040756 TGATCTCTGT
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
56 1 0.01
57 102 0.97
58 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (57 bp):
CTTTGTGGCAAAACTCTGGAAAGGTAAGGTTTTGTGGTGAACCTGTTAAAGGATAGC
Found at i:17045262 original size:42 final size:41
Alignment explanation
Indices: 17045172--17045249 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
17045162 TTATGAACCA
* *
17045172 TATCCAATGGTAAACCAACCGATTGGAACAAATGTTTTAAAT
1 TATCCAATGGTAAACCAACCAATTGGAAC-AATCTTTTAAAT
17045214 TATCCAATGGTAAACCAACCAATTGGAAC-ATCTTTT
1 TATCCAATGGTAAACCAACCAATTGGAACAATCTTTT
17045250 TCATTAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 6 0.18
42 28 0.82
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (41 bp):
TATCCAATGGTAAACCAACCAATTGGAACAATCTTTTAAAT
Found at i:17046909 original size:13 final size:13
Alignment explanation
Indices: 17046890--17046918 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17046880 AGTATTCTAG
17046890 CTTTTTTT-TTTT
1 CTTTTTTTCTTTT
17046902 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
17046915 CTTT
1 CTTT
17046919 ACTTTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
CTTTTTTTCTTTT
Found at i:17047291 original size:153 final size:154
Alignment explanation
Indices: 17047115--17047394 Score: 465
Period size: 154 Copynumber: 1.8 Consensus size: 154
17047105 TAAAAAAACT
* *
17047115 GAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTTAGTCATATTAAAGGAAAATTTTAA-ATT
1 GAAAGATTAGATTTTTAAAATAAAAATATG-TTTTTTAGTCATATTAAAGGAAAAGTTTAATATT
* *
17047179 CTTAAAAC-AAAGTTTTCATCTTTTTCAACTATTTCGAAATAAAGTTTTTATTTTTAAGAAAAAT
65 CTTAAAACTAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAAAT
17047243 AACGATTTTTTAAATAAAAAATAGA
130 AACGATTTTTTAAATAAAAAATAGA
* * *
17047268 GAAAGATTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAGTTTAATTTTT
1 GAAAGATTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAGTTTAATATTC
*
17047333 TTTAAACTAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAA
66 TTAAAACTAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAA
17047395 GTAGTAATTT
Statistics
Matches: 117, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
152 28 0.24
153 37 0.32
154 52 0.44
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (154 bp):
GAAAGATTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAGTTTAATATTC
TTAAAACTAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAAATA
ACGATTTTTTAAATAAAAAATAGA
Found at i:17048339 original size:27 final size:27
Alignment explanation
Indices: 17048309--17048370 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
17048299 TAAGTAGGTG
*
17048309 TTACATTTTAATGAAACCATAAGGTTT
1 TTACATTTTAATAAAACCATAAGGTTT
*
17048336 TTACATTTTAATAAAACCTTAAGGTTT
1 TTACATTTTAATAAAACCATAAGGTTT
17048363 TTACATTT
1 TTACATTT
17048371 GAATTTAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.45
Consensus pattern (27 bp):
TTACATTTTAATAAAACCATAAGGTTT
Found at i:17052914 original size:32 final size:32
Alignment explanation
Indices: 17052872--17052946 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
17052862 TTCGGGCTCG
*
17052872 TTCTCAAGCTC-AGTCTTTTTCGACCTCAAATT
1 TTCTCAAGCTCAAGTCCTTTTCGA-CTCAAATT
* * *
17052904 TTCTCTAGCTCAAGTCCTTTTGGACTCAGATT
1 TTCTCAAGCTCAAGTCCTTTTCGACTCAAATT
* *
17052936 TTTTCGAGCTC
1 TTCTCAAGCTC
17052947 TGATTTTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.41
Consensus pattern (32 bp):
TTCTCAAGCTCAAGTCCTTTTCGACTCAAATT
Found at i:17054284 original size:108 final size:109
Alignment explanation
Indices: 17054093--17054289 Score: 272
Period size: 108 Copynumber: 1.8 Consensus size: 109
17054083 ATAGAGGTGT
* * *
17054093 CATGGGTTTCAACCACATGGGCTTACACATAATTTCATGTCGTGATCTGCCAGTCCAGTTTACAT
1 CATGGGTTTCAACCACATGGACTTACACAT-ACTTCATGTCGTGATCTGCCAGTCCAATTTACAT
* *
17054158 ATTACCGAAGGCATCACCAGGAGTATTCATTTTATCATATCATGC
65 ATCACCGAAGGCAACACCAGGAGTATTCATTTTATCATATCATGC
* *
17054203 CATGGGTTTCAACCACATGGACTTACACAT-CTTCATGTCGTGATCTGTCAGTCCAATCTT-CTT
1 CATGGGTTTCAACCACATGGACTTACACATACTTCATGTCGTGATCTGCCAGTCCAAT-TTACAT
* * *
17054266 CTCACTGAAGGCAACACCATGAGT
65 ATCACCGAAGGCAACACCAGGAGT
17054290 GTTTTTAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
108 45 0.59
109 2 0.03
110 29 0.38
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (109 bp):
CATGGGTTTCAACCACATGGACTTACACATACTTCATGTCGTGATCTGCCAGTCCAATTTACATA
TCACCGAAGGCAACACCAGGAGTATTCATTTTATCATATCATGC
Found at i:17054305 original size:108 final size:108
Alignment explanation
Indices: 17054093--17054317 Score: 258
Period size: 108 Copynumber: 2.1 Consensus size: 108
17054083 ATAGAGGTGT
* * *
17054093 CATGGGTTTCAACCACATGGGCTTACACATAATTTCATGTCGTGATCTGCCAGTCCAGTTTACAT
1 CATGGGTTTCAACCACATGGACTTACACAT-ACTTCATGTCGTGATCTGCCAGTCCAATTTACAT
* * * *
17054158 ATTACCGAAGGCATCACCAGGAGTATTCATTTTATCATATCATGC
65 ATCACCGAAGGCAACACCAGGAGTATT-ATTTTACCATATAATGC
* *
17054203 CATGGGTTTCAACCACATGGACTTACACAT-CTTCATGTCGTGATCTGTCAGTCCAATCTT-CTT
1 CATGGGTTTCAACCACATGGACTTACACATACTTCATGTCGTGATCTGCCAGTCCAAT-TTACAT
* * * *
17054266 CTCACTGAAGGCAACACCATGAGTGTT-TTTAATACCATATAATGC
65 ATCACCGAAGGCAACACCAGGAGTATTATTT--TACCATATAATGC
*
17054311 CAAGGGT
1 CATGGGT
17054318 CTTAGTGGAA
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
106 3 0.03
108 64 0.65
109 2 0.02
110 29 0.30
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (108 bp):
CATGGGTTTCAACCACATGGACTTACACATACTTCATGTCGTGATCTGCCAGTCCAATTTACATA
TCACCGAAGGCAACACCAGGAGTATTATTTTACCATATAATGC
Found at i:17059900 original size:13 final size:13
Alignment explanation
Indices: 17059882--17059909 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17059872 CTTGTACAAG
17059882 TAAACTTCATAAA
1 TAAACTTCATAAA
17059895 TAAACTTCATAAA
1 TAAACTTCATAAA
17059908 TA
1 TA
17059910 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTCATAAA
Found at i:17060480 original size:34 final size:35
Alignment explanation
Indices: 17060422--17060488 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
17060412 CAAACACCAG
* * *
17060422 AAAATATTTTTCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
17060457 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17060489 ACAGACCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17065240 original size:22 final size:22
Alignment explanation
Indices: 17065215--17065257 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17065205 AAAATGACCT
17065215 CTTC-AGGCTTTAATGTCGCGAC
1 CTTCTAGGC-TTAATGTCGCGAC
* *
17065237 CTTCTATGCTTGATGTCGCGA
1 CTTCTAGGCTTAATGTCGCGA
17065258 TTTCCTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (22 bp):
CTTCTAGGCTTAATGTCGCGAC
Found at i:17067350 original size:68 final size:68
Alignment explanation
Indices: 17067054--17067333 Score: 310
Period size: 68 Copynumber: 4.1 Consensus size: 68
17067044 GAGGTATAAG
* ** * * *
17067054 GTGTAAGACCATAGCTCGATTATGGTAACCAATAGAGTCCGCTAGGACATTAAACATGGGGTTAA
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACAAGGACATTAAACATGGGGTTAC
17067119 AAA
66 AAA
* * * * * *
17067122 GTGAAAGGCCATAGCTAGACTATGACAACCAATAGAGTCCACAAGGACCTTAAATATTGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACAAGGACATTAAACATGGGGTTAC
17067187 AAA
66 AAA
** * ** ** * * *
17067190 GTGTAAGATTAAAGCTCGACTACAACAACCAATAGAGTTTACCAGGACAGTAAACATGAGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACAAGGACATTAAACATGGGGTTAC
*
17067255 AAT
66 AAA
**
17067258 GTGTAAGACCATAGCTC-AGCTATGACAACCAATAGAGTCTGCAAGGACATTAAACATGGGGTTA
1 GTGTAAGACCATAGCTCGA-CTATGACAACCAATAGAGTCCACAAGGACATTAAACATGGGGTTA
*
17067322 CAAG
65 CAAA
17067326 GTGTAAGA
1 GTGTAAGA
17067334 TTATAGGTTG
Statistics
Matches: 171, Mismatches: 40, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
67 1 0.01
68 170 0.99
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACAAGGACATTAAACATGGGGTTAC
AAA
Found at i:17069053 original size:35 final size:35
Alignment explanation
Indices: 17069014--17069084 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
17069004 TCTAGGATCA
*
17069014 CATATCTCTGAAGATCACCTTCCATATCTGCCAAG
1 CATATCTCTGAAGATCACCTTCCATATCTACCAAG
* * *
17069049 CATATCTTTGAAGATCACTTTCCATATTTACCAAG
1 CATATCTCTGAAGATCACCTTCCATATCTACCAAG
17069084 C
1 C
17069085 TCCGGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (35 bp):
CATATCTCTGAAGATCACCTTCCATATCTACCAAG
Found at i:17069145 original size:22 final size:22
Alignment explanation
Indices: 17069113--17069166 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
17069103 ATCTCTCCAA
*
17069113 GCAATGAACCAGTCCGATTGGG
1 GCAATGGACCAGTCCGATTGGG
17069135 GCAATGGACCAGTCCGATTGGG
1 GCAATGGACCAGTCCGATTGGG
* *
17069157 CCAATTGACC
1 GCAATGGACC
17069167 TCCCTCGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (22 bp):
GCAATGGACCAGTCCGATTGGG
Found at i:17074199 original size:35 final size:35
Alignment explanation
Indices: 17074129--17074199 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
17074119 TATAGGATCA
* **
17074129 CATATCTCTGAAGATCACCTTCCATATTTGTCAAG
1 CATATCTCTGAAGACCACCTTCCATATTTACCAAG
* *
17074164 CATATCTTTGAAGACCACTTTCCATATTTACCAAG
1 CATATCTCTGAAGACCACCTTCCATATTTACCAAG
17074199 C
1 C
17074200 TCCGGAGACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (35 bp):
CATATCTCTGAAGACCACCTTCCATATTTACCAAG
Found at i:17074916 original size:22 final size:22
Alignment explanation
Indices: 17074888--17074968 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
17074878 GATACATAAA
17074888 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
17074910 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
* * * **
17074932 AACTAAACCCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
17074954 TACTAAGCTCTCATG
1 TACTAAGCTCTCATG
17074969 GATTCCTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:17078857 original size:68 final size:67
Alignment explanation
Indices: 17078679--17079035 Score: 292
Period size: 68 Copynumber: 5.3 Consensus size: 67
17078669 TCAAAAGTGA
* * * * * * * *
17078679 TACAATGTGTAAAACCATAGCTCGACTATGACAACCAATAGAGTCCACCAGGACATTAAACATGG
1 TACAAGGTGTAAGACCATAGCTCAACTAAG-CAACCAATAGAGTCCGCTAGGACATTAAATATAG
17078744 GGT
65 GGT
* * * ** *
17078747 TAAAAGGT-TTA-CCCATAGCTTTACT-AGACAACCAATAGAGTCCGCTAGGACATTCAATATAG
1 TACAAGGTGTAAGACCATAGCTCAACTAAG-CAACCAATAGAGTCCGCTAGGACATTAAATATAG
*
17078809 GTT
65 GGT
* * * *
17078812 TACAGGGTGTAAGGCCATAGCTCAACTATAGCAACCAATAAAGTCCG-TCATGACATTAAACT-T
1 TACAAGGTGTAAGACCATAGCTCAACTA-AGCAACCAATAGAGTCCGCT-AGGACATTAAA-TAT
17078875 AGGGT
63 AGGGT
* * ** * ** * *
17078880 TACAAGATGTAAAACCATAGCTCAGTTACAACAAGAAATAGAGTTCGTTAGGACATTAAATATAG
1 TACAAGGTGTAAGACCATAGCTCAACTA-AGCAACCAATAGAGTCCGCTAGGACATTAAATATAG
17078945 GGT
65 GGT
** * * * * *
17078948 TACAAGGTGTAAGACCATAGCTTGACTACGACAACCAATAGAGTCCGCTAGGATATTCAACATGG
1 TACAAGGTGTAAGACCATAGCTCAACTAAG-CAACCAATAGAGTCCGCTAGGACATTAAATATAG
17079013 GGT
65 GGT
*
17079016 TACAAGGTGTAAGGCCATAG
1 TACAAGGTGTAAGACCATAG
17079036 GTCGATTATG
Statistics
Matches: 227, Mismatches: 53, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
65 39 0.17
66 13 0.06
67 15 0.07
68 156 0.69
69 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (67 bp):
TACAAGGTGTAAGACCATAGCTCAACTAAGCAACCAATAGAGTCCGCTAGGACATTAAATATAGG
GT
Found at i:17079027 original size:136 final size:134
Alignment explanation
Indices: 17078679--17079027 Score: 375
Period size: 136 Copynumber: 2.6 Consensus size: 134
17078669 TCAAAAGTGA
* * * *
17078679 TACAATGTGTAAAACCATAGCTCGACTATGACAACCAATAGAGTCCACCAGGACATTAAACATGG
1 TACAAGGTGTAAGACCATAGCTCGACTA-GACAACCAATAGAGTCCGCTAGGACATTAAACATGG
* * * * *
17078744 GGTTAAAAGGT-T-TACCCATAGCTTTACTAGACAACCAATAGAGTCCGCTAGGACATTCAATAT
65 GGTTACAAGGTGTAAAACCATAGCTTTACTAGACAACAAATAGAGTCCGCTAGGACATTAAATAT
*
17078807 AGGTT
130 AGGGT
* * * * * * * *
17078812 TACAGGGTGTAAGGCCATAGCTCAACTATAGCAACCAATAAAGTCCG-TCATGACATTAAACTTA
1 TACAAGGTGTAAGACCATAGCTCGACTAGA-CAACCAATAGAGTCCGCT-AGGACATTAAACATG
* * * *
17078876 GGGTTACAAGATGTAAAACCATAGCTCAGTTAC-A-ACAAGAAATAGAGTTCGTTAGGACATTAA
64 GGGTTACAAGGTGTAAAACCATAGCT---TTACTAGACAACAAATAGAGTCCGCTAGGACATTAA
17078939 ATATAGGGT
126 ATATAGGGT
* * *
17078948 TACAAGGTGTAAGACCATAGCTTGACTACGACAACCAATAGAGTCCGCTAGGATATTCAACATGG
1 TACAAGGTGTAAGACCATAGCTCGACTA-GACAACCAATAGAGTCCGCTAGGACATTAAACATGG
17079013 GGTTACAAGGTGTAA
65 GGTTACAAGGTGTAA
17079028 GGCCATAGGT
Statistics
Matches: 173, Mismatches: 34, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
132 1 0.01
133 59 0.34
134 1 0.01
135 9 0.05
136 96 0.55
137 3 0.02
138 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (134 bp):
TACAAGGTGTAAGACCATAGCTCGACTAGACAACCAATAGAGTCCGCTAGGACATTAAACATGGG
GTTACAAGGTGTAAAACCATAGCTTTACTAGACAACAAATAGAGTCCGCTAGGACATTAAATATA
GGGT
Found at i:17081894 original size:21 final size:21
Alignment explanation
Indices: 17081854--17081916 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
17081844 TCGGGGCTAC
* *
17081854 ATGTTTAGAGACATTGGCCTGT
1 ATGTTCAGAGACA-TAGCCTGT
*
17081876 ATG-TCAGAGACATAAGCCTAT
1 ATGTTCAGAGACAT-AGCCTGT
17081897 ATGTTTC-GAGACATAGCCTG
1 ATG-TTCAGAGACATAGCCTG
17081917 CCAACAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 10 0.29
23 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
ATGTTCAGAGACATAGCCTGT
Found at i:17089737 original size:18 final size:18
Alignment explanation
Indices: 17089702--17089734 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17089692 GAATGATGGT
17089702 TTTAACTATTATTTATAA
1 TTTAACTATTATTTATAA
17089720 TTTAA-TATT-TTTATA
1 TTTAACTATTATTTATA
17089735 TAACATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAACTATTATTTATAA
Found at i:17089783 original size:23 final size:21
Alignment explanation
Indices: 17089731--17089793 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
17089721 TTAATATTTT
17089731 TATATAACATTATTA-TT-AAA
1 TATAT-ACATTATTATTTCAAA
17089751 TATATA-ATTACTTATTTCAAA
1 TATATACATTA-TTATTTCAAA
17089772 TATATATCATTATATATTTCAA
1 TATATA-CATTAT-TATTTCAA
17089794 CTTGTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 7 0.19
21 9 0.24
22 1 0.03
23 12 0.32
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATACATTATTATTTCAAA
Found at i:17090400 original size:21 final size:21
Alignment explanation
Indices: 17090361--17090401 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17090351 GTTTAGGGGC
*
17090361 AGAGGTGATGGAGGGAGAGGG
1 AGAGGTGATGGAGGAAGAGGG
* *
17090382 AGAGGTGGTGGTGGAAGAGG
1 AGAGGTGATGGAGGAAGAGG
17090402 TGGCGATAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.61, T:0.12
Consensus pattern (21 bp):
AGAGGTGATGGAGGAAGAGGG
Found at i:17090477 original size:15 final size:15
Alignment explanation
Indices: 17090457--17090485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17090447 TGGTGGCCGC
17090457 GGTGGAGGAAGAGGG
1 GGTGGAGGAAGAGGG
17090472 GGTGGAGGAAGAGG
1 GGTGGAGGAAGAGG
17090486 TGGAATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.66, T:0.07
Consensus pattern (15 bp):
GGTGGAGGAAGAGGG
Found at i:17110650 original size:45 final size:45
Alignment explanation
Indices: 17110578--17110687 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 45
17110568 AAAAAATACC
* * *
17110578 AAAAAGGAAGTAAAGTGAAAAAACAACCACATCCATGTCTAGACA
1 AAAAAGGAAGCAAAGTGGAAAAACAACCACATCCATGTCTAAACA
* * *
17110623 AAAAAGGAAGCAATGTGGAAAAGCAACCACATTCATGTCTAAACA
1 AAAAAGGAAGCAAAGTGGAAAAACAACCACATCCATGTCTAAACA
*
17110668 AAAAAGGAAGC-ACGTGGAAA
1 AAAAAGGAAGCAAAGTGGAAA
17110688 CAATCACATC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 8 0.14
45 50 0.86
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (45 bp):
AAAAAGGAAGCAAAGTGGAAAAACAACCACATCCATGTCTAAACA
Found at i:17111399 original size:27 final size:27
Alignment explanation
Indices: 17111346--17111399 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
17111336 GAAAGGTGTG
*
17111346 GAGAAAGCGAATGTGAAAGAGGCGGTA
1 GAGAAAGCGAATGTGAAAGAGGAGGTA
17111373 GAGAAAGCGAA-G-GAGAAGAGGAAGGTA
1 GAGAAAGCGAATGTGA-AAGAGG-AGGTA
17111400 AATTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 7 0.29
27 15 0.62
ACGTcount: A:0.44, C:0.06, G:0.43, T:0.07
Consensus pattern (27 bp):
GAGAAAGCGAATGTGAAAGAGGAGGTA
Found at i:17113522 original size:20 final size:19
Alignment explanation
Indices: 17113492--17113539 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
17113482 TCTCTCACAA
17113492 CAAAA-TTATAAAAAAATT
1 CAAAATTTATAAAAAAATT
*
17113510 CAAATATTTAT-AAAAATTT
1 CAAA-ATTTATAAAAAAATT
17113529 CAAAATTTATA
1 CAAAATTTATA
17113540 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
CAAAATTTATAAAAAAATT
Found at i:17113974 original size:26 final size:26
Alignment explanation
Indices: 17113945--17114003 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
17113935 ATACGTATTT
* *
17113945 AATTATTTATATTTAGTC-ATATAATA
1 AATTATTTA-ATATAATCAATATAATA
*
17113971 AATTA-TTAATATAATCAATATAATT
1 AATTATTTAATATAATCAATATAATA
17113996 AATTATTT
1 AATTATTT
17114004 TTAATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.21
25 15 0.54
26 7 0.25
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (26 bp):
AATTATTTAATATAATCAATATAATA
Found at i:17117236 original size:3 final size:3
Alignment explanation
Indices: 17117228--17117275 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
17117218 CTCCGCTCTC
17117228 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17117276 GACACCTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17118174 original size:19 final size:19
Alignment explanation
Indices: 17118150--17118189 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17118140 TTGAAACCAC
*
17118150 TGCCCACCATAATCAAATT
1 TGCCCACCACAATCAAATT
*
17118169 TGCCCACCGCAATCAAATT
1 TGCCCACCACAATCAAATT
17118188 TG
1 TG
17118190 TTATTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.25
Consensus pattern (19 bp):
TGCCCACCACAATCAAATT
Found at i:17120322 original size:53 final size:55
Alignment explanation
Indices: 17120153--17120332 Score: 181
Period size: 55 Copynumber: 3.3 Consensus size: 55
17120143 CCCTTCAAAC
** * * *
17120153 CCTTTTACTTTCCTCC-CAAAAAAATTA-TTTCCCTCAAACTGC-CATAACTATTTTT
1 CCTTTTACTTTCC-CCTCAAAAATTTTACTTTCCCCCAAAC-CCTCAAAACT-TTTTT
*
17120208 CCTTTTACTTTCCCCCTTAAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTT
1 CCTTTTACTTT-CCCCTCAAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTT
* ***
17120264 TCTTTTACTTTCCCCTCAAAAATTTTAC-TTCTTTCAAA-CCTCAAAACTTTTTT
1 CCTTTTACTTTCCCCTCAAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTT
**
17120317 CCTTTTGTTTTCCCCT
1 CCTTTTACTTTCCCCT
17120333 AAACCCCCCA
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
53 28 0.26
54 7 0.07
55 29 0.27
56 26 0.24
57 17 0.16
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.44
Consensus pattern (55 bp):
CCTTTTACTTTCCCCTCAAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTT
Found at i:17120726 original size:18 final size:19
Alignment explanation
Indices: 17120705--17120740 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17120695 GATGAAAGTT
17120705 AATA-ACAAATTTGATTAC
1 AATAGACAAATTTGATTAC
*
17120723 AATAGGCAAATTTGATTA
1 AATAGACAAATTTGATTA
17120741 TTGTGGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (19 bp):
AATAGACAAATTTGATTAC
Found at i:17125453 original size:25 final size:26
Alignment explanation
Indices: 17125425--17125476 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
17125415 AAGTTGTAAA
17125425 TAAAAAAATATC-TCTAGA-AATTTTC
1 TAAAAAAATATCTTC-AGAGAATTTTC
* *
17125450 TAAAATAATCTCTTCAGAGAATTTTC
1 TAAAAAAATATCTTCAGAGAATTTTC
17125476 T
1 T
17125477 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (26 bp):
TAAAAAAATATCTTCAGAGAATTTTC
Found at i:17125610 original size:15 final size:16
Alignment explanation
Indices: 17125592--17125621 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17125582 TTAATATTAA
17125592 ATTAAGAT-AATATTT
1 ATTAAGATAAATATTT
17125607 ATTAAGATAAATATT
1 ATTAAGATAAATATT
17125622 AAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTAAGATAAATATTT
Found at i:17125756 original size:68 final size:65
Alignment explanation
Indices: 17125575--17125771 Score: 192
Period size: 62 Copynumber: 3.0 Consensus size: 65
17125565 GATTAAATTT
* *
17125575 AATCACTTTAATATTAAATTAAGATAATATTTATTAAGATAAATATTAAATTAAATTTAATATT-
1 AATCACTTTAAT-TTAAATTAAAAAAATATTTATTAAGATAAATATTAAATTAAATTTAATATTA
17125639 A
65 A
* * * * *
17125640 AAT--C-TT-A-TTAAAATAATAGAATATTTATCTACAAGAAAAACATTAAATTAAATTTAATAT
1 AATCACTTTAATTTAAATTAAAAAAATATTTAT-T--AAGATAAATATTAAATTAAATTTAATAT
17125700 TAA
63 TAA
* *
17125703 GATGATCACTTTAATTTTAAATTAAAAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATA
1 -A--ATCACTTTAA-TTTAAATTAAAAAAATATTTATTAAGATAAATATTAAATTAAATTTAATA
17125767 TTAA
62 TTAA
17125771 A
1 A
17125772 CTATTAAAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
59 18 0.17
60 1 0.01
61 1 0.01
62 29 0.27
63 2 0.02
64 1 0.01
65 3 0.03
66 2 0.02
67 1 0.01
68 29 0.27
69 2 0.02
70 2 0.02
71 3 0.03
72 13 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (65 bp):
AATCACTTTAATTTAAATTAAAAAAATATTTATTAAGATAAATATTAAATTAAATTTAATATTAA
Found at i:17125759 original size:37 final size:36
Alignment explanation
Indices: 17125713--17125789 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
17125703 GATGATCACT
* *
17125713 TTAATTTTAAATTAA-AAAAATACTATTAAGATAAATA
1 TTAAATTTAAATTAATAAAAA-ACTATTAAAAT-AATA
* **
17125750 TTAAATTTAATTTAATATTAAACTATTAAAATAATA
1 TTAAATTTAAATTAATAAAAAACTATTAAAATAATA
17125786 TTAA
1 TTAA
17125790 GACGAACTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 8 0.24
37 23 0.68
38 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
TTAAATTTAAATTAATAAAAAACTATTAAAATAATA
Found at i:17126732 original size:23 final size:23
Alignment explanation
Indices: 17126702--17126767 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
17126692 CAATGAGACA
17126702 ATACAAAATTTGCCACAAAGGCC
1 ATACAAAATTTGCCACAAAGGCC
* *
17126725 ATACAAAATATGCCACAAAGGCT
1 ATACAAAATTTGCCACAAAGGCC
** *
17126748 ATACGGAATTCGCCACAAAG
1 ATACAAAATTTGCCACAAAG
17126768 ACTTTGCAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (23 bp):
ATACAAAATTTGCCACAAAGGCC
Found at i:17128451 original size:24 final size:25
Alignment explanation
Indices: 17128424--17128490 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
17128414 GTTATTAGGG
* *
17128424 TTATCAATTC-CAGCTCTTATGAGC
1 TTATCAATACTCAGCTCGTATGAGC
*
17128448 TTATCGATACTCAGCTCGTATGAGC
1 TTATCAATACTCAGCTCGTATGAGC
* * *
17128473 TTACCATTATTCAGCTCG
1 TTATCAATACTCAGCTCG
17128491 GAGAAGTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 8 0.23
25 27 0.77
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (25 bp):
TTATCAATACTCAGCTCGTATGAGC
Found at i:17128486 original size:25 final size:25
Alignment explanation
Indices: 17128434--17128546 Score: 81
Period size: 25 Copynumber: 4.6 Consensus size: 25
17128424 TTATCAATTC
* * *
17128434 CAGCTCTTATGAGCTTATCGA-TACT
1 CAGCTCGTATGAGCTTA-CCATTATT
17128459 CAGCTCGTATGAGCTTACCATTATT
1 CAGCTCGTATGAGCTTACCATTATT
* * *
17128484 CAGCTCGGA-GAAGTTTACCGTTATT
1 CAGCTCGTATG-AGCTTACCATTATT
* * * *
17128509 TAGCTCGGAGGAGCTTACC-TTTTAT
1 CAGCTCGTATGAGCTTACCATTAT-T
17128534 CA-CTCGTATGAGC
1 CAGCTCGTATGAGC
17128547 ATACATGTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
24 15 0.21
25 56 0.78
26 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCATTATT
Found at i:17128935 original size:25 final size:25
Alignment explanation
Indices: 17128901--17128953 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
17128891 TTCTGTGTTA
17128901 TACGAACTTACTAAGCTTAATTGCT
1 TACGAACTTACTAAGCTTAATTGCT
17128926 TACGAACTTACTAAGCTTAATTGCT
1 TACGAACTTACTAAGCTTAATTGCT
17128951 TAC
1 TAC
17128954 TCTGTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (25 bp):
TACGAACTTACTAAGCTTAATTGCT
Found at i:17138699 original size:16 final size:17
Alignment explanation
Indices: 17138678--17138715 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17138668 TAATTTTTTT
*
17138678 AAAAATAATTT-TACAA
1 AAAAATAATTTGAACAA
*
17138694 AAAAATTATTTGAACAA
1 AAAAATAATTTGAACAA
17138711 AAAAA
1 AAAAA
17138716 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATAATTTGAACAA
Found at i:17140432 original size:21 final size:21
Alignment explanation
Indices: 17140388--17140458 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
17140378 ATAACAGATT
* * *
17140388 CAGATCATGCTTAACA-AATA
1 CAGATCATACTTATCATATTA
17140408 CAGATCATACTTATCATATTA
1 CAGATCATACTTATCATATTA
** * *
17140429 CAGATTGTACTTATCTTATCA
1 CAGATCATACTTATCATATTA
17140450 CAGATCATA
1 CAGATCATA
17140459 TTGGGCATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (21 bp):
CAGATCATACTTATCATATTA
Found at i:17141216 original size:41 final size:41
Alignment explanation
Indices: 17141171--17141253 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
17141161 AGTCTAGCAT
* *
17141171 ATGGCTTGGCACACG-TTCATATGTCACACACGACTTACCAC
1 ATGGCATGGCACACGCCT-ATATGTCACACACGACTTACCAC
* *
17141212 ATGGCATGTCACACGCCTATGTGTCACACACGACTTACCAC
1 ATGGCATGGCACACGCCTATATGTCACACACGACTTACCAC
17141253 A
1 A
17141254 CAGCCATGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (41 bp):
ATGGCATGGCACACGCCTATATGTCACACACGACTTACCAC
Found at i:17152433 original size:43 final size:43
Alignment explanation
Indices: 17152283--17152442 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 43
17152273 TTGTACAACA
* * * *
17152283 CCAACGTCCCAGACGTGGTCTTACATGTAAACA-TAGATCGATG
1 CCAACGTCCCAGACATGGTCTTACACGAAAACACAAG-TCGATG
* *
17152326 CC-ACTGTCCCAGACAGGGTCTTACACGAAAATACAAGTCGATG
1 CCAAC-GTCCCAGACATGGTCTTACACGAAAACACAAGTCGATG
* * * *
17152369 CCAACATTCCAGACGTGGTCTTACATGAAAACACAAGTCGATG
1 CCAACGTCCCAGACATGGTCTTACACGAAAACACAAGTCGATG
* *
17152412 CCAACGTCCCAGACATTGTCTTGCACGAAAA
1 CCAACGTCCCAGACATGGTCTTACACGAAAA
17152443 AATTTATCAA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 2 0.02
43 90 0.94
44 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (43 bp):
CCAACGTCCCAGACATGGTCTTACACGAAAACACAAGTCGATG
Found at i:17165679 original size:40 final size:40
Alignment explanation
Indices: 17165627--17165737 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
17165617 TAGGCACAAA
* *
17165627 ACATTGTCGGTTTATCCGACTAGTGCTGGGCACACATTTG
1 ACATCGTCGGTTTATTCGACTAGTGCTGGGCACACATTTG
*
17165667 ACATCGTCGGTTTATTCGACTAGTGTTGGGCACACATTTG
1 ACATCGTCGGTTTATTCGACTAGTGCTGGGCACACATTTG
*
17165707 ACATCGTCGGTTTATTCGACTACTGCTGGGC
1 ACATCGTCGGTTTATTCGACTAGTGCTGGGC
17165738 GCAAGATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (40 bp):
ACATCGTCGGTTTATTCGACTAGTGCTGGGCACACATTTG
Found at i:17168778 original size:2 final size:2
Alignment explanation
Indices: 17168771--17168806 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17168761 TTGAGAAATC
17168771 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17168807 TTGTGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17170014 original size:33 final size:33
Alignment explanation
Indices: 17169966--17170048 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
17169956 TCCAAGAATT
17169966 ATTTATTGGTGGGTTTATTAGAGTCTTTAATTGA
1 ATTTATT-GTGGGTTTATTAGAGTCTTTAATTGA
*
17170000 ATTTATTGTGGGTTTATTAGAGTCTTTACTTGA
1 ATTTATTGTGGGTTTATTAGAGTCTTTAATTGA
*
17170033 ATTTATTG-GGATTTAT
1 ATTTATTGTGGGTTTAT
17170049 ATATCAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 7 0.15
33 33 0.70
34 7 0.15
ACGTcount: A:0.23, C:0.04, G:0.22, T:0.52
Consensus pattern (33 bp):
ATTTATTGTGGGTTTATTAGAGTCTTTAATTGA
Found at i:17185750 original size:19 final size:20
Alignment explanation
Indices: 17185726--17185768 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
17185716 TAGATTTATT
17185726 CTTAATTAATC-TGAATTAA
1 CTTAATTAATCATGAATTAA
*
17185745 CTTAATTAATCATTAATTAA
1 CTTAATTAATCATGAATTAA
17185765 -TTAA
1 CTTAA
17185769 ACTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (20 bp):
CTTAATTAATCATGAATTAA
Done.