Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 131 of 325
Found at i:39561521 original size:94 final size:94
Alignment explanation
Indices: 39561352--39561525 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 94
39561342 GTTATTGTGG
* *
39561352 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACTATGTC
1 GCTAGTGTAAGACACGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
39561417 TGGGACATGGCATCGGCATCGAAACGAGT
66 TGGGACATGGCATCGGCATCGAAACGAGT
* * * *
39561446 GCTAGTGTAAGACACGTCTGGTACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGT
1 GCTAGTGTAAGACACGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGACCATGT
*
39561510 CCT-GGATATGGCATCG
65 -CTGGGACATGGCATCG
39561526 ACTTGAGATA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
94 68 0.96
95 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACACGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCGGCATCGAAACGAGT
Found at i:39561559 original size:94 final size:93
Alignment explanation
Indices: 39561355--39561571 Score: 244
Period size: 94 Copynumber: 2.3 Consensus size: 93
39561345 ATTGTGGGCT
*
39561355 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACTATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
* *
39561420 GACATGGCATCGGCATCGAAACGAGTGCT
66 GACATGGCATCGACATCGAAACGAG-GCA
* * * * *
39561449 AGTGTAAGACACGTCTGGTACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGTCCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGACCATGT-CT
* * *
39561513 -GGATATGGCATCGAC-TTGAGATATGA-GCA
64 GGGACATGGCATCGACATCGA-A-ACGAGGCA
39561542 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
39561572 AACATTCTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
93 14 0.13
94 79 0.76
95 11 0.11
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATCGAAACGAGGCA
Found at i:39567276 original size:30 final size:30
Alignment explanation
Indices: 39567242--39567302 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39567232 TCCTTAACTC
39567242 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39567272 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39567302 A
1 A
39567303 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39574229 original size:21 final size:20
Alignment explanation
Indices: 39574191--39574229 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39574181 TCAGATTTTC
*
39574191 TTGAAATAAAAATTTTGTTT
1 TTGAAATAAAAATGTTGTTT
*
39574211 TTGAAGTACAAAATGTTGT
1 TTGAAATA-AAAATGTTGT
39574230 CTGAACCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGAAATAAAAATGTTGTTT
Found at i:39587036 original size:48 final size:48
Alignment explanation
Indices: 39586965--39587187 Score: 257
Period size: 48 Copynumber: 4.6 Consensus size: 48
39586955 GTGAATTTTT
* * * *
39586965 CGATGCCATGTCCTAGACATGGTCTGACACTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * ** * * * *
39587013 CGATGCCATGTCCCAGACGTGGTCTTACACTAGCTCTTGTCTCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * *
39587061 CGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCCTATGGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* ** *
39587109 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAGGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
*
39587157 CGATTCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
39587188 AGCACACACA
Statistics
Matches: 147, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 147 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
Found at i:39589993 original size:3 final size:3
Alignment explanation
Indices: 39589987--39590011 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39589977 ATGATGAAAT
39589987 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
39590012 AAACAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39592478 original size:47 final size:47
Alignment explanation
Indices: 39592414--39592533 Score: 231
Period size: 47 Copynumber: 2.6 Consensus size: 47
39592404 GCGAATGTCC
*
39592414 GAACTCGTTGAGTTGAGTCTGAGTTCGTGAAATGTAACTAGGCATCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCT
39592461 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCT
39592508 GAACTCGTTGAGTTGAGTCCGAGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC
39592534 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (47 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCT
Found at i:39603415 original size:71 final size:71
Alignment explanation
Indices: 39603327--39603490 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
39603317 GAGATGTATC
39603327 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39603392 AGGACA
66 AGGACA
*
39603398 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39603463 AGGACA
66 AGGACA
39603469 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39603491 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39610952 original size:71 final size:71
Alignment explanation
Indices: 39610864--39611027 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
39610854 GAGATGTATC
39610864 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39610929 AGGACA
66 AGGACA
*
39610935 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
39611000 CGGACA
66 AGGACA
39611006 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39611028 AGACAAATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39616861 original size:26 final size:26
Alignment explanation
Indices: 39616832--39616907 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
39616822 CAGTGACTGG
*
39616832 TTTGACCAACTAATTCTAATACCTAA
1 TTTGACCAACTAATTCTAATAACTAA
39616858 TTTGACCAACTAATTCTAATAACTAA
1 TTTGACCAACTAATTCTAATAACTAA
* * *
39616884 TTAGACCAACTGATTCTATTAACT
1 TTTGACCAACTAATTCTAATAACT
39616908 GTTTATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (26 bp):
TTTGACCAACTAATTCTAATAACTAA
Found at i:39619489 original size:2 final size:2
Alignment explanation
Indices: 39619467--39619512 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
39619457 CATAAAATTT
39619467 TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39619506 TA TA TA T
1 TA TA TA T
39619513 TTTACATTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:39622847 original size:18 final size:18
Alignment explanation
Indices: 39622824--39622867 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39622814 AATTTATATG
**
39622824 AAAATCCTTGAAGAATTT
1 AAAATCCTAAAAGAATTT
*
39622842 AAAATCCCAAAAGAATTT
1 AAAATCCTAAAAGAATTT
39622860 AAAATCCT
1 AAAATCCT
39622868 CGAATGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (18 bp):
AAAATCCTAAAAGAATTT
Found at i:39624987 original size:15 final size:17
Alignment explanation
Indices: 39624959--39624994 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
39624949 CACTACGAGC
39624959 AATAATATCACGAACAA
1 AATAATATCACGAACAA
39624976 AATAATA-C-CGAACAA
1 AATAATATCACGAACAA
39624991 AATA
1 AATA
39624995 CTGTGCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (17 bp):
AATAATATCACGAACAA
Found at i:39630132 original size:47 final size:45
Alignment explanation
Indices: 39630064--39630423 Score: 210
Period size: 47 Copynumber: 7.7 Consensus size: 45
39630054 GATTTGTGCA
*
39630064 CCAGTGTAAGACATGTCTGGGACATGCTTCAGCCACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACA-TATGAGAG
* * * * *
39630110 CCAGTATAAGACCATGTCTGGGACATGGCATC-GGCATTCAGACGAGGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA--CATATGAGAG
* * * * * *
39630158 CTAGTGTAAGACATGTTTGGAACATGCATCAGCCATACTATAATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACA-TATGAGAG
* * * *
39630204 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGAACAGAGATGAGTA-
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CCACATATGAG-AG
* * * *
39630252 TCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGACAGA-GATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAG-C-C-ACATATGAGAG
* * * * * * * *
39630299 CCAGTGTAAGACGA-GTTTAGGACACGCATCGGCTA-AGA-GTTGTG
1 CCAGTGTAAGAC-ATGTCTGGGACATGCATCAGCCACATATG-AGAG
* * *
39630343 CTAGTGTAAGACATGTCTGGGACATGCATCAACACGCGTATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGC-CAC--ATATGAGAG
*
39630391 CCAGTGTAAGACCATATCTGGGACATGGCATCA
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCA
39630424 ACAATGTATC
Statistics
Matches: 237, Mismatches: 54, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
43 5 0.02
44 27 0.11
45 1 0.00
46 36 0.15
47 86 0.36
48 56 0.24
49 20 0.08
50 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (45 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATATGAGAG
Found at i:39630227 original size:94 final size:92
Alignment explanation
Indices: 39630066--39630422 Score: 332
Period size: 94 Copynumber: 3.8 Consensus size: 92
39630056 TTTGTGCACC
* * * * *
39630066 AGTGTAAGACATGTCTGGGACATGCTTCAGCCACATTATGAGAGCCAGTATAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATAAGAGCCAGTGTAAGACCATGTCTGG
39630131 GACATGGCATCGGCATTCAGACGAGGGCT
66 GACATGGCATCGGCA-TCAGA-GAGGGCT
* * *
39630160 AGTGTAAGACATGTTTGGAACATGCATCAGCCATACTATAATAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATAAGAGCCAGTGTAAGACCATGTCTGG
* **
39630225 GACATGGCATCGG-AACAGAGATGAGTAT
66 GACATGGCATCGGCATCAGAGA-G-GGCT
* * * *
39630253 CAGTGTAAGACATGTCTAGGACATGCATCAGCC-TCGAC-AGAGATAGCCAGTGTAAGACGA-GT
1 -AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTATA-AGAGCCAGTGTAAGACCATGT
* * * * * *
39630315 TTAGGACA-CGCATCGGC-TAAGAGTTGTGCT
62 CTGGGACATGGCATCGGCATCAGAG-AGGGCT
* * * *
39630345 AGTGTAAGACATGTCTGGGACATGCATCAACACGCGTA-TATGAGAGCCAGTGTAAGACCATATC
1 AGTGTAAGACATGTCTGGGACATGCATC-A-GC-CATACTATAAGAGCCAGTGTAAGACCATGTC
39630409 TGGGACATGGCATC
63 TGGGACATGGCATC
39630423 AACAATGTAT
Statistics
Matches: 213, Mismatches: 35, Indels: 30
0.77 0.13 0.11
Matches are distributed among these distances:
91 29 0.14
92 23 0.11
93 26 0.12
94 115 0.54
95 20 0.09
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATAAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGGCATCAGAGAGGGCT
Found at i:39647323 original size:30 final size:30
Alignment explanation
Indices: 39647289--39647345 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
39647279 ACCTTTATAG
39647289 AAAATTTACAATAACATTTAAAAATAAAAA
1 AAAATTTACAATAACATTTAAAAATAAAAA
39647319 AAAATTTACAATAACATTTAAAAATAA
1 AAAATTTACAATAACATTTAAAAATAA
39647346 TAATAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAATTTACAATAACATTTAAAAATAAAAA
Found at i:39650358 original size:21 final size:20
Alignment explanation
Indices: 39650334--39650540 Score: 92
Period size: 22 Copynumber: 9.8 Consensus size: 20
39650324 TTTAATGATA
39650334 ATAATATATAGATAAAAATGT
1 ATAATATATA-ATAAAAATGT
39650355 ATAATA-AT-ATAAAAATGACAT
1 ATAATATATAATAAAAATG---T
39650376 AATAATATATAATAAAATAAT-T
1 -ATAATATATAAT-AAA-AATGT
39650398 ATAATATATAATATATATAAT-T
1 ATAATATATAATA-A-A-AATGT
*
39650420 AATAAATATATAAT-ACAA-GT
1 -AT-AATATATAATAAAAATGT
* *
39650440 A-AAAATATAATAATAA--T
1 ATAATATATAATAAAAATGT
* *
39650457 AT-ATAAATAATAAACTAATAT
1 ATAATATATAATAAA--AATGT
* *
39650478 ATAATAAATAATAATAATGT
1 ATAATATATAATAAAAATGT
*
39650498 AAATAATATATAATAAAATAATTAT
1 --ATAATATATAAT-AAA-AA-TGT
39650523 ATAATATATAATATAAAA
1 ATAATATATAATA-AAAA
39650541 ATAAGGTTAA
Statistics
Matches: 149, Mismatches: 11, Indels: 51
0.71 0.05 0.24
Matches are distributed among these distances:
17 20 0.13
18 12 0.08
19 3 0.02
20 10 0.07
21 23 0.15
22 39 0.26
23 20 0.13
24 14 0.09
25 5 0.03
26 3 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAATATATAATAAAAATGT
Found at i:39650377 original size:19 final size:18
Alignment explanation
Indices: 39650345--39650384 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
39650335 TAATATATAG
*
39650345 ATAAAAATGTATAATAAT
1 ATAAAAATGCATAATAAT
39650363 ATAAAAATGACATAATAAT
1 ATAAAAATG-CATAATAAT
39650382 ATA
1 ATA
39650385 TAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAAAAATGCATAATAAT
Found at i:39650429 original size:17 final size:16
Alignment explanation
Indices: 39650380--39650613 Score: 102
Period size: 16 Copynumber: 14.3 Consensus size: 16
39650370 TGACATAATA
39650380 ATATATAAT-A-AAAT
1 ATATATAATAATAAAT
39650394 A-ATTATAAT-ATATAAT
1 ATA-TATAATAATA-AAT
39650410 ATATATAATTAATAAAT
1 ATATATAA-TAATAAAT
*
39650427 ATATAATACA-AGTAAA-
1 ATAT-ATA-ATAATAAAT
39650443 A-ATATAATAAT-AAT
1 ATATATAATAATAAAT
39650457 ATATA-AATAATAAACT
1 ATATATAATAATAAA-T
39650473 A-ATAT-ATAATAAAT
1 ATATATAATAATAAAT
*
39650487 A-ATAATAAT-GTAAAT
1 ATAT-ATAATAATAAAT
*
39650502 AATATATAATAAAATAAT
1 -ATATATAATAATA-AAT
39650520 -TATATAATATATAATAT
1 ATATATAATA-ATAA-AT
* *
39650537 AAAAATAAGGTTAAATAAA-
1 ATATATAA---T-AATAAAT
* * *
39650556 ACAAATAACAATATAAT
1 ATATATAATAATA-AAT
*
39650573 ATATATATATATATATAT
1 ATATATA-ATA-ATAAAT
39650591 ATAATAATAATAATAAAT
1 AT-AT-ATAATAATAAAT
39650609 ATATA
1 ATATA
39650614 GGGTTAGATT
Statistics
Matches: 172, Mismatches: 15, Indels: 64
0.69 0.06 0.25
Matches are distributed among these distances:
13 4 0.02
14 24 0.14
15 30 0.17
16 33 0.19
17 28 0.16
18 27 0.16
19 16 0.09
20 4 0.02
21 5 0.03
22 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
ATATATAATAATAAAT
Found at i:39650430 original size:45 final size:44
Alignment explanation
Indices: 39650376--39650528 Score: 150
Period size: 45 Copynumber: 3.3 Consensus size: 44
39650366 AAAATGACAT
*
39650376 AATAATATATAATAAAATAATTATAATATATAATATATATAATT
1 AATAATATATAATAAAATAATTATAATATATAATATATATAATA
* *
39650420 AATAAATATATAATACAAGTAAAAATATAATA-ATAATATATAAATAATA
1 AAT-AATATATAATA-AA--ATAATTATAATATATAATATAT--ATAATA
* *
39650469 AACTAATATATAAT-AAATAATAATAATGTA-AATAATATATAATAA
1 AA-TAATATATAATAAAATAATTATAATATATAAT-ATATATAAT-A
39650514 AATAATTATATAATA
1 AATAA-TATATAATA
39650529 TATAATATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
44 11 0.12
45 33 0.37
46 7 0.08
47 11 0.12
48 10 0.11
49 17 0.19
50 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (44 bp):
AATAATATATAATAAAATAATTATAATATATAATATATATAATA
Found at i:39650453 original size:94 final size:93
Alignment explanation
Indices: 39650346--39650528 Score: 239
Period size: 94 Copynumber: 2.0 Consensus size: 93
39650336 AATATATAGA
* *
39650346 TAAAAATGTATAATAATATAAAAATGACAT-AA-TAATATATAATAAAATAATTATAATATATAA
1 TAAAAATATATAATAATATAAAAAT-A-ATAAACTAATATATAAT-AAATAATAATAATATA-AA
*
39650409 T-ATATATAAT-TAATAAATATATAATACAAG
62 TAATATATAATAAAATAAATATATAATACAAG
* *
39650439 TAAAAATATAATAATAATATATAAATAATAAACTAATATATAATAAATAATAATAATGTAAATAA
1 TAAAAATAT-ATAATAATATAAAAATAATAAACTAATATATAATAAATAATAATAATATAAATAA
*
39650504 TATATAATAAAATAATTATATAATA
65 TATATAATAAAATAAATATATAATA
39650529 TATAATATAA
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
92 5 0.06
93 34 0.43
94 40 0.51
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (93 bp):
TAAAAATATATAATAATATAAAAATAATAAACTAATATATAATAAATAATAATAATATAAATAAT
ATATAATAAAATAAATATATAATACAAG
Found at i:39650509 original size:125 final size:123
Alignment explanation
Indices: 39650284--39650544 Score: 304
Period size: 125 Copynumber: 2.1 Consensus size: 123
39650274 AGTTATTAAC
* * * *
39650284 ATATAAATAATAATAAGTATATAATACAAGTTAGAAAACCTTTAATGATAATAATATATAGATAA
1 ATATAAATAATAATAAATATATAATACAAGTTAGAAAA-CTATAATAATAATAATAAATAGATAA
* *
39650349 AAATGTATAATAATATAAAAATGACATAATAATATATAATAAAATAA-T-TATAATATATA
65 AAATATATAATAATATAAAAATGAAAT-A-AATATATAATAAAATAATTATATAATATATA
*
39650408 ATATATATAATTAATAAATATATAATACAAG-TA-AAAA-TATAATAATAATATATAAATA-ATA
1 ATATAAATAA-TAATAAATATATAATACAAGTTAGAAAACTATAATAATAATA-ATAAATAGATA
*
39650469 AACTAATATATAATAAATAATAATAATGTAAAT-AATATATAATAAAATAATTATATAATATATA
64 AA--AATATATAAT-AAT-ATAAAAATG-AAATAAATATATAATAAAATAATTATATAATATATA
39650533 ATATAAA-AATAA
1 ATATAAATAATAA
39650545 GGTTAAATAA
Statistics
Matches: 119, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
121 16 0.13
122 6 0.05
123 33 0.28
124 17 0.14
125 44 0.37
126 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (123 bp):
ATATAAATAATAATAAATATATAATACAAGTTAGAAAACTATAATAATAATAATAAATAGATAAA
AATATATAATAATATAAAAATGAAATAAATATATAATAAAATAATTATATAATATATA
Found at i:39650578 original size:2 final size:2
Alignment explanation
Indices: 39650566--39650613 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
39650556 ACAAATAACA
39650566 AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39650603 AT AA AT AT AT A
1 AT AT AT AT AT A
39650614 GGGTTAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
1 5 0.13
2 34 0.87
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:39650608 original size:56 final size:55
Alignment explanation
Indices: 39650392--39650609 Score: 149
Period size: 56 Copynumber: 3.8 Consensus size: 55
39650382 ATATAATAAA
* * * *
39650392 ATAATTATAATATATA-ATATATATAAT--TAATAAATATATAATACAAGTAAAAAT
1 ATAATAATAATATATATATATATATAATAATAAT-AATAAATAAAACAAAT-AAAAT
* * * *
39650446 ATAATAATAATATATAAATAATAAACTAATATATAATAA-ATAATAATAATGTAAATAATAT
1 ATAATAATAATATATATAT-ATATA-TAATA-ATAATAATA-AATAA-AA--CAAATAAAAT
* ***
39650507 ATAATAAAATAATTATATAATATATAATATAAAAATAAGGTTAAATAAAACAAATAACAAT
1 ATAAT--AATAA-TATAT-ATATAT-ATATAATAATAATAATAAATAAAACAAATAA-AAT
39650568 ATAAT-ATATATATATATATATATATAATAATAATAATAAATA
1 ATAATAATA-ATATATATATATATATAATAATAATAATAAATA
39650610 TATAGGGTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 34
0.71 0.11 0.19
Matches are distributed among these distances:
54 15 0.12
55 2 0.02
56 21 0.17
57 10 0.08
58 9 0.07
59 7 0.06
60 11 0.09
61 16 0.13
62 5 0.04
63 14 0.11
64 12 0.09
65 5 0.04
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (55 bp):
ATAATAATAATATATATATATATATAATAATAATAATAAATAAAACAAATAAAAT
Found at i:39652650 original size:119 final size:120
Alignment explanation
Indices: 39652267--39652743 Score: 778
Period size: 120 Copynumber: 4.0 Consensus size: 120
39652257 CTTGAGTCTG
* * *
39652267 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTTGATTTGTTTCATGTAAACACAAGAATAT
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
* * * * *
39652332 CAAATCATCTTAGATCTTGCTTCAGTGTAAACATCTGAAGGCTAGATCTGCCATG
66 CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
* * * * * *
39652387 TCTGAGAACATCTGAGAGTCAAATCTACTATGTCCTTGATTTCTTCCTTGTAAACACAAGAATAT
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
39652452 CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
66 CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
* *
39652507 TTTGGGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
39652572 CAAATCATCTTGGATC-TGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
66 CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
39652626 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
* *
39652691 CAAATTATCTTGGATC-TGCTTCAGTATAAACATCTGAAAACTAGATCTGCTAT
66 CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTAT
39652744 TCTTCGGCCT
Statistics
Matches: 335, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
119 152 0.45
120 183 0.55
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (120 bp):
TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
Found at i:39652703 original size:239 final size:239
Alignment explanation
Indices: 39652267--39652743 Score: 776
Period size: 239 Copynumber: 2.0 Consensus size: 239
39652257 CTTGAGTCTG
* * *
39652267 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTTGATTTGTTTCATGTAAACACAAGAATAT
1 TTTGAGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCATGTAAACACAAGAATAC
* * *
39652332 CAAATCATCTTAGATCTTGCTTCAGTGTAAACATCTGAAGGCTAGATCTGCCATGTCTGAGAACA
66 CAAATCATCTTAGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCCATATCTGAGAACA
* *
39652397 TCTGAGAGTCAAATCTACTATGTCCTTGATTTCTTCCTTGTAAACACAAGAATATCAAATCATCT
131 TCTGAGAGTCAAATCTACTATGTCCTCGATTTCTTCCTTGTAAACACAAGAATACCAAATCATCT
*
39652462 TGGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
196 TGGATC-TGCTTCAGTATAAACATCTGAAAACTAGATCTGCTATA
* *
39652507 TTTGGGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCATGTAAACACAAGAATAC
* * *
39652572 CAAATCATCTTGGATC-TGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATATTTGAGAACA
66 CAAATCATCTTAGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCCATATCTGAGAACA
* * * *
39652636 TCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCAAATTATCT
131 TCTGAGAGTCAAATCTACTATGTCCTCGATTTCTTCCTTGTAAACACAAGAATACCAAATCATCT
39652701 TGGATCTGCTTCAGTATAAACATCTGAAAACTAGATCTGCTAT
196 TGGATCTGCTTCAGTATAAACATCTGAAAACTAGATCTGCTAT
39652744 TCTTCGGCCT
Statistics
Matches: 219, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
238 36 0.16
239 108 0.49
240 75 0.34
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (239 bp):
TTTGAGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCATGTAAACACAAGAATAC
CAAATCATCTTAGATCTTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCCATATCTGAGAACA
TCTGAGAGTCAAATCTACTATGTCCTCGATTTCTTCCTTGTAAACACAAGAATACCAAATCATCT
TGGATCTGCTTCAGTATAAACATCTGAAAACTAGATCTGCTATA
Found at i:39660734 original size:15 final size:15
Alignment explanation
Indices: 39660692--39660741 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
39660682 ATAACTTTGA
*
39660692 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
39660706 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
39660721 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
39660735 ATGCAAA
1 ATGCAAA
39660742 AAGAATATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:39664511 original size:20 final size:18
Alignment explanation
Indices: 39664488--39664524 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
39664478 CTAAGATATT
39664488 ACATAACATATAAATACATA
1 ACATAACA-AT-AATACATA
39664508 ACATAACAATAATACAT
1 ACATAACAATAATACAT
39664525 TAATACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (18 bp):
ACATAACAATAATACATA
Found at i:39664718 original size:19 final size:19
Alignment explanation
Indices: 39664694--39664733 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39664684 ATTGGCTTAG
*
39664694 TAAAATAATGTATAA-AATT
1 TAAAAT-ATGTAAAAGAATT
39664713 TAAAATATGTAAAAGAATT
1 TAAAATATGTAAAAGAATT
39664732 TA
1 TA
39664734 TATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
TAAAATATGTAAAAGAATT
Found at i:39664934 original size:3 final size:3
Alignment explanation
Indices: 39664921--39665123 Score: 91
Period size: 3 Copynumber: 64.7 Consensus size: 3
39664911 TAAAAACCTT
* * * *
39664921 TAA TGA TAA TAA TATA TAGA TAA AAA TGTA TAA TAA T-A TAA AAA TGACA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA T-AA TAA TAA TAA TAA TAA T-A-A
*
39664970 TAA TAA TATA TAA TAA -AA TAA TTA TAA TATA TAA T-A TATA TAA TTAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA -TAA
* *
39665017 TAAA TAGA TAA TACA -AG TAA AAA T-A TAA TAA TAA TATA TAAA TAA
1 T-AA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA
* *
39665062 TAA -AC TAA TATA TAA TAAA TAA TAA TAA T-G TAAA TAA TATA TAA TAA
1 TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA T-AA TAA TA-A TAA TAA
*
39665109 -AA TAA TTA T-A TAA TA
1 TAA TAA TAA TAA TAA TA
39665124 TTTAATATAA
Statistics
Matches: 154, Mismatches: 20, Indels: 52
0.68 0.09 0.23
Matches are distributed among these distances:
2 14 0.09
3 94 0.61
4 43 0.28
5 3 0.02
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39664953 original size:21 final size:20
Alignment explanation
Indices: 39664929--39665110 Score: 78
Period size: 22 Copynumber: 8.8 Consensus size: 20
39664919 TTTAATGATA
39664929 ATAATATATAGATAAAAATGT
1 ATAATATATA-ATAAAAATGT
39664950 ATAATA-AT-ATAAAAATGACAT
1 ATAATATATAATAAAAATG---T
39664971 AATAATATATAATAAAATAAT-T
1 -ATAATATATAAT-AAA-AATGT
39664993 ATAATATATAATATATATAAT-T
1 ATAATATATAATA-A-A-AATGT
* *
39665015 AATAAATAGATAAT-ACAA-GT
1 -AT-AATATATAATAAAAATGT
* *
39665035 A-AAAATATAATAATAA--T
1 ATAATATATAATAAAAATGT
* *
39665052 AT-ATAAATAATAAACTAATAT
1 ATAATATATAATAAA--AATGT
* *
39665073 ATAATAAATAATAATAATGT
1 ATAATATATAATAAAAATGT
39665093 AAATAATATATAATAAAA
1 --ATAATATATAATAAAA
39665111 TAATTATATA
Statistics
Matches: 127, Mismatches: 12, Indels: 43
0.70 0.07 0.24
Matches are distributed among these distances:
17 19 0.15
18 12 0.09
19 3 0.02
20 10 0.08
21 23 0.18
22 39 0.31
23 4 0.03
24 11 0.09
25 3 0.02
26 3 0.02
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (20 bp):
ATAATATATAATAAAAATGT
Found at i:39664972 original size:19 final size:18
Alignment explanation
Indices: 39664940--39664979 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
39664930 TAATATATAG
*
39664940 ATAAAAATGTATAATAAT
1 ATAAAAATGCATAATAAT
39664958 ATAAAAATGACATAATAAT
1 ATAAAAATG-CATAATAAT
39664977 ATA
1 ATA
39664980 TAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAAAAATGCATAATAAT
Found at i:39665132 original size:123 final size:122
Alignment explanation
Indices: 39664880--39665132 Score: 300
Period size: 123 Copynumber: 2.0 Consensus size: 122
39664870 AGTTATTAAC
* * * * * *
39664880 ATATAAATAATAATAAGTATATAATACAAGTTAAAAACCTTTAATGATAATAATATATAGATAAA
1 ATATATATAATAATAAATAGATAATACAAGTTAAAAA-CTATAATAATAATAATAAATAGATAAA
*
39664945 AATGTATAATAATATAAAAATGACATAATAATATATAATAAAATAATTATAATATATA
65 AATATATAATAATATAAAAATGACATAATAATATATAATAAAATAATTATAATATATA
39665003 ATATATATAATTAATAAATAGATAATACAAG-TAAAAA-TATAATAATAATATATAAATA-ATAA
1 ATATATATAA-TAATAAATAGATAATACAAGTTAAAAACTATAATAATAATA-ATAAATAGATAA
* * *
39665065 ACTAATATATAATAAATAATAATAATG-TA-AATAATATATAATAAAATAATTATATAATATTTA
64 A--AATATATAAT-AAT-ATAAAAATGACATAATAATATATAATAAAATAA-T-TATAATATATA
39665128 ATATA
1 ATATA
39665133 AAAATAAGGT
Statistics
Matches: 112, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
121 16 0.14
122 6 0.05
123 44 0.39
124 23 0.21
125 23 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (122 bp):
ATATATATAATAATAAATAGATAATACAAGTTAAAAACTATAATAATAATAATAAATAGATAAAA
ATATATAATAATATAAAAATGACATAATAATATATAATAAAATAATTATAATATATA
Found at i:39665683 original size:8 final size:8
Alignment explanation
Indices: 39665670--39665694 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39665660 CCTTCGTACG
39665670 CCACGCGC
1 CCACGCGC
39665678 CCACGCGC
1 CCACGCGC
39665686 CCACGCGC
1 CCACGCGC
39665694 C
1 C
39665695 GCCCTAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.64, G:0.24, T:0.00
Consensus pattern (8 bp):
CCACGCGC
Found at i:39666824 original size:22 final size:22
Alignment explanation
Indices: 39666799--39666841 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
39666789 ATCGTGAATC
39666799 ATCCTCTCAAAACTCATATCAT
1 ATCCTCTCAAAACTCATATCAT
*
39666821 ATCCTCTCAAAACTCTTATCA
1 ATCCTCTCAAAACTCATATCA
39666842 AACTGAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
ATCCTCTCAAAACTCATATCAT
Found at i:39670509 original size:5 final size:5
Alignment explanation
Indices: 39670495--39670536 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
39670485 TAATAAAATA
* * *
39670495 ATTAG ATTAT ATTAT ATTGT ATTAT ATTAT ACTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
39670537 AGATTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:39672839 original size:40 final size:40
Alignment explanation
Indices: 39672742--39672850 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 40
39672732 ATTGAATGAT
* * * * *
39672742 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * * *
39672782 AT-CAGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
39672821 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
39672851 AAATTGTGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 30 0.54
40 26 0.46
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:39675837 original size:40 final size:40
Alignment explanation
Indices: 39675792--39675958 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
39675782 CGGAATATAA
39675792 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
39675832 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
39675872 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
39675912 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
39675951 CCGGATAT
1 CCGGATAT
39675959 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:39675942 original size:80 final size:79
Alignment explanation
Indices: 39675792--39675958 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
39675782 CGGAATATAA
* *
39675792 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
39675857 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
39675872 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
39675934 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
39675951 CCGGATAT
1 CCGGATAT
39675959 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:39676806 original size:17 final size:19
Alignment explanation
Indices: 39676783--39676828 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
39676773 AAGAAGCATG
39676783 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
39676801 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
39676819 AATCATGCTC
1 AATCATGCTC
39676829 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:39683892 original size:39 final size:40
Alignment explanation
Indices: 39683786--39683950 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39683776 CGGAATATAA
*
39683786 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAATTGCCTTCGGGTCTTAGC
* * * *
39683826 CCGGATAGAATAACTCGCACGAA-TGCCTTC-GGCCTTAGC
1 CCGGATATAATCACTAGCAC-AATTGCCTTCGGGTCTTAGC
* *
39683865 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
** * * *
39683905 CCGGATATAATTTCCAGCATAATTGTCTTC-GG-CTTAGC
1 CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
39683943 CCGGATAT
1 CCGGATAT
39683951 CATTCAATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
38 15 0.14
39 34 0.32
40 54 0.51
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
Found at i:39683935 original size:79 final size:78
Alignment explanation
Indices: 39683786--39683950 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 78
39683776 CGGAATATAA
* *
39683786 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
39683851 CCTTCGGCCTTAGC
66 CCTTCGG-CTTAGC
* * ** *
39683865 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
39683927 TTGTCTTCGGCTTAGC
64 -TGCCTTCGGCTTAGC
39683943 CCGGATAT
1 CCGGATAT
39683951 CATTCAATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
78 18 0.24
79 57 0.76
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGCTTAGC
Found at i:39684793 original size:17 final size:19
Alignment explanation
Indices: 39684770--39684815 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
39684760 AAGAAGCATG
39684770 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
39684788 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
39684806 AATCATGCTC
1 AATCATGCTC
39684816 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:39688751 original size:40 final size:40
Alignment explanation
Indices: 39688706--39688872 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
39688696 CGGAATATAA
*
39688706 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
39688746 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
39688786 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
39688826 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
39688865 CCGGATAT
1 CCGGATAT
39688873 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:39691324 original size:40 final size:40
Alignment explanation
Indices: 39691280--39691465 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
39691270 GCTACTCGTT
* * *
39691280 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
39691320 CAAATGCCTTGGGGACTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
39691360 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* *
39691400 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
39691441 CAGA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39691466 CATCATTCGA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39698541 original size:33 final size:33
Alignment explanation
Indices: 39698504--39698611 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
39698494 TGTATACGTG
*
39698504 TAAGACCATAGCTGGGCTATGGTATCCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATCCTGATGA
* * * *
39698537 TAAGACCATAACTGGGTTATGACATTAC-GAGTG-
1 TAAGACCATAGCTGGGCTATGGCA-TCCTGA-TGA
* *
39698570 TAAGACCATAGTTGGGCTACGGCATCCT-ATGA
1 TAAGACCATAGCTGGGCTATGGCATCCTGATGA
39698602 TAAGACCATA
1 TAAGACCATA
39698612 ATTGGATTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.03
32 13 0.22
33 41 0.68
34 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCATCCTGATGA
Found at i:39698628 original size:65 final size:66
Alignment explanation
Indices: 39698501--39698643 Score: 225
Period size: 65 Copynumber: 2.2 Consensus size: 66
39698491 ATATGTATAC
* * * *
39698501 GTGTAAGACCATAGCTGGGCTATGGTATCCTGATGATAAGACCATAACTGGGTTATGACATTACG
1 GTGTAAGACCATAGCTGGGCTACGGCATCCTGATGATAAGACCATAACTGGATTATGACATTACA
39698566 A
66 A
* *
39698567 GTGTAAGACCATAGTTGGGCTACGGCATCCT-ATGATAAGACCATAATTGGATTATGACATTACA
1 GTGTAAGACCATAGCTGGGCTACGGCATCCTGATGATAAGACCATAACTGGATTATGACATTACA
39698631 A
66 A
39698632 GTGTAAGACCAT
1 GTGTAAGACCAT
39698644 GGCAAGGCCA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 43 0.61
66 28 0.39
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (66 bp):
GTGTAAGACCATAGCTGGGCTACGGCATCCTGATGATAAGACCATAACTGGATTATGACATTACA
A
Found at i:39701966 original size:49 final size:50
Alignment explanation
Indices: 39701897--39702070 Score: 164
Period size: 49 Copynumber: 3.6 Consensus size: 50
39701887 ACATCAAAGT
* *
39701897 CGATGCCATGTTCCAGACAGGTCTTACACTGACTTTCATATACT-GAGGC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATACTCGAGGC
* * * * *
39701946 CGATGCCGTGTCCCAAACAGGTCTTACACTGGCTCTCATCTA-TCG-GTGT
1 CGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATACTCGAG-GC
* * * *
39701995 TGATGCCATGTCCCAGATAGGTCTTACTCT-AGCTTGT-ATAT-CTCGAGGC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGA-CTT-TCATATACTCGAGGC
*
39702044 CGATG-CATGTCCCAAACATGTCTTACA
1 CGATGCCATGTCCCAAACAGGTCTTACA
39702071 TTAGTTCTCG
Statistics
Matches: 98, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
48 20 0.20
49 76 0.78
50 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
CGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATACTCGAGGC
Found at i:39702105 original size:46 final size:46
Alignment explanation
Indices: 39702044--39702164 Score: 233
Period size: 46 Copynumber: 2.6 Consensus size: 46
39702034 ATCTCGAGGC
*
39702044 CGATGCATGTCCCAAACATGTCTTACATTAGTTCTCGTCTTAATGT
1 CGATGCATGTCCCAAACATGTCTTACACTAGTTCTCGTCTTAATGT
39702090 CGATGCATGTCCCAAACATGTCTTACACTAGTTCTCGTCTTAATGT
1 CGATGCATGTCCCAAACATGTCTTACACTAGTTCTCGTCTTAATGT
39702136 CGATGCATGTCCCAAACATGTCTTACACT
1 CGATGCATGTCCCAAACATGTCTTACACT
39702165 GGCTGGTATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (46 bp):
CGATGCATGTCCCAAACATGTCTTACACTAGTTCTCGTCTTAATGT
Found at i:39702174 original size:140 final size:143
Alignment explanation
Indices: 39701954--39702215 Score: 332
Period size: 140 Copynumber: 1.9 Consensus size: 143
39701944 GCCGATGCCG
* ** * * *
39701954 TGTCCCAAACAGGTCTTACACTGGCTCTCATCTATCGGTGTTGATGCCATGTCCCAGATAGGTCT
1 TGTCCCAAACAGGTCTTACACTAGCTCTCATCTATCAATGTCGATGCCATGTCCCAAACAGGTCT
* * * * *
39702019 TACTCTAGCTTGTATATCTCGAGGCCGATGCATGTCCCAAACATGTCTTACATTAGTTCTCGTCT
66 TACACTAGCTGGTATATCTCGAGGCCGATACATGTCCCAAACATATCTTACACTAGTTCTCGTCT
39702084 TAATGTCGATGCA
131 TAATGTCGATGCA
* * * *
39702097 TGTCCCAAACATGTCTTACACTAGTTCTCGTCT-T-AATGTCGATG-CATGTCCCAAACATGTCT
1 TGTCCCAAACAGGTCTTACACTAGCTCTCATCTATCAATGTCGATGCCATGTCCCAAACAGGTCT
* * * *
39702159 TACACTGGCTGGTATATCTTGAGGCTGATACATGTCCCAGACATATCTTACACTAGT
66 TACACTAGCTGGTATATCTCGAGGCCGATACATGTCCCAAACATATCTTACACTAGT
39702216 ACACATATCA
Statistics
Matches: 100, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
140 63 0.63
141 7 0.07
142 1 0.01
143 29 0.29
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (143 bp):
TGTCCCAAACAGGTCTTACACTAGCTCTCATCTATCAATGTCGATGCCATGTCCCAAACAGGTCT
TACACTAGCTGGTATATCTCGAGGCCGATACATGTCCCAAACATATCTTACACTAGTTCTCGTCT
TAATGTCGATGCA
Found at i:39706042 original size:28 final size:28
Alignment explanation
Indices: 39706007--39706089 Score: 157
Period size: 28 Copynumber: 3.0 Consensus size: 28
39705997 TGGTACATAT
39706007 ATCACCATTCACTTATAAAAAATTATAC
1 ATCACCATTCACTTATAAAAAATTATAC
*
39706035 ATCACCATTCAATTATAAAAAATTATAC
1 ATCACCATTCACTTATAAAAAATTATAC
39706063 ATCACCATTCACTTATAAAAAATTATA
1 ATCACCATTCACTTATAAAAAATTATA
39706090 TTATCATTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (28 bp):
ATCACCATTCACTTATAAAAAATTATAC
Found at i:39709024 original size:53 final size:55
Alignment explanation
Indices: 39708956--39709149 Score: 169
Period size: 53 Copynumber: 3.6 Consensus size: 55
39708946 TTCCTTTTTC
* *
39708956 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTA-AG-
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATAGT
* * * * * *
39709009 AACTCACCATTGCCATGCCTTGGCAAGGTCTTACATGGGATCTTTGCCTTATCGT
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATAGT
** * * *** * * *
39709064 AGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTGCTTGCCTTGTA-A
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATAGT
* * * *
39709118 AACTTACCAATGACATGCCTTGGCATGGTCTT
1 AACTTACCATTGCCATGTCTTGACATGGTCTT
39709150 TCTTAGTATC
Statistics
Matches: 109, Mismatches: 30, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 44 0.40
54 27 0.25
55 38 0.35
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (55 bp):
AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATAGT
Found at i:39715230 original size:53 final size:54
Alignment explanation
Indices: 39715162--39715368 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
39715152 TTCCTTTTTA
* * *
39715162 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * ** * * *
39715215 AACTCACCATTGCCATGCCTTGGTATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * * *
39715269 TAGTTTATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCTTACCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
39715324 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
39715369 AAACCCTGAT
Statistics
Matches: 119, Mismatches: 33, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 45 0.38
54 37 0.31
55 37 0.31
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:39717719 original size:16 final size:16
Alignment explanation
Indices: 39717698--39717731 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39717688 CACGTGAATT
39717698 ACGTATGAATGCACTA
1 ACGTATGAATGCACTA
39717714 ACGTATGAATGCACTA
1 ACGTATGAATGCACTA
39717730 AC
1 AC
39717732 ATGTGTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (16 bp):
ACGTATGAATGCACTA
Found at i:39719839 original size:291 final size:293
Alignment explanation
Indices: 39719375--39720435 Score: 954
Period size: 291 Copynumber: 3.6 Consensus size: 293
39719365 TGTATGAAAA
* * * * * * * *
39719375 AAAATGAAGTTTTGGTTGAGTGGTAAATTTAATATTTTACTACTCCAATTGACAT-AGGTTTAAA
1 AAAATAAAGCTTTGATTGAGTGATAAATTTAAGATTTTACTAATCCAATTGGCATGA-GTTCAAA
* * * * *
39719439 TACCACCATATGCATATTTTTCTTTGATTTTTGTTAAAATAAATAGACTAAAACACCATTGAATA
65 TCCCACCACATGCATATTTTTC-TTG-TTTTTGTTAAAATAAAAAGACTAAAATACCTTTGAATA
* ** * * *
39719504 GTATTACTTATTTTAATTATGGGAGGACA-TTTCTATACTTTCCTAACCGAGTTGGCACCCAGTT
128 ATAAGACTTATTTTAATTATGGAAGGACATTTTC-ATAATTTCCTAACCGAGTTGGTACCCAGTT
*
39719568 AAACTATGACACC-ACTCAACCAGGGGTTTTATTAATAGTATAAAAATATAACTGGTGAAGATAA
192 AAACTATGACACCAACTCAATCAGGGGTTTTATTAATAGTATAAAAATATAACTGGTGAAGATAA
*
39719632 TAAATTGTGAATATTTAAAAAATTGTATAAAA-AAATC
257 TAAATTGTGAATATTTAAAAAA-TGTATAAAATATATC
* * * *
39719669 AAAATAAAGCTTTGATTGAGTTG-TAAATTTAAGGTTTTACTAATCCAATTGGCACGAGTTTAAC
1 AAAATAAAGCTTTGATTGAG-TGATAAATTTAAGATTTTACTAATCCAATTGGCATGAGTTCAAA
* *
39719733 TCCCACCACATGCATATTTTTCTTGTTTTT-TCT-AAATAAAAAGACTAAAGTGCCTTTGAATAA
65 TCCCACCACATGCATATTTTTCTTGTTTTTGT-TAAAATAAAAAGACTAAAATACCTTTGAATAA
* *
39719796 TAAGATTTATTTTTATTATGGAAGGACATTTTCATAATTTCCTAA-CGAGTTGGTACCCAGTTAA
129 TAAGACTTATTTTAATTATGGAAGGACATTTTCATAATTTCCTAACCGAGTTGGTACCCAGTTAA
* * * * * * * * **
39719860 CCTATGGCACCAACTTAATCAGAGGTTTTATTAATAGTATAGATATACAACTGGCGGGGATAATA
194 ACTATGACACCAACTCAATCAGGGGTTTTATTAATAGTATAAAAATATAACTGGTGAAGATAATA
* *
39719925 AATTAT-ATATATATTAAAAAGAATGTATAAAATATATT
259 AATTGTGA-ATAT-TT-AAAA-AATGTATAAAATATATC
* * ** * * ** *
39719963 AAAATAAAGTTTTGCTCAAGTGATAAATTTAAGGTTTTACTAATCAAATTGGTGTGGGTTCAAA-
1 AAAATAAAGCTTTGATTGAGTGATAAATTTAAGATTTTACTAATCCAATTGGCATGAGTTCAAAT
* * * *
39720027 --C-CC-CAT-C--A---TT-TGGTTTCTGTTAAAATGAAAAAAATTAAAATACCTTTGAATAAT
66 CCCACCACATGCATATTTTTCTTGTTTTTGTTAAAAT-AAAAAGACTAAAATACCTTTGAATAAT
* * * * **
39720081 ATA-ACTCATTTTAATTATAGAAGGACATTTCCATAATTTCCTAATCGAGTTGGTACCTGGTTAA
130 A-AGACTTATTTTAATTATGGAAGGACATTTTCATAATTTCCTAACCGAGTTGGTACCCAGTTAA
* * ** *
39720145 CAC-GTGACACCAACTCAGTTTGGGGTATTATTAATAGTAAGTATATACATATATAACTGGTGAA
194 -ACTATGACACCAACTCAATCAGGGGTTTTATTAATAGT-A-TA-A-A-A-ATATAACTGGTGAA
* *
39720209 GATAATAAATTGTGCATA-TTAAAAGA-GTATAAAATATTATC
252 GATAATAAATTGTGAATATTTAAAAAATGTATAAAATA-TATC
* * * *
39720250 AAAGTAAAACATT-AGTTGAGTGATAAATTTAAGATTTTACTAATCCAATTGGCATGGGTTCAAA
1 AAAATAAAGCTTTGA-TTGAGTGATAAATTTAAGATTTTACTAATCCAATTGGCATGAGTTCAAA
* * * * * *
39720314 TCTCACCATATGCATATTTTTCTTGGTTTTTGTTAAAATGAAAAGACTAAAATGCCCTCT-AATG
65 TCCCACCACATGCATATTTTTCTT-GTTTTTGTTAAAATAAAAAGACTAAAAT-ACCTTTGAATA
* * * * * *
39720378 ATATGATTTATTTTAATTA-CGAATGGATATTTTCGTAATTTTCTAACCGAGTTGGTAC
128 ATAAGACTTATTTTAATTATGGAA-GGACATTTTCATAATTTCCTAACCGAGTTGGTAC
39720436 AAGGTTAACC
Statistics
Matches: 615, Mismatches: 110, Indels: 79
0.76 0.14 0.10
Matches are distributed among these distances:
282 7 0.01
283 7 0.01
284 60 0.10
285 45 0.07
286 13 0.02
287 58 0.09
288 5 0.01
289 6 0.01
290 31 0.05
291 140 0.23
292 14 0.02
293 19 0.03
294 125 0.20
295 4 0.01
298 5 0.01
299 59 0.10
300 17 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (293 bp):
AAAATAAAGCTTTGATTGAGTGATAAATTTAAGATTTTACTAATCCAATTGGCATGAGTTCAAAT
CCCACCACATGCATATTTTTCTTGTTTTTGTTAAAATAAAAAGACTAAAATACCTTTGAATAATA
AGACTTATTTTAATTATGGAAGGACATTTTCATAATTTCCTAACCGAGTTGGTACCCAGTTAAAC
TATGACACCAACTCAATCAGGGGTTTTATTAATAGTATAAAAATATAACTGGTGAAGATAATAAA
TTGTGAATATTTAAAAAATGTATAAAATATATC
Found at i:39722522 original size:40 final size:39
Alignment explanation
Indices: 39722477--39722643 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 39
39722467 CGGAATATAA
39722477 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
39722517 CCGGATAGAATAACTTGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
39722557 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * *
39722597 CCGGATATAATTTC-CAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAA--TCACTGCACAAATGCCTTCGGGTCTTAGC
39722636 CCGGATAT
1 CCGGATAT
39722644 CATTCAATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 14 0.13
40 91 0.85
41 1 0.01
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAATCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39722627 original size:80 final size:79
Alignment explanation
Indices: 39722477--39722643 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 79
39722467 CGGAATATAA
* * **
39722477 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTTGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCACGAATG
39722542 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
39722557 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCA-TAAT
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCACGAA-
*
39722620 TGTCTTCGGGCTTAGC
64 TGCCTTCGGGCTTAGC
39722636 CCGGATAT
1 CCGGATAT
39722644 CATTCAATTT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 17 0.23
80 58 0.77
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCACGAATG
CCTTCGGGCTTAGC
Found at i:39723493 original size:17 final size:19
Alignment explanation
Indices: 39723470--39723515 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
39723460 AAGAAGCATG
39723470 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
39723488 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
39723506 AATCATGCTC
1 AATCATGCTC
39723516 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:39725237 original size:10 final size:9
Alignment explanation
Indices: 39725198--39725354 Score: 60
Period size: 10 Copynumber: 17.4 Consensus size: 9
39725188 ACATGTGACA
39725198 AAAAATTAT
1 AAAAATTAT
39725207 AAAAA--AT
1 AAAAATTAT
*
39725214 AAAAATCAAT
1 AAAAAT-TAT
*
39725224 AAAAGTTAT
1 AAAAATTAT
39725233 AAAAATTATT
1 AAAAATTA-T
**
39725243 AAACTTTAAT
1 AAAAATT-AT
39725253 AAAAATT-T
1 AAAAATTAT
39725261 AAAAA--AT
1 AAAAATTAT
* *
39725268 TAAATTTA-
1 AAAAATTAT
39725276 AAAAATTA-
1 AAAAATTAT
*
39725284 AAATA-TAT
1 AAAAATTAT
* *
39725292 ATAAATTGT
1 AAAAATTAT
*
39725301 AAAAAATATT
1 AAAAATTA-T
* *
39725311 AAAATTTGT
1 AAAAATTAT
*
39725320 AAAATTTTAT
1 AAAA-ATTAT
*
39725330 AAAAATCATT
1 AAAAATTA-T
39725340 AAAAAAGTTAT
1 -AAAAA-TTAT
39725351 AAAA
1 AAAA
39725355 TGCATCAAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
7 13 0.12
8 19 0.18
9 29 0.27
10 38 0.35
11 7 0.06
12 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:39725245 original size:19 final size:20
Alignment explanation
Indices: 39725211--39725259 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
39725201 AATTATAAAA
*
39725211 AATAAAAATCAATAAAAGTT
1 AATAAAAATTAATAAAAGTT
* **
39725231 -ATAAAAATTATTAAACTTT
1 AATAAAAATTAATAAAAGTT
39725250 AATAAAAATT
1 AATAAAAATT
39725260 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAATTAATAAAAGTT
Found at i:39725254 original size:29 final size:25
Alignment explanation
Indices: 39725198--39725280 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 25
39725188 ACATGTGACA
* * *
39725198 AAAAATTATAAAAAATAAAAATCAAT
1 AAAAATT-TAAAAAATTAAATTTAAT
*
39725224 AAAAGTTATAAAAATTATTAAACTTTAAT
1 AAAAATT-TAAAAA--ATTAAA-TTTAAT
39725253 AAAAATTTAAAAAATTAAATTTAA-
1 AAAAATTTAAAAAATTAAATTTAAT
39725277 AAAA
1 AAAA
39725281 TTAAAATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 4 0.08
25 5 0.10
26 19 0.39
28 11 0.22
29 10 0.20
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (25 bp):
AAAAATTTAAAAAATTAAATTTAAT
Found at i:39725274 original size:14 final size:14
Alignment explanation
Indices: 39725255--39725285 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39725245 ACTTTAATAA
39725255 AAATTTAAAAAATT
1 AAATTTAAAAAATT
39725269 AAATTTAAAAAATT
1 AAATTTAAAAAATT
39725283 AAA
1 AAA
39725286 ATATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTTAAAAAATT
Found at i:39725304 original size:68 final size:69
Alignment explanation
Indices: 39725200--39725335 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 69
39725190 ATGTGACAAA
* *
39725200 AAATTATAAAAAATAAAAATCAATAAAAGTTATAAAAATTATTAAACTTTAATAAAAATTTA-AA
1 AAATTATAAAAAATAAAAATCAATAAAAGTTATAAAAAATATTAAAATTT-ATAAAAATTTATAA
39725264 AAATT
65 AAATT
* * * *
39725269 AAATT-TAAAAAATTAAAAT-ATATATAAA-TTGTAAAAAATATTAAAATTTGTAAAATTTTATA
1 AAATTATAAAAAATAAAAATCA-ATA-AAAGTTATAAAAAATATTAAAATTTATAAAAATTTATA
39725331 AAAAT
64 AAAAT
39725336 CATTAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
67 10 0.17
68 40 0.69
69 8 0.14
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (69 bp):
AAATTATAAAAAATAAAAATCAATAAAAGTTATAAAAAATATTAAAATTTATAAAAATTTATAAA
AATT
Found at i:39725309 original size:18 final size:19
Alignment explanation
Indices: 39725283--39725323 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
39725273 TTAAAAAATT
39725283 AAAATATATATAAA-TTGTAA
1 AAAATAT-TA-AAATTTGTAA
39725303 AAAATATTAAAATTTGTAA
1 AAAATATTAAAATTTGTAA
39725322 AA
1 AA
39725324 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 10 0.50
20 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAATATTAAAATTTGTAA
Found at i:39725350 original size:21 final size:21
Alignment explanation
Indices: 39725326--39725368 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39725316 TTGTAAAATT
*
39725326 TTATAAAAAT-CATTAAAAAAG
1 TTAT-AAAATGCATCAAAAAAG
39725347 TTATAAAATGCATCAAAAAAG
1 TTATAAAATGCATCAAAAAAG
39725368 T
1 T
39725369 CATTTAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (21 bp):
TTATAAAATGCATCAAAAAAG
Found at i:39725632 original size:19 final size:18
Alignment explanation
Indices: 39725610--39725664 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
39725600 GTTTTCTATA
39725610 TTTCTATATATTTTATAAT
1 TTTCTATA-ATTTTATAAT
*
39725629 TTTCTACAATTTTTATAAT
1 TTTCTATAA-TTTTATAAT
*
39725648 TTTTTATAATTTT-TAAT
1 TTTCTATAATTTTATAAT
39725665 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 23 0.72
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCTATAATTTTATAAT
Found at i:39725666 original size:10 final size:9
Alignment explanation
Indices: 39725620--39725662 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
39725610 TTTCTATATA
39725620 TTTTATAAT
1 TTTTATAAT
*
39725629 TTTCTACAAT
1 TTT-TATAAT
39725639 TTTTATAATT
1 TTTTATAA-T
39725649 TTTTATAAT
1 TTTTATAAT
39725658 TTTTA
1 TTTTA
39725663 ATAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 13 0.43
10 17 0.57
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:39725719 original size:29 final size:29
Alignment explanation
Indices: 39725643--39725722 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
39725633 TACAATTTTT
*
39725643 ATAATTTTTTATAATTTTTAATAAAAATTA
1 ATAA-TTTTTATAATTTTTATTAAAAATTA
* *
39725673 A-ATATTTCTTGT-ATTTTTATTAAAATTTA
1 ATA-ATTT-TTATAATTTTTATTAAAAATTA
*
39725702 ATAATTTTTATAACTTTTATT
1 ATAATTTTTATAATTTTTATT
39725723 TATTTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.07
29 32 0.78
30 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (29 bp):
ATAATTTTTATAATTTTTATTAAAAATTA
Found at i:39725926 original size:23 final size:23
Alignment explanation
Indices: 39725894--39725945 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
39725884 GTTTAATTTT
39725894 TTTTTG-AAAAAGATTAAGAGTC
1 TTTTTGAAAAAAGATTAAGAGTC
* *
39725916 TTTTTGAAAAAAGTTTGAGAGTC
1 TTTTTGAAAAAAGATTAAGAGTC
39725939 TTTTTGA
1 TTTTTGA
39725946 TGTATTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (23 bp):
TTTTTGAAAAAAGATTAAGAGTC
Found at i:39728130 original size:17 final size:17
Alignment explanation
Indices: 39728099--39728131 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39728089 AAGTGAAACT
39728099 AGGGAGGAAATAATAAA
1 AGGGAGGAAATAATAAA
39728116 AGGGTAGGAAA-AATAA
1 AGGG-AGGAAATAATAA
39728132 TTAGAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (17 bp):
AGGGAGGAAATAATAAA
Found at i:39739818 original size:21 final size:21
Alignment explanation
Indices: 39739784--39739830 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39739774 GAACAATTTC
*
39739784 ACTCG-ATTTAATTTGACTTG
1 ACTCGAATTTAATTTGACTCG
* *
39739804 ACTCGAATTTCATTTTACTCG
1 ACTCGAATTTAATTTGACTCG
39739825 ACTCGA
1 ACTCGA
39739831 TTAAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (21 bp):
ACTCGAATTTAATTTGACTCG
Found at i:39740425 original size:13 final size:13
Alignment explanation
Indices: 39740409--39740460 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
39740399 ATTCTAAAAA
39740409 ATAAATAAAAATT
1 ATAAATAAAAATT
* *
39740422 ATAAAAAAAAATA
1 ATAAATAAAAATT
39740435 AT-AATAAAAA-T
1 ATAAATAAAAATT
*
39740446 GT-AATAAAAATT
1 ATAAATAAAAATT
39740458 ATA
1 ATA
39740461 GAAATATATC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 9 0.29
12 9 0.29
13 13 0.42
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:39740432 original size:25 final size:27
Alignment explanation
Indices: 39740404--39740455 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
39740394 AATAGATTCT
39740404 AAAAAAT-A-AATAAAAAT-T-ATAAA
1 AAAAAATAATAATAAAAATGTAATAAA
39740427 AAAAAATAATAATAAAAATGTAATAAA
1 AAAAAATAATAATAAAAATGTAATAAA
39740454 AA
1 AA
39740456 TTATAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.28
24 1 0.04
25 9 0.36
26 1 0.04
27 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (27 bp):
AAAAAATAATAATAAAAATGTAATAAA
Found at i:39741920 original size:14 final size:14
Alignment explanation
Indices: 39741903--39741931 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39741893 AATATTTTGT
39741903 ATACAATAAATGTA
1 ATACAATAAATGTA
39741917 ATACAATAAATGTA
1 ATACAATAAATGTA
39741931 A
1 A
39741932 ACTTTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
ATACAATAAATGTA
Found at i:39750421 original size:12 final size:12
Alignment explanation
Indices: 39750376--39750434 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
39750366 AATTTGTGTA
* *
39750376 TTGTTTTAAGAA
1 TTGTTTTAATAT
*
39750388 TTGTTTTAGTA-
1 TTGTTTTAATAT
*
39750399 TTATTTT--TAT
1 TTGTTTTAATAT
39750409 TTGTTTTAATAT
1 TTGTTTTAATAT
39750421 TTGTTTTAATAT
1 TTGTTTTAATAT
39750433 TT
1 TT
39750435 TTAAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 6 0.15
12 26 0.65
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:39750477 original size:25 final size:26
Alignment explanation
Indices: 39750417--39750466 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
39750407 ATTTGTTTTA
*
39750417 ATATTTG-TTT-TAATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
39750441 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
39750467 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:39752600 original size:69 final size:68
Alignment explanation
Indices: 39752485--39752619 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 68
39752475 TTTGTATAGC
* *
39752485 TGGGAGCTTTGCTTTCACTAACTATTTTAGAGGTCGCGGCTCTTCTCCTGA-GAGCTTTGATTTT
1 TGGGAGCTTTGCTCTCACTAACTATTTTAGAGGTCGCGACTCTTCT-CT-ACGAGCTTTGATTTT
39752549 ACAGT
64 ACAGT
* * *
39752554 TGGGAGCTTTAG-TCTCGCTAATTATTTTAGAGGTCGCGACTTTTCTCTACGAGCTTTGATTTTA
1 TGGGAGCTTT-GCTCTCACTAACTATTTTAGAGGTCGCGACTCTTCTCTACGAGCTTTGATTTTA
39752618 CA
65 CA
39752620 TCACTGATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 1 0.02
68 18 0.31
69 39 0.66
70 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (68 bp):
TGGGAGCTTTGCTCTCACTAACTATTTTAGAGGTCGCGACTCTTCTCTACGAGCTTTGATTTTAC
AGT
Found at i:39752730 original size:69 final size:67
Alignment explanation
Indices: 39752657--39753046 Score: 210
Period size: 69 Copynumber: 5.7 Consensus size: 67
39752647 CTTCGCCTAC
* * *
39752657 GAGCCTTGATTTTACAGTTAGGAGCTTTGCTCTCTCTAATTAGTTTGGGGATCGTGACTCTTCAC
1 GAGCCTTGATTTTACAGCTAGGAGCTTTGCTCTCTCTAACT-GTTTGAGG-TCGTGACTCTTCAC
39752722 TTGT
64 TTGT
* * * * * * *
39752726 GAGCCCTAATTTTACAACTAGGATCTTTGCT-TTTGCTAACTGTTTGAAAGGTCATGACTCTTCG
1 GAGCCTTGATTTTACAGCTAGGAGCTTTGCTCTCT-CTAACTGTTTG--AGGTCGTGACTCTTCA
*
39752790 CTTGC
63 CTTGT
* * * * * * * * *
39752795 GAACCTTGATTTTATAGGTGGGAGCTTTGCTCTCGCTAACTGTTTTAGAGGTCGCGGCTTTTTAC
1 GAGCCTTGATTTTACAGCTAGGAGCTTTGCTCTCTCTAACTG-TTT-GAGGTCGTGACTCTTCAC
39752860 TTGT
64 TTGT
* * ** * * * * * *
39752864 GAGCCTTGATTTTATAGGTTTGAGCTTTGTTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGC
1 GAGCCTTGATTTTACAGCTAGGAGCTTTGCTCTCTCTAACT-GTTT-GAGGTCGTGACTCTTCAC
*
39752929 TTGC
64 TTGT
* * * * * * * * * * * *
39752933 AAACCTTTATTTTATAG-TTGTGAACTTTGGTCCCGCTAACTGTTTTGAAGGTCGCGGCTCTTCG
1 GAGCCTTGATTTTACAGCTAG-GAGCTTTGCTCTCTCTAACTG-TTTG-AGGTCGTGACTCTTCA
*
39752997 CTTGC
63 CTTGT
* * * *
39753002 AAACCTTGATTTTACAGCT-GTGAGCTTTGGTCTCGCTAACTGTTT
1 GAGCCTTGATTTTACAGCTAG-GAGCTTTGCTCTCTCTAACTGTTT
39753047 TGGAGGTTGC
Statistics
Matches: 256, Mismatches: 54, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
68 13 0.05
69 235 0.92
70 7 0.03
71 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.40
Consensus pattern (67 bp):
GAGCCTTGATTTTACAGCTAGGAGCTTTGCTCTCTCTAACTGTTTGAGGTCGTGACTCTTCACTT
GT
Found at i:39753047 original size:69 final size:69
Alignment explanation
Indices: 39752760--39753081 Score: 369
Period size: 69 Copynumber: 4.7 Consensus size: 69
39752750 CTTTGCTTTT
** * * *
39752760 GCTAACTG-TTTGAAAGGTCATGACTCTTCGCTTGCGAACCTTGATTTTATAGGTGGGAGCTTTG
1 GCTAACTGTTTTG-AAGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTATAGGTGTGAGCTTTG
*
39752824 CTCTC
65 GTCTC
* ** ** * *
39752829 GCTAACTGTTTT-AGAGGTCGCGGCTTTTTACTTGTGAGCCTTGATTTTATAGGTTTGAGCTTTG
1 GCTAACTGTTTTGA-AGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTATAGGTGTGAGCTTTG
*
39752893 TTCTC
65 GTCTC
* * * * * * *
39752898 GCTAACTATTTTGGAGGTTGTGGCTCTTCGCTTGCAAACCTTTATTTTATAGTTGTGAACTTTGG
1 GCTAACTGTTTTGAAGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTATAGGTGTGAGCTTTGG
*
39752963 TCCC
66 TCTC
* *
39752967 GCTAACTGTTTTGAAGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTACAGCTGTGAGCTTTGG
1 GCTAACTGTTTTGAAGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTATAGGTGTGAGCTTTGG
39753032 TCTC
66 TCTC
* * *
39753036 GCTAACTGTTTTGGAGGTTGCGGCTCTTCGCTTGCAAACCTCGATT
1 GCTAACTGTTTTGAAGGTCGCGGCTCTTCGCTTGCAAACCTTGATT
39753082 CATGACTCTT
Statistics
Matches: 211, Mismatches: 39, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
68 1 0.00
69 207 0.98
70 3 0.01
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (69 bp):
GCTAACTGTTTTGAAGGTCGCGGCTCTTCGCTTGCAAACCTTGATTTTATAGGTGTGAGCTTTGG
TCTC
Found at i:39757548 original size:40 final size:40
Alignment explanation
Indices: 39757449--39757666 Score: 266
Period size: 40 Copynumber: 5.5 Consensus size: 40
39757439 TGGATGATAA
*
39757449 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
39757490 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39757530 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39757570 CCGGGCTAAGTCTCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39757610 CCGGGCTATGTCTCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
39757649 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39757667 TACTTGGCTT
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 14 0.09
39 15 0.09
40 102 0.65
41 23 0.15
42 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39759172 original size:66 final size:65
Alignment explanation
Indices: 39759066--39759203 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 65
39759056 ATGTTCTAGG
* * * * *
39759066 CCGTGTGCTAGGCCGTGCCAAACCTATAGGGTATATTGACTTATGCTACACGGCCAAGTCACATG
1 CCGTGTGCTAGGCCGTGCCAAACCTAGAGGGTACACTGACTTATGCCACACGGCCAA-TCACACG
39759131 C
65 C
* * * * *
39759132 CCGTGTGCTAGGCCGTGTGCAAA-TTAGGGGGTACACTGACTTATGCCACGCGGCCGATCACACG
1 CCGTGTGCTAGGCCGTG-CCAAACCTAGAGGGTACACTGACTTATGCCACACGGCCAATCACACG
39759196 C
65 C
39759197 CCGTGTG
1 CCGTGTG
39759204 TGAGATCGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 14 0.23
66 43 0.70
67 4 0.07
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.22
Consensus pattern (65 bp):
CCGTGTGCTAGGCCGTGCCAAACCTAGAGGGTACACTGACTTATGCCACACGGCCAATCACACGC
Found at i:39775083 original size:104 final size:104
Alignment explanation
Indices: 39774886--39775089 Score: 268
Period size: 104 Copynumber: 2.0 Consensus size: 104
39774876 TGCTCTTAGT
*
39774886 TGATGTTTAAAGGTTAGATGAGTTATACTCATAACCTTCATTTATTTGAGTAAGCTGAGTCAAGC
1 TGATGTTTAAAGGTCAGATGAGTTATACTCATAACCTTCATTTATTTGAGTAAGCTGAGTCAAGC
* *** *
39774951 TCACTACTCTGAAACAGTTCATGGACCTATGCTCCCAAC
66 TCACTACTCTGAAACAGCTCACAAACCTATACTCCCAAC
* * *
39774990 TGATGTTTTAAGGTCAGATGAGTTATACTCATAACCTTTATTTATTTGAGTAAGTTGAG-CTAAG
1 TGATGTTTAAAGGTCAGATGAGTTATACTCATAACCTTCATTTATTTGAGTAAGCTGAGTC-AAG
* * *
39775054 CTCGCTACT-TCGGAATAGCTCACAAACCTATACTCC
65 CTCACTACTCT-GAAACAGCTCACAAACCTATACTCC
39775090 TAGCTGACAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 2 0.02
104 84 0.98
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (104 bp):
TGATGTTTAAAGGTCAGATGAGTTATACTCATAACCTTCATTTATTTGAGTAAGCTGAGTCAAGC
TCACTACTCTGAAACAGCTCACAAACCTATACTCCCAAC
Found at i:39775478 original size:16 final size:16
Alignment explanation
Indices: 39775457--39775487 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39775447 CATTAGTAAA
*
39775457 TCAACTTAAAATTTTT
1 TCAACTCAAAATTTTT
39775473 TCAACTCAAAATTTT
1 TCAACTCAAAATTTT
39775488 CATTCCATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (16 bp):
TCAACTCAAAATTTTT
Found at i:39778267 original size:33 final size:33
Alignment explanation
Indices: 39778221--39778295 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
39778211 TACTCTTTGT
*
39778221 GTGTGTTGATTGGATTAGCTCTTATGAGCATTG
1 GTGTGTTGGTTGGATTAGCTCTTATGAGCATTG
39778254 GTGTGTTGGTTGGATTAGCTCTTATGAGCATTG
1 GTGTGTTGGTTGGATTAGCTCTTATGAGCATTG
39778287 GTGTGTTGG
1 GTGTGTTGG
39778296 AGGGATTGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.08, G:0.35, T:0.43
Consensus pattern (33 bp):
GTGTGTTGGTTGGATTAGCTCTTATGAGCATTG
Found at i:39778302 original size:33 final size:33
Alignment explanation
Indices: 39778232--39778307 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
39778222 TGTGTTGATT
**
39778232 GGATTAGCTCTTATGAGCATTGGTGTGTTGGTT
1 GGATTAGCTCTTATGAGCATTGGTGTGTTGGAG
39778265 GGATTAGCTCTTATGAGCATTGGTGTGTTGGAG
1 GGATTAGCTCTTATGAGCATTGGTGTGTTGGAG
*
39778298 GGATTGGCTC
1 GGATTAGCTC
39778308 GAGTGAGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.38
Consensus pattern (33 bp):
GGATTAGCTCTTATGAGCATTGGTGTGTTGGAG
Found at i:39778315 original size:33 final size:33
Alignment explanation
Indices: 39778232--39778327 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
39778222 TGTGTTGATT
* **
39778232 GGATTAGCTCTTATGAGCATTGGTGTGTTGGTT
1 GGATTAGCTCTGATGAGCATTGGTGTGTTGGAG
*
39778265 GGATTAGCTCTTATGAGCATTGGTGTGTTGGAG
1 GGATTAGCTCTGATGAGCATTGGTGTGTTGGAG
* *
39778298 GGATTGGCTC-GAGTGAGCATCTAGTGTGTT
1 GGATTAGCTCTGA-TGAGCAT-TGGTGTGTT
39778328 TGTTTGGACT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
32 1 0.02
33 47 0.84
34 8 0.14
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (33 bp):
GGATTAGCTCTGATGAGCATTGGTGTGTTGGAG
Found at i:39783716 original size:22 final size:22
Alignment explanation
Indices: 39783685--39783738 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
39783675 GTACCAGGGT
39783685 CACACGGGCGGGTCCCTTAGAC
1 CACACGGGCGGGTCCCTTAGAC
*
39783707 CACACAGGCGGGTCCCTTAGAC
1 CACACGGGCGGGTCCCTTAGAC
39783729 CACACGGGCG
1 CACACGGGCG
39783739 TGTGAGCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.37, G:0.31, T:0.11
Consensus pattern (22 bp):
CACACGGGCGGGTCCCTTAGAC
Found at i:39788543 original size:19 final size:19
Alignment explanation
Indices: 39788516--39788554 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39788506 AGTGAGACTG
*
39788516 GTCGGGAAAGGGCCAAGGT
1 GTCGAGAAAGGGCCAAGGT
**
39788535 GTCGAGAAAGTTCCAAGGT
1 GTCGAGAAAGGGCCAAGGT
39788554 G
1 G
39788555 AATAAAGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.41, T:0.15
Consensus pattern (19 bp):
GTCGAGAAAGGGCCAAGGT
Found at i:39799691 original size:19 final size:19
Alignment explanation
Indices: 39799669--39799757 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
39799659 CTTTTTCATA
39799669 ATTTTATATAAT-TTTTAAT
1 ATTTT-TATAATATTTTAAT
* *
39799688 ATTTTTTTAATATTTTATT
1 ATTTTTATAATATTTTAAT
*
39799707 ATTTTTAATAA-ATTTTATAA
1 ATTTTT-ATAATATTTTA-AT
* *
39799727 ATTTTTA-AAAATTCT-AT
1 ATTTTTATAATATTTTAAT
39799744 A-TTTTATAATATTT
1 ATTTTTATAATATTT
39799758 AAAAAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
16 5 0.09
17 7 0.12
18 7 0.12
19 28 0.50
20 9 0.16
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTATAATATTTTAAT
Found at i:39799693 original size:20 final size:20
Alignment explanation
Indices: 39799660--39799733 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
39799650 ATGCAAATTC
* *
39799660 TTTTTCATAATTTTATATAA
1 TTTTTAATATTTTTATATAA
39799680 TTTTTAATATTTTT-T-TAA
1 TTTTTAATATTTTTATATAA
*
39799698 TATTTTATTATTTTTA-ATAAA
1 T-TTTTAATATTTTTATAT-AA
39799719 TTTTATAA-ATTTTTA
1 TTTT-TAATATTTTTA
39799734 AAAATTCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.09
19 13 0.29
20 23 0.51
21 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAATATTTTTATATAA
Found at i:39799710 original size:28 final size:31
Alignment explanation
Indices: 39799660--39799716 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
39799650 ATGCAAATTC
*
39799660 TTTTTCATAATTTTATATAATTTTTAATATT
1 TTTTTAATAATTTTATATAATTTTTAATATT
39799691 TTTTTAAT-ATTTTAT-T-ATTTTTAATA
1 TTTTTAATAATTTTATATAATTTTTAATA
39799717 AATTTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 1 0.04
30 7 0.28
31 7 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTTAATAATTTTATATAATTTTTAATATT
Found at i:39799722 original size:28 final size:30
Alignment explanation
Indices: 39799660--39799731 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 30
39799650 ATGCAAATTC
* **
39799660 TTTTTCATAATTTTATATAATTTTTAATATT
1 TTTTTAAT-ATTTTATATAATTTTTAATAAA
39799691 TTTTTAATATTTTAT-T-ATTTTTAATAAA
1 TTTTTAATATTTTATATAATTTTTAATAAA
39799719 TTTTATAA-ATTTT
1 TTTT-TAATATTTT
39799732 TAAAAATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 19 0.51
29 4 0.11
30 7 0.19
31 7 0.19
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTAATATTTTATATAATTTTTAATAAA
Found at i:39799773 original size:25 final size:26
Alignment explanation
Indices: 39799718--39799775 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
39799708 TTTTTAATAA
* * *
39799718 ATTTTATAAATTTTTAAAAATTCTAT
1 ATTTTATAAATATTTAAAAAATATAT
39799744 ATTTTAT-AATATTTAAAAAATATAT
1 ATTTTATAAATATTTAAAAAATATAT
*
39799769 TTTTTAT
1 ATTTTAT
39799776 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTATAAATATTTAAAAAATATAT
Found at i:39810558 original size:40 final size:40
Alignment explanation
Indices: 39810503--39810665 Score: 202
Period size: 40 Copynumber: 4.1 Consensus size: 40
39810493 TGAATGATAC
* *
39810503 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
39810543 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
39810583 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
39810623 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
39810663 CCG
1 CCG
39810666 ACTAAATTCC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:39812651 original size:26 final size:26
Alignment explanation
Indices: 39812599--39812669 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
39812589 TGTTCCGACC
**
39812599 CACAGCTCATGTGAGCAGGCCCATTT
1 CACAGCTCATGTGAGCATACCCATTT
* *
39812625 CACAGCTCATGTGAGCATACTCTTTT
1 CACAGCTCATGTGAGCATACCCATTT
* *
39812651 CACAGCTCCTATGAGCATA
1 CACAGCTCATGTGAGCATA
39812670 TATGTAAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (26 bp):
CACAGCTCATGTGAGCATACCCATTT
Found at i:39815810 original size:144 final size:144
Alignment explanation
Indices: 39815550--39815879 Score: 452
Period size: 144 Copynumber: 2.3 Consensus size: 144
39815540 TGAATTGTCG
* * * * * *
39815550 ATGCCATGTTCCAAACATGGTCTTAAACTAGCTCACATGTCAAGGCCAATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAGGCCAATGCCACGTCCCAGACA
* * * *
39815615 TGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTC
66 TGGTCTTACACTAGCTCTCGACACAATGCCAATGCCATGTCCTAAACATGGTCTTACACTGGCTC
39815680 TCATAAT-GTGGCCA
131 TCAT-ATCGTGGCCA
* * * *
39815694 ATGCCATGTCCCAGACATGGCCTTACACTAGCGCACATATCAATGCCAATGCCACGTCCTAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAGGCCAATGCCACGTCCCAGACA
39815759 TGGTCTTACACTAGCTCTC-ACA-ACATCGCCAATGCCATGTTCC-AAACATGGTCTTACACTGG
66 TGGTCTTACACTAGCTCTCGACACA-AT-GCCAATGCCATG-TCCTAAACATGGTCTTACACTGG
*
39815821 CTCTCATATCGTGGCCG
128 CTCTCATATCGTGGCCA
*
39815838 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA
39815880 CCCAAATGTC
Statistics
Matches: 165, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
142 1 0.01
143 5 0.03
144 156 0.95
145 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAGGCCAATGCCACGTCCCAGACA
TGGTCTTACACTAGCTCTCGACACAATGCCAATGCCATGTCCTAAACATGGTCTTACACTGGCTC
TCATATCGTGGCCA
Found at i:39815878 original size:48 final size:48
Alignment explanation
Indices: 39815550--39815866 Score: 361
Period size: 48 Copynumber: 6.6 Consensus size: 48
39815540 TGAATTGTCG
* * * * * *
39815550 ATGCCATGTTCCAAACATGGTCTTAAACTAGCTCACATGTCAAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCCA
* * *
39815598 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAAT-GCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-ATGGCCA
* * *
39815646 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCATGGCCA
* * *
39815694 ATGCCATGTCCCAGACATGGCCTTACACTAGCGCACATATCAAT-GCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-ATGGCCA
* * * * *
39815742 ATGCCACGTCCTAGACATGGTCTTACACTAGCTCTCACAACATCGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCCA
* * * * *
39815790 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCCA
39815838 ATGCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
39815867 GGCACACATA
Statistics
Matches: 224, Mismatches: 39, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
47 5 0.02
48 216 0.96
49 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCCA
Found at i:39822352 original size:25 final size:23
Alignment explanation
Indices: 39822323--39822370 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39822313 TTTAGTACTT
39822323 CTCTTTTACTTGTAATGATATTTCA
1 CTCTTTT-CTT-TAATGATATTTCA
* *
39822348 CTCTTTTGTTTAATGTTATTTCA
1 CTCTTTTCTTTAATGATATTTCA
39822371 ATTTTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (23 bp):
CTCTTTTCTTTAATGATATTTCA
Found at i:39823943 original size:40 final size:40
Alignment explanation
Indices: 39823914--39824058 Score: 159
Period size: 40 Copynumber: 3.6 Consensus size: 40
39823904 CTACTCGTTT
* *
39823914 AAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCAC
* *
39823954 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCAC
* ** * *
39823994 AAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTTAGCAC
1 AAATGCCTTCGGGA-CATAACCCGGATATAGTAAC-TCGCAC
* *
39824035 AAA-GCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGGACATAACCCGGA
39824059 CATCATTCGA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
39 3 0.03
40 80 0.85
41 11 0.12
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
AAATGCCTTCGGGACATAACCCGGATATAGTAACTCGCAC
Found at i:39836033 original size:41 final size:44
Alignment explanation
Indices: 39835971--39836095 Score: 159
Period size: 43 Copynumber: 2.9 Consensus size: 44
39835961 TGCTATCACG
** * *
39835971 TATCGATGCCTCTGTCTCAGACAGGGTCTTACAC-AAATCAT-A
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATCA
* *
39836013 TA-CGATGCCAATGTCCCAGACATGGTCTTACACGTAATC-TCC
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATCA
*
39836055 TATCGATGCCAATGTCCCAAACATGGTCTTACACGAAATCA
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCA
39836096 CAACTCGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 28 0.39
42 8 0.11
43 35 0.49
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (44 bp):
TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATCA
Found at i:39836241 original size:2 final size:2
Alignment explanation
Indices: 39836229--39836258 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
39836219 AATTCGGCAC
39836229 AT AT A- 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 A
39836259 CAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39839405 original size:31 final size:31
Alignment explanation
Indices: 39839370--39839508 Score: 192
Period size: 31 Copynumber: 4.5 Consensus size: 31
39839360 CCAATGATAT
* *
39839370 ACGGGCGTGTGCGCCCACACGACGCACATAC
1 ACGGGCGTGTGCGCCCACACGACCCACACAC
* *
39839401 ACGGGCATGTGCGCCCACACGGCCCACACAC
1 ACGGGCGTGTGCGCCCACACGACCCACACAC
*
39839432 ACGGGCGTGTGCGCCCACAC-AGCCCACACAT
1 ACGGGCGTGTGCGCCCACACGA-CCCACACAC
*
39839463 ACGGGCGTGTGCGCCCACACGGCCCACACAC
1 ACGGGCGTGTGCGCCCACACGACCCACACAC
*
39839494 AAGGGCGTGTG-GCCC
1 ACGGGCGTGTGCGCCC
39839509 TCCAAAGCTA
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
30 4 0.04
31 92 0.96
ACGTcount: A:0.21, C:0.41, G:0.29, T:0.09
Consensus pattern (31 bp):
ACGGGCGTGTGCGCCCACACGACCCACACAC
Found at i:39841136 original size:17 final size:17
Alignment explanation
Indices: 39841110--39841144 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39841100 AGTTAGAATT
39841110 CAATTCCACATTAAAAG
1 CAATTCCACATTAAAAG
*
39841127 CAATTTCACATTAAAAG
1 CAATTCCACATTAAAAG
39841144 C
1 C
39841145 GATGTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (17 bp):
CAATTCCACATTAAAAG
Found at i:39842231 original size:50 final size:50
Alignment explanation
Indices: 39842156--39842264 Score: 200
Period size: 50 Copynumber: 2.2 Consensus size: 50
39842146 AAGATAATAG
*
39842156 TATATATATGTATATATTTATCCCAAAACAACATACAGTGATGTTGGCGAA
1 TATA-ATAAGTATATATTTATCCCAAAACAACATACAGTGATGTTGGCGAA
39842207 TATAATAAGTATATATTTATCCCAAAACAACATACAGTGATGTTGGCGAA
1 TATAATAAGTATATATTTATCCCAAAACAACATACAGTGATGTTGGCGAA
39842257 TATAATAA
1 TATAATAA
39842265 TAGTTGAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 53 0.93
51 4 0.07
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (50 bp):
TATAATAAGTATATATTTATCCCAAAACAACATACAGTGATGTTGGCGAA
Found at i:39843468 original size:15 final size:15
Alignment explanation
Indices: 39843450--39843478 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39843440 TTACATATAA
39843450 AATATATACACACAC
1 AATATATACACACAC
39843465 AATATATACACACA
1 AATATATACACACA
39843479 ATTATAATAA
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:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (15 bp):
AATATATACACACAC
Found at i:39849769 original size:2 final size:2
Alignment explanation
Indices: 39849717--39849749 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39849707 AATGGTCATT
*
39849717 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39849750 GTTTGTGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:39860755 original size:2 final size:2
Alignment explanation
Indices: 39860748--39860795 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
39860738 CGTTTTAGAA
*
39860748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39860790 TT AT AT
1 AT AT AT
39860796 TTTTTGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:39861318 original size:25 final size:26
Alignment explanation
Indices: 39861277--39861328 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39861267 AAGGGAGAAT
*
39861277 ATTAAAAAAATAAATTT-ATTTTAAA
1 ATTAAAAAAATAAATTTAATTTCAAA
*
39861302 ATTAATAAAAA-ATATTTAATTTCAAA
1 ATTAA-AAAAATAAATTTAATTTCAAA
39861328 A
1 A
39861329 AGTGATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTAAAAAAATAAATTTAATTTCAAA
Found at i:39870068 original size:16 final size:18
Alignment explanation
Indices: 39870047--39870086 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39870037 AATTTACTCG
39870047 ACAAATG-TA-AAGATTT
1 ACAAATGCTACAAGATTT
39870063 ACAAATGCTACAAGATTT
1 ACAAATGCTACAAGATTT
39870081 ATCAAA
1 A-CAAA
39870087 CTAAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 8 0.38
19 4 0.19
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (18 bp):
ACAAATGCTACAAGATTT
Found at i:39870683 original size:19 final size:19
Alignment explanation
Indices: 39870659--39870698 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
39870649 AATATATGGC
39870659 AATTCCATCAAAATCAATA
1 AATTCCATCAAAATCAATA
39870678 AATTCCATCAAAATCAATA
1 AATTCCATCAAAATCAATA
39870697 AA
1 AA
39870699 CAAGTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (19 bp):
AATTCCATCAAAATCAATA
Found at i:39870917 original size:40 final size:39
Alignment explanation
Indices: 39870873--39871005 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 39
39870863 CACCAGACAG
39870873 AAGCTCATAAGAGCTAATCCAACCGAAACACGTCAAGCAA
1 AAGCTCATAAGAGCTAATCCAACCGAAACACG-CAAGCAA
* * * *
39870913 AAGCTCATAAGAGCTGATCCAACCAAAACACGCCAAACAG
1 AAGCTCATAAGAGCTAATCCAACCGAAACACG-CAAGCAA
* *
39870953 AAGCTCATAAGAGGTAATTCAACCGAAACACGCTAAGCAA
1 AAGCTCATAAGAGCTAATCCAACCGAAACACGC-AAGCAA
39870993 AAGCTCATAAGAG
1 AAGCTCATAAGAG
39871006 TTGATCTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 80 0.99
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (39 bp):
AAGCTCATAAGAGCTAATCCAACCGAAACACGCAAGCAA
Found at i:39870992 original size:80 final size:80
Alignment explanation
Indices: 39870859--39871029 Score: 245
Period size: 80 Copynumber: 2.1 Consensus size: 80
39870849 AGATCAACTG
* *
39870859 AACACACCAGACAGAAGCTCATAAGAGCTAATCCAACCGAAACACGTCAAGCAAAAGCTCATAAG
1 AACACGCCAAACAGAAGCTCATAAGAGCTAATCCAACCGAAACACGTCAAGCAAAAGCTCATAAG
39870924 AGCTGATCCAACCAA
66 AGCTGATCCAACCAA
* *
39870939 AACACGCCAAACAGAAGCTCATAAGAGGTAATTCAACCGAAACACG-CTAAGCAAAAGCTCATAA
1 AACACGCCAAACAGAAGCTCATAAGAGCTAATCCAACCGAAACACGTC-AAGCAAAAGCTCATAA
* * **
39871003 GAGTTGATCTAATGAA
65 GAGCTGATCCAACCAA
*
39871019 AACATGCCAAA
1 AACACGCCAAA
39871030 AAAAGAGTAC
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 80 0.99
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (80 bp):
AACACGCCAAACAGAAGCTCATAAGAGCTAATCCAACCGAAACACGTCAAGCAAAAGCTCATAAG
AGCTGATCCAACCAA
Found at i:39871022 original size:40 final size:40
Alignment explanation
Indices: 39870873--39871022 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
39870863 CACCAGACAG
* *
39870873 AAGCTCATAAGAGCTAATCCAACCG-AAACACG-TCAAGCAA
1 AAGCTCATAAGAGCTGATCTAA-CGAAAACACGCT-AAGCAA
* * * * *
39870913 AAGCTCATAAGAGCTGATCCAACCAAAACACGCCAAACAG
1 AAGCTCATAAGAGCTGATCTAACGAAAACACGCTAAGCAA
* *
39870953 AAGCTCATAAGAGGTAAT-TCAACCG-AAACACGCTAAGCAA
1 AAGCTCATAAGAGCTGATCT-AA-CGAAAACACGCTAAGCAA
* *
39870993 AAGCTCATAAGAGTTGATCTAATGAAAACA
1 AAGCTCATAAGAGCTGATCTAACGAAAACA
39871023 TGCCAAAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.02
40 85 0.96
41 2 0.02
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (40 bp):
AAGCTCATAAGAGCTGATCTAACGAAAACACGCTAAGCAA
Found at i:39876352 original size:28 final size:29
Alignment explanation
Indices: 39876254--39876352 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
39876244 TCACAAATTG
* *
39876254 GCACTAAGTGTGCGGGTTCAAAT-TGTATA
1 GCACTAAGTGTGCGAGTTCGAATAT-TATA
* * *
39876283 GCACTAAGTGTGCAAGTTTGATTA-TATA
1 GCACTAAGTGTGCGAGTTCGAATATTATA
*
39876311 GCACTAAGTGTGCGAGTTCGACTATTA-A
1 GCACTAAGTGTGCGAGTTCGAATATTATA
39876339 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39876353 GGCTTATTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 40 0.67
29 20 0.33
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTCGAATATTATA
Found at i:39884041 original size:28 final size:29
Alignment explanation
Indices: 39883943--39884041 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
39883933 TCACAAATTG
* *
39883943 GCACTAAGTGTGCGGGTTCAAAT-TGTATA
1 GCACTAAGTGTGCGAGTTCGAATAT-TATA
* * *
39883972 GCACTAAGTGTGCAAGTTTGATTA-TATA
1 GCACTAAGTGTGCGAGTTCGAATATTATA
*
39884000 GCACTAAGTGTGCGAGTTCGACTATTA-A
1 GCACTAAGTGTGCGAGTTCGAATATTATA
39884028 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39884042 GGCTTATTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 40 0.67
29 20 0.33
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTCGAATATTATA
Found at i:39891376 original size:42 final size:42
Alignment explanation
Indices: 39891317--39891400 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
39891307 TTCGGTAAGT
*
39891317 ATGCGCGGTAAGTGTTCTGATAGTATGTAAATAGTTAGGATA
1 ATGCGCGGTAAGTGTTCTGATAGTATGTAAATAGTCAGGATA
39891359 ATGCGCGGTAAGTGTTCTGATAGTATGTAAATAGTCAGGATA
1 ATGCGCGGTAAGTGTTCTGATAGTATGTAAATAGTCAGGATA
39891401 TGCATGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (42 bp):
ATGCGCGGTAAGTGTTCTGATAGTATGTAAATAGTCAGGATA
Found at i:39891644 original size:27 final size:26
Alignment explanation
Indices: 39891604--39891744 Score: 165
Period size: 27 Copynumber: 5.2 Consensus size: 26
39891594 AGGAAGCGTC
*
39891604 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
39891631 CTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
39891658 TTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
39891685 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
39891712 CTGGTGGCTCTACCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
39891739 CTGGTG
1 CTGGTG
39891745 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.10
27 85 0.88
28 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:39891687 original size:54 final size:53
Alignment explanation
Indices: 39891604--39891744 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 53
39891594 AGGAAGCGTC
*
39891604 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
39891658 TTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * *
39891712 CTGGTGGCTCTACCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
39891745 ACTTCGTCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 7 0.09
54 72 0.91
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:39894432 original size:26 final size:26
Alignment explanation
Indices: 39894396--39894448 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39894386 TGATTCATCG
* * *
39894396 AGCCATATGAAATTATAGAAAGAATC
1 AGCCACATGAAATTAAAGAAAAAATC
39894422 AGCCACATGAAATTAAAGAAAAAATC
1 AGCCACATGAAATTAAAGAAAAAATC
39894448 A
1 A
39894449 AACCTGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (26 bp):
AGCCACATGAAATTAAAGAAAAAATC
Found at i:39915431 original size:40 final size:41
Alignment explanation
Indices: 39915381--39915505 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 41
39915371 ATCGAACACA
* *
39915381 CCAAAAAAAAGCTCATAAAAGCTAATCCAATCGAAACACGT
1 CCAAACAAAAGCTCATAAGAGCTAATCCAATCGAAACACGT
* * *
39915422 -CAAGCAAAAGCTCATAAGAGCTTATCCAATTGAAACAC-T
1 CCAAACAAAAGCTCATAAGAGCTAATCCAATCGAAACACGT
* * *
39915461 CCAAACAGAAGCTCATAAGAGCTGATCCAATCGGAACACG-
1 CCAAACAAAAGCTCATAAGAGCTAATCCAATCGAAACACGT
39915501 CCAAA
1 CCAAA
39915506 TAAAGAGCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.15
Consensus pattern (41 bp):
CCAAACAAAAGCTCATAAGAGCTAATCCAATCGAAACACGT
Done.