Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 122 of 145
Found at i:40191537 original size:31 final size:31
Alignment explanation
Indices: 40191502--40191563 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
40191492 AGTGTCAATG
40191502 AGCTCTATCAAGTTTTCATCATTTCTTTCAT
1 AGCTCTATCAAGTTTTCATCATTTCTTTCAT
*
40191533 AGCTCTATCAAGTTTTCATTATTTCTTTCAT
1 AGCTCTATCAAGTTTTCATCATTTCTTTCAT
40191564 TCTCCTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (31 bp):
AGCTCTATCAAGTTTTCATCATTTCTTTCAT
Found at i:40195048 original size:82 final size:83
Alignment explanation
Indices: 40194955--40195196 Score: 407
Period size: 83 Copynumber: 2.9 Consensus size: 83
40194945 CGGCAATTTA
*
40194955 AATTCGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAATTGTCA-TTTTTATGAACTT
1 AATTTGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAATTGTCACTTTTTATGAACTT
40195019 ATTTGGTGAACATAATTG
66 ATTTGGTGAACATAATTG
* *
40195037 AATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTACTTTTTATGAACTT
1 AATTTGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAATTGTCACTTTTTATGAACTT
*
40195102 ATTCGGTGAACATAATTG
66 ATTTGGTGAACATAATTG
* *
40195120 AATTTGGTTAATGTATACT-TTTAATTGCTTTTAATTTATTTGAAATTGTCATTTTTTATGAACT
1 AATTTGGTTAATGTATA-TATTTAATTGCTTTTAATTTATTTTAAATTGTCACTTTTTATGAACT
40195184 TATTTGGTGAACA
65 TATTTGGTGAACA
40195197 CTCATGACTA
Statistics
Matches: 149, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
82 48 0.32
83 100 0.67
84 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (83 bp):
AATTTGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAATTGTCACTTTTTATGAACTT
ATTTGGTGAACATAATTG
Found at i:40196301 original size:24 final size:24
Alignment explanation
Indices: 40196269--40196368 Score: 200
Period size: 24 Copynumber: 4.2 Consensus size: 24
40196259 AGGGACATCC
40196269 TTATTTCGTTGCTAAGATTAAAGT
1 TTATTTCGTTGCTAAGATTAAAGT
40196293 TTATTTCGTTGCTAAGATTAAAGT
1 TTATTTCGTTGCTAAGATTAAAGT
40196317 TTATTTCGTTGCTAAGATTAAAGT
1 TTATTTCGTTGCTAAGATTAAAGT
40196341 TTATTTCGTTGCTAAGATTAAAGT
1 TTATTTCGTTGCTAAGATTAAAGT
40196365 TTAT
1 TTAT
40196369 GTTCTCCAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (24 bp):
TTATTTCGTTGCTAAGATTAAAGT
Found at i:40199593 original size:135 final size:135
Alignment explanation
Indices: 40199348--40199758 Score: 687
Period size: 135 Copynumber: 3.0 Consensus size: 135
40199338 AAGCAACTAG
* * *
40199348 AGAAGAAAAACTGGAAAAGTCGAGGAATTGGGCCAAGAAAGATGGAGGAGGATCTGATTCGTCTG
1 AGAAGAAAAACAGGAAAAGACGAGGAATTGGGCCAAGAAAGAT---GGAGGATCTGATTTGTCTG
*
40199413 CTTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGACATAGACAA
63 CTTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGATATAGACAA
40199478 TATGATCC
128 TATGATCC
* * *
40199486 AGAAGAAAAACAGGAAAAGACGAGGAATTGGGCCAAAAAAGATGGAGGATCCGATTTTTCTGCTT
1 AGAAGAAAAACAGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGATCTGATTTGTCTGCTT
* * * *
40199551 CAAACTTGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCGTCGGATATAGACAATAT
66 CAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGATATAGACAATAT
40199616 GATCC
131 GATCC
*
40199621 AGAAGAAAAACCGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGATCTGATTTGTCTGCTT
1 AGAAGAAAAACAGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGATCTGATTTGTCTGCTT
40199686 CAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGATATAGACAATAT
66 CAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGATATAGACAATAT
40199751 GATCC
131 GATCC
40199756 AGA
1 AGA
40199759 GCCTCCCACT
Statistics
Matches: 254, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
135 214 0.84
138 40 0.16
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (135 bp):
AGAAGAAAAACAGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGATCTGATTTGTCTGCTT
CAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATACCATTGGATATAGACAATAT
GATCC
Found at i:40202120 original size:31 final size:28
Alignment explanation
Indices: 40202064--40202128 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
40202054 AAAATTTCAC
*
40202064 ATATAAAATTACACAAATTCAAAATTCTT
1 ATATAAAATTACACAAAATCAAAATT-TT
* *
40202093 GTATAAAATTACATATTAAATCAAAATTTT
1 ATATAAAATTACACA--AAATCAAAATTTT
40202123 ATATAA
1 ATATAA
40202129 TTTTGAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 13 0.43
30 7 0.23
31 10 0.33
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (28 bp):
ATATAAAATTACACAAAATCAAAATTTT
Found at i:40216243 original size:22 final size:22
Alignment explanation
Indices: 40216196--40216268 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
40216186 CGAGGGTAGG
** *
40216196 ATATGATATGATATATGTTA-A
1 ATATGATATGCGATATGCTACA
* *
40216217 TATATGATATGTGTTATGCTACA
1 -ATATGATATGCGATATGCTACA
* **
40216240 ATATGACATGCGATATGCTATG
1 ATATGATATGCGATATGCTACA
40216262 ATATGAT
1 ATATGAT
40216269 TTGAGACTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 39 0.98
23 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (22 bp):
ATATGATATGCGATATGCTACA
Found at i:40216280 original size:22 final size:22
Alignment explanation
Indices: 40216255--40216313 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
40216245 ACATGCGATA
40216255 TGCTATGATATGATT-TGAGACT-
1 TGCTATGATATG-TTATGAGA-TG
*
40216277 TGCTAAGATATGTTATGAGATG
1 TGCTATGATATGTTATGAGATG
*
40216299 TGTTATGATATGTTA
1 TGCTATGATATGTTA
40216314 CACGATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (22 bp):
TGCTATGATATGTTATGAGATG
Found at i:40219786 original size:6 final size:6
Alignment explanation
Indices: 40219775--40219815 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
40219765 AAATATTATT
40219775 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
40219816 TAATAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:40229310 original size:15 final size:14
Alignment explanation
Indices: 40229290--40229323 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
40229280 AAAATAAACA
40229290 TTAAAAAAT-TATTT
1 TTAAAAAATATA-TT
40229304 TTAAAAAATATATT
1 TTAAAAAATATATT
40229318 TTAAAA
1 TTAAAA
40229324 TTAAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAAAAAATATATT
Found at i:40233402 original size:59 final size:60
Alignment explanation
Indices: 40233309--40233427 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 60
40233299 TTGTGATTTT
40233309 TATTTTATAAGCGATTTATTAAGTTCAAGTGGTATGACCCTAAGGTCAAGTGGTTTCATA
1 TATTTTATAAGCGATTTATTAAGTTCAAGTGGTATGACCCTAAGGTCAAGTGGTTTCATA
40233369 TATTTTATAA-CGATTTATTAAGTTCAAGTGGTATGACCCTAAGGTCAAGTGGTTTCATA
1 TATTTTATAAGCGATTTATTAAGTTCAAGTGGTATGACCCTAAGGTCAAGTGGTTTCATA
40233428 AATTGAGGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 49 0.83
60 10 0.17
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (60 bp):
TATTTTATAAGCGATTTATTAAGTTCAAGTGGTATGACCCTAAGGTCAAGTGGTTTCATA
Found at i:40240464 original size:46 final size:46
Alignment explanation
Indices: 40240411--40240503 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
40240401 ACAAAAAGGA
40240411 TAGGGAGTAGAAATGTAGGTTTTCACACAGTAGTGAGGCAAGATGG
1 TAGGGAGTAGAAATGTAGGTTTTCACACAGTAGTGAGGCAAGATGG
40240457 TAGGGAGTAGAAATGTAGGTTTTCACACAGTAGTGAGGCAAGATGG
1 TAGGGAGTAGAAATGTAGGTTTTCACACAGTAGTGAGGCAAGATGG
40240503 T
1 T
40240504 TTACTTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.09, G:0.34, T:0.25
Consensus pattern (46 bp):
TAGGGAGTAGAAATGTAGGTTTTCACACAGTAGTGAGGCAAGATGG
Found at i:40242570 original size:105 final size:101
Alignment explanation
Indices: 40242461--40242654 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 101
40242451 TTTTTAGTGC
* **
40242461 CATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACACATGTATTT
1 CATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTT--ACAT-T-TGA
*
40242526 ATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
62 ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
* * * *
40242566 CATAACCTAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATTTGAACAT
1 CATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACATTTGAACAC
40242631 TGCCATGGTCCAACCATGGTCTTA
66 TGCCATGGTCCAACCATGGTCTTA
40242655 TCCGTCAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 27 0.33
102 1 0.01
103 4 0.05
105 49 0.60
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (101 bp):
CATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACATTTGAACAC
TGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
Found at i:40243826 original size:56 final size:56
Alignment explanation
Indices: 40243760--40243871 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
40243750 ATAATTTGAA
* * **
40243760 TATACTGACTTGTGACACATGGCTGAGCCACACGCCCATGTGCTAAGCCGTGTGAG
1 TATACTGACTTGGGACACACGGCCAAGCCACACGCCCATGTGCTAAGCCGTGTGAG
* * *
40243816 TATACTGACTTGGGTCACACGGCCAAGCCACACGCCCGTGTGTTAAGCCGTGTGAG
1 TATACTGACTTGGGACACACGGCCAAGCCACACGCCCATGTGCTAAGCCGTGTGAG
40243872 CCTACTGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (56 bp):
TATACTGACTTGGGACACACGGCCAAGCCACACGCCCATGTGCTAAGCCGTGTGAG
Found at i:40247427 original size:20 final size:20
Alignment explanation
Indices: 40247390--40247430 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40247380 AAAAAAGACA
* *
40247390 TATAATTATTCATCTAATAT
1 TATAACTATTCAACTAATAT
*
40247410 TATAACTATTCAAGTAATAT
1 TATAACTATTCAACTAATAT
40247430 T
1 T
40247431 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAACTATTCAACTAATAT
Found at i:40251141 original size:40 final size:41
Alignment explanation
Indices: 40251070--40251194 Score: 105
Period size: 40 Copynumber: 3.1 Consensus size: 41
40251060 AGCGGCGTTT
* * * *
40251070 TTAGCGGCGATTG-GACAAAAAACGCCACTAAAAATCTAGCA
1 TTAGCGGCGATTGTTA-GAAAAACGCCGCTAAAAATCAAGCA
* * * ** *
40251111 TTAGCGGTGCTT-TTCGAAAAACGCCGCTAAAGGTCGAGCA
1 TTAGCGGCGATTGTTAGAAAAACGCCGCTAAAAATCAAGCA
* *
40251151 CTAGCGGCGATTGTTAG-AAAACACCGCTAAAAA-CAAGCA
1 TTAGCGGCGATTGTTAGAAAAACGCCGCTAAAAATCAAGCA
40251190 TTAGC
1 TTAGC
40251195 AACGTTTTTT
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
39 9 0.14
40 42 0.66
41 13 0.20
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGATTGTTAGAAAAACGCCGCTAAAAATCAAGCA
Found at i:40251314 original size:41 final size:41
Alignment explanation
Indices: 40251257--40251393 Score: 211
Period size: 41 Copynumber: 3.3 Consensus size: 41
40251247 TGAGTTTTTG
* * *
40251257 GGGCCTGTAGTGGCGTTTTTTAAGAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTC
* *
40251298 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTC
*
40251339 GGGCCTTTAGCGGCGTTTTTTAAGCAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTC
*
40251380 TGGCCTTTAGCGGC
1 GGGCCTTTAGCGGC
40251394 ACTTCTTCAA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTC
Found at i:40261309 original size:19 final size:19
Alignment explanation
Indices: 40261267--40261310 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40261257 TCCCAAATAA
*
40261267 TAAAAAGTAATTTAGAAAG
1 TAAAAAGTAATATAGAAAG
* * *
40261286 GAAAAATTAATATAGAAAT
1 TAAAAAGTAATATAGAAAG
40261305 TAAAAA
1 TAAAAA
40261311 AACCCGAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (19 bp):
TAAAAAGTAATATAGAAAG
Found at i:40263053 original size:96 final size:96
Alignment explanation
Indices: 40262932--40263126 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
40262922 GTTTAAACTT
*
40262932 AAAAATATGTACTTTATGGTGATGTTTTTCTTGTTTCTTTGGGGATTGTTAACTACTTCAAGGGG
1 AAAAATATGTACTTTATGGTGATGTTTTTCTTGTTACTTTGGGGATTGTTAACTACTTCAAGGGG
40262997 TTAATTCTTAACAATAAGCATAAGCTAGTTG
66 TTAATTCTTAACAATAAGCATAAGCTAGTTG
40263028 AAAAATATGTACTTTATGGTGATGTTTTTCTTGTTACTTTGGGGATTGTTAACTACTTCAAGGGG
1 AAAAATATGTACTTTATGGTGATGTTTTTCTTGTTACTTTGGGGATTGTTAACTACTTCAAGGGG
40263093 TTAATTCTTAACAATAAGCATAAGCTAGTTG
66 TTAATTCTTAACAATAAGCATAAGCTAGTTG
40263124 AAA
1 AAA
40263127 TTTGTGCATT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (96 bp):
AAAAATATGTACTTTATGGTGATGTTTTTCTTGTTACTTTGGGGATTGTTAACTACTTCAAGGGG
TTAATTCTTAACAATAAGCATAAGCTAGTTG
Found at i:40272651 original size:71 final size:72
Alignment explanation
Indices: 40272561--40272706 Score: 285
Period size: 71 Copynumber: 2.0 Consensus size: 72
40272551 ATTAAATATT
40272561 TTTATTTTAAAATCATAAATTTGTTTTATAATAAATTTATACTGATTAATAATTTTTTTTCAATT
1 TTTATTTTAAAATCATAAATTTGTTTTATAATAAATTTATACTGATTAATAATTTTTTTTCAATT
40272626 TTATTGA
66 TTATTGA
40272633 TTTATTTT-AAATCATAAATTTGTTTTATAATAAATTTATACTGATTAATAATTTTTTTTCAATT
1 TTTATTTTAAAATCATAAATTTGTTTTATAATAAATTTATACTGATTAATAATTTTTTTTCAATT
40272697 TTATTGA
66 TTATTGA
40272704 TTT
1 TTT
40272707 TAATTTCATT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 66 0.89
72 8 0.11
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (72 bp):
TTTATTTTAAAATCATAAATTTGTTTTATAATAAATTTATACTGATTAATAATTTTTTTTCAATT
TTATTGA
Found at i:40273658 original size:16 final size:17
Alignment explanation
Indices: 40273633--40273666 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40273623 TAGATTTTAT
40273633 TTACAGATATAA-AAAA
1 TTACAGATATAAGAAAA
*
40273649 TTACATATATAAGAAAA
1 TTACAGATATAAGAAAA
40273666 T
1 T
40273667 ACAAACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
TTACAGATATAAGAAAA
Found at i:40273850 original size:91 final size:90
Alignment explanation
Indices: 40273685--40273940 Score: 271
Period size: 91 Copynumber: 2.8 Consensus size: 90
40273675 TCTACAAAAT
* * * * ** * * * *
40273685 GAAAATATATAATTCAATCAACAAATAATACCAATTAAATTTTATTTACAGATACAAAAATAATA
1 GAAAATATAAAATTCGACCAAAAAATAATACGGACTAAAATTGATTTACAAATACAAAAATAATA
* * *
40273750 CGAACATTTTAGAAAATTGATATAC
66 CAAACATTTTACAAAATTAATATAC
* * * * * *
40273775 GAAAATATAAAATTCGACCGATAAATAATACGGGCTAAAAATAT-TTTTACATATCCAAAAATAA
1 GAAAATATAAAATTCGACCAAAAAATAATACGGACT-AAAAT-TGATTTACAAATACAAAAATAA
*
40273839 TACAAATATTTTACAAAATTAATATAC
64 TACAAACATTTTACAAAATTAATATAC
* *
40273866 GAAAATATAAAATTTGACCAAAAAATAATACTGACTAAAATTGATTTACAAATACAAAAATAATA
1 GAAAATATAAAATTCGACCAAAAAATAATACGGACTAAAATTGATTTACAAATACAAAAATAATA
**
40273931 TGAACATTTT
66 CAAACATTTT
40273941 GAATAATAGT
Statistics
Matches: 135, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
89 1 0.01
90 58 0.43
91 75 0.56
92 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (90 bp):
GAAAATATAAAATTCGACCAAAAAATAATACGGACTAAAATTGATTTACAAATACAAAAATAATA
CAAACATTTTACAAAATTAATATAC
Found at i:40277224 original size:49 final size:49
Alignment explanation
Indices: 40277160--40277258 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
40277150 TTCATCATGT
40277160 TAGTAGAGTTAATTCAGGTAAAATCTTCATTTCCTACCCAAAATTTTAC
1 TAGTAGAGTTAATTCAGGTAAAATCTTCATTTCCTACCCAAAATTTTAC
40277209 TAGTAGAGTTAATTCAGGTAAAATCTTCATTTCCTACCCAAAATTTTAC
1 TAGTAGAGTTAATTCAGGTAAAATCTTCATTTCCTACCCAAAATTTTAC
40277258 T
1 T
40277259 CTATTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (49 bp):
TAGTAGAGTTAATTCAGGTAAAATCTTCATTTCCTACCCAAAATTTTAC
Found at i:40277441 original size:6 final size:6
Alignment explanation
Indices: 40277430--40277460 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40277420 GAGTGTTATA
*
40277430 TATATG TATATG TATATG TACATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG T
40277461 CGGGCATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:40292153 original size:20 final size:20
Alignment explanation
Indices: 40292093--40292154 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
40292083 CATTTATGCA
*
40292093 CCAGGAATGCACTTTGTGTG
1 CCAGGAATGTACTTTGTGTG
* * * *
40292113 CCA--AATATGCGCTTATGTG
1 CCAGGAATGTAC-TTTGTGTG
40292132 CCAGGAATGTACTTTGTGTG
1 CCAGGAATGTACTTTGTGTG
40292152 CCA
1 CCA
40292155 AGTATGCTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 4 0.13
19 9 0.30
20 12 0.40
21 5 0.17
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (20 bp):
CCAGGAATGTACTTTGTGTG
Found at i:40293869 original size:5 final size:5
Alignment explanation
Indices: 40293859--40293884 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40293849 CTCGAAAATT
40293859 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
40293885 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:40300704 original size:41 final size:41
Alignment explanation
Indices: 40300659--40300761 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
40300649 AGGTTTGTGC
* * *
40300659 CTAGCAAACTTAGTGCCGGTGAAATATTTTAGACTATACGT
1 CTAGCAAGCTTAATGCCGGTGAAATATTTCAGACTATACGT
* *
40300700 CTAGCAGGCTTAATGCTGGTGAAATATTTCAGACTATACGT
1 CTAGCAAGCTTAATGCCGGTGAAATATTTCAGACTATACGT
40300741 CTAGCAAGCTTAATGCCGGTG
1 CTAGCAAGCTTAATGCCGGTG
40300762 TACTGGATCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (41 bp):
CTAGCAAGCTTAATGCCGGTGAAATATTTCAGACTATACGT
Found at i:40301547 original size:2 final size:2
Alignment explanation
Indices: 40301540--40301564 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40301530 TATAAGCTGA
40301540 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 A
40301565 ATGATAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40302688 original size:20 final size:20
Alignment explanation
Indices: 40302648--40302688 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40302638 ATCGTGATTT
*
40302648 AAAAAGTTATTCCTTTTAAA
1 AAAAAGTTATTCCTTTCAAA
40302668 AAAAAGTTATTACC-TTCAAA
1 AAAAAGTTATT-CCTTTCAAA
40302688 A
1 A
40302689 CCTTGCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAAGTTATTCCTTTCAAA
Found at i:40305750 original size:27 final size:26
Alignment explanation
Indices: 40305692--40305791 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
40305682 TTAACCTATA
* * *
40305692 AGGGTATTTCGATAATTTTCCAAAATG
1 AGGGTCTTTCGATAATTTTAC-AAATC
40305719 AGGGTCTTTCGATAATTTTACAAATC
1 AGGGTCTTTCGATAATTTTACAAATC
* *
40305745 AGGGGTACTTT-GGTAATTTTACAAGTC
1 A-GGGT-CTTTCGATAATTTTACAAATC
* **
40305772 GAGGGTATTTTAATAATTTT
1 -AGGGTCTTTCGATAATTTT
40305792 CTAAACCGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
26 8 0.13
27 48 0.79
28 5 0.08
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (26 bp):
AGGGTCTTTCGATAATTTTACAAATC
Found at i:40313164 original size:72 final size:73
Alignment explanation
Indices: 40313045--40313190 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 73
40313035 TTTTTCTTTT
40313045 TAATATTAGATTTTAAATATATTTAATCCTATTTTGACATATATGTCAAAAATTTAGTATTATTT
1 TAATATTAGA-TTTAAATATATTTAATCCTATTTTGACATATATGTCAAAAATTTAGTATTATTT
40313110 TAATATTTA
65 TAATATTTA
40313119 TAATATTAG-TTTAAATATATTTAATCCTATTTTGACATATATGTCAAAAATTTAGTATTATTTT
1 TAATATTAGATTTAAATATATTTAATCCTATTTTGACATATATGTCAAAAATTTAGTATTATTTT
40313183 AATATTTA
66 AATATTTA
40313191 GGTTTTGATA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 63 0.88
74 9 0.12
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (73 bp):
TAATATTAGATTTAAATATATTTAATCCTATTTTGACATATATGTCAAAAATTTAGTATTATTTT
AATATTTA
Found at i:40318036 original size:71 final size:70
Alignment explanation
Indices: 40317915--40318105 Score: 240
Period size: 71 Copynumber: 2.7 Consensus size: 70
40317905 TACAGCTTAT
* * * * **
40317915 AAGATGAGATAGAAGTCCTAAGATCGACGTAAATGATCCCGTTTAATTTGTTCTAGACTAGAATT
1 AAGATGAGATAGAAGTCCTAAAATCG-TGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAATT
40317980 CCGAAA
65 CCGAAA
*
40317986 AAGATGAGACAGAAGTCCTAAAATCAGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAATT
1 AAGATGAGATAGAAGTCCTAAAATC-GTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAATT
*
40318051 CCGATA
65 CCGAAA
* * * *
40318057 AA-ATGAGATAGAAGTCCTAAAATTGGTGCAAATTACCCCATCTTGTTTG
1 AAGATGAGATAGAAGTCCTAAAA-TCGTGTAAATGACCCCATTTTGTTTG
40318106 ATCAAGAATT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
70 40 0.38
71 64 0.61
72 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (70 bp):
AAGATGAGATAGAAGTCCTAAAATCGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAATTC
CGAAA
Found at i:40318095 original size:70 final size:70
Alignment explanation
Indices: 40317913--40318149 Score: 238
Period size: 71 Copynumber: 3.4 Consensus size: 70
40317903 CATACAGCTT
* * * * *
40317913 ATAAGATGAGATAGAAGTCCTAAGATCGACGT--AAATGATCCCGT-TTAATTTGTTCTAGACTA
1 ATAAAATGAGATAGAAGTCCTAAAATC-A-GTGCAAATGACCCCATCTT-GTTTGTTCTAGACTA
40317975 GAATTCCG
63 GAATTCCG
* * * *
40317983 AAAAAGATGAGACAGAAGTCCTAAAATCAGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGA
1 ATAAA-ATGAGATAGAAGTCCTAAAATCAGTGCAAATGACCCCATCTTGTTTGTTCTAGACTAGA
40318048 ATTCCG
65 ATTCCG
** * *
40318054 ATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATTACCCCATCTTGTTTGATC---A--AGAA
1 ATAAAATGAGATAGAAGTCCTAAAATCAGTGCAAATGACCCCATCTTGTTTGTTCTAGACTAGAA
*
40318114 TTCTG
66 TTCCG
* *
40318119 ATAAAATGAGATAAAAGTCCTAAGATCAGTG
1 ATAAAATGAGATAGAAGTCCTAAAATCAGTG
40318150 TGAATGATGA
Statistics
Matches: 143, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
65 35 0.24
67 1 0.01
69 2 0.01
70 47 0.33
71 56 0.39
72 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (70 bp):
ATAAAATGAGATAGAAGTCCTAAAATCAGTGCAAATGACCCCATCTTGTTTGTTCTAGACTAGAA
TTCCG
Found at i:40318195 original size:68 final size:66
Alignment explanation
Indices: 40318045--40318293 Score: 186
Period size: 65 Copynumber: 3.7 Consensus size: 66
40318035 GTTCTAGACT
* * * ** * * * ** *
40318045 AGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAA--ATTACCCCATCTTGTTTGAT
1 AGAATTCTGAT-AAATGAGATAAAAGTCCTAAGATCAGTGTAATGATGACTCCATCTCATTTGTT
40318108 CA
65 CA
* *
40318110 AGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTGAATGATGAGTCCATCTCCTTTGT
1 AGAATTCTGAT-AAATGAGATAAAAGTCCTAAGATCAGTGT-AATGATGACTCCATCTCATTTGT
*
40318175 TCT
64 TCA
* * **
40318178 AGAATTCTGATCAAATGAGGA-AGAAAGTCCTAGGCTTGGTGTAA--ATGACTCCATCTCATTTG
1 AGAATTCTGAT-AAATGA-GATA-AAAGTCCTAAGATCAGTGTAATGATGACTCCATCTCATTTG
40318240 TTCA
63 TTCA
* * *
40318244 AGAATTCCT-ATAAATTGAGATAGATGTTCTAAGATCAGTGTAAATGATGA
1 AGAATT-CTGATAAA-TGAGATAAAAGTCCTAAGATCAGTGT-AATGATGA
40318294 TCCCGTCTCA
Statistics
Matches: 145, Mismatches: 28, Indels: 19
0.76 0.15 0.10
Matches are distributed among these distances:
65 52 0.36
66 35 0.24
67 2 0.01
68 39 0.27
69 17 0.12
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (66 bp):
AGAATTCTGATAAATGAGATAAAAGTCCTAAGATCAGTGTAATGATGACTCCATCTCATTTGTTC
A
Found at i:40318248 original size:134 final size:133
Alignment explanation
Indices: 40318043--40318293 Score: 317
Period size: 134 Copynumber: 1.9 Consensus size: 133
40318033 TTGTTCTAGA
* **
40318043 CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATTACCCCATCTTGTTTGAT
1 CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTGAT
*
40318108 CAAGAATT-CTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTGAATGATGAGTCCATCTCCTT
66 CAAGAATTCCT-ATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGAGTCCATCTCCTT
40318172 TGTT
130 TGTT
* * *** * *
40318176 CTAGAATTCTGATCAAATGAGGA-AGAAAGTCCTAGGCTTGGTGTAAATGACTCCATCTCATTTG
1 CTAGAATTCCGATAAAATGA-GATAG-AAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTG
* * * * *
40318240 TTCAAGAATTCCTATAAATTGAGATAGATGTTCTAAGATCAGTGTAAATGATGA
64 ATCAAGAATTCCTATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGA
40318294 TCCCGTCTCA
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
133 20 0.20
134 77 0.78
135 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (133 bp):
CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTGAT
CAAGAATTCCTATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGAGTCCATCTCCTTT
GTT
Found at i:40322944 original size:3 final size:3
Alignment explanation
Indices: 40322938--40322971 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
40322928 TGATTTCTTC
40322938 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
40322972 AATGAAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40323789 original size:52 final size:52
Alignment explanation
Indices: 40323727--40323877 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
40323717 AATAATTGTT
* *
40323727 TTTCACTTTGTGAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGTC
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
*
40323779 TTTCACTTTGTAAAAACAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
* *
40323831 TTACACTTTGTAAAAGCAGATTTCCTCTTATCTGCTCGTTTAGCTTT
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
40323878 TATCCCCTAT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 93 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (52 bp):
TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
Found at i:40324629 original size:3 final size:3
Alignment explanation
Indices: 40324621--40324647 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40324611 TGATTCTTTA
40324621 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
40324648 GGTTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40324905 original size:18 final size:19
Alignment explanation
Indices: 40324866--40324907 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40324856 ATAAATTTTA
*
40324866 AAAAATTAAAAAATTATCT
1 AAAAATTAAAAAATTATAT
40324885 AAAAA-TAAATAAATTA-AT
1 AAAAATTAAA-AAATTATAT
40324903 AAAAA
1 AAAAA
40324908 AGAGTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTAAAAAATTATAT
Found at i:40324907 original size:19 final size:18
Alignment explanation
Indices: 40324858--40324908 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
40324848 TGACGAGCAT
*
40324858 AAATTTTAAAAAATTAAA
1 AAATTATAAAAAATTAAA
*
40324876 AAATTATCTAAAAA-TAAA
1 AAATTAT-AAAAAATTAAA
40324894 TAAATTAATAAAAAA
1 -AAATT-ATAAAAAA
40324909 GAGTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.37
19 15 0.56
20 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTATAAAAAATTAAA
Found at i:40342799 original size:139 final size:139
Alignment explanation
Indices: 40342537--40342888 Score: 390
Period size: 139 Copynumber: 2.5 Consensus size: 139
40342527 AAGTATTGCT
* * *
40342537 TCCCTGAAGTTGCAGTGGA-ACAGACTGAAGCCACTAATCCTATTTCCCTGAAGTTGCAGTGAAG
1 TCCCTGAAGTTGCAGTGGAGA-AGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAG
* * * *
40342601 CGGATTAAAACGAGAAATCCTATACCTTTGAAGTTGCAGAGGGCCAGATTAAATTTTATCATAGC
65 CGGATTAAAACAAGAAATCATATACCTTTGAAGTTGCAGAGGGCCAGATTAAATCTTATCAGAGC
**
40342666 AATTCTTATC
130 AAACCTTATC
* *
40342676 TCCCTGAAGTTGCAGTGGGGTAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 TCCCTGAAGTTGCAGTGGAGAAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
* * * * *
40342741 GGATTCAAACAATG-AATCATATACCTTTGAAGTTGCAGTAGGTCGA-ATTAGATCTTATCAGAT
66 GGATTAAAACAA-GAAATCATATACCTTTGAAGTTGCAG-AGGGCCAGATTAAATCTTATCAGAG
40342804 CAAACCTTATC
129 CAAACCTTATC
* ** ** * * *
40342815 TCCTTGGAA-TCACAGTGGAGAAGGTTGAAGATAC-AAGTCTTATCTCCCTGAGGTTGCAGTGGA
1 TCCCT-GAAGTTGCAGTGGAGAAGACTGAAGCTACTAA-TCCTATCTCCCTGAAGTTGCAGTGGA
* *
40342878 GCAGACTAAAA
64 GCGGATTAAAA
40342889 ACCACAAACT
Statistics
Matches: 179, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
138 2 0.01
139 168 0.94
140 9 0.05
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (139 bp):
TCCCTGAAGTTGCAGTGGAGAAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
GGATTAAAACAAGAAATCATATACCTTTGAAGTTGCAGAGGGCCAGATTAAATCTTATCAGAGCA
AACCTTATC
Found at i:40350545 original size:29 final size:30
Alignment explanation
Indices: 40350488--40350545 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
40350478 ACTTCACTAT
40350488 AATAATTACAGAGACCTTCTCAAAAAGAAAG
1 AATAATTACAGAGA-CTTCTCAAAAAGAAAG
*
40350519 AATAATTACAGAG-TTTCTCAAAAAGAA
1 AATAATTACAGAGACTTCTCAAAAAGAA
40350546 GAGACCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (30 bp):
AATAATTACAGAGACTTCTCAAAAAGAAAG
Found at i:40353104 original size:145 final size:149
Alignment explanation
Indices: 40352933--40353230 Score: 469
Period size: 152 Copynumber: 2.0 Consensus size: 149
40352923 GTATTTGTTT
* *
40352933 TTTTACAACTCATTTGTAACAGAACGAAAAAGGAAAGGAAAATGAGTACTTACC-G-AT-TTT-G
1 TTTTACAACTCATTTGTAACAAAACGAAAAAGGAAAGGAAAAGGAGTACTTACCGGTATGTTTCG
* * *
40352994 AAATCCCGTTACCGGAAACCTTCTTCAATGTTGGAATCGGACCGAAAAGGGTACGAAAGACCCCT
66 AAAGCCCGTCACCGGAAACCTTCTTCAATGTTGGAATCGAACCGAAAAGGGTACGAAAGACCCCT
40353059 CCTTTTTCAGCCTCTTGGG
131 CCTTTTTCAGCCTCTTGGG
*
40353078 TTTTACAACTCATTTGTAACAAAACGAAAAAGGAAAGGAAAAGGAGTACTTACCGGTTTCGGGTT
1 TTTTACAACTCATTTGTAACAAAACGAAAAAGGAAAGGAAAAGGAGTACTTACCGGTAT---GTT
* *
40353143 TCGAAAGCCCGTCACTGGAAACCTTCTTCAATGTTGGAATCGAACTGAAAAGGGTACGAAAGACC
63 TCGAAAGCCCGTCACCGGAAACCTTCTTCAATGTTGGAATCGAACCGAAAAGGGTACGAAAGACC
40353208 CCTCCTTTTTCAGCCTCTTGGG
128 CCTCCTTTTTCAGCCTCTTGGG
40353230 T
1 T
40353231 CCAGAGAGTC
Statistics
Matches: 138, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
145 52 0.38
146 1 0.01
147 1 0.01
151 3 0.02
152 81 0.59
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (149 bp):
TTTTACAACTCATTTGTAACAAAACGAAAAAGGAAAGGAAAAGGAGTACTTACCGGTATGTTTCG
AAAGCCCGTCACCGGAAACCTTCTTCAATGTTGGAATCGAACCGAAAAGGGTACGAAAGACCCCT
CCTTTTTCAGCCTCTTGGG
Found at i:40353568 original size:169 final size:165
Alignment explanation
Indices: 40353285--40353620 Score: 582
Period size: 169 Copynumber: 2.0 Consensus size: 165
40353275 GCCCATCTTT
* ** *
40353285 TTCTGGCTCCGACCACCGCTCACGGCAGAGTTATGGCGAAGCTATGACGGCAACATGCCGGAGCC
1 TTCTGGCTCCAACCACCGCTCACGGCAGAGCCACGGCGAAGCTATGACGGCAACATGCCGGAGCC
*
40353350 GGCCGCCATCTGGTCTGAAATCCAGAGGAAAAATAAAAGAAGAAAATTTTGAAAAAAGGGGGAGG
66 AGCCGCCATCTGGTCTGAAATCCAGAGGAAAAATAAAAGAAGAAAATTTTGAAAAAA---GG-GG
40353415 GGGCGGCTGTTAAATGAATTTTAGGTTAAAATTTTATTA
127 GGGCGGCTGTTAAATGAATTTTAGGTTAAAATTTTATTA
40353454 TTCTGGCTCCAACCACCGCTCACGGCAGAGCCACGGCGAAGCTATGACGGCAACATGCCGGAGCC
1 TTCTGGCTCCAACCACCGCTCACGGCAGAGCCACGGCGAAGCTATGACGGCAACATGCCGGAGCC
*
40353519 AGCCGCCATCTGGTCTGAAATCCAGAGGAAAAATAAAAGAAGGAAATTTTGAAAAAAGGGGGGGC
66 AGCCGCCATCTGGTCTGAAATCCAGAGGAAAAATAAAAGAAGAAAATTTTGAAAAAAGGGGGGGC
40353584 GGCTGTTAAATGAATTTTAGGTTAAAATTTTATTA
131 GGCTGTTAAATGAATTTTAGGTTAAAATTTTATTA
40353619 TT
1 TT
40353621 TATAACAATG
Statistics
Matches: 161, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
165 43 0.27
166 2 0.01
169 116 0.72
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (165 bp):
TTCTGGCTCCAACCACCGCTCACGGCAGAGCCACGGCGAAGCTATGACGGCAACATGCCGGAGCC
AGCCGCCATCTGGTCTGAAATCCAGAGGAAAAATAAAAGAAGAAAATTTTGAAAAAAGGGGGGGC
GGCTGTTAAATGAATTTTAGGTTAAAATTTTATTA
Found at i:40360635 original size:5 final size:5
Alignment explanation
Indices: 40360627--40360651 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40360617 TGGGGGATAG
40360627 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
40360652 GTAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:40366397 original size:6 final size:6
Alignment explanation
Indices: 40366388--40366413 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40366378 AAAAATAGAT
40366388 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
40366414 ATGACTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:40387313 original size:2 final size:2
Alignment explanation
Indices: 40387306--40387334 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40387296 TTAGGGTAAC
40387306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40387335 TCAAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40387397 original size:2 final size:2
Alignment explanation
Indices: 40387390--40387416 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40387380 TTAGGGTAAC
40387390 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40387417 TCAAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40387416 original size:84 final size:82
Alignment explanation
Indices: 40387275--40387440 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
40387265 CTAATTCGAA
40387275 TGCAATTCCATGATTGCTTTGTTAGGGTAACTATATATATATATATATATATATATATATTCAAA
1 TGCAATTCCATGATTGCTTTGTTAGGGTAAC--TATATATATATATATATATATATATATTCAAA
*
40387340 TAAAGTGCTTTTTAGGCTT
64 TAAAGTGATTTTTAGGCTT
40387359 TGCAATTCCATGATTGCTTTGTTAGGGTAACTATATATATATATATATATATATATATTCAAATA
1 TGCAATTCCATGATTGCTTTGTTAGGGTAACTATATATATATATATATATATATATATTCAAATA
40387424 AAGTGATTTTTAGGCTT
66 AAGTGATTTTTAGGCTT
40387441 CTTGGGAGCC
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
82 50 0.62
84 31 0.38
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (82 bp):
TGCAATTCCATGATTGCTTTGTTAGGGTAACTATATATATATATATATATATATATATTCAAATA
AAGTGATTTTTAGGCTT
Found at i:40393182 original size:13 final size:13
Alignment explanation
Indices: 40393164--40393194 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40393154 GTATTAAAAT
40393164 ATATTTATACCAA
1 ATATTTATACCAA
*
40393177 ATATTTATATCAA
1 ATATTTATACCAA
40393190 ATATT
1 ATATT
40393195 CATTACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTTATACCAA
Found at i:40393461 original size:20 final size:19
Alignment explanation
Indices: 40393436--40393482 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
40393426 TTTTGAAGAG
40393436 TTTTTATTTTTTTAATAATT
1 TTTTTATTTTTTT-ATAATT
*
40393456 TTTTTAATTTTTTTGTAATT
1 TTTTT-ATTTTTTTATAATT
40393476 TTTTTAT
1 TTTTTAT
40393483 AAATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTTTTATAATT
Found at i:40393463 original size:9 final size:9
Alignment explanation
Indices: 40393436--40393506 Score: 52
Period size: 11 Copynumber: 7.2 Consensus size: 9
40393426 TTTTGAAGAG
*
40393436 TTTTTATTT
1 TTTTTAATT
40393445 TTTTAATAATT
1 TTTT--TAATT
40393456 TTTTTAATTT
1 TTTTTAA-TT
40393466 TTTTGTAATTT
1 TTTT-TAA-TT
*
40393477 TTTTATAAAT
1 TTTT-TAATT
*
40393487 ATTTTAATT
1 TTTTTAATT
*
40393496 TTTATAATT
1 TTTTTAATT
40393505 TT
1 TT
40393507 AAAATTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 20 0.39
10 10 0.20
11 21 0.41
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTTTAATT
Found at i:40394037 original size:14 final size:13
Alignment explanation
Indices: 40394018--40394047 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
40394008 TTATTATATA
40394018 ATAAAATATAGAAT
1 ATAAAATATA-AAT
40394032 ATAAAATATAAAT
1 ATAAAATATAAAT
40394045 ATA
1 ATA
40394048 TATAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:40395113 original size:30 final size:30
Alignment explanation
Indices: 40395079--40395138 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
40395069 TATTTTATTA
40395079 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
40395109 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
40395139 CTTNNNNNNN
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:40397045 original size:16 final size:16
Alignment explanation
Indices: 40397024--40397074 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
40397014 GGTTGGGGGG
40397024 AATGGAATAGGGCTGT
1 AATGGAATAGGGCTGT
*
40397040 AATGGAATAGGACTGT
1 AATGGAATAGGGCTGT
* **
40397056 AATGAAATAAAGCTGT
1 AATGGAATAGGGCTGT
40397072 AAT
1 AAT
40397075 TAATAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.25
Consensus pattern (16 bp):
AATGGAATAGGGCTGT
Found at i:40397229 original size:3 final size:3
Alignment explanation
Indices: 40397221--40397248 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40397211 TAGGTAGATG
40397221 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
40397249 AATTTTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:40400819 original size:25 final size:22
Alignment explanation
Indices: 40400790--40400842 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
40400780 ATATACATCA
40400790 AAATAAAAATAAAAATAAAAATTT
1 AAATAAAAAT-AAAAT-AAAATTT
* *
40400814 ATAATATAGATAAAATAAAATTT
1 A-AATAAAAATAAAATAAAATTT
40400837 AAATAA
1 AAATAA
40400843 TAGAACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 4 0.16
23 8 0.32
24 6 0.24
25 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATAAAAATAAAATAAAATTT
Found at i:40400837 original size:23 final size:24
Alignment explanation
Indices: 40400801--40400846 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
40400791 AATAAAAATA
40400801 AAAATAAAAATTTATAAT-ATAGAT
1 AAAATAAAAATTTA-AATAATAGAT
40400825 AAAAT-AAAATTTAAATAATAGA
1 AAAATAAAAATTTAAATAATAGA
40400847 ACAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 13 0.62
24 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAATAAAAATTTAAATAATAGAT
Found at i:40400852 original size:24 final size:24
Alignment explanation
Indices: 40400801--40400853 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
40400791 AATAAAAATA
*
40400801 AAAATAAAAATTTATAATATAGAT
1 AAAATAAAAATTTATAATATAGAC
40400825 AAAAT-AAAATTTA-AATAATAGAAC
1 AAAATAAAAATTTATAAT-ATAG-AC
40400849 AAAAT
1 AAAAT
40400854 TTAAATAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 12 0.46
24 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAATAAAAATTTATAATATAGAC
Found at i:40403226 original size:20 final size:20
Alignment explanation
Indices: 40403188--40403226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40403178 CGTGATCCAA
* * *
40403188 TTGAAACATGAGAATTTTTT
1 TTGAAACACGAAAACTTTTT
40403208 TTGAAACACGAAAACTTTT
1 TTGAAACACGAAAACTTTT
40403227 GAAATACGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGAAACACGAAAACTTTTT
Found at i:40403228 original size:17 final size:17
Alignment explanation
Indices: 40403205--40403444 Score: 198
Period size: 17 Copynumber: 13.8 Consensus size: 17
40403195 ATGAGAATTT
40403205 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * *
40403222 CTTTTGAAATACGAGAA
1 TTTTTGAAACACGAAAA
* *
40403239 -TTTTAAGAACACAAAAA
1 TTTTTGA-AACACGAAAA
*
40403256 TTTTTAAAACACGAAAA
1 TTTTTGAAACACGAAAA
*
40403273 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* **
40403291 TTTGTGAAACACGGGAA
1 TTTTTGAAACACGAAAA
* *
40403308 TTGTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
* *
40403326 TTTTTGAAACACGGGAAT
1 TTTTTGAAACAC-GAAAA
40403344 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
40403362 TTTTTAAAACACCGGAAA
1 TTTTTGAAACA-CGAAAA
*
40403380 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
*
40403397 TTTTTGAAACACCG-GAA
1 TTTTTGAAACA-CGAAAA
* *
40403414 TTTTTGAAAACAGGAAGA
1 TTTTTG-AAACACGAAAA
40403432 TTTTTGAAACACG
1 TTTTTGAAACACG
40403445 GTTTTTTTAA
Statistics
Matches: 177, Mismatches: 34, Indels: 24
0.75 0.14 0.10
Matches are distributed among these distances:
16 5 0.03
17 86 0.49
18 80 0.45
19 6 0.03
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:40403292 original size:35 final size:35
Alignment explanation
Indices: 40403205--40403445 Score: 260
Period size: 35 Copynumber: 6.9 Consensus size: 35
40403195 ATGAGAATTT
* *
40403205 TTTTTG-AAACACGAAAACTTTTGAAATAC-GAGAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGGA-AA
* * *
40403239 -TTTT-AAGAACACAAAAATTTTTAAAACACGAAAA
1 TTTTTGAA-AACACGAAAATTTTTGAAACACGGAAA
* * *
40403273 TTTTTGAAAACACGGAAATTTGTGAAACACGGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGGAAA
* * *
40403308 TTGTTGAAAACATGAAAATTTTTGAAACACGGGAAT
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-GGAAA
*
40403344 TTTTTGAAAACACGAAAATTTTTAAAACACCGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGGAAA
*
40403380 -TTTTGAAAACACGAAGATTTTTGAAACACCGG-AA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGGAAA
* *
40403414 TTTTTGAAAACAGGAAGATTTTTGAAACACGG
1 TTTTTGAAAACACGAAAATTTTTGAAACACGG
40403446 TTTTTTTAAA
Statistics
Matches: 175, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
33 5 0.03
34 25 0.14
35 109 0.62
36 35 0.20
37 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGGAAA
Found at i:40403418 original size:18 final size:17
Alignment explanation
Indices: 40403253--40403440 Score: 143
Period size: 18 Copynumber: 10.7 Consensus size: 17
40403243 AAGAACACAA
*
40403253 AAATTTTT-AAAACACGA
1 AAATTTTTGAAAAC-CGG
40403270 AAATTTTTGAAAACACGG
1 AAATTTTTGAAAAC-CGG
*
40403288 AAATTTGTG-AAACACGG
1 AAATTTTTGAAAAC-CGG
* * * *
40403305 GAATTGTTGAAAACATGA
1 AAATTTTTGAAAAC-CGG
*
40403323 AAATTTTTGAAACACGGG
1 AAATTTTTGAAA-ACCGG
* *
40403341 AATTTTTTGAAAACACGA
1 AAATTTTTGAAAAC-CGG
*
40403359 AAATTTTTAAAACACCGG
1 AAATTTTTGAAA-ACCGG
40403377 AAA-TTTTGAAAACAC-G
1 AAATTTTTGAAAAC-CGG
40403393 AAGATTTTTGAAACACCGG
1 AA-ATTTTTGAAA-ACCGG
*
40403412 -AATTTTTGAAAACAGG
1 AAATTTTTGAAAACCGG
40403428 AAGATTTTTGAAA
1 AA-ATTTTTGAAA
40403441 CACGGTTTTT
Statistics
Matches: 140, Mismatches: 19, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.06
17 44 0.31
18 80 0.57
19 7 0.05
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (17 bp):
AAATTTTTGAAAACCGG
Found at i:40404352 original size:10 final size:10
Alignment explanation
Indices: 40404334--40404427 Score: 56
Period size: 10 Copynumber: 9.6 Consensus size: 10
40404324 GACCCGACTA
40404334 TTCTATTTTT-
1 TTCT-TTTTTC
40404344 TTCTTTTTTC
1 TTCTTTTTTC
40404354 TTCTTTTTTC
1 TTCTTTTTTC
*
40404364 --CCTTTTT-
1 TTCTTTTTTC
**
40404371 TTC-TTTCCC
1 TTCTTTTTTC
*
40404380 TTTCTTCTTTC
1 -TTCTTTTTTC
40404391 TT-TTTTTTC
1 TTCTTTTTTC
*
40404400 TTCCTTCTTTC
1 TT-CTTTTTTC
*
40404411 TTCTCTTCTTC
1 TTCT-TTTTTC
40404422 TTCTTT
1 TTCTTT
40404428 CCCTTCGACC
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 9 0.14
9 14 0.22
10 23 0.35
11 19 0.29
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:40404384 original size:27 final size:27
Alignment explanation
Indices: 40404354--40404432 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 27
40404344 TTCTTTTTTC
40404354 TTCTTTTTTCCCTTTTTTTCTTTCCCT
1 TTCTTTTTTCCCTTTTTTTCTTTCCCT
* *
40404381 TTCTTCTTT-CTTTTTTTTC-TT-CC-
1 TTCTTTTTTCCCTTTTTTTCTTTCCCT
* * *
40404404 TTCTTTCTTCTCTTCTTCTTCTTTCCCT
1 TTCTTTTTTCCCTT-TTTTTCTTTCCCT
40404432 T
1 T
40404433 CGACCTTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
23 7 0.17
24 4 0.10
25 7 0.17
26 11 0.28
27 10 0.25
28 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (27 bp):
TTCTTTTTTCCCTTTTTTTCTTTCCCT
Found at i:40404425 original size:11 final size:12
Alignment explanation
Indices: 40404382--40404425 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
40404372 TCTTTCCCTT
40404382 TCTTCTTTCTT-
1 TCTTCTTTCTTC
40404393 T-TT-TTTCTTC
1 TCTTCTTTCTTC
40404403 -CTTCTTTCTTC
1 TCTTCTTTCTTC
40404414 TCTTC-TTCTTC
1 TCTTCTTTCTTC
40404425 T
1 T
40404426 TTCCCTTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.21
10 4 0.14
11 15 0.52
12 4 0.14
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTCTTC
Found at i:40404433 original size:27 final size:26
Alignment explanation
Indices: 40404334--40404433 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 26
40404324 GACCCGACTA
* ** *
40404334 TTCTATTTTTTTCTTTTTTCTTCTTTT
1 TTCTCTTTTTTTC-TTTCCCTTCTTTC
*
40404361 TTCCCTTTTTTTCTTTCCCTT-TCTTC
1 TTCTCTTTTTTTCTTTCCCTTCT-TTC
40404387 TT-TCTTTTTTT-TCTT-CCTTCTTTC
1 TTCTCTTTTTTTCT-TTCCCTTCTTTC
*
40404411 TTCTCTTCTTCTTCTTTCCCTTC
1 TTCTCTT-TTTTTCTTTCCCTTC
40404434 GACCTTGCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
24 10 0.17
25 16 0.27
26 16 0.27
27 17 0.29
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (26 bp):
TTCTCTTTTTTTCTTTCCCTTCTTTC
Found at i:40404512 original size:11 final size:11
Alignment explanation
Indices: 40404496--40404525 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40404486 CGGCGTCTCC
40404496 TCTTCTCTTCT
1 TCTTCTCTTCT
40404507 TCTTCTCTTCT
1 TCTTCTCTTCT
40404518 T-TTCTCTT
1 TCTTCTCTT
40404526 TTTTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TCTTCTCTTCT
Found at i:40404614 original size:15 final size:15
Alignment explanation
Indices: 40404596--40404629 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40404586 CGACGATGTT
*
40404596 GTGGTTGCGGTGGCG
1 GTGGTTGCGGTGACG
40404611 GTGGTTGCGGTGACG
1 GTGGTTGCGGTGACG
40404626 GTGG
1 GTGG
40404630 GGGAATCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.12, G:0.59, T:0.26
Consensus pattern (15 bp):
GTGGTTGCGGTGACG
Found at i:40404951 original size:29 final size:31
Alignment explanation
Indices: 40404903--40404974 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
40404893 TTTCTAGGAT
40404903 AAAAGTGTAA-TTTTAGGAAAATAT-GAGGCC
1 AAAA-TGTAATTTTTAGGAAAATATAGAGGCC
* * *
40404933 AAAATGTAATTTTTA-GAAAGTTTAGGGGCC
1 AAAATGTAATTTTTAGGAAAATATAGAGGCC
*
40404963 TAAATGTAATTT
1 AAAATGTAATTT
40404975 ACAAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (31 bp):
AAAATGTAATTTTTAGGAAAATATAGAGGCC
Found at i:40404968 original size:30 final size:30
Alignment explanation
Indices: 40404934--40405063 Score: 110
Period size: 30 Copynumber: 4.4 Consensus size: 30
40404924 TATGAGGCCA
40404934 AAATGTAATTTTTAG-AAAGTTTAGGGGCCT
1 AAATGTAATTTTTAGAAAAGTTTAGGGG-CT
* * *
40404964 AAATGTAA--TTTA-CAAATTATTAGGGGTT
1 AAATGTAATTTTTAGAAAAGT-TTAGGGGCT
** *
40404992 AAGATGTAA-TTTTAGAAAAAATTAGGGGTCA
1 AA-ATGTAATTTTTAGAAAAGTTTAGGGG-CT
*
40405023 AAATGTAATTTTT-GAAAAGTTCAGGGGCT
1 AAATGTAATTTTTAGAAAAGTTTAGGGGCT
40405052 AAAATGTAATTT
1 -AAATGTAATTT
40405064 GTATTTTTTG
Statistics
Matches: 81, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
28 11 0.14
29 14 0.17
30 47 0.58
31 9 0.11
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (30 bp):
AAATGTAATTTTTAGAAAAGTTTAGGGGCT
Found at i:40405480 original size:76 final size:76
Alignment explanation
Indices: 40405398--40406116 Score: 761
Period size: 75 Copynumber: 9.5 Consensus size: 76
40405388 CATTTCTCAG
** * * *
40405398 ATTATGAGTTGACCTTTGAAAAATAGAAATTGAAAAATACCTCGGCATATGACCCTAGGCTCAAC
1 ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTCAAC
*
40405463 TCACATCTCGC
66 TCACCTCTCGC
* * * *
40405474 AATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAATGCCTCGGCGTAT-AGCCCGAGGCTCAA
1 ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGA-CCCGAGGCTCAA
40405537 CTCACCTCTCGC
65 CTCACCTCTCGC
* *
40405549 ATTATGAGTTGATTTTTTTGGAAAACAAGAAATT-AAAAATACCTCAGCGTA--ACCCGAGGCTC
1 ATTATGAGTTGA--TTTTTGAAAAAC-AGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTC
40405611 AACTCACCTCTCGC
63 AACTCACCTCTCGC
* * *
40405625 ATTATGAGTTGATTTTTTTTGGAAAACAGGAATT-AAAAATACCTCAGCGTA--ACCCGAGGCTC
1 ATTATGAGTTGA---TTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTC
40405687 AACTCACCTCTCGC
63 AACTCACCTCTCGC
* * * * *
40405701 ATTATGAGTTGATTTTTGGAAAATAGAAATT-AAAATATACCTCAACATGTGACCTGAGGCTCAA
1 ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAA-ATACCTCAGCATATGACCCGAGGCTCAA
**
40405765 CTCATTTCTCGC
65 CTCACCTCTCGC
* *
40405777 AATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAATACCTCAGC--GTGACCCGAGGCTCA
1 ATTATGAGTTGA--TTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTCA
40405839 ACTCACCTCTCGC
64 ACTCACCTCTCGC
* ** * *
40405852 AATATGAGTTGATATTTTTGAAAAGTAGAAATTG-AAAATACCTCAGC--ATGGCCCGAGGCTTA
1 ATTATGAGTTG--ATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTCA
*
40405914 ACTCACTTCTCGC
64 ACTCACCTCTCGC
* * * *
40405927 ATTATGAGTTGATTTTTGAAAAATAGAAATTG-AAAATACCTCAGGATGTGACTCGAGGCTCAAC
1 ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTCAAC
*
40405991 CCACCTCTCGC
66 TCACCTCTCGC
* * ** * *
40406002 ATTATGAGTTAAATTTTTTTTTGAAAAACAGAAATTGAGAAATACCTTGGCATGTG-CCCAAGGC
1 ATTATGAGTT-GA----TTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGC
*
40406066 TCAACTCACCTCTTGC
61 TCAACTCACCTCTCGC
***
40406082 ATTATGAGTTGATTTAAAAAAAACAGAAATTGAAA
1 ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAA
40406117 CATATTTCTT
Statistics
Matches: 564, Mismatches: 58, Indels: 43
0.85 0.09 0.06
Matches are distributed among these distances:
73 53 0.09
74 11 0.02
75 201 0.36
76 157 0.28
77 36 0.06
78 42 0.07
79 1 0.00
80 49 0.09
81 14 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (76 bp):
ATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATATGACCCGAGGCTCAAC
TCACCTCTCGC
Found at i:40405809 original size:227 final size:225
Alignment explanation
Indices: 40405412--40406096 Score: 847
Period size: 227 Copynumber: 3.0 Consensus size: 225
40405402 TGAGTTGACC
** * * *
40405412 TTTGAAAAATAGAAATTGAAAAATACCTCGGCATATGACCCTAGGCTCAACTCACATCTCGCAAT
1 TTTGAAAAGCAGAAATT-AAAAATACCTCAGCATA--ACCCGAGGCTCAACTCACATCTCGCATT
* * * * * *
40405477 ATGAGTTGATTTTTGAAAAACAGAAATTAAAAATGCCTCGGCGTAT-AGCCCGAGGCTCAACTCA
63 ATGAGTTGATTTTTGAAAAATAGAAATTAAAAATACCTCAGCATGTGA-CCTGAGGCTCAACTCA
*
40405541 CCTCTCGCATTATGAGTTGATTTTTTTGGAAAACAAGAAATTAAAAATACCTCAGCGTAACCCGA
127 CCTCTCGCATTATGAGTTGATTTTTTTGAAAAAC-AGAAATTAAAAATACCTCAGCGT-ACCCGA
40405606 GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
190 GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
* * *
40405642 TTTGGAAAA-CAGGAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCATTAT
1 TTT-GAAAAGCAGAAATTAAAAATACCTCAGCATAACCCGAGGCTCAACTCACATCTCGCATTAT
* * **
40405706 GAGTTGATTTTTGGAAAATAGAAATTAAAATATACCTCAACATGTGACCTGAGGCTCAACTCATT
65 GAGTTGATTTTTGAAAAATAGAAATTAAAA-ATACCTCAGCATGTGACCTGAGGCTCAACTCACC
* *
40405771 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGC
129 TCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGT-ACCCGAGGC
* *
40405836 TCAACTCACCTCTCGCAATATGAGTTGA-TATT
193 TCAACTCACCTCTCGCATTATGAGTTGATTTTT
* * ** * *
40405868 TTTGAAAAGTAGAAATTGAAAATACCTCAGCATGGCCCGAGGCTTAACTCACTTCTCGCATTATG
1 TTTGAAAAGCAGAAATTAAAAATACCTCAGCATAACCCGAGGCTCAACTCACATCTCGCATTATG
* * *
40405933 AGTTGATTTTTGAAAAATAGAAATTGAAAATACCTCAGGATGTGA-CTCGAGGCTCAACCCACCT
66 AGTTGATTTTTGAAAAATAGAAATTAAAAATACCTCAGCATGTGACCT-GAGGCTCAACTCACCT
* * ** * *
40405997 CTCGCATTATGAGTTAAATTTTTTTTTGAAAAACAGAAATTGAGAAATACCTTGGCATGTGCCCA
130 CTCGCATTATGAGTT-GA--TTTTTTTGAAAAACAGAAATT-AAAAATACCTCAGC--GTACCCG
*
40406062 AGGCTCAACTCACCTCTTGCATTATGAGTTGATTT
189 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
40406097 AAAAAAAACA
Statistics
Matches: 394, Mismatches: 49, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
224 2 0.01
225 46 0.12
226 82 0.21
227 113 0.29
228 75 0.19
229 26 0.07
230 42 0.11
231 8 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (225 bp):
TTTGAAAAGCAGAAATTAAAAATACCTCAGCATAACCCGAGGCTCAACTCACATCTCGCATTATG
AGTTGATTTTTGAAAAATAGAAATTAAAAATACCTCAGCATGTGACCTGAGGCTCAACTCACCTC
TCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTACCCGAGGCTCA
ACTCACCTCTCGCATTATGAGTTGATTTTT
Found at i:40417748 original size:20 final size:20
Alignment explanation
Indices: 40417710--40417748 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40417700 CGTGATCCAA
* * *
40417710 TTGAAACATGAGAATTTTTT
1 TTGAAACACGAAAACTTTTT
40417730 TTGAAACACGAAAACTTTT
1 TTGAAACACGAAAACTTTT
40417749 GAAATACGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGAAACACGAAAACTTTTT
Found at i:40417750 original size:17 final size:17
Alignment explanation
Indices: 40417727--40417986 Score: 204
Period size: 18 Copynumber: 14.9 Consensus size: 17
40417717 ATGAGAATTT
40417727 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * **
40417744 CTTTTGAAATACGAGCA
1 TTTTTGAAACACGAAAA
* *
40417761 -TTTTAAGAACACAAAAA
1 TTTTTGA-AACACGAAAA
* *
40417778 TTTTTAAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
40417795 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* * **
40417813 TTTGTGAAACATGGGAA
1 TTTTTGAAACACGAAAA
*
40417830 TTGTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
40417848 TTTTTGAAAACAACG-AAA
1 TTTTTG-AAAC-ACGAAAA
* * *
40417866 TTTTTGAAAGACAGGAAT
1 TTTTTGAAACAC-GAAAA
40417884 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
40417902 TTTTTAAAACATCGGAAA
1 TTTTTGAAACA-CGAAAA
*
40417920 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
40417937 TTTTTGAAACAC-AGAAA
1 TTTTTGAAACACGA-AAA
*
40417954 TTTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
40417972 TTTTTGAAACACGAA
1 TTTTTGAAACACGAA
40417987 TTTTTTTTAA
Statistics
Matches: 194, Mismatches: 35, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
16 8 0.04
17 85 0.44
18 92 0.47
19 9 0.05
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.29
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:40417798 original size:34 final size:34
Alignment explanation
Indices: 40417734--40417798 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
40417724 TTTTTTTTGA
* * **
40417734 AACACGAAAACTTTTGAAATACGAGCATTTTAAG
1 AACACAAAAACTTTTAAAATACGAAAATTTTAAG
*
40417768 AACACAAAAATTTTTAAAATACGAAAATTTT
1 AACACAAAAACTTTTAAAATACGAAAATTTT
40417799 TGAAAACACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.29
Consensus pattern (34 bp):
AACACAAAAACTTTTAAAATACGAAAATTTTAAG
Found at i:40417814 original size:35 final size:35
Alignment explanation
Indices: 40417775--40417992 Score: 214
Period size: 35 Copynumber: 6.2 Consensus size: 35
40417765 AAGAACACAA
*
40417775 AAATTTTTAAAATACGAAAATTTTTGAAAACACGG
1 AAATTTTTAAAACACGAAAATTTTTGAAAACACGG
* * * ** * *
40417810 AAATTTGTGAAACATGGGAATTGTTGAAAACACGA
1 AAATTTTTAAAACACGAAAATTTTTGAAAACACGG
40417845 AAATTTTTGAAAACAACG-AAATTTTTGAAAGACA-GG
1 AAATTTTT-AAAAC-ACGAAAATTTTTGAAA-ACACGG
*
40417881 AATTTTTTGAAAACACGAAAATTTTT-AAAACATCGG
1 AAATTTTT-AAAACACGAAAATTTTTGAAAACA-CGG
* * *
40417917 AAATTTTGAAAACACGAAGATTTTTG-AAACACAG
1 AAATTTTTAAAACACGAAAATTTTTGAAAACACGG
*
40417951 AAATTTTTGAAAACACGAAGATTTTTG-AAACAC-G
1 AAATTTTT-AAAACACGAAAATTTTTGAAAACACGG
*
40417985 AATTTTTT
1 AAATTTTT
40417993 TTAAAAGAAA
Statistics
Matches: 154, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
34 20 0.13
35 85 0.55
36 44 0.29
37 5 0.03
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (35 bp):
AAATTTTTAAAACACGAAAATTTTTGAAAACACGG
Found at i:40417848 original size:53 final size:51
Alignment explanation
Indices: 40417727--40417991 Score: 224
Period size: 53 Copynumber: 5.1 Consensus size: 51
40417717 ATGAGAATTT
* * * * *
40417727 TTTTTG-AAACACGAAAACTTTTG-AAATACGAGCATTTTAAGAACACAA-AAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACACGA-AATTTT-TGAA-ACAAGGAA
* * *
40417778 TTTTT-AAAATACGAAAATTTTTGAAAACACGGAAATTTGTGAAACATGGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACAC-GAAATTTTTGAAACA-AGGAA
* *
40417830 TTGTTGAAAACACGAAAATTTTTGAAAACAACGAAATTTTTGAAAGACAGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAC-ACGAAATTTTTGAAACA-AGGAA
* *
40417883 TTTTTTGAAAACACGAAAATTTTT-AAAACATCGGAAA-TTTTGAAAACACGAAGA
1 -TTTTTGAAAACACGAAAATTTTTGAAAACA-C-GAAATTTTTG-AAACAAGGA-A
*
40417937 TTTTTG-AAACAC-AGAAATTTTTGAAAACACGAAGATTTTTGAAAC-ACGAA
1 TTTTTGAAAACACGA-AAATTTTTGAAAACACGAA-ATTTTTGAAACAAGGAA
40417987 TTTTT
1 TTTTT
40417992 TTTAAAAGAA
Statistics
Matches: 177, Mismatches: 21, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
50 9 0.05
51 28 0.16
52 36 0.20
53 71 0.40
54 33 0.19
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (51 bp):
TTTTTGAAAACACGAAAATTTTTGAAAACACGAAATTTTTGAAACAAGGAA
Found at i:40417993 original size:17 final size:17
Alignment explanation
Indices: 40417775--40417991 Score: 214
Period size: 18 Copynumber: 12.5 Consensus size: 17
40417765 AAGAACACAA
*
40417775 AAATTTTT-AAAATACG
1 AAATTTTTGAAAACACG
40417791 AAAATTTTTGAAAACACGG
1 -AAATTTTTGAAAACAC-G
* *
40417810 AAATTTGTG-AAACATGG
1 AAATTTTTGAAAACA-CG
* *
40417827 GAATTGTTGAAAACACG
1 AAATTTTTGAAAACACG
40417844 AAAATTTTTGAAAACAACG
1 -AAATTTTTGAAAAC-ACG
*
40417863 AAATTTTTGAAAGACAGG
1 AAATTTTTGAAA-ACACG
*
40417881 AATTTTTTGAAAACACG
1 AAATTTTTGAAAACACG
40417898 AAAATTTTT-AAAACATCGG
1 -AAATTTTTGAAAACA-C-G
40417917 AAA-TTTTGAAAACACG
1 AAATTTTTGAAAACACG
40417933 AAGATTTTTG-AAACACAG
1 AA-ATTTTTGAAAACAC-G
40417951 AAATTTTTGAAAACACG
1 AAATTTTTGAAAACACG
40417968 AAGATTTTTG-AAACACG
1 AA-ATTTTTGAAAACACG
40417985 -AATTTTT
1 AAATTTTT
40417992 TTTAAAAGAA
Statistics
Matches: 171, Mismatches: 13, Indels: 34
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.04
16 4 0.02
17 60 0.35
18 94 0.55
19 7 0.04
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (17 bp):
AAATTTTTGAAAACACG
Found at i:40417993 original size:35 final size:34
Alignment explanation
Indices: 40417727--40417992 Score: 206
Period size: 35 Copynumber: 7.6 Consensus size: 34
40417717 ATGAGAATTT
* *
40417727 TTTTTGAAACACGAAAACTTTTG-AAATACG-AGCA
1 TTTTTGAAACACG-AAATTTTTGAAAACACGAAG-A
* * * *
40417761 -TTTTAAGAACACAAAAATTTTT-AAAATACGAAAA
1 TTTTTGA-AACAC-GAAATTTTTGAAAACACGAAGA
* * *
40417795 TTTTTGAAAACACGGAAATTTGTG-AAACATG-GGAA
1 TTTTTG-AAACAC-GAAATTTTTGAAAACACGAAG-A
*
40417830 TTGTTGAAAACACGAAAATTTTTGAAAACAACGAA-A
1 TTTTTG-AAACACG-AAATTTTTGAAAAC-ACGAAGA
* * *
40417866 TTTTTGAAAGACAGGAATTTTTTGAAAACACGAAAA
1 TTTTTG-AA-ACACGAAATTTTTGAAAACACGAAGA
*
40417902 TTTTTAAAACATCGGAAA-TTTTGAAAACACGAAGA
1 TTTTTGAAACA-C-GAAATTTTTGAAAACACGAAGA
40417937 TTTTTGAAACACAGAAATTTTTGAAAACACGAAGA
1 TTTTTGAAACAC-GAAATTTTTGAAAACACGAAGA
*
40417972 TTTTTGAAACACGAATTTTTT
1 TTTTTGAAACACGAAATTTTT
40417993 TTAAAAGAAA
Statistics
Matches: 189, Mismatches: 26, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
33 5 0.03
34 37 0.20
35 105 0.56
36 36 0.19
37 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (34 bp):
TTTTTGAAACACGAAATTTTTGAAAACACGAAGA
Found at i:40418224 original size:19 final size:18
Alignment explanation
Indices: 40418197--40418232 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40418187 TGTGATTATA
40418197 TTAAAACACGAGAAATTTT
1 TTAAAACACGA-AAATTTT
*
40418216 TTAACACACGAAAATTT
1 TTAAAACACGAAAATTT
40418233 GTGAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (18 bp):
TTAAAACACGAAAATTTT
Found at i:40418565 original size:7 final size:7
Alignment explanation
Indices: 40418550--40418602 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
40418540 ACTTGGGCCC
40418550 TTTTTCT
1 TTTTTCT
*
40418557 TTCTTCT
1 TTTTTCT
40418564 TTTTTCT
1 TTTTTCT
40418571 TTTTT-T
1 TTTTTCT
40418577 TTCTTT-T
1 TT-TTTCT
*
40418584 TTTCTCT
1 TTTTTCT
40418591 TTTTTCT
1 TTTTTCT
40418598 TTTTT
1 TTTTT
40418603 GGCTGGGCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:40418571 original size:10 final size:9
Alignment explanation
Indices: 40418549--40418602 Score: 65
Period size: 9 Copynumber: 5.8 Consensus size: 9
40418539 GACTTGGGCC
40418549 CTTTTTCTTT
1 CTTTTT-TTT
40418559 CTTCTTTTTT
1 CTT-TTTTTT
40418569 CTTTTTTTT
1 CTTTTTTTT
40418578 -TCTTTTTTT
1 CT-TTTTTTT
*
40418587 CTCTTTTTT
1 CTTTTTTTT
40418596 CTTTTTT
1 CTTTTTT
40418603 GGCTGGGCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 1 0.03
9 25 0.64
10 10 0.26
11 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:40418574 original size:20 final size:20
Alignment explanation
Indices: 40418549--40418599 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
40418539 GACTTGGGCC
40418549 CTTTTTCTTTCTTCTTTTT-T
1 CTTTTTCTTTCTT-TTTTTCT
*
40418569 CTTTTTTTTTCTTTTTTTCT
1 CTTTTTCTTTCTTTTTTTCT
40418589 CTTTTTTCTTT
1 C-TTTTTCTTT
40418600 TTTGGCTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 14 0.52
21 8 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTTTCTTTCTTTTTTTCT
Found at i:40418582 original size:17 final size:17
Alignment explanation
Indices: 40418550--40418602 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
40418540 ACTTGGGCCC
*
40418550 TTTTTCTTTCTTCTTTT
1 TTTTTCTTTTTTCTTTT
40418567 TTCTTT-TTTTTTCTTTT
1 TT-TTTCTTTTTTCTTTT
*
40418584 TTTCTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
40418601 TT
1 TT
40418603 GGCTGGGCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.06
17 27 0.84
18 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTT
Found at i:40418740 original size:25 final size:23
Alignment explanation
Indices: 40418704--40418767 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
40418694 GCTATTGGGC
40418704 TGCTGTTGGCCTGCTTCCTTTTTTTT
1 TGCT-TTGGCCTGCTT-C-TTTTTTT
* *
40418730 TGCTTTTGCCTTCTTCTTTTTTT
1 TGCTTTGGCCTGCTTCTTTTTTT
*
40418753 TGCTTTGGACTGCTT
1 TGCTTTGGCCTGCTT
40418768 GAGTTGTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 19 0.58
24 1 0.03
25 9 0.27
26 4 0.12
ACGTcount: A:0.02, C:0.22, G:0.17, T:0.59
Consensus pattern (23 bp):
TGCTTTGGCCTGCTTCTTTTTTT
Found at i:40418897 original size:8 final size:8
Alignment explanation
Indices: 40418879--40418951 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
40418869 GACCCGACTA
40418879 TTCTATTTT
1 TTCT-TTTT
40418888 TTCTTTTT
1 TTCTTTTT
40418896 TTCCCTTTTT
1 TT--CTTTTT
*
40418906 TTCTTTCCCT
1 TTCTTT--TT
*
40418916 TTC-TTCT
1 TTCTTTTT
40418923 TTCTTTTT
1 TTCTTTTT
40418931 TTCTTTTT
1 TTCTTTTT
* *
40418939 TTCCTTCT
1 TTCTTTTT
40418947 TTCTT
1 TTCTT
40418952 CTCTTCTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
7 5 0.09
8 31 0.57
9 6 0.11
10 12 0.22
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.75
Consensus pattern (8 bp):
TTCTTTTT
Found at i:40418945 original size:24 final size:24
Alignment explanation
Indices: 40418900--40418951 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
40418890 CTTTTTTTCC
40418900 CTTTTTTTCTTTCCCTTTCTTCTTT
1 CTTTTTTTCTTT-CCTTTCTTCTTT
*
40418925 CTTTTTTTCTTT-TTTTCCTTCTTT
1 CTTTTTTTCTTTCCTTT-CTTCTTT
40418949 CTT
1 CTT
40418952 CTCTTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 3 0.12
24 10 0.40
25 12 0.48
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
CTTTTTTTCTTTCCTTTCTTCTTT
Found at i:40418957 original size:12 final size:12
Alignment explanation
Indices: 40418914--40418967 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 12
40418904 TTTTCTTTCC
40418914 CTTTCTTCT-TT
1 CTTTCTTCTCTT
*
40418925 CTTT-TTTTCTT
1 CTTTCTTCTCTT
40418936 -TTT-TTC-CTT
1 CTTTCTTCTCTT
40418945 CTTTCTTCTCTT
1 CTTTCTTCTCTT
40418957 C-TTCTTC-CTT
1 CTTTCTTCTCTT
40418967 C
1 C
40418968 CCTTCGACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 3 0.08
10 15 0.41
11 15 0.41
12 4 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTTCTTCTCTT
Found at i:40418958 original size:8 final size:7
Alignment explanation
Indices: 40418914--40418967 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
40418904 TTTTCTTTCC
40418914 CTTTCTT
1 CTTTCTT
40418921 CTTTCTT
1 CTTTCTT
40418928 -TTT-TT
1 CTTTCTT
40418933 CTTT-TT
1 CTTTCTT
*
40418939 -TTCCTT
1 CTTTCTT
40418945 CTTTCTT
1 CTTTCTT
40418952 CTCTTCTT
1 CT-TTCTT
*
40418960 CTTCCTT
1 CTTTCTT
40418967 C
1 C
40418968 CCTTCGACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.10
6 10 0.25
7 19 0.47
8 7 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
CTTTCTT
Found at i:40419509 original size:30 final size:30
Alignment explanation
Indices: 40419474--40419626 Score: 102
Period size: 30 Copynumber: 5.1 Consensus size: 30
40419464 AAAAGTGCAA
40419474 TTTTAGGAAAATAT-GGGGCCAAAATGTAAT
1 TTTTA-GAAAATATAGGGGCCAAAATGTAAT
* * *
40419504 TTTTAGAAAGTTTAGGGGCCCAAATGTAA-
1 TTTTAGAAAATATAGGGGCCAAAATGTAAT
* * ** *
40419533 -TTTACAAATTATTAGGGGTTAAGATGTAA-
1 TTTTAGAAAATA-TAGGGGCCAAAATGTAAT
* *
40419562 ATTTAGAAAAAAATATAGGGGTCAAAATGTAAT
1 TTTTAG---AAAATATAGGGGCCAAAATGTAAT
*
40419595 TTTT-GAAAA-ATTCAGGGGCTAAAATGTAAT
1 TTTTAGAAAATA-T-AGGGGCCAAAATGTAAT
40419625 TT
1 TT
40419627 GTATTTTTTG
Statistics
Matches: 97, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
28 9 0.09
29 24 0.25
30 40 0.41
32 16 0.16
33 8 0.08
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (30 bp):
TTTTAGAAAATATAGGGGCCAAAATGTAAT
Found at i:40435715 original size:18 final size:18
Alignment explanation
Indices: 40435678--40435721 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40435668 TTTAATAATT
40435678 AATTAAGATAAAAAATTAA
1 AATTAA-ATAAAAAATTAA
* *
40435697 AATTAAATTAAACATTAA
1 AATTAAATAAAAAATTAA
*
40435715 AGTTAAA
1 AATTAAA
40435722 ATCAACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTAAATAAAAAATTAA
Found at i:40437810 original size:22 final size:23
Alignment explanation
Indices: 40437785--40437834 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
40437775 AAAAAAATGG
*
40437785 GTATTCATTTATT-TATAATTT-T
1 GTATTCATTT-TTATAAAATTTAT
*
40437807 GTATTTATTTTTATAAAATTTAT
1 GTATTCATTTTTATAAAATTTAT
40437830 GTATT
1 GTATT
40437835 TTTTTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (23 bp):
GTATTCATTTTTATAAAATTTAT
Found at i:40440820 original size:26 final size:26
Alignment explanation
Indices: 40440748--40440823 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
40440738 AGCGAGTTAT
*
40440748 ATCGGGAAGCTC-TGGAGAGCCATAA
1 ATCGGGAAGCTCATGAAGAGCCATAA
* ** * * *
40440773 ATCAGGAAGCTCACAAACAGCCTTTA
1 ATCGGGAAGCTCATGAAGAGCCATAA
*
40440799 ATTGGGAAGCTCATGAAGAGCCATA
1 ATCGGGAAGCTCATGAAGAGCCATA
40440824 TATCAAGACG
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
25 11 0.31
26 25 0.69
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (26 bp):
ATCGGGAAGCTCATGAAGAGCCATAA
Found at i:40447282 original size:20 final size:18
Alignment explanation
Indices: 40447258--40447306 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40447248 AATAGTATTT
40447258 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
40447276 GTGATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
40447296 T-TTAATTTAAT
1 TATTAATTTAAT
40447307 GTTTATCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 4 0.15
20 14 0.52
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:40463209 original size:15 final size:17
Alignment explanation
Indices: 40463189--40463228 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40463179 ATTTATAAAG
40463189 AAAAATAATC-TC-TTA
1 AAAAATAATCTTCTTTA
*
40463204 AAAAAT-GTCTTCTTTA
1 AAAAATAATCTTCTTTA
40463220 AAAAATAAT
1 AAAAATAAT
40463229 TACATAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.10
15 8 0.40
16 9 0.45
17 1 0.05
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAAATAATCTTCTTTA
Found at i:40464475 original size:42 final size:42
Alignment explanation
Indices: 40464420--40464577 Score: 217
Period size: 42 Copynumber: 3.8 Consensus size: 42
40464410 TTCTGCTGTG
* * * * *
40464420 TCCGTCGACGGTTTCGTCGCTGATTGTTTAGATTCCGAGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
** *
40464462 TCTTTCGAAGGTTTCGTCGCCGGTGGTTTGGATTCCGGGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
*
40464504 TCCGTCGAAGGTTTCGTCGCCGGTTTTTTGGATTCCGGGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
* *
40464546 TCCGACGAAGGTTTCGTCGCCGGTTGCTTGGA
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGA
40464578 GTCAGCGGTT
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.36
Consensus pattern (42 bp):
TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
Found at i:40464597 original size:33 final size:33
Alignment explanation
Indices: 40464559--40464658 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
40464549 GACGAAGGTT
* * * *
40464559 TCGTCGCCGGTTGCTTGGAGTCAGCGGTTTCTG
1 TCGTCGCCGGTGGTTTGGAATCAGCGGTTTCCG
* *
40464592 TCGTCGCCGGCGGTTTGGAACCAGCGGTTTCCG
1 TCGTCGCCGGTGGTTTGGAATCAGCGGTTTCCG
*
40464625 TCGTCTCCGGTGGTTTGGAATCAGCGGTTTCCG
1 TCGTCGCCGGTGGTTTGGAATCAGCGGTTTCCG
40464658 T
1 T
40464659 GGAAGGTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.08, C:0.26, G:0.35, T:0.31
Consensus pattern (33 bp):
TCGTCGCCGGTGGTTTGGAATCAGCGGTTTCCG
Found at i:40468215 original size:23 final size:23
Alignment explanation
Indices: 40468188--40468243 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
40468178 AATGATGAAA
* *
40468188 TTATAAATTCATACATAATAAAT
1 TTATAAATTAATACATAAAAAAT
** *
40468211 TTATATTTTAATATATAAAAAAT
1 TTATAAATTAATACATAAAAAAT
40468234 TTAT-AATTAA
1 TTATAAATTAA
40468244 ATTCCGATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAAATTAATACATAAAAAAT
Found at i:40470018 original size:24 final size:22
Alignment explanation
Indices: 40469974--40470026 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 22
40469964 AAGTATACAT
40469974 ATTTTTTAAAAATTTATTTTTA
1 ATTTTTTAAAAATTTATTTTTA
40469996 ATTTTTTCAGAAATATTTA-TTTTA
1 ATTTTTT-A-AAA-ATTTATTTTTA
40470020 ATTTTTT
1 ATTTTTT
40470027 TAGTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 15 0.54
25 5 0.18
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTTTAAAAATTTATTTTTA
Found at i:40474265 original size:15 final size:15
Alignment explanation
Indices: 40474241--40474283 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
40474231 ATTTAATAAA
*
40474241 TAAAAATAAAAATCC
1 TAAAACTAAAAATCC
*
40474256 TAAAACTAAAAGT-C
1 TAAAACTAAAAATCC
*
40474270 TAAACCTAAAAATC
1 TAAAACTAAAAATC
40474284 GCTACAGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAACTAAAAATCC
Found at i:40479123 original size:10 final size:10
Alignment explanation
Indices: 40479096--40479127 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
40479086 TGTTTTTGGG
40479096 TTGGTTTATT
1 TTGGTTTATT
40479106 TT--TTTATT
1 TTGGTTTATT
40479114 TTGGTTTATT
1 TTGGTTTATT
40479124 TTGG
1 TTGG
40479128 ATTAGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (10 bp):
TTGGTTTATT
Found at i:40481385 original size:26 final size:26
Alignment explanation
Indices: 40481303--40481385 Score: 86
Period size: 25 Copynumber: 3.3 Consensus size: 26
40481293 TGGCTTTTCG
* *
40481303 GAGC-TTCCCGCTACATGGCTCATAT
1 GAGCATTCCCGTTATATGGCTCATAT
*
40481328 GAGC-TTCCCGTTATATGGCTCGA-AA
1 GAGCATTCCCGTTATATGGCTC-ATAT
40481353 GAG-ATTCCCGTT-TATGTGCTCATAT
1 GAGCATTCCCGTTATATG-GCTCATAT
40481378 GAGCATTC
1 GAGCATTC
40481386 TCGAATATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.10
25 39 0.80
26 5 0.10
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (26 bp):
GAGCATTCCCGTTATATGGCTCATAT
Found at i:40503435 original size:16 final size:17
Alignment explanation
Indices: 40503414--40503447 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40503404 ATGTCTAGAT
40503414 AAATT-ATTAATTGAGG
1 AAATTAATTAATTGAGG
40503430 AAATTAGATTAATTGAGG
1 AAATTA-ATTAATTGAGG
40503448 GGTTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
AAATTAATTAATTGAGG
Found at i:40513209 original size:16 final size:17
Alignment explanation
Indices: 40513182--40513223 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40513172 AATACTTACT
40513182 ATATACATACATATATAC
1 ATATA-ATACATATATAC
*
40513200 ATA-AATACATATATGC
1 ATATAATACATATATAC
40513216 ATATAATA
1 ATATAATA
40513224 TATACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 5 0.23
18 3 0.14
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAATACATATATAC
Found at i:40515801 original size:322 final size:322
Alignment explanation
Indices: 40515203--40515851 Score: 1118
Period size: 322 Copynumber: 2.0 Consensus size: 322
40515193 GTAGATAGGC
* *
40515203 ACTAATCTTAGCTGTTGATATAATTCAATATGTACCGTCGGATCTAGGGGAGATCAATTATAAAT
1 ACTAATCTTAGCTGTTGATATAATTCAATATGTACCATCGGATCTAGGGGAGATCAACTATAAAT
* *
40515268 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
66 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAAGTAAGAGAATAATTTTGAGAGCATTTA
*
40515333 CTCAAACATTTGGTGTGTTATTGTTTTCTTGTGGCTTTATTGTTCAATTCAAGTCCATTTGTCTT
131 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTATTGTTCAATTCAAGTCCATTTGTCTT
* * *
40515398 TTCGAGTATATTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
196 TTCGAGTATATTACGCTTTACTTCGATGCATTAGAGAATCTCTCTTGAGAATTATCACTTTCGAA
* *
40515463 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
261 AGATAGGATAACTTAGGCAGATTTAAAGCAAAGGAATGACCTAAGGCCACACGGTTTGCCAA
* * *
40515525 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
1 ACTAATCTTAGCTGTTGATATAATTCAATATGTACCATCGGATCTAGGGGAGATCAACTATAAAT
40515590 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAAGTAAGAGAATAATTTTGAGAGCATTTA
66 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAAGTAAGAGAATAATTTTGAGAGCATTTA
* *
40515655 CTCAAACATTTGGTGTGCTATTGTTTTTTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
131 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTATTGTTCAATTCAAGTCCATTTGTCTT
*
40515720 TTCGAGTATCTTACGCTTTACTTCGATGCATTAGAGAATCTCTCTTGAGAATTATCACTTTCGAA
196 TTCGAGTATATTACGCTTTACTTCGATGCATTAGAGAATCTCTCTTGAGAATTATCACTTTCGAA
* * * *
40515785 AGGTAGGATGACTTAGGCAGATTTAAAGCAAAGGAATGACCTAAGGCCGCACGGTTTGCCTA
261 AGATAGGATAACTTAGGCAGATTTAAAGCAAAGGAATGACCTAAGGCCACACGGTTTGCCAA
40515847 ACTAA
1 ACTAA
40515852 AGTTCTAGCC
Statistics
Matches: 307, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
322 307 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (322 bp):
ACTAATCTTAGCTGTTGATATAATTCAATATGTACCATCGGATCTAGGGGAGATCAACTATAAAT
AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAAGTAAGAGAATAATTTTGAGAGCATTTA
CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTATTGTTCAATTCAAGTCCATTTGTCTT
TTCGAGTATATTACGCTTTACTTCGATGCATTAGAGAATCTCTCTTGAGAATTATCACTTTCGAA
AGATAGGATAACTTAGGCAGATTTAAAGCAAAGGAATGACCTAAGGCCACACGGTTTGCCAA
Found at i:40519062 original size:23 final size:25
Alignment explanation
Indices: 40519036--40519084 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
40519026 TGTAAATAAG
*
40519036 AAAATTATCTC-TAGA-AATTTTCT
1 AAAATAATCTCTTAGAGAATTTTCT
40519059 AAAATAATCTCTTTAGAGAATTTTCT
1 AAAATAATCTC-TTAGAGAATTTTCT
40519085 CTCTACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
25 4 0.18
26 8 0.36
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAATAATCTCTTAGAGAATTTTCT
Found at i:40519200 original size:21 final size:22
Alignment explanation
Indices: 40519174--40519214 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
40519164 TTCAACTATG
40519174 ATTAAACTTAAT-T-ATTTTAAT
1 ATTAAA-TTAATATAATTTTAAT
40519195 ATTAAATTAATATAATTTTA
1 ATTAAATTAATATAATTTTA
40519215 TCAAGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAAATTAATATAATTTTAAT
Found at i:40524120 original size:27 final size:27
Alignment explanation
Indices: 40524090--40524162 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
40524080 ACACGCCAAA
* *
40524090 AAAATAGAAGCCTTTGTGGTAATTTAT
1 AAAATGGAAGCCTTTGTGGCAATTTAT
** *
40524117 AAAATGGAATTCTTTGTGGCGATTTAT
1 AAAATGGAAGCCTTTGTGGCAATTTAT
* **
40524144 GATGTGGAAGCCTTTGTGG
1 AAAATGGAAGCCTTTGTGG
40524163 AGATCTGAGG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (27 bp):
AAAATGGAAGCCTTTGTGGCAATTTAT
Found at i:40524341 original size:27 final size:27
Alignment explanation
Indices: 40524311--40524370 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
40524301 TGACGAACAT
40524311 TGAAGGGATAGTATGTACGGCAAACTC
1 TGAAGGGATAGTATGTACGGCAAACTC
40524338 TGAAGGGATAGTATGTACGGCAAACTC
1 TGAAGGGATAGTATGTACGGCAAACTC
*
40524365 TAAAGG
1 TGAAGG
40524371 AACGGTAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (27 bp):
TGAAGGGATAGTATGTACGGCAAACTC
Found at i:40528549 original size:24 final size:24
Alignment explanation
Indices: 40528522--40528567 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40528512 GGTAAAGAAG
40528522 ATGTTGGA-ACTGAGGGTGGGGACA
1 ATGTT-GATACTGAGGGTGGGGACA
*
40528546 ATGTTGATAGTGAGGGTGGGGA
1 ATGTTGATACTGAGGGTGGGGA
40528568 AGATGATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.24, C:0.04, G:0.48, T:0.24
Consensus pattern (24 bp):
ATGTTGATACTGAGGGTGGGGACA
Found at i:40528577 original size:24 final size:24
Alignment explanation
Indices: 40528532--40528577 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40528522 ATGTTGGAAC
*
40528532 TGAGGGTGGGGACAATGTTGATAG
1 TGAGGGTGGGGACAATGATGATAG
40528556 TGAGGGTGGGGA-AGATGATGAT
1 TGAGGGTGGGGACA-ATGATGAT
40528578 GTCTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.26, C:0.02, G:0.48, T:0.24
Consensus pattern (24 bp):
TGAGGGTGGGGACAATGATGATAG
Found at i:40531467 original size:19 final size:19
Alignment explanation
Indices: 40531434--40531481 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
40531424 CTTCACCTGC
* * *
40531434 ACAACAAGGAAAGAAATAA
1 ACAACAAAGATAGAAAGAA
40531453 ACAACAAAGATAGAAAGAA
1 ACAACAAAGATAGAAAGAA
*
40531472 A-ATCAAAGAT
1 ACAACAAAGAT
40531482 TCGTAAATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.67, C:0.10, G:0.15, T:0.08
Consensus pattern (19 bp):
ACAACAAAGATAGAAAGAA
Found at i:40534980 original size:37 final size:37
Alignment explanation
Indices: 40534936--40535051 Score: 232
Period size: 37 Copynumber: 3.1 Consensus size: 37
40534926 AAACCATGTG
40534936 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
1 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
40534973 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
1 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
40535010 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
1 ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
40535047 ATAAC
1 ATAAC
40535052 CCTGTCGTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (37 bp):
ATAACTATACTTGAAATAAAAAGTGACACGCAACCAT
Found at i:40538398 original size:22 final size:24
Alignment explanation
Indices: 40538367--40538410 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40538357 AATTCGAGAC
40538367 ATTATATA-TTT-ATATAAATTTT
1 ATTATATATTTTAATATAAATTTT
*
40538389 ATTATTTATTTTAATATAAATT
1 ATTATATATTTTAATATAAATT
40538411 GTGATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATATATTTTAATATAAATTTT
Found at i:40541374 original size:17 final size:17
Alignment explanation
Indices: 40541334--40541390 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
40541324 TTAATGTAAA
*
40541334 ATATATTTATTATAATTA
1 ATAT-TTTATTATAATTT
*
40541352 ATTATTTTTTTATAATTT
1 A-TATTTTATTATAATTT
* *
40541370 ATATTTTATTAGATTTT
1 ATATTTTATTATAATTT
40541387 ATAT
1 ATAT
40541391 AATTTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 17 0.52
18 13 0.39
19 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTTATTATAATTT
Found at i:40550064 original size:3 final size:3
Alignment explanation
Indices: 40550058--40550083 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40550048 TAATAATAAT
40550058 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
40550084 AGAAAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40551886 original size:49 final size:48
Alignment explanation
Indices: 40551813--40551913 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 48
40551803 ACTTAAAGAA
*
40551813 AAATGATGAGTTAGAGTAACATAGGTTAAAATTGAACTAGTGTTTGAT
1 AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
40551861 AAATGATGAGTTAAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
1 AAATGATGAGTT-AGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
40551910 AAAT
1 AAAT
40551914 TAAAAATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 12 0.24
49 39 0.76
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (48 bp):
AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
Found at i:40554301 original size:21 final size:21
Alignment explanation
Indices: 40554277--40554322 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40554267 TATACAATTA
40554277 CATTACATCAACAAATTCAAC
1 CATTACATCAACAAATTCAAC
**
40554298 CATTGGATCAACAAATTCAAC
1 CATTACATCAACAAATTCAAC
40554319 CATT
1 CATT
40554323 GGATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.26
Consensus pattern (21 bp):
CATTACATCAACAAATTCAAC
Found at i:40554323 original size:21 final size:21
Alignment explanation
Indices: 40554283--40554326 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40554273 ATTACATTAC
40554283 ATCAACAAATTCAACCATTGG
1 ATCAACAAATTCAACCATTGG
40554304 ATCAACAAATTCAACCATTGG
1 ATCAACAAATTCAACCATTGG
40554325 AT
1 AT
40554327 TATTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (21 bp):
ATCAACAAATTCAACCATTGG
Found at i:40560502 original size:18 final size:18
Alignment explanation
Indices: 40560479--40560514 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40560469 TATTTTGGTC
40560479 ACTCTAAATAAGATAATT
1 ACTCTAAATAAGATAATT
40560497 ACTCTAAATAAGATAATT
1 ACTCTAAATAAGATAATT
40560515 GCTCGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
ACTCTAAATAAGATAATT
Done.