Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 128 of 332
Found at i:41819986 original size:11 final size:11
Alignment explanation
Indices: 41819972--41820004 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41819962 ATTTTATAAA
41819972 AAAATATTTTT
1 AAAATATTTTT
41819983 AAAAT-TTTTT
1 AAAATATTTTT
41819993 AGAAATATTTTT
1 A-AAATATTTTT
41820005 TACAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.30
11 9 0.45
12 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:41820011 original size:23 final size:24
Alignment explanation
Indices: 41819953--41820015 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
41819943 TTTTAAATAA
*
41819953 ATTTTTAAAATTTTATAAAAAAAT
1 ATTTTTAAAATTTTTTAAAAAAAT
* *
41819977 ATTTTTAAAATTTTTTAGAAATAT
1 ATTTTTAAAATTTTTTAAAAAAAT
*
41820001 -TTTTTACAATTTTTT
1 ATTTTTAAAATTTTTT
41820016 TATATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTTAAAATTTTTTAAAAAAAT
Found at i:41820024 original size:21 final size:21
Alignment explanation
Indices: 41820000--41820046 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41819990 TTTAGAAATA
* * *
41820000 TTTTTTACAATTTTTTTATAT
1 TTTTTTACAATTCTCTTACAT
*
41820021 TTTTTTACTATTCTCTTACAT
1 TTTTTTACAATTCTCTTACAT
41820042 TTTTT
1 TTTTT
41820047 GTAATAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTACAATTCTCTTACAT
Found at i:41820106 original size:14 final size:15
Alignment explanation
Indices: 41820089--41820123 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41820079 TTTAGTTATC
41820089 TTTTTTAATTT-TAA
1 TTTTTTAATTTATAA
*
41820103 TTTTATAATTTATAA
1 TTTTTTAATTTATAA
41820118 TTTTTT
1 TTTTTT
41820124 TCTATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTAATTTATAA
Found at i:41820149 original size:11 final size:10
Alignment explanation
Indices: 41820120--41820154 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
41820110 ATTTATAATT
41820120 TTTTTCTATA
1 TTTTTCTATA
41820130 -TTTTCTATA
1 TTTTTCTATA
41820139 TTTTTCATATA
1 TTTTTC-TATA
41820150 TTTTT
1 TTTTT
41820155 AATGTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 5 0.22
11 9 0.39
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTCTATA
Found at i:41824090 original size:16 final size:16
Alignment explanation
Indices: 41824069--41824102 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
41824059 TATAAATTAA
41824069 TTTTAATTA-ATTAATT
1 TTTTAATTATA-TAATT
41824085 TTTTAATTATATAATT
1 TTTTAATTATATAATT
41824101 TT
1 TT
41824103 CACAACTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTATATAATT
Found at i:41825381 original size:28 final size:27
Alignment explanation
Indices: 41825294--41825383 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
41825284 CTGACAGAGT
* *
41825294 CACCAGATACAAATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
41825323 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
*
41825350 CACCAGAACAGATAATTTATGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
41825378 CACCAG
1 CACCAG
41825384 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 23 0.46
28 20 0.40
29 7 0.14
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:41825536 original size:28 final size:28
Alignment explanation
Indices: 41825490--41825552 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
41825480 AATTAACCCC
*
41825490 AGGGGTATAGAGGTCATTTTGCATACAT
1 AGGGGTATAGAGGTAATTTTGCATACAT
41825518 AGGGGTATA-ATGGTAATTTTGCATACAT
1 AGGGGTATAGA-GGTAATTTTGCATACAT
41825546 AGGGGTA
1 AGGGGTA
41825553 CTCTAGTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (28 bp):
AGGGGTATAGAGGTAATTTTGCATACAT
Found at i:41829366 original size:53 final size:52
Alignment explanation
Indices: 41829291--41829450 Score: 189
Period size: 52 Copynumber: 3.1 Consensus size: 52
41829281 CGGATCACAT
* * *
41829291 ATCATATCGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCAC
* *
41829344 ATCATACCGATGCCATAGCCCAGCTATGATCTTATACGGGAGT-ACGAT-TCAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATAC-GGAATCAC-ATATCAC
** * * *
41829396 ATTGTACCGATGCCATAGCCCTGCTATGGTCTTATACGGAAGCACATATTAC
1 ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCAC
41829448 ATC
1 ATC
41829451 TTTTCCGTCA
Statistics
Matches: 90, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
51 5 0.06
52 44 0.49
53 36 0.40
54 5 0.06
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (52 bp):
ATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCAC
Found at i:41833409 original size:19 final size:19
Alignment explanation
Indices: 41833385--41833429 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
41833375 CATCATTAAC
41833385 AGAAGCTCGAAAGCTGAAT
1 AGAAGCTCGAAAGCTGAAT
41833404 AGAAGCTCGAAAGCTGAAT
1 AGAAGCTCGAAAGCTGAAT
41833423 AGAAGCT
1 AGAAGCT
41833430 TGTAAGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.16
Consensus pattern (19 bp):
AGAAGCTCGAAAGCTGAAT
Found at i:41833447 original size:21 final size:21
Alignment explanation
Indices: 41833382--41833609 Score: 157
Period size: 21 Copynumber: 11.1 Consensus size: 21
41833372 GTACATCATT
* *
41833382 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTA
* * *
41833401 AATAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTA
* **
41833420 AATAGAAGCTTGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
41833441 AACAGAAACCCATAAGGGTTT
1 AACAGAAGCTCATAAGAGCTA
41833462 AACAGAAGCTCATAAGAGCTGA
1 AACAGAAGCTCATAAGAGCT-A
* * *
41833484 AA-A-AAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
41833503 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * *
41833524 AACAAAAACTCATAAGAG-TT
1 AACAGAAGCTCATAAGAGCTA
41833544 AACAGAAGCTCGA-AAGAGCTA
1 AACAGAAGCTC-ATAAGAGCTA
** * * *
41833565 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
*
41833586 AATAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
41833607 AAC
1 AAC
41833610 GAAAAGTAAA
Statistics
Matches: 162, Mismatches: 39, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
19 31 0.19
20 31 0.19
21 98 0.60
22 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:41833513 original size:41 final size:40
Alignment explanation
Indices: 41833423--41833608 Score: 205
Period size: 41 Copynumber: 4.5 Consensus size: 40
41833413 AAAGCTGAAT
** * * * *
41833423 AGAAGCTTGTAAGAGCTAAACAGAAACCCATAAGGGTTTAAC
1 AGAAGCTCATAAGAGCTAAA-A-AAACTCATATGAGTTAAAC
41833465 AGAAGCTCATAAGAGCTGAAAAAAACTCATATGAGTTAAAC
1 AGAAGCTCATAAGAGCT-AAAAAAACTCATATGAGTTAAAC
*
41833506 AGAAGCTCATAAGAGCTAAACAAAAACTCATAAGAGTT-AAC
1 AGAAGCTCATAAGAGCT-AA-AAAAACTCATATGAGTTAAAC
* *
41833547 AGAAGCTCGA-AAGAGCTAAATGGAAACTCATATGAGTTAAAT
1 AGAAGCTC-ATAAGAGCTAAA--AAAACTCATATGAGTTAAAC
41833589 AGAAGCTCATAAGAGCTAAA
1 AGAAGCTCATAAGAGCTAAA
41833609 CGAAAAGTAA
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 67 0.53
42 53 0.42
43 3 0.02
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (40 bp):
AGAAGCTCATAAGAGCTAAAAAAACTCATATGAGTTAAAC
Found at i:41833520 original size:83 final size:82
Alignment explanation
Indices: 41833423--41833613 Score: 262
Period size: 83 Copynumber: 2.3 Consensus size: 82
41833413 AAAGCTGAAT
** *
41833423 AGAAGCTTGTAAGAGCTAAACAGAAACCCATAAGGGTTTAACAGAAGCTC-ATAAGAGCTGAAA-
1 AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAG-TTAACAGAAGCTCGA-AAGAGCT-AAAG
41833486 AAAACTCATATGAGTTAAAC
63 AAAACTCATATGAGTTAAAC
* * *
41833506 AGAAGCTCATAAGAGCTAAACAAAAACTCATAAGAGTTAACAGAAGCTCGAAAGAGCTAAATGGA
1 AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAACAGAAGCTCGAAAGAGCTAAA-GAA
*
41833571 AACTCATATGAGTTAAAT
65 AACTCATATGAGTTAAAC
41833589 AGAAGCTCATAAGAGCTAAAC-GAAA
1 AGAAGCTCATAAGAGCTAAACAGAAA
41833614 AGTAAAACAT
Statistics
Matches: 97, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
81 3 0.03
82 23 0.24
83 71 0.73
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (82 bp):
AGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAACAGAAGCTCGAAAGAGCTAAAGAAA
ACTCATATGAGTTAAAC
Found at i:41838689 original size:29 final size:29
Alignment explanation
Indices: 41838650--41838719 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
41838640 ATGGCTTGAG
41838650 ACACGGGCGTGTCATTGGTCGTGTGAGCC
1 ACACGGGCGTGTCATTGGTCGTGTGAGCC
* * *
41838679 ATACGGACGTGTCATTGGTCGTTTGAGCC
1 ACACGGGCGTGTCATTGGTCGTGTGAGCC
41838708 ACACGGGCGTGT
1 ACACGGGCGTGT
41838720 GTCACTTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.26
Consensus pattern (29 bp):
ACACGGGCGTGTCATTGGTCGTGTGAGCC
Found at i:41840685 original size:12 final size:12
Alignment explanation
Indices: 41840668--41840699 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41840658 CAATAATCAG
*
41840668 TAACAGTAGCAA
1 TAACAGTAACAA
41840680 TAACAGTAACAA
1 TAACAGTAACAA
41840692 TAACAGTA
1 TAACAGTA
41840700 TTCAACACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (12 bp):
TAACAGTAACAA
Found at i:41840739 original size:51 final size:51
Alignment explanation
Indices: 41840671--41840791 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 51
41840661 TAATCAGTAA
* * *
41840671 CAGTAGCAATAACAGTAACAATAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCCGAAT
* * *
41840722 C-G-----GTACCGGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCCGAAT
*
41840767 CAGTAACAGTAACGGTAACAATAAC
1 CAGTAACAGTAACAGTAACAATAAC
41840792 GGTAACAGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
45 39 0.68
46 1 0.02
50 1 0.02
51 16 0.28
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (51 bp):
CAGTAACAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:41840779 original size:45 final size:45
Alignment explanation
Indices: 41840680--41840786 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
41840670 ACAGTAGCAA
* * *
41840680 TAACAGTAACAATAACAGTATTCAACACACAAAGTGCTGAATCGG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCAG
* *
41840725 TACCGGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCAG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCAG
*
41840770 TAACAGTAACGGTAACA
1 TAACAGTAACAGTAACA
41840787 ATAACGGTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCAG
Found at i:41840786 original size:12 final size:12
Alignment explanation
Indices: 41840769--41840802 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41840759 TGCCGAATCA
41840769 GTAACAGTAACG
1 GTAACAGTAACG
*
41840781 GTAACAATAACG
1 GTAACAGTAACG
41840793 GTAACAGTAA
1 GTAACAGTAA
41840803 TAGTAGTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.18
Consensus pattern (12 bp):
GTAACAGTAACG
Found at i:41841052 original size:40 final size:40
Alignment explanation
Indices: 41841006--41841089 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
41840996 AATCCATTAC
* * *
41841006 TTCAGTAATTTCACAGTTCAATGCAGTA-TACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACT-CAAAACAATA
*
41841046 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACTCAAAACAATA
41841086 TTCA
1 TTCA
41841090 ATATTCCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.32
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACTCAAAACAATA
Found at i:41841070 original size:21 final size:21
Alignment explanation
Indices: 41841006--41841073 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
41840996 AATCCATTAC
* *
41841006 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
41841027 TGCAGTATACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
41841046 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
41841067 TTCAGTA
1 TTCAGTA
41841074 CTCAAAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
21 15 0.43
22 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Found at i:41841184 original size:18 final size:18
Alignment explanation
Indices: 41841161--41841198 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41841151 TTTACTAAAC
41841161 ACTTACCTTAAAATACTT
1 ACTTACCTTAAAATACTT
41841179 ACTTACCTTAAAATACTT
1 ACTTACCTTAAAATACTT
41841197 AC
1 AC
41841199 CACACATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (18 bp):
ACTTACCTTAAAATACTT
Found at i:41854916 original size:56 final size:55
Alignment explanation
Indices: 41854829--41854977 Score: 226
Period size: 56 Copynumber: 2.7 Consensus size: 55
41854819 AGGGGGGTGT
41854829 TAGGATATTATTATAGGATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTA
1 TAGGATATTATTAT-GGATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTA
* * * *
41854885 TAGGATATTATTCTGTGATACTATCTCTTAGCAATTTGATTCCTAATGGGATATTA
1 TAGGATATTATTATG-GATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTA
*
41854941 TATGATATTATTATGAGATATTATCTTTTAGCAATTT
1 TAGGATATTATTATG-GATATTATCTTTTAGCAATTT
41854978 AATTTCTACG
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 1 0.01
56 82 0.99
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (55 bp):
TAGGATATTATTATGGATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTA
Found at i:41855771 original size:9 final size:9
Alignment explanation
Indices: 41855754--41855792 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
41855744 GCTTCCCTCA
*
41855754 AACTTTCTC
1 AACTCTCTC
41855763 AACTCTCTC
1 AACTCTCTC
*
41855772 ACACTTTCTC
1 A-ACTCTCTC
41855782 AACTCTCTC
1 AACTCTCTC
41855791 AA
1 AA
41855793 GCTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (9 bp):
AACTCTCTC
Found at i:41855777 original size:19 final size:19
Alignment explanation
Indices: 41855750--41855797 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
41855740 ACGTGCTTCC
41855750 CTCAAACTTTCTCAACTCT
1 CTCAAACTTTCTCAACTCT
*
41855769 CTCACACTTTCTCAACTCT
1 CTCAAACTTTCTCAACTCT
*
41855788 CTCAAGCTTT
1 CTCAAACTTT
41855798 TTATTACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.38
Consensus pattern (19 bp):
CTCAAACTTTCTCAACTCT
Found at i:41867606 original size:8 final size:7
Alignment explanation
Indices: 41867575--41867604 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41867565 TAAGAATAAG
*
41867575 AATAACA
1 AATAAAA
41867582 AATAAAA
1 AATAAAA
41867589 AATAAAA
1 AATAAAA
41867596 AATAAAA
1 AATAAAA
41867603 AA
1 AA
41867605 ATGGAATCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:41869405 original size:22 final size:23
Alignment explanation
Indices: 41869371--41869420 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
41869361 GGCAACATAT
41869371 AGAATACGCCACAAAA-GCTATC
1 AGAATACGCCACAAAAGGCTATC
* *
41869393 AGAATATGTCACAAAAGGCTATC
1 AGAATACGCCACAAAAGGCTATC
41869416 AGAAT
1 AGAAT
41869421 TGTAACACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (23 bp):
AGAATACGCCACAAAAGGCTATC
Found at i:41870811 original size:39 final size:39
Alignment explanation
Indices: 41870751--41870872 Score: 163
Period size: 39 Copynumber: 3.1 Consensus size: 39
41870741 ACTTCCAATA
* * * ** **
41870751 CACCAGCACACATCCTACTAGGCACAAAGCATGAATAAT
1 CACCAGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
* *
41870790 CACCGGCACAAAGCTTGCTAGGCACTTAGCCCGAATAAT
1 CACCAGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
41870829 CACCAGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
1 CACCAGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
41870868 CACCA
1 CACCA
41870873 TATTTCTATT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.35, C:0.33, G:0.16, T:0.16
Consensus pattern (39 bp):
CACCAGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
Found at i:41872990 original size:21 final size:21
Alignment explanation
Indices: 41872942--41873148 Score: 100
Period size: 21 Copynumber: 10.0 Consensus size: 21
41872932 CTTTCTATTT
**
41872942 AGCTCTTACAAGCTTCTGTTTA
1 AGCTCTTATGAGCTTCTG-TTA
* * *
41872964 A-TTCTTATGAGTTTTTGTTA
1 AGCTCTTATGAGCTTCTGTTA
* *
41872984 AGCTCTTACGAGCTTTTGTTCA
1 AGCTCTTATGAGCTTCTGTT-A
* **
41873006 A-CTCTTAAGAATTTCTGTTA
1 AGCTCTTATGAGCTTCTGTTA
* * * *
41873026 AGCTCTCACGAGCTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTA
* * *
41873047 AGTTTTTTTGAGCTTCTGTTA
1 AGCTCTTATGAGCTTCTGTTA
* * * *
41873068 A-CCCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTA
*
41873088 AGCTCTTTTGAGCTTCTGTTCA
1 AGCTCTTATGAGCTTCTGTT-A
* * * * *
41873110 A-CCCTTATG-GTTTTTTTTT
1 AGCTCTTATGAGCTTCTGTTA
*
41873129 AGCTCTCATGAGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
41873149 CAGCCTTCAG
Statistics
Matches: 130, Mismatches: 48, Indels: 15
0.67 0.25 0.08
Matches are distributed among these distances:
19 1 0.01
20 31 0.24
21 94 0.72
22 4 0.03
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTA
Found at i:41872990 original size:42 final size:42
Alignment explanation
Indices: 41872933--41873047 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
41872923 TGTGTTTTAC
* * * * * * * *
41872933 TTTCTATTTAGCTCTTACAAGCTTCTGTTTAATTCTTATGAG
1 TTTCTGTTAAGCTCTTACGAGCTTTTGTTCAACTCTTAAGAA
*
41872975 TTTTTGTTAAGCTCTTACGAGCTTTTGTTCAACTCTTAAGAA
1 TTTCTGTTAAGCTCTTACGAGCTTTTGTTCAACTCTTAAGAA
*
41873017 TTTCTGTTAAGCTCTCACGAGCTTTTGTTCA
1 TTTCTGTTAAGCTCTTACGAGCTTTTGTTCA
41873048 GTTTTTTTGA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (42 bp):
TTTCTGTTAAGCTCTTACGAGCTTTTGTTCAACTCTTAAGAA
Found at i:41873064 original size:42 final size:42
Alignment explanation
Indices: 41872942--41873107 Score: 138
Period size: 42 Copynumber: 4.0 Consensus size: 42
41872932 CTTTCTATTT
* * * ** * * *
41872942 AGCTCTTACAAGCTTCTGTTTAATTCTTATGAGTTTTTGTTA
1 AGCTCTTACGAGCTTTTGTTCAGCTCTTTTGAGCTTCTGTTA
* ** **
41872984 AGCTCTTACGAGCTTTTGTTCAACTCTTAAGAATTTCTGTTA
1 AGCTCTTACGAGCTTTTGTTCAGCTCTTTTGAGCTTCTGTTA
* * *
41873026 AGCTCTCACGAGCTTTTGTTCAGTTTTTTTGAGCTTCTGTTA
1 AGCTCTTACGAGCTTTTGTTCAGCTCTTTTGAGCTTCTGTTA
* * *
41873068 A-CCCTTATG-GGTTTCTGTTCAGCTCTTTTGAGCTTCTGTT
1 AGCTCTTACGAGCTTT-TGTTCAGCTCTTTTGAGCTTCTGTT
41873108 CAACCCTTAT
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
40 4 0.04
41 28 0.27
42 70 0.69
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (42 bp):
AGCTCTTACGAGCTTTTGTTCAGCTCTTTTGAGCTTCTGTTA
Found at i:41873097 original size:41 final size:41
Alignment explanation
Indices: 41873042--41873150 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 41
41873032 CACGAGCTTT
* *
41873042 TGTTCAGTTTTTTTGAGCTTCTGTT-AACCCTTATGGGTTTC
1 TGTTCAGCTCTTTTGAGCTTCTGTTCAACCCTTAT-GGTTTC
*
41873083 TGTTCAGCTCTTTTGAGCTTCTGTTCAACCCTTATGGTTTT
1 TGTTCAGCTCTTTTGAGCTTCTGTTCAACCCTTATGGTTTC
* * **
41873124 TTTTTAGCTCTCATGAGCTTCTGTTCA
1 TGTTCAGCTCTTTTGAGCTTCTGTTCA
41873151 GCCTTCAGGC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 51 0.85
42 9 0.15
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (41 bp):
TGTTCAGCTCTTTTGAGCTTCTGTTCAACCCTTATGGTTTC
Found at i:41876182 original size:21 final size:21
Alignment explanation
Indices: 41876158--41876224 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
41876148 TTTAACCCTC
41876158 ATGAGTTTCCGTTCAGCTCTT
1 ATGAGTTTCCGTTCAGCTCTT
* * *
41876179 ATGAGCTTCCGTTCAAC-CCT
1 ATGAGTTTCCGTTCAGCTCTT
* * * *
41876199 ACGGGTTTCCGTTTAGCTCTC
1 ATGAGTTTCCGTTCAGCTCTT
41876220 ATGAG
1 ATGAG
41876225 CTTCAATTCA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGAGTTTCCGTTCAGCTCTT
Found at i:41876197 original size:42 final size:41
Alignment explanation
Indices: 41876120--41876228 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
41876110 ACCTTAATAG
* * * * *
41876120 GTTTCTGTTAAGCTC-TATTGAGATTCTGTTTAACCCTCATGA
1 GTTTCCGTTAAGCTCTTA-TGAGCTTCCGTTCAACCCT-ACGA
* *
41876162 GTTTCCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTACGG
1 GTTTCCGTTAAGCTCTTATGAGCTTCCGTTCAACCCTACGA
* *
41876203 GTTTCCGTTTAGCTCTCATGAGCTTC
1 GTTTCCGTTAAGCTCTTATGAGCTTC
41876229 AATTCAGCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 26 0.46
42 29 0.51
43 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (41 bp):
GTTTCCGTTAAGCTCTTATGAGCTTCCGTTCAACCCTACGA
Found at i:41879664 original size:3 final size:3
Alignment explanation
Indices: 41879656--41879698 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
41879646 AATTTATTTG
*
41879656 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41879699 CGATAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:41879742 original size:15 final size:16
Alignment explanation
Indices: 41879711--41879749 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
41879701 ATAATTTAAT
*
41879711 ATAATAATTTAAATAA
1 ATAATTATTTAAATAA
*
41879727 ATATTTATTT-AATAA
1 ATAATTATTTAAATAA
41879742 ATAATTAT
1 ATAATTAT
41879750 AAGTATTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTATTTAAATAA
Found at i:41879756 original size:25 final size:25
Alignment explanation
Indices: 41879684--41879757 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 25
41879674 ATAATAATAA
41879684 TAAT-AATAATTATAACG-A-TAATT
1 TAATAAATAATTATAA-GTATTAATT
* *
41879707 TAATATAATAATTTAAATAAATATTTATT
1 TAATA-AATAA-TT--ATAAGTATTAATT
41879736 TAATAAATAATTATAAGTATTA
1 TAATAAATAATTATAAGTATTA
41879758 CAAATGTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
23 4 0.10
25 13 0.32
26 2 0.05
27 2 0.05
28 10 0.25
29 9 0.22
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (25 bp):
TAATAAATAATTATAAGTATTAATT
Found at i:41879851 original size:14 final size:17
Alignment explanation
Indices: 41879832--41879869 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
41879822 ATTTATTTCT
41879832 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
41879846 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
41879863 TAATATA
1 TAATATA
41879870 CTTATAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:41879863 original size:23 final size:24
Alignment explanation
Indices: 41879831--41879894 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
41879821 AATTTATTTC
*
41879831 TTAATATAATATTTATA-ATATAA
1 TTAATTTAATATTTATACATATAA
* *
41879854 TTAATTTAATA-ATATACTTATAA
1 TTAATTTAATATTTATACATATAA
*
41879877 TCAATTTATATATTTATA
1 TTAATTTA-ATATTTATA
41879895 TAATTAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
23 22 0.67
24 3 0.09
25 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAATTTAATATTTATACATATAA
Found at i:41880434 original size:25 final size:24
Alignment explanation
Indices: 41880332--41880439 Score: 75
Period size: 25 Copynumber: 4.5 Consensus size: 24
41880322 GTTACAAGAG
*
41880332 TACACCACAAATGCAACATACAAAA
1 TACACCACAAA-GGAACATACAAAA
**
41880357 TATGCCACAAAGGTTAA-AT--AAAA
1 TACACCACAAAGG--AACATACAAAA
*
41880380 TACACCACAAA-G-AC-TATCAAAG
1 TACACCACAAAGGAACATA-CAAAA
**
41880402 TATGCCACAAAGGAAACATACAAAA
1 TACACCACAAAGG-AACATACAAAA
41880427 TACACCACAAAGG
1 TACACCACAAAGG
41880440 CCAAATAGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
19 2 0.03
22 13 0.21
23 14 0.23
24 1 0.02
25 28 0.45
26 4 0.06
ACGTcount: A:0.53, C:0.23, G:0.10, T:0.14
Consensus pattern (24 bp):
TACACCACAAAGGAACATACAAAA
Found at i:41883417 original size:39 final size:38
Alignment explanation
Indices: 41883373--41883570 Score: 288
Period size: 39 Copynumber: 5.1 Consensus size: 38
41883363 ATGCAAGACA
* *
41883373 CTGGAAATGTATCTAGGCTAAAGTCTCGCAGGCTTCGTG
1 CTGGAAATGTATC-CGGCTAAAGTCCCGCAGGCTTCGTG
41883412 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTG
* *
41883451 CTGGAAATATATCCGAGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCG-GCTAAAGTCCCGCAGGCTTCGTG
41883490 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCG-GCTAAAGTCCCGCAGGCTTCGTG
* * *
41883529 CTGGAAATGTATCCGGGTTAATGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTG
41883568 CTG
1 CTG
41883571 ATAATATAAT
Statistics
Matches: 147, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
38 1 0.01
39 145 0.99
40 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (38 bp):
CTGGAAATGTATCCGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:41885928 original size:29 final size:29
Alignment explanation
Indices: 41885896--41885972 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
41885886 TTAAAATTTC
41885896 AAAAAAATATAAAATATTTTTAAAAAA-T
1 AAAAAAATATAAAATATTTTTAAAAAAGT
* *
41885924 AAAAATCAT-TAAAAT-TATTTAAAAAAGT
1 AAAAA-AATATAAAATATTTTTAAAAAAGT
*
41885952 ATAAAAATATAAAAATATTTT
1 AAAAAAATAT-AAAATATTTT
41885973 AAATATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
27 12 0.31
28 17 0.44
29 7 0.18
30 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAAAAATATAAAATATTTTTAAAAAAGT
Found at i:41887215 original size:26 final size:27
Alignment explanation
Indices: 41887172--41887225 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
41887162 CTAAAAGTCT
* *
41887172 AAAACACGATTATGAAATGATTAACAAA
1 AAAACACGATTATAAAAT-ATCAACAAA
41887200 AAAACAC-ATTA-AAAATATCAACAAA
1 AAAACACGATTATAAAATATCAACAAA
41887225 A
1 A
41887226 GAAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 4 0.17
27 4 0.17
28 7 0.29
ACGTcount: A:0.63, C:0.13, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAACACGATTATAAAATATCAACAAA
Found at i:41890572 original size:14 final size:15
Alignment explanation
Indices: 41890547--41890579 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41890537 TTAATTTTTT
41890547 TTAAATTTAAATTAA
1 TTAAATTTAAATTAA
*
41890562 TTAAA-TTAAATTAT
1 TTAAATTTAAATTAA
41890576 TTAA
1 TTAA
41890580 TTTTTTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:41891030 original size:12 final size:12
Alignment explanation
Indices: 41891013--41891038 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41891003 TATTACTCAA
41891013 TTTAAATTTTAT
1 TTTAAATTTTAT
41891025 TTTAAATTTTAT
1 TTTAAATTTTAT
41891037 TT
1 TT
41891039 CAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTAAATTTTAT
Found at i:41896633 original size:16 final size:16
Alignment explanation
Indices: 41896612--41896645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41896602 TGATATAACA
41896612 AATAAAAATGTTTTTG
1 AATAAAAATGTTTTTG
**
41896628 AATAAAGTTGTTTTTG
1 AATAAAAATGTTTTTG
41896644 AA
1 AA
41896646 CAAAGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AATAAAAATGTTTTTG
Found at i:41896650 original size:16 final size:16
Alignment explanation
Indices: 41896620--41896650 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41896610 CAAATAAAAA
*
41896620 TGTTTTTGAATAAAGT
1 TGTTTTTGAACAAAGT
41896636 TGTTTTTGAACAAAG
1 TGTTTTTGAACAAAG
41896651 AAATTATAAA
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:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (16 bp):
TGTTTTTGAACAAAGT
Found at i:41896779 original size:20 final size:20
Alignment explanation
Indices: 41896751--41896793 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
41896741 AAAATGGTTT
41896751 AAAC-TTTTTAAACTCAATTG
1 AAACATTTTTAAA-TCAATTG
41896771 AAACATTTTTAAATCAATTG
1 AAACATTTTTAAATCAATTG
41896791 AAA
1 AAA
41896794 AATTACTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (20 bp):
AAACATTTTTAAATCAATTG
Found at i:41896974 original size:18 final size:18
Alignment explanation
Indices: 41896948--41896982 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41896938 TTTAAAAAAG
*
41896948 TATCGATACCATCTTTGA
1 TATCAATACCATCTTTGA
*
41896966 TATCAATACCATTTTTG
1 TATCAATACCATCTTTG
41896983 TATTCTGACG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (18 bp):
TATCAATACCATCTTTGA
Found at i:41897058 original size:20 final size:20
Alignment explanation
Indices: 41897009--41897050 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
41896999 CAAACAATTA
*
41897009 TAAAAAGTATTGATACCTTT
1 TAAAAAGTATTAATACCTTT
41897029 TAAAAAGTATTAATACCTTT
1 TAAAAAGTATTAATACCTTT
41897049 TA
1 TA
41897051 CCAGGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (20 bp):
TAAAAAGTATTAATACCTTT
Found at i:41899285 original size:40 final size:40
Alignment explanation
Indices: 41899240--41899315 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
41899230 TCACACCATG
* *
41899240 TGGGGATAGAATCGACCCACCCAACCCTATACACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
** *
41899280 TGGGGATTTAATCAACCCATCCAACCCTACACACCA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCA
41899316 TAAGGTACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:41899794 original size:17 final size:17
Alignment explanation
Indices: 41899756--41899806 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
41899746 GTGTGATTCA
* *
41899756 CCGTGTGGGCCCACAAGC
1 CCGTGT-GGCCCACACGT
*
41899774 CCGTGTGGCCTACACGT
1 CCGTGTGGCCCACACGT
41899791 CCGTGTGGCCCACACG
1 CCGTGTGGCCCACACG
41899807 GCCCATTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.14, C:0.39, G:0.31, T:0.16
Consensus pattern (17 bp):
CCGTGTGGCCCACACGT
Found at i:41902575 original size:24 final size:24
Alignment explanation
Indices: 41902548--41902593 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41902538 GGAAACAAAT
41902548 TATATATA-AATAAATTTTAAAAAA
1 TATATATATAATAAA-TTTAAAAAA
*
41902572 TATATATATAATAGATTTAAAA
1 TATATATATAATAAATTTAAAA
41902594 GAAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TATATATATAATAAATTTAAAAAA
Found at i:41903799 original size:21 final size:20
Alignment explanation
Indices: 41903762--41903800 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41903752 TGTCATTTAC
* *
41903762 TGGCTTATTTTTTTTGTTAT
1 TGGCTTATTTCTATTGTTAT
41903782 TGGCATTATTTCTATTGTT
1 TGGC-TTATTTCTATTGTT
41903801 TCTTCTCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (20 bp):
TGGCTTATTTCTATTGTTAT
Found at i:41904595 original size:223 final size:220
Alignment explanation
Indices: 41904270--41904668 Score: 565
Period size: 223 Copynumber: 1.8 Consensus size: 220
41904260 TTATTAATTA
* * * *
41904270 TTATAAATCGTTTGTGTTTAGTTTAGTGTTTTTGTGATTTTTTATGAATATAAATTTTTTATTTT
1 TTATAAATCGTTTGTGTTTAGTTCAGTGTTTTTGGGACTTGTTATGAATATAAATTTTTTATTTT
*
41904335 TTTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTT
66 TTTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTTT
* ** * *
41904400 A-TTTTA-GTGTTTTGTGATTTTTTATGAATGTAATTTTTTTTTGTTTTTTTAAAATTATTTTAT
129 AGTTTAATGTGCATTGTGATTTGTTAT-AATGTAA-TTTTATTTGTTTTTTTAAAATTATTTTAT
41904463 AGTTATTTTGTTAGTAATTTATGATTAGG
192 AGTTATTTTGTTAGTAATTTATGATTAGG
* *
41904492 TTATAAATTGTTTGTGTTTAGTTCAGTGTTTATTGGGACTTGTTAT-AA-ATGAATTTTTT-TTT
1 TTATAAATCGTTTGTGTTTAGTTCAGTGTTT-TTGGGACTTGTTATGAATATAAATTTTTTATTT
**
41904554 GTGTTCTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGT
65 -T-TT-TAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGT
41904619 TTAGTTTAATGTGCATTGTGATTTGTTATAATGTAATTTTATTTGTTTTT
127 TTAGTTTAATGTGCATTGTGATTTGTTATAATGTAATTTTATTTGTTTTT
41904669 GATTTATTTG
Statistics
Matches: 157, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
220 3 0.02
221 30 0.19
222 46 0.29
223 78 0.50
ACGTcount: A:0.25, C:0.01, G:0.15, T:0.59
Consensus pattern (220 bp):
TTATAAATCGTTTGTGTTTAGTTCAGTGTTTTTGGGACTTGTTATGAATATAAATTTTTTATTTT
TTTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAG
TTTAATGTGCATTGTGATTTGTTATAATGTAATTTTATTTGTTTTTTTAAAATTATTTTATAGTT
ATTTTGTTAGTAATTTATGATTAGG
Found at i:41904618 original size:112 final size:109
Alignment explanation
Indices: 41904270--41904668 Score: 504
Period size: 111 Copynumber: 3.6 Consensus size: 109
41904260 TTATTAATTA
* *
41904270 TTATAAATCGTTTGTGTTTAGTTTAGTGTTTTTGTGATTTTTTATGAATATAAATTTTTTATTT-
1 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTTGTGATTTTTTAT-AA-ATGAATTTTTT-TTTG
**
41904334 TTTTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
63 TTTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* *
41904381 TTATAAATTGTTTGTGTTTATTTTAGTG-TTTTGTGATTTTTTATGAATGTAATTTTTTTTTGTT
1 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTTGTGATTTTTTATAAATG-AATTTTTTTTTG-T
*
41904445 TTTTTAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
64 TTTTT-AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * * *
41904492 TTATAAATTGTTTGTGTTTAGTTCAGTGTTTATTGGGACTTGTTATAAATGAATTTTTTTTTGTG
1 TTATAAATTGTTTGTGTTTAGTTTAGTGTTT-TTGTGATTTTTTATAAATGAATTTTTTTTTGT-
41904557 TTCTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
64 TT-TTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * ** * *
41904604 TTATAAATT-ATT-TGTTTAGTTTAATGTGCATTGTGATTTGTTAT-AATGTAA-TTTTATTTGT
1 TTATAAATTGTTTGTGTTTAGTTTAGTGT-TTTTGTGATTTTTTATAAATG-AATTTTTTTTTGT
41904665 TTTT
64 TTTT
41904669 GATTTATTTG
Statistics
Matches: 256, Mismatches: 22, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
107 2 0.01
108 7 0.03
109 22 0.09
110 47 0.18
111 95 0.37
112 65 0.25
113 18 0.07
ACGTcount: A:0.25, C:0.01, G:0.15, T:0.59
Consensus pattern (109 bp):
TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTTGTGATTTTTTATAAATGAATTTTTTTTTGTTT
TTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
Found at i:41906268 original size:97 final size:97
Alignment explanation
Indices: 41906102--41906296 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
41906092 TTTATAGCAA
41906102 ATTTCACATTTTAATGAATTTCCATGGATTAGATAGCACATTAAGCATACATAACACCAAATATG
1 ATTTCACATTTTAATGAATTTCCATGGATTAGATAGCACATTAAGCATACATAACACCAAATATG
41906167 ATCTTGATTAGCCATTGCAATGGCTAATCATT
66 ATCTTGATTAGCCATTGCAATGGCTAATCATT
41906199 ATTTCACATTTTAATGAATTTCCATGGATTAGATAGCACATTAAGCATACATAACACCAAATATG
1 ATTTCACATTTTAATGAATTTCCATGGATTAGATAGCACATTAAGCATACATAACACCAAATATG
41906264 ATCTTGATTAGCCATTGCAATGGCTAATCATT
66 ATCTTGATTAGCCATTGCAATGGCTAATCATT
41906296 A
1 A
41906297 CCAAACATTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (97 bp):
ATTTCACATTTTAATGAATTTCCATGGATTAGATAGCACATTAAGCATACATAACACCAAATATG
ATCTTGATTAGCCATTGCAATGGCTAATCATT
Found at i:41909899 original size:23 final size:21
Alignment explanation
Indices: 41909873--41909943 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 21
41909863 AAAATATAAA
41909873 TGTAACAAACTTTAGACTAACTT
1 TGTAACAAA-TTTAGA-TAACTT
41909896 TGTAATTCAAA-TTAGATTAA--T
1 TGTAA--CAAATTTAGA-TAACTT
41909917 TGTAACAAATTTTAGATAAACTT
1 TGTAACAAA-TTTAGAT-AACTT
41909940 TGTA
1 TGTA
41909944 TTTATTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
19 4 0.10
20 1 0.03
21 13 0.32
23 18 0.45
25 4 0.10
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
TGTAACAAATTTAGATAACTT
Found at i:41909931 original size:21 final size:21
Alignment explanation
Indices: 41909873--41909939 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
41909863 AAAATATAAA
*
41909873 TGTAACAAACTTTAGACTAACTT
1 TGTAACAAA-TTTAGATTAAC-T
41909896 TGTAATTCAAA-TTAGATTAA-T
1 TGTAA--CAAATTTAGATTAACT
*
41909917 TGTAACAAATTTTAGATAAACT
1 TGTAACAAA-TTTAGATTAACT
41909939 T
1 T
41909940 TGTATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 4 0.11
21 14 0.38
22 2 0.05
23 13 0.35
25 4 0.11
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (21 bp):
TGTAACAAATTTAGATTAACT
Found at i:41913661 original size:11 final size:11
Alignment explanation
Indices: 41913645--41913685 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41913635 AGTAACTAAG
*
41913645 AAAATAACTTT
1 AAAATAACTTA
*
41913656 AAAATAAATTA
1 AAAATAACTTA
*
41913667 AAAATAACATA
1 AAAATAACTTA
41913678 AAAATAAC
1 AAAATAAC
41913686 AATAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAACTTA
Found at i:41913686 original size:11 final size:11
Alignment explanation
Indices: 41913645--41913691 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
41913635 AGTAACTAAG
* *
41913645 AAAATAACTTT
1 AAAATAACATA
41913656 AAAATAA-ATTA
1 AAAATAACA-TA
41913667 AAAATAACATA
1 AAAATAACATA
41913678 AAAATAACAATA
1 AAAATAAC-ATA
41913690 AA
1 AA
41913692 TAAACTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAACATA
Found at i:41915354 original size:25 final size:26
Alignment explanation
Indices: 41915307--41915356 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41915297 TAAATAAAAA
* * *
41915307 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAATAAAACAAATAC
41915333 ATTTAAAAACATAA-AAAACAAATA
1 ATTTAAAAACATAATAAAACAAATA
41915357 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (26 bp):
ATTTAAAAACATAATAAAACAAATAC
Found at i:41915381 original size:19 final size:19
Alignment explanation
Indices: 41915345--41915381 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41915335 TTAAAAACAT
**
41915345 AAAAAACAAATATTAAAAC
1 AAAAAACAAATAAAAAAAC
41915364 AAAAAACAAATAAAAAAA
1 AAAAAACAAATAAAAAAA
41915382 TGAGACAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAACAAATAAAAAAAC
Found at i:41915597 original size:11 final size:11
Alignment explanation
Indices: 41915583--41915681 Score: 90
Period size: 11 Copynumber: 8.9 Consensus size: 11
41915573 CACAAAAAGT
41915583 AACACCAAAAC
1 AACACCAAAAC
*
41915594 AACACCAAAAT
1 AACACCAAAAC
* *
41915605 AGCAACAAAAC
1 AACACCAAAAC
* *
41915616 AGCACCAAAAT
1 AACACCAAAAC
* *
41915627 AGCAACAAAAC
1 AACACCAAAAC
*
41915638 AGCACCAAAAC
1 AACACCAAAAC
* *
41915649 AACATCACCAAC
1 AACACCA-AAAC
*
41915661 AACACCAAAAT
1 AACACCAAAAC
41915672 AACACCAAAA
1 AACACCAAAA
41915682 ACCTGCAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
11 63 0.88
12 9 0.12
ACGTcount: A:0.61, C:0.31, G:0.04, T:0.04
Consensus pattern (11 bp):
AACACCAAAAC
Found at i:41915616 original size:22 final size:22
Alignment explanation
Indices: 41915554--41915681 Score: 121
Period size: 22 Copynumber: 5.7 Consensus size: 22
41915544 TAAATAACTG
* * *
41915554 CAAAAGAACAATAAAACACCAC
1 CAAAATAACAACAAAACAACAC
* *
41915576 AAAAAGTAACACCAAAACAACAC
1 CAAAA-TAACAACAAAACAACAC
* *
41915599 CAAAATAGCAACAAAACAGCAC
1 CAAAATAACAACAAAACAACAC
* *
41915621 CAAAATAGCAACAAAACAGCAC
1 CAAAATAACAACAAAACAACAC
* * *
41915643 CAAAACAACATCACCAACAACAC
1 CAAAATAACAACA-AAACAACAC
*
41915666 CAAAATAACACCAAAA
1 CAAAATAACAACAAAA
41915682 ACCTGCAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
22 52 0.60
23 35 0.40
ACGTcount: A:0.62, C:0.29, G:0.05, T:0.05
Consensus pattern (22 bp):
CAAAATAACAACAAAACAACAC
Found at i:41915623 original size:33 final size:33
Alignment explanation
Indices: 41915583--41915681 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
41915573 CACAAAAAGT
*
41915583 AACACCAAAACAACACCAAAATAGCAACAAAAC
1 AACACCAAAACAACACCAAAATAGCACCAAAAC
* * * * *
41915616 AGCACCAAAATAGCAACAAAACAGCACCAAAAC
1 AACACCAAAACAACACCAAAATAGCACCAAAAC
* * *
41915649 AACATCACCAACAACACCAAAATAACACCAAAA
1 AACACCA-AAACAACACCAAAATAGCACCAAAA
41915682 ACCTGCAAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
33 32 0.63
34 19 0.37
ACGTcount: A:0.61, C:0.31, G:0.04, T:0.04
Consensus pattern (33 bp):
AACACCAAAACAACACCAAAATAGCACCAAAAC
Found at i:41915625 original size:67 final size:67
Alignment explanation
Indices: 41915554--41915681 Score: 150
Period size: 67 Copynumber: 1.9 Consensus size: 67
41915544 TAAATAACTG
* * *
41915554 CAAAAGAACAATAAAACACCACAAAAAGTAACACCA-AAACAACACCAAAATAGCAACAAAACAG
1 CAAAAGAACAACAAAACACCACAAAAA-CAACACCACAAACAACACCAAAATAACAACAAAACAG
41915618 CAC
65 CAC
* * * * * * *
41915621 CAAAATAGCAACAAAACAGCACCAAAACAACATCACCAACAACACCAAAATAACACCAAAA
1 CAAAAGAACAACAAAACACCACAAAAACAACACCACAAACAACACCAAAATAACAACAAAA
41915682 ACCTGCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 6 0.12
67 44 0.88
ACGTcount: A:0.62, C:0.29, G:0.05, T:0.05
Consensus pattern (67 bp):
CAAAAGAACAACAAAACACCACAAAAACAACACCACAAACAACACCAAAATAACAACAAAACAGC
AC
Found at i:41919747 original size:20 final size:19
Alignment explanation
Indices: 41919705--41919754 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
41919695 AAAGTTAAAG
*
41919705 TTAAAAATAAAAAAAAGGA
1 TTAAAAATAAAAAAAAGAA
* *
41919724 TTAAAAATAAAATAAATAA
1 TTAAAAATAAAAAAAAGAA
* *
41919743 TTTAATATAAAA
1 TTAAAAATAAAA
41919755 TTCGGCCCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
TTAAAAATAAAAAAAAGAA
Found at i:41921236 original size:10 final size:9
Alignment explanation
Indices: 41921216--41921311 Score: 71
Period size: 10 Copynumber: 10.8 Consensus size: 9
41921206 TTTATAACTT
41921216 TATTATATA
1 TATTATATA
41921225 TATTAT-TA
1 TATTATATA
41921233 TA-TATAT-
1 TATTATATA
* *
41921240 TCTTA-ATG
1 TATTATATA
41921248 T-TTA-AGTA
1 TATTATA-TA
41921256 TA-TATATTA
1 TATTATA-TA
41921265 TATTATATTA
1 TATTATA-TA
41921275 TATTATACTA
1 TATTATA-TA
41921285 TATTATATTA
1 TATTATA-TA
41921295 TATTATATTA
1 TATTATA-TA
41921305 TATTATA
1 TATTATA
41921312 ACAAACAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
7 10 0.13
8 12 0.16
9 11 0.15
10 42 0.56
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (9 bp):
TATTATATA
Found at i:41921268 original size:5 final size:5
Alignment explanation
Indices: 41921254--41921311 Score: 100
Period size: 5 Copynumber: 11.8 Consensus size: 5
41921244 AATGTTTAAG
*
41921254 TATA- TATAT TATAT TATAT TATAT TATAC TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
41921303 TATAT TATA
1 TATAT TATA
41921312 ACAAACAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 4 0.08
5 47 0.92
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:41921334 original size:10 final size:10
Alignment explanation
Indices: 41921319--41921348 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
41921309 ATAACAAACA
41921319 AAAAAGAAAG
1 AAAAAGAAAG
41921329 AAAAAGAAAG
1 AAAAAGAAAG
41921339 AGAAAAGAAA
1 A-AAAAGAAA
41921349 AAGAGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:41921359 original size:17 final size:16
Alignment explanation
Indices: 41921320--41921359 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
41921310 TAACAAACAA
41921320 AAAAG-AAAGAAAAAG
1 AAAAGAAAAGAAAAAG
41921335 AAAGAGAAAAGAAAAAG
1 AAA-AGAAAAGAAAAAG
41921352 AGAAAGAA
1 A-AAAGAA
41921360 GAAAGGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.14
16 2 0.09
17 15 0.68
18 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:41921364 original size:13 final size:13
Alignment explanation
Indices: 41921327--41921364 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
41921317 CAAAAAAGAA
41921327 AGAAA-AAGAAAG
1 AGAAAGAAGAAAG
41921339 AGAAAAGAA-AAAG
1 AG-AAAGAAGAAAG
41921352 AGAAAGAAGAAAG
1 AGAAAGAAGAAAG
41921365 GAAGCCACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAG
Found at i:41921364 original size:19 final size:17
Alignment explanation
Indices: 41921322--41921364 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
41921312 ACAAACAAAA
41921322 AAGAAAGAAAAAGAAAG
1 AAGAAAGAAAAAGAAAG
41921339 -AGAAAAGAAAAAGAGAAAG
1 AAG-AAAG-AAAA-AGAAAG
41921358 AAGAAAG
1 AAGAAAG
41921365 GAAGCCACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.09
17 4 0.18
18 4 0.18
19 10 0.45
20 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAAAGAAAG
Found at i:41923630 original size:20 final size:20
Alignment explanation
Indices: 41923605--41923642 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41923595 GTAACTATGG
41923605 TTGAATGATATGCATATGAC
1 TTGAATGATATGCATATGAC
41923625 TTGAATGATATGCATATG
1 TTGAATGATATGCATATG
41923643 GAATAAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGAATGATATGCATATGAC
Found at i:41924376 original size:23 final size:24
Alignment explanation
Indices: 41924331--41924376 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
41924321 AGAGTGTATT
*
41924331 TAAATGAGTTTTAAATTGGTTGAA
1 TAAATGAGTTTTAAATTGCTTGAA
* *
41924355 TAAATG-GTTTTGAGTTGCTTGA
1 TAAATGAGTTTTAAATTGCTTGA
41924377 TGTGCAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (24 bp):
TAAATGAGTTTTAAATTGCTTGAA
Found at i:41925291 original size:30 final size:30
Alignment explanation
Indices: 41925257--41925313 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
41925247 ACTTAACAAG
41925257 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
41925287 CAAATTCTTTTAAAATAATAACAAAAT
1 CAAATGCCTCTAAAATAATAACAAAAT
41925314 AAATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41925324 original size:12 final size:12
Alignment explanation
Indices: 41925297--41925329 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41925287 CAAATTCTTT
41925297 TAAAAT-AATAA
1 TAAAATAAATAA
*
41925308 CAAAATAAATAA
1 TAAAATAAATAA
41925320 TAAAATAAAT
1 TAAAATAAAT
41925330 TTTATACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAATAAATAA
Found at i:41926392 original size:32 final size:33
Alignment explanation
Indices: 41926356--41926423 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
41926346 ATATTTCATT
* *
41926356 TATCAAATATTATTATTTTT-AAT-TGATTCTAA
1 TATCAAATA-TAATATTTTTAAATGTGATACTAA
**
41926388 TATCAGTTATAATATTTTTAAATGTGATACTAA
1 TATCAAATATAATATTTTTAAATGTGATACTAA
41926421 TAT
1 TAT
41926424 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 9 0.30
32 10 0.33
33 11 0.37
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (33 bp):
TATCAAATATAATATTTTTAAATGTGATACTAA
Found at i:41932779 original size:5 final size:6
Alignment explanation
Indices: 41932764--41932799 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
41932754 CCTTTTTGAG
41932764 TTTTTA TTTTTA TTTTTA -TTTTA TTTTTA TATTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA
41932800 AGTGTCAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:41932785 original size:11 final size:11
Alignment explanation
Indices: 41932764--41932793 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
41932754 CCTTTTTGAG
41932764 TTTTTATTTTTA
1 TTTTTA-TTTTA
41932776 TTTTTATTTTA
1 TTTTTATTTTA
41932787 TTTTTAT
1 TTTTTAT
41932794 ATTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:41932787 original size:17 final size:18
Alignment explanation
Indices: 41932765--41932799 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
41932755 CTTTTTGAGT
41932765 TTTTATTTTTAT-TTTTA
1 TTTTATTTTTATATTTTA
41932782 TTTTATTTTTATATTTTA
1 TTTTATTTTTATATTTTA
41932800 AGTGTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTATATTTTA
Found at i:41945874 original size:43 final size:43
Alignment explanation
Indices: 41945815--41945916 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
41945805 GTTAAGATAT
*
41945815 TATTAT-GGGATATTATCTTTTAGCAAATTGATTCATAATAGGA
1 TATTATAGGG-TATTATCTATTAGCAAATTGATTCATAATAGGA
* * *
41945858 TATTATAGGGTATTATCTATTAGTAATTTGATTCCTAATAGGA
1 TATTATAGGGTATTATCTATTAGCAAATTGATTCATAATAGGA
*
41945901 TATTATAGGCTATTAT
1 TATTATAGGGTATTAT
41945917 TATGAGATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
43 50 0.94
44 3 0.06
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (43 bp):
TATTATAGGGTATTATCTATTAGCAAATTGATTCATAATAGGA
Found at i:41947800 original size:12 final size:12
Alignment explanation
Indices: 41947783--41947840 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
41947773 TTTCATGCTA
41947783 TTTTTTATAATT
1 TTTTTTATAATT
41947795 TTTTTTATAATT
1 TTTTTTATAATT
* *
41947807 TTTTTAGAAAATT
1 TTTTT-TATAATT
*
41947820 TTTTGTA-AATT
1 TTTTTTATAATT
*
41947831 ATTTTTATAA
1 TTTTTTATAA
41947841 AAATTTGCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 9 0.24
12 20 0.53
13 9 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:41948264 original size:8 final size:8
Alignment explanation
Indices: 41948253--41948333 Score: 101
Period size: 8 Copynumber: 10.2 Consensus size: 8
41948243 TTTTATAATT
41948253 TTTTTAAA
1 TTTTTAAA
41948261 TTTTTAAA
1 TTTTTAAA
41948269 TTTTTAAA
1 TTTTTAAA
41948277 TTTTTAAA
1 TTTTTAAA
41948285 TTTTTAAA
1 TTTTTAAA
*
41948293 TTCTTAAA
1 TTTTTAAA
*
41948301 TTTTT-GA
1 TTTTTAAA
* *
41948308 TTTTTGAT
1 TTTTTAAA
**
41948316 TTTTTTTA
1 TTTTTAAA
41948324 TTTTTAAA
1 TTTTTAAA
41948332 TT
1 TT
41948334 ATTTTTTGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
7 6 0.10
8 56 0.90
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (8 bp):
TTTTTAAA
Found at i:41949913 original size:19 final size:19
Alignment explanation
Indices: 41949879--41949926 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
41949869 ATCATTCTAC
*
41949879 TAAAATCATGAAATGA-ATAA
1 TAAAAT-ATTAAATGATA-AA
41949899 TAAAATATTAAATGATAAA
1 TAAAATATTAAATGATAAA
*
41949918 TATAATATT
1 TAAAATATT
41949927 GTATAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAAATATTAAATGATAAA
Found at i:41952958 original size:18 final size:18
Alignment explanation
Indices: 41952927--41952961 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41952917 AATGATATCG
*
41952927 ATATTGATTATAGTGACA
1 ATATTGATGATAGTGACA
*
41952945 ATATTGATGCTAGTGAC
1 ATATTGATGATAGTGAC
41952962 GCTATTGATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (18 bp):
ATATTGATGATAGTGACA
Found at i:41955614 original size:12 final size:12
Alignment explanation
Indices: 41955599--41955643 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
41955589 AAAACAGGGG
41955599 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
41955611 AGAAAAAGGGAA
1 AGAAAAAGAGAA
* *
41955623 AAAAAAAGAAAA
1 AGAAAAAGAGAA
41955635 AGGAAAAAG
1 A-GAAAAAG
41955644 CTAGAGATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:41955639 original size:17 final size:18
Alignment explanation
Indices: 41955609--41955642 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41955599 AGAAAAAGAG
41955609 AAAGAAAAAGGGAAAAAA
1 AAAGAAAAAGGGAAAAAA
41955627 AAAGAAAAA-GGAAAAA
1 AAAGAAAAAGGGAAAAA
41955643 GCTAGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGGGAAAAAA
Found at i:41956425 original size:45 final size:45
Alignment explanation
Indices: 41956357--41956502 Score: 256
Period size: 45 Copynumber: 3.2 Consensus size: 45
41956347 TATTGTTTCC
* *
41956357 GTTACTGTTACCGATTCAGCACTTTGTGTGTCGAATACTGTTACT
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACT
*
41956402 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACT
*
41956447 GTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACT
41956492 GTTACTGTTAC
1 GTTACTGTTAC
41956503 TGCTACTGCT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACT
Found at i:41956493 original size:6 final size:6
Alignment explanation
Indices: 41956482--41956528 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
41956472 GTGTGTTGAA
* * *
41956482 TACTGT TACTGT TACTGT TACTGC TACTGC TACCGT TACTGAT TACT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACT
41956529 ATTTAGGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:41958819 original size:50 final size:50
Alignment explanation
Indices: 41958739--41958833 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
41958729 GCTAAATGAC
* * *
41958739 CATGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTTAT
1 CATGTATATTCGACCACATAGATATATACATATGTGATGTTATATTTTAT
*
41958789 CATGTATATTCGACCATATAGATATATACATATGTGATGTTATAT
1 CATGTATATTCGACCACATAGATATATACATATGTGATGTTATAT
41958834 ATTTGATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (50 bp):
CATGTATATTCGACCACATAGATATATACATATGTGATGTTATATTTTAT
Found at i:41963759 original size:5 final size:5
Alignment explanation
Indices: 41963743--41963811 Score: 56
Period size: 5 Copynumber: 14.0 Consensus size: 5
41963733 GAATAAACTT
41963743 TTAAA TTAAAA TTAAA TTAAA --AGAA TTAAA TTAAA TTAAA TTATAA
1 TTAAA TT-AAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTA-AA
* * *
41963789 --AAA ATAAA TTTAA TTATA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
41963812 ACTTTTCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 38 0.73
6 8 0.15
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (5 bp):
TTAAA
Found at i:41963778 original size:24 final size:23
Alignment explanation
Indices: 41963743--41963812 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 23
41963733 GAATAAACTT
41963743 TTAAATTAAAATTAAATTAAAAGAA
1 TTAAATT-AAATTAAATTAAAA-AA
41963768 TTAAATTAAATTAAATTATAAAAA
1 TTAAATTAAATTAAATTA-AAAAA
* * *
41963792 ATAAATTTAATTATATTAAAA
1 TTAAATTAAATTAAATTAAAA
41963813 CTTTTCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 3 0.07
24 28 0.68
25 10 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (23 bp):
TTAAATTAAATTAAATTAAAAAA
Found at i:41978572 original size:59 final size:59
Alignment explanation
Indices: 41978473--41978585 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
41978463 CAAGAGGCCT
* *
41978473 AAACCGACGCTGGCCCAACTCTTGCTCTATAGTTGGTCTGCCATAAGAGCCATGGGCTC
1 AAACCGACGCTGGCCCAACTCTTGCTCCATAGTTGATCTGCCATAAGAGCCATGGGCTC
* * * * *
41978532 AAACCGATGCTGGTCCAATTCTTGCTCCATGGTTGATCTGCCATAAGGGCCATG
1 AAACCGACGCTGGCCCAACTCTTGCTCCATAGTTGATCTGCCATAAGAGCCATG
41978586 ATACATACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (59 bp):
AAACCGACGCTGGCCCAACTCTTGCTCCATAGTTGATCTGCCATAAGAGCCATGGGCTC
Found at i:41982522 original size:28 final size:28
Alignment explanation
Indices: 41982456--41982583 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
41982446 GTTGATTTCG
* * **
41982456 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
41982485 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41982513 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
41982542 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41982570 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
41982584 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41982545 original size:57 final size:57
Alignment explanation
Indices: 41982456--41982583 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
41982446 GTTGATTTCG
*
41982456 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
41982513 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
41982570 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
41982584 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:41986155 original size:23 final size:23
Alignment explanation
Indices: 41986136--41986188 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
41986126 CAGCTCATTG
41986136 GAGCTTACCGATTCAACTCATAT
1 GAGCTTACCGATTCAACTCATAT
* *
41986159 GAGCTTACC-ACTCAGCTCGATA-
1 GAGCTTACCGATTCAACTC-ATAT
41986181 GAGCTTAC
1 GAGCTTAC
41986189 TATTTCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (23 bp):
GAGCTTACCGATTCAACTCATAT
Found at i:41986204 original size:23 final size:23
Alignment explanation
Indices: 41986123--41986225 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
41986113 AGCCTACTGT
* * *
41986123 TTTCAGCTCATTGGAGCTTACCGA
1 TTTCAGCTCAATAGAGCTTA-CTA
* *
41986147 -TTCAACTC-ATATGAGCTTACCA
1 TTTCAGCTCAATA-GAGCTTACTA
* *
41986169 -CTCAGCTCGATAGAGCTTACTA
1 TTTCAGCTCAATAGAGCTTACTA
41986191 TTTCAGCTCAATAGAGCTTACTA
1 TTTCAGCTCAATAGAGCTTACTA
41986214 TTTATCAGCTCA
1 -TT-TCAGCTCA
41986226 GGAGGAGCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.28
23 37 0.57
24 2 0.03
25 8 0.12
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (23 bp):
TTTCAGCTCAATAGAGCTTACTA
Found at i:41986406 original size:20 final size:20
Alignment explanation
Indices: 41986369--41986426 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
41986359 TACCGATCAT
*
41986369 ATGAATGAGCTA-TGTTGAA
1 ATGAATGAACTACTGTTGAA
* *
41986388 ATGGATGAATTACTGTTGAA
1 ATGAATGAACTACTGTTGAA
*
41986408 ATGAATGAACTACTATTGA
1 ATGAATGAACTACTGTTGA
41986427 TACAGATGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGAATGAACTACTGTTGAA
Found at i:41991529 original size:126 final size:126
Alignment explanation
Indices: 41991300--41991681 Score: 568
Period size: 126 Copynumber: 3.0 Consensus size: 126
41991290 TTTCTGCAAG
* * ** *
41991300 AATAATTCTGAGCAGACGTTTCTGGAA-AAATAATGTTGGAAAACGCTTCAAGTAGGATGCACTG
1 AATAATTCTGAGTAGACGTTTCT-GAACAAATAGTG-CCGAAAACGCTTCAAGCAGGATGCACTG
* * * * *
41991364 TCAGCAAAATTTCTGGAAAAAGCTTCCACGTGGATGCTCTTTTCCGACAGTAATTCGTAGAAA
64 TCAGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* *
41991427 AATAATTCTGAGTAGACGTTTCTAAACAAATAGTGCCGAAGACGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
*
41991492 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCATAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
41991553 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCAAAAATGCTTCAAGCAGGATGCAATGTT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
41991618 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
41991679 AAT
1 AAT
41991682 GAGGCTATAA
Statistics
Matches: 232, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
126 203 0.88
127 29 0.12
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:41993832 original size:14 final size:15
Alignment explanation
Indices: 41993813--41993869 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
41993803 AATCTTTAAG
41993813 GATATG-CAATCTTA
1 GATATGACAATCTTA
41993827 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
41993844 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
41993863 GATATGA
1 GATATGA
41993870 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:41993854 original size:36 final size:38
Alignment explanation
Indices: 41993813--41993891 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
41993803 AATCTTTAAG
41993813 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
41993849 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
41993889 GAT
1 GAT
41993892 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:41993860 original size:19 final size:19
Alignment explanation
Indices: 41993813--41993891 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
41993803 AATCTTTAAG
41993813 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41993832 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41993849 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41993868 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
41993889 GAT
1 GAT
41993892 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:42000873 original size:93 final size:92
Alignment explanation
Indices: 42000715--42000884 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 92
42000705 GCCCATAAGT
***
42000715 GAACTCGGACTCAACTCAACGAGCTGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
42000780 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
42000807 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42000872 CGAGTTCGGATGC
65 CGAGTTCGGATGC
42000885 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 24 0.33
93 49 0.67
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42000874 original size:46 final size:46
Alignment explanation
Indices: 42000707--42000881 Score: 207
Period size: 45 Copynumber: 3.8 Consensus size: 46
42000697 TGTAACCCGC
* ***
42000707 CCATAAGTGAACTCGGACTCAACTCAACGAGCT-GGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42000752 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
42000802 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42000845 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42000882 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 34 0.31
46 31 0.28
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42006222 original size:47 final size:46
Alignment explanation
Indices: 42006153--42006328 Score: 225
Period size: 47 Copynumber: 3.8 Consensus size: 46
42006143 TGTAACCCGC
*
42006153 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCA-TTCGCAT
*
42006200 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCAT
* * *
42006250 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
42006293 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
42006329 ATGCTCAACC
Statistics
Matches: 112, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 28 0.25
47 63 0.56
48 2 0.02
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
Found at i:42006321 original size:93 final size:94
Alignment explanation
Indices: 42006161--42006332 Score: 319
Period size: 93 Copynumber: 1.8 Consensus size: 94
42006151 GCCCATAAGT
*
42006161 GAACTCGGACTCAACTCAACGAGCTCGGGCATTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTCGCATCCATAAGTGAACTCGGACTCAACTCA
42006226 ACGAGTTCGGATGCCTAGTTACATCTCAC
66 ACGAGTTCGGATGCCTAGTTACATCTCAC
*
42006255 GAACTCGGACTCAACTCAACGAGTTCGGACA-TTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTCGCATCCATAAGTGAACTCGGACTCAACTCA
42006319 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42006333 TCAACCATCT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 47 0.62
94 29 0.38
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (94 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42007663 original size:16 final size:15
Alignment explanation
Indices: 42007631--42007684 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
42007621 CTTCTATTTC
42007631 AAAAAAAGA-AAAGAA
1 AAAAAAAGATAAA-AA
42007646 AAGAAAAAGATAAAAA
1 AA-AAAAAGATAAAAA
* *
42007662 AAATAAATATAAAAA
1 AAAAAAAGATAAAAA
42007677 AATAAAAA
1 AA-AAAAA
42007685 AGACAAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 15 0.45
16 15 0.45
17 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.09
Consensus pattern (15 bp):
AAAAAAAGATAAAAA
Found at i:42007692 original size:23 final size:23
Alignment explanation
Indices: 42007649--42007692 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42007639 AAAAGAAAAG
* *
42007649 AAAAAGATAAAAAAAATAAATAT
1 AAAAAAATAAAAAAAACAAATAT
*
42007672 AAAAAAATAAAAAAGACAAAT
1 AAAAAAATAAAAAAAACAAAT
42007693 GGAGAGGCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (23 bp):
AAAAAAATAAAAAAAACAAATAT
Found at i:42008994 original size:205 final size:205
Alignment explanation
Indices: 42008633--42009384 Score: 1271
Period size: 205 Copynumber: 3.7 Consensus size: 205
42008623 GCAGATCTGG
*
42008633 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* ** *
42008698 GATTTGGTTTTCGTGTGCTTACGCTGACGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
42008763 AAAACAAATCGAAGTTTTGTATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTC
130 AGAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACATAGCAGATCTAACCTTC
42008828 AGATGTTTATA
195 AGATGTTTATA
42008839 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
*
42008904 ATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
42008969 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGTAGATACATAGCAGATCTAACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACATAGCAGATCTAACCTTCA
42009034 GATGTTTATA
196 GATGTTTATA
*
42009044 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGGCATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* * *
42009109 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGTTTTTGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
42009174 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACATAACAGATCTAACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACATAGCAGATCTAACCTTCA
42009239 GATG-----A
196 GATGTTTATA
*
42009244 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCAAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* * *
42009309 ATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTTAGA
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
42009374 GAACAAATCGA
131 GAACAAATCGA
42009385 GGAAACAGAT
Statistics
Matches: 519, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
200 134 0.26
205 378 0.73
206 7 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (205 bp):
CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACATAGCAGATCTAACCTTCA
GATGTTTATA
Found at i:42011147 original size:47 final size:47
Alignment explanation
Indices: 42011088--42011474 Score: 657
Period size: 47 Copynumber: 8.2 Consensus size: 47
42011078 TCGGGACTTA
* * * *
42011088 TCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
* * * * * *
42011135 TCACATATATACACCTTCACATCCATCACATCGTCCATTAGGCTTTA
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
42011182 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
42011229 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
*
42011276 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
42011323 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
*
42011370 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
*
42011417 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
42011464 TCACATATATA
1 TCACATATATA
42011475 TATCTTGAAC
Statistics
Matches: 323, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 323 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTG
Found at i:42014054 original size:18 final size:19
Alignment explanation
Indices: 42014015--42014079 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
42014005 ATGGAAATAT
*
42014015 AATCTTAGAAATGATATGC
1 AATCTTAGATATGATATGC
42014034 AATCTTAGATATGAT-TGC
1 AATCTTAGATATGATATGC
* *
42014052 AATATTAGATATGATATGT
1 AATCTTAGATATGATATGC
42014071 AATCTTAGA
1 AATCTTAGA
42014080 AGATATGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 17 0.41
19 24 0.59
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (19 bp):
AATCTTAGATATGATATGC
Found at i:42014085 original size:22 final size:23
Alignment explanation
Indices: 42014058--42014102 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
42014048 TTGCAATATT
42014058 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
42014080 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
42014103 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:42014112 original size:22 final size:23
Alignment explanation
Indices: 42014068--42014112 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42014058 AGATATGATA
*
42014068 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
42014091 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
42014113 GTAGATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:42015516 original size:12 final size:12
Alignment explanation
Indices: 42015501--42015526 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42015491 CAAAACTCGA
42015501 TTTAAAAATGGT
1 TTTAAAAATGGT
42015513 TTTAAAAATGGT
1 TTTAAAAATGGT
42015525 TT
1 TT
42015527 CGACACCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTAAAAATGGT
Found at i:42020842 original size:126 final size:125
Alignment explanation
Indices: 42020617--42020998 Score: 622
Period size: 126 Copynumber: 3.0 Consensus size: 125
42020607 TTATAGCCTC
42020617 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGT-GGAGCTTTTTCCAGAAATTTTGCTG
* *
42020682 ACAGTGCATCCTGCTTGAAGCATTTTCGGCACTATTTGTTCAGAAACATCTACTCAGAATT
65 ACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
42020743 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTAGGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGT-GGAGCTTTTTCCAGAAATTTTGCTG
42020808 ACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
65 ACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
* * * *
42020869 ATTTTTCTACTAACTACTGTAGCAAAATAGCGTCCACGTGAGAGCTTTTTCTAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTG-GAGCTTTTTCCAGAAATTTTGCTG
* * * *
42020934 ACAGTGCATCTTGCTTGAAGTGTTTTCCGACACTATTT-TTCCAGAAACGTCTGCTCAGAATT
65 ACAGTGCATCCTGCTTGAAGCGTTTT-CGGCACTATTTGTT-CAGAAACGTCTACTCAGAATT
42020996 ATT
1 ATT
42020999 CTTGCAGAAA
Statistics
Matches: 242, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
125 1 0.00
126 208 0.86
127 33 0.14
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (125 bp):
ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTGGAGCTTTTTCCAGAAATTTTGCTGA
CAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:42021386 original size:22 final size:22
Alignment explanation
Indices: 42021323--42021386 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 22
42021313 AACTCGAAAT
42021323 TTAATCAATTAACCCTAA-ACCC
1 TTAATCAATTAACCCTAATA-CC
* *
42021345 TAAATCAA-T--CCATAAT---
1 TTAATCAATTAACCCTAATACC
42021361 TTAATCAATTAACCCTAATACC
1 TTAATCAATTAACCCTAATACC
42021383 TTAA
1 TTAA
42021387 ACTCTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
16 7 0.23
17 1 0.03
19 11 0.35
21 1 0.03
22 11 0.35
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (22 bp):
TTAATCAATTAACCCTAATACC
Found at i:42022531 original size:41 final size:41
Alignment explanation
Indices: 42022453--42022536 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
42022443 CAAAAGAGCG
* * *
42022453 TCCACGTGGGAGCTTTTTCCAGAAATTTTGCTAACAGTGCA
1 TCCACGTGGGAGCTTTCTCCAGAAATTTTACTAACAGTACA
* * * *
42022494 TCCATGTGGGAGCTTTCTCTAGAAATTTTATTGACAGTACA
1 TCCACGTGGGAGCTTTCTCCAGAAATTTTACTAACAGTACA
42022535 TC
1 TC
42022537 TTGCTTTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (41 bp):
TCCACGTGGGAGCTTTCTCCAGAAATTTTACTAACAGTACA
Found at i:42024220 original size:126 final size:126
Alignment explanation
Indices: 42023995--42024376 Score: 584
Period size: 126 Copynumber: 3.0 Consensus size: 126
42023985 TTATAGACTC
42023995 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
*
42024060 ACAGTACATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
42024121 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
* * * ** * * *
42024186 ACAGTGTATCCTGCATGAAGCGTTTTCGGTACTATTTGTTCAGAAATGTATACTTAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* * * * *
42024247 ATTTTTCTACAAAATACTGTAGCAAAAGAGTGTCTACGTGGGAGCTTTTTCTAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
* * * * *
42024312 ACAGTGCATCCTGCTTAAAGAATTTTTCGACGCTATTTTTTCAGAAACGTCTGCTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCA-TTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
42024374 ATT
1 ATT
42024377 CTTGCAGAAA
Statistics
Matches: 228, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
126 194 0.85
127 34 0.15
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (126 bp):
ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:42024777 original size:39 final size:37
Alignment explanation
Indices: 42024702--42024779 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 37
42024692 ATCCTAAATT
42024702 TAATCAATTAACCCTAAACCCTAAATCAATCCATAATA
1 TAATCAATTAACCCTAAACCCTAAATCAAT-CATAATA
*
42024740 TAATCAATTAACCTTAATACCCTAAACTCTAAT-ATAATA
1 TAATCAATTAACCCTAA-ACCCTAAA-TC-AATCATAATA
42024779 T
1 T
42024780 TTAGCATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 16 0.44
39 15 0.42
40 2 0.06
41 3 0.08
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (37 bp):
TAATCAATTAACCCTAAACCCTAAATCAATCATAATA
Done.