Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 157 of 318
Found at i:49370161 original size:120 final size:119
Alignment explanation
Indices: 49369820--49370174 Score: 430
Period size: 120 Copynumber: 3.0 Consensus size: 119
49369810 CGAATACACG
* * * *
49369820 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGG-ATATAACACCAGCACGAATGCTCTTCGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTATATAAC-TC-GCACGAATGCTCTTCGGG
** *
49369884 GTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
64 ACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * * * *
49369940 TCACTAGCATGAATGCTCTTCAGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG-TATATAACTCGCACGAATGCTCTTCGGGA
*
49370005 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
65 CTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
*
49370060 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC-CTTCGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGG-TATA-TAACTCGCACGAATGCTCTTCGGG
* * * * * * *
49370124 ACTTAACCCAGATTTAGTAACTCGCACCAATGC-CTTCGG-GCTTAGCCCGGA
64 ACTTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
49370175 ATTAGTAACT
Statistics
Matches: 201, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
119 11 0.05
120 160 0.80
121 25 0.12
122 5 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (119 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTATATAACTCGCACGAATGCTCTTCGGGAC
TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:49372164 original size:37 final size:37
Alignment explanation
Indices: 49372108--49372186 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
49372098 TTATTACGAA
* *
49372108 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
* *
49372145 TTCTTACCCGGACAAAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
49372182 GTCTT
1 GTCTT
49372187 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:49372383 original size:47 final size:47
Alignment explanation
Indices: 49372305--49372808 Score: 893
Period size: 47 Copynumber: 10.7 Consensus size: 47
49372295 CCCTTCGGGA
* * * * * *
49372305 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-C
* *
49372353 CCT-TCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372399 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372446 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49372493 CTTATCACATATATACACTTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372540 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372587 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49372634 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372681 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49372728 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49372775 CTTATCACATATATACACTTTCACATTCATCACA
1 CTTATCACATATATACACTTTCACATTCATCACA
49372809 AATATAGATT
Statistics
Matches: 442, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
46 3 0.01
47 437 0.99
48 2 0.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:49372384 original size:25 final size:25
Alignment explanation
Indices: 49372356--49372433 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
49372346 CTCGGCCCCT
49372356 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
49372381 TCACAT-TGGCCA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
49372403 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
49372428 TCACAT
1 TCACAT
49372434 CGGCCATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:49377285 original size:15 final size:15
Alignment explanation
Indices: 49377265--49377301 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
49377255 ATTTACTTTC
*
49377265 AATAAATTGGTTATT
1 AATAAATTGGTGATT
49377280 AATAAATTGGTGATT
1 AATAAATTGGTGATT
49377295 AATAAAT
1 AATAAAT
49377302 AGGAGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATAAATTGGTGATT
Found at i:49379529 original size:13 final size:13
Alignment explanation
Indices: 49379511--49379536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49379501 AAATGGGTTG
49379511 TACAAAGCTCTCC
1 TACAAAGCTCTCC
49379524 TACAAAGCTCTCC
1 TACAAAGCTCTCC
49379537 ACTTTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
TACAAAGCTCTCC
Found at i:49379852 original size:18 final size:18
Alignment explanation
Indices: 49379824--49379866 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
49379814 AATCATCATT
*
49379824 AAAAAGTTATTTACTTTC
1 AAAACGTTATTTACTTTC
* *
49379842 AGAACGTTATTTATTTTC
1 AAAACGTTATTTACTTTC
49379860 AAAACGT
1 AAAACGT
49379867 CACTTATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (18 bp):
AAAACGTTATTTACTTTC
Found at i:49409700 original size:19 final size:20
Alignment explanation
Indices: 49409676--49409713 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49409666 AAGAAAAGAT
*
49409676 ATCAAGT-TTTCTGTAGGTG
1 ATCAAGTGTTTCTGAAGGTG
49409695 ATCAAGTGTTTCTGAAGGT
1 ATCAAGTGTTTCTGAAGGT
49409714 ATCTCCATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (20 bp):
ATCAAGTGTTTCTGAAGGTG
Found at i:49411298 original size:42 final size:42
Alignment explanation
Indices: 49411232--49411312 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
49411222 TGACCTAAGA
*
49411232 TCACACGATCAAGGACAAGGGTGTGTGCCCAGGCCGTGTGAG
1 TCACACGATCAAGGACAAGAGTGTGTGCCCAGGCCGTGTGAG
* * *
49411274 TCACACG-TGCAAGGACACGAGTGTGTGTCCAGGTCGTGT
1 TCACACGAT-CAAGGACAAGAGTGTGTGCCCAGGCCGTGT
49411313 AACTCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.22, C:0.23, G:0.35, T:0.20
Consensus pattern (42 bp):
TCACACGATCAAGGACAAGAGTGTGTGCCCAGGCCGTGTGAG
Found at i:49422755 original size:17 final size:17
Alignment explanation
Indices: 49422733--49422765 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49422723 GGGCCGTATG
*
49422733 GGCCCAATGGGCTTGTA
1 GGCCCAACGGGCTTGTA
49422750 GGCCCAACGGGCTTGT
1 GGCCCAACGGGCTTGT
49422766 GGGCTCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.21
Consensus pattern (17 bp):
GGCCCAACGGGCTTGTA
Found at i:49424876 original size:21 final size:22
Alignment explanation
Indices: 49424831--49424884 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
49424821 TTTCCCAAGC
49424831 AAAATAAAAATAATAAGTAGAT
1 AAAATAAAAATAATAAGTAGAT
* **
49424853 AAAATAAATA-AATAAGTATCT
1 AAAATAAAAATAATAAGTAGAT
49424874 AAAACTAAAAA
1 AAAA-TAAAAA
49424885 AAACAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATAAAAATAATAAGTAGAT
Found at i:49434153 original size:12 final size:12
Alignment explanation
Indices: 49434136--49434167 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
49434126 ATGACACACA
49434136 GCCGTGTGGTAG
1 GCCGTGTGGTAG
49434148 GCCGTGTGGTAG
1 GCCGTGTGGTAG
*
49434160 GTCGTGTG
1 GCCGTGTG
49434168 CCATAGCATT
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:0.06, C:0.16, G:0.50, T:0.28
Consensus pattern (12 bp):
GCCGTGTGGTAG
Found at i:49439052 original size:130 final size:130
Alignment explanation
Indices: 49438869--49439127 Score: 421
Period size: 130 Copynumber: 2.0 Consensus size: 130
49438859 TAATTATTTA
*
49438869 TTTAAAAATTATTTAAAACAAAGGTAATGCTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCG
1 TTTAAAAATTATTCAAAACAAAGGTAATGCTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCG
*
49438934 TGCTGGGTTGCGATTTCCCGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGTC
66 TGCTGGGTTGCGATTTCCCGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGTC
* * * *
49438999 TTTAAAAATTCTTCAAAACGAAGGTAATG-TTGATGTTTGGCAATTTGGGGAATCGTGCCCTATC
1 TTTAAAAATTATTCAAAACAAAGGTAATGCTCGATGTTTGGCAATTT-GAGAATCGTGCCCTATC
* * *
49439063 GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAATAATCGGATATTCCTTTAGAATTTCACTCATGT
65 GTGCTGGGTTGCGATTTCCCGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGT
49439128 TCTCTAAATT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 16 0.13
130 103 0.87
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (130 bp):
TTTAAAAATTATTCAAAACAAAGGTAATGCTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCG
TGCTGGGTTGCGATTTCCCGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGTC
Found at i:49439225 original size:127 final size:129
Alignment explanation
Indices: 49438873--49439206 Score: 356
Period size: 130 Copynumber: 2.6 Consensus size: 129
49438863 TATTTATTTA
* * * * * * *
49438873 AAAATTATTTAAAACAAAGGTAATGCTCGATGTTTGGCAATTTGA-GAATCGTGCCCTATCGTGC
1 AAAATTCTTCAAAACGAAGGCAATG-TCGATGTTTAGAAATTCGAGGAATCGTGCCCTATCGTGC
* ** * * *
49438937 TGGGTTGCGATTTCCCGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGTCTTT
65 TGGGTTGCGATTTCCTGTTTGGACAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTCTCT
* * * * * *
49439002 AAAAATTCTTCAAAACGAAGGTAATGTTGATGTTTGGCAATTTGGGGAATCGTGCCCTATCGTGC
1 -AAAATTCTTCAAAACGAAGGCAATGTCGATGTTTAGAAATTCGAGGAATCGTGCCCTATCGTGC
** *
49439067 TGGGTTGCGATTTCCTGTTTGTTCAAAATAATCGGATATTCCTTTAGAATTTCACTCATGTTCTC
65 TGGGTTGCGATTTCCTGTTTGGACAAAATAATCGAATATTCCTTTAGAATTTCACTCATG-TCTC
49439132 T
129 T
* *
49439133 -AAATTC-T-AAAA-TAAGGCAATGTCCGATGTTTAGAAATTCGAGGAATCGTGCCCTA-CTTTG
1 AAAATTCTTCAAAACGAAGGCAATGT-CGATGTTTAGAAATTCGAGGAATCGTGCCCTATC-GTG
*
49439193 CTGGGTTTCGATTT
64 CTGGGTTGCGATTT
49439207 TTTCGTTGGA
Statistics
Matches: 181, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
126 10 0.06
127 46 0.25
128 1 0.01
129 23 0.13
130 97 0.54
131 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (129 bp):
AAAATTCTTCAAAACGAAGGCAATGTCGATGTTTAGAAATTCGAGGAATCGTGCCCTATCGTGCT
GGGTTGCGATTTCCTGTTTGGACAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTCTCT
Found at i:49442287 original size:23 final size:23
Alignment explanation
Indices: 49442260--49442306 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
49442250 ATATTCGGCC
49442260 TAAAT-AGGAAACTCATAAGAGTT
1 TAAATCAGGAAACTCAT-AGAGTT
*
49442283 TAAATCAGGAAGCTCATAGAGTT
1 TAAATCAGGAAACTCATAGAGTT
49442306 T
1 T
49442307 TTTAATAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (23 bp):
TAAATCAGGAAACTCATAGAGTT
Found at i:49445543 original size:16 final size:16
Alignment explanation
Indices: 49445518--49445560 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
49445508 GTAGATCAAC
49445518 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
* *
49445534 AAAAGTCGAAATGCTG
1 AAAAGCCGAAATGCCG
*
49445550 AAAAGCTGAAA
1 AAAAGCCGAAA
49445561 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:49445852 original size:28 final size:29
Alignment explanation
Indices: 49445769--49445864 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
49445759 GAAAGCATGT
*
49445769 ATATGAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
49445798 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
49445827 ATATGAATATGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
49445855 ATATGCATGT
1 ATATGAATGT
49445865 ATGTAGACTT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
28 23 0.37
29 39 0.63
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:49452946 original size:19 final size:20
Alignment explanation
Indices: 49452922--49452959 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49452912 GGTACCACCA
49452922 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
49452941 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
49452960 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:49453767 original size:29 final size:30
Alignment explanation
Indices: 49453734--49453792 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
49453724 ATTTAATACG
*
49453734 AACTTTAATAAAATTACACTTTT-CCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
** *
49453763 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
49453793 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (30 bp):
AACTTTAACAAAATTACACTTTTGCCCCTA
Found at i:49460462 original size:19 final size:20
Alignment explanation
Indices: 49460438--49460475 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49460428 GGTACCACCA
49460438 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
49460457 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
49460476 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:49460802 original size:47 final size:45
Alignment explanation
Indices: 49460748--49460871 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 45
49460738 ATCCATAAAT
*
49460748 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC-AC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTACATC-CAAA
*
49460795 GAACTCGGACTCAACTCAACGAGTTCGGA---CATTGCATCCATAA
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTACATCCA-AA
49460838 GTTAACTCGGACTCAACTCAACGAGTTCGGATGC
1 G--AACTCGGACTCAACTCAACGAGTTCGGATGC
49460872 TCAACCATCC
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
41 1 0.01
42 6 0.09
43 3 0.04
44 1 0.01
45 28 0.41
47 29 0.43
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTACATCCAAA
Found at i:49460860 original size:45 final size:47
Alignment explanation
Indices: 49460736--49460868 Score: 152
Period size: 45 Copynumber: 2.9 Consensus size: 47
49460726 CTGGGCGTTC
*
49460736 GCATCCATAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT
1 GCATCCATAAGT-AACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTT
* *
49460786 ACAT-C-TCACG-AACTCGGACTCAACTCAACGAGTTCGGA-C-A-TT
1 GCATCCAT-AAGTAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT
49460828 GCATCCATAAGTTAACTCGGACTCAACTCAACGAGTTCGGA
1 GCATCCATAAG-TAACTCGGACTCAACTCAACGAGTTCGGA
49460869 TGCTCAACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
42 5 0.07
43 4 0.05
44 2 0.03
45 28 0.38
47 28 0.38
48 1 0.01
49 2 0.03
50 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (47 bp):
GCATCCATAAGTAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT
Found at i:49461321 original size:30 final size:29
Alignment explanation
Indices: 49461287--49461345 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
49461277 ATTTAATACG
*
49461287 AACTTTAATAAAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTT-CCCCTA
** *
49461317 AACTTTTGCATAATTACACTTTTCCCCTA
1 AACTTTAACAAAATTACACTTTTCCCCTA
49461346 GGCTCGGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTTAACAAAATTACACTTTTCCCCTA
Found at i:49467808 original size:19 final size:20
Alignment explanation
Indices: 49467784--49467821 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49467774 TGGTACACCA
49467784 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
49467803 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
49467822 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:49468205 original size:44 final size:47
Alignment explanation
Indices: 49468082--49468213 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 47
49468072 CTGGGCGTTC
*
49468082 GCATCCATAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT
1 GCATCCATAAGT-AACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTT
* *
49468132 ACAT-C-TCACG-AACTCGGACTCAACTCAACGAGTTCGGA-C-A-TT
1 GCATCCAT-AAGTAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT
49468174 GCATCCATAAGTAACTCGGACTCAACTCAACGAGTTCGGA
1 GCATCCATAAGTAACTCGGACTCAACTCAACGAGTTCGGA
49468214 TGCTCAACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
42 5 0.07
43 4 0.05
44 30 0.41
47 28 0.38
48 1 0.01
49 2 0.03
50 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (47 bp):
GCATCCATAAGTAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT
Found at i:49475172 original size:19 final size:20
Alignment explanation
Indices: 49475148--49475185 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49475138 GGTACCACCA
49475148 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
49475167 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
49475186 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:49476033 original size:30 final size:30
Alignment explanation
Indices: 49475999--49476058 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
49475989 ATTTAATACG
*
49475999 AACTTTAATAAAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
** *
49476029 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAACAAAATTACACTTTTGCCCCTA
49476059 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTAACAAAATTACACTTTTGCCCCTA
Found at i:49477169 original size:39 final size:39
Alignment explanation
Indices: 49477121--49477199 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
49477111 CTTAACATTA
**
49477121 ATTCAAGCTATATTGGGCATATAATTTATTTCATAATTT
1 ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
*
49477160 ATTCAAGCTATATCAGGCATATAATTTATTTCATACTTT
1 ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
49477199 A
1 A
49477200 AACATTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (39 bp):
ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
Found at i:49481578 original size:46 final size:46
Alignment explanation
Indices: 49481522--49481694 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
49481512 CGGTTGAGCA
*
49481522 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
49481568 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
49481615 TCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
49481661 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49481695 GGGGTGGGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.57
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:49481678 original size:93 final size:93
Alignment explanation
Indices: 49481519--49481689 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
49481509 GGACGGTTGA
* * * * *
49481519 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCTGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
49481584 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
49481612 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
49481677 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
49481690 ACTTAGGGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:49481955 original size:19 final size:20
Alignment explanation
Indices: 49481918--49481955 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49481908 ATAAGGTGGT
49481918 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
49481938 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
49481956 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:49489144 original size:46 final size:46
Alignment explanation
Indices: 49489091--49489263 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
49489081 CGGTTGAGCA
49489091 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
49489137 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
49489182 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
49489230 CCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49489264 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 58 0.55
47 29 0.27
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:49489247 original size:93 final size:93
Alignment explanation
Indices: 49489088--49489258 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
49489078 GGACGGTTGA
* *
49489088 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCATTGAGT
49489153 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
49489181 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCATTGAGT
*
49489246 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
49489259 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:49489524 original size:19 final size:20
Alignment explanation
Indices: 49489487--49489524 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49489477 ATAAGGTGGT
49489487 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
49489507 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
49489525 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:49490173 original size:21 final size:20
Alignment explanation
Indices: 49490130--49490173 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
49490120 CTGTTCTGAC
*
49490130 TTTAAAAAATAATAATAAAT
1 TTTAAAAAATAATAAGAAAT
* *
49490150 TTTAATAAAATAATTAGAAGT
1 TTTAA-AAAATAATAAGAAAT
49490171 TTT
1 TTT
49490174 TATTTATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTAAAAAATAATAAGAAAT
Found at i:49491323 original size:17 final size:18
Alignment explanation
Indices: 49491279--49491313 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49491269 TTCATGCAGG
*
49491279 CGAATTAAATGAACATGA
1 CGAATTAAATAAACATGA
49491297 CGAATTAAATAAACATG
1 CGAATTAAATAAACATG
49491314 CAACTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (18 bp):
CGAATTAAATAAACATGA
Found at i:49491354 original size:40 final size:40
Alignment explanation
Indices: 49491309--49491391 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
49491299 AATTAAATAA
49491309 ACATGCAACTTAAATCACCTTATTTAAAATGAAAACAAAC
1 ACATGCAACTTAAATCACCTTATTTAAAATGAAAACAAAC
49491349 ACATGCAACTTAAATCACCTTATTTAAAATGAAAACAAAC
1 ACATGCAACTTAAATCACCTTATTTAAAATGAAAACAAAC
49491389 ACA
1 ACA
49491392 CTTTAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (40 bp):
ACATGCAACTTAAATCACCTTATTTAAAATGAAAACAAAC
Found at i:49491574 original size:52 final size:50
Alignment explanation
Indices: 49491490--49491638 Score: 142
Period size: 50 Copynumber: 2.9 Consensus size: 50
49491480 AAATGCATGG
* * *
49491490 TTTAAGATGCAAA-TTATATGAACAA-ATGAGTTACTTAATGCATGACTTAA
1 TTTATGATGCAAACTTAAAT-AACAAGA-GAGTTACATAATGCATGACTTAA
* * * *
49491540 TTTAATGTTGCACACTTTAAATAACAAGGGAGTTACATAATGCAT-ATCATAA
1 TTT-ATGATGCAAAC-TTAAATAACAAGAGAGTTACATAATGCATGA-CTTAA
* * *
49491592 TTTATGATGCAAACTTAACTAACATGAGAGTTACATAATTCATGACT
1 TTTATGATGCAAACTTAAATAACAAGAGAGTTACATAATGCATGACT
49491639 ATATTAAATG
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
50 29 0.37
51 18 0.23
52 27 0.34
53 5 0.06
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (50 bp):
TTTATGATGCAAACTTAAATAACAAGAGAGTTACATAATGCATGACTTAA
Found at i:49502482 original size:6 final size:6
Alignment explanation
Indices: 49502468--49502500 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
49502458 AAACAACATG
*
49502468 AAAAGA AAAATA AAAATA AAAAT- AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
49502501 ATTAAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:49502502 original size:12 final size:12
Alignment explanation
Indices: 49502468--49502500 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
49502458 AAACAACATG
*
49502468 AAAAGAAAAATA
1 AAAATAAAAATA
49502480 AAAATAAAAAT-
1 AAAATAAAAATA
49502491 AAAATAAAAA
1 AAAATAAAAA
49502501 ATTAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:49506865 original size:48 final size:48
Alignment explanation
Indices: 49506669--49506895 Score: 187
Period size: 48 Copynumber: 4.8 Consensus size: 48
49506659 GTTATGTGCG
**
49506669 ATCCCATGTAAGACCATGTCTGGGACATGGTTTTGGCATCGATATGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTA
** * * * * * *
49506717 ATTTCGTGTAAGACCATAG-CTAGG-C-T---ATCGGAATTGATATGTG
1 ATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGTA
* * * * * ***
49506760 ATCCCATGTAAGACCATGTTTGCGTCATGGCATTGGCATTGATCTACG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTA
*
49506808 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATATGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTA
* * * * *
49506856 ATCCTATGTAAGGCCATATCCGGGATATGGCATTGGCATC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
49506896 CTGCCATGTG
Statistics
Matches: 137, Mismatches: 35, Indels: 14
0.74 0.19 0.08
Matches are distributed among these distances:
42 1 0.01
43 28 0.20
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 103 0.75
49 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTA
Found at i:49516047 original size:40 final size:40
Alignment explanation
Indices: 49515947--49516132 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
49515937 GCTCCTCGTT
* * * *
49515947 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
49515987 C-AATGCCTTCGGAACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
49516026 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
49516066 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
*
49516106 CAAATGCCTTC-GGATCTTAGCCCGGAT
1 CAAATGCCTTCGGGA-CTTAACCCGGAT
49516133 ATATTCACTT
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.30
40 86 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:49523231 original size:40 final size:40
Alignment explanation
Indices: 49523131--49523355 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
49523121 GCTCCTCGTT
* * * *
49523131 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
49523171 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
49523210 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
49523250 CAAAGGCCTTCGGGGCTTAACCCAGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGATTTAGTAACTCGCA
** * * * *
49523290 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
49523331 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
49523356 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 41 0.26
40 101 0.64
41 16 0.10
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:49523364 original size:41 final size:41
Alignment explanation
Indices: 49523287--49523364 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
49523277 TTTGTATCTC
* * *
49523287 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
49523328 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
49523365 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:49532159 original size:46 final size:45
Alignment explanation
Indices: 49532105--49532226 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 45
49532095 CTCGTAATCA
* *
49532105 ATGCATGTCCCAAACATGTCTTACACTG-ACTTACGTCTCGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGCACTT--GTCTCAAGGCCG
* *
49532151 ATGCATGTCCCAGACATGTCTTACAATAGCACTTGTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACT-GCACTTGTCTCAAGGCCG
49532197 ATGCCATGTCCCAGACATGGTCTTACACTG
1 ATG-CATGTCCCAGACAT-GTCTTACACTG
49532227 GCTCTCATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
46 38 0.57
47 16 0.24
48 13 0.19
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTGCACTTGTCTCAAGGCCG
Found at i:49532249 original size:94 final size:93
Alignment explanation
Indices: 49532008--49532267 Score: 248
Period size: 94 Copynumber: 2.8 Consensus size: 93
49531998 GTAAGGTGTA
* **
49532008 GATGCCATGTCCCGGACATGGTCTTACACAAGCTCTAGCATATATGT-GCCAATGCCATGTCCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTA-CATA-ATGTGGCCAATG-CATGTCCCA
*
49532072 GACATGGTCTTACATTGACACATCTCGTAATC
63 GACAT-GTCTTACATAGACACATCTCGTAATC
* * * * * * *
49532104 AATG-CATGTCCCAAACAT-GTCTTACACTGACT-TACGT-CTCGAGGCCGATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATAAT-GTGGCCAATGCATGTCCCAGA
* *
49532165 CATGTCTTACAATAG-CACTTGTC-TCAATGCC
65 CATGTCTTAC-ATAGACACATCTCGT-AAT--C
* *
49532196 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGTGGCCAATGCATATCCTAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATAATGTGGCCAATGCATGTCCCAGAC
49532260 ATGTCTTA
66 ATGTCTTA
49532268 GACTAGCTCA
Statistics
Matches: 132, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
89 1 0.01
90 17 0.13
91 18 0.14
92 12 0.09
93 15 0.11
94 52 0.39
95 14 0.11
96 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATAATGTGGCCAATGCATGTCCCAGAC
ATGTCTTACATAGACACATCTCGTAATC
Found at i:49538617 original size:52 final size:52
Alignment explanation
Indices: 49538534--49538647 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
49538524 AAGGGCACAT
* * *
49538534 ACCCGTGTGGCTTACACGCCTTAGGCAATGAAGGGACACGCCCGTGTCTTCC
1 ACCCATGTGGCTCACACGCCTTAGGCAATGAAGGGACACGCCCGTGTCCTCC
49538586 ACCCATGTGGCTCACACGCCTTAGGCAATGAAGGGACACGCCCGTGTCCTCC
1 ACCCATGTGGCTCACACGCCTTAGGCAATGAAGGGACACGCCCGTGTCCTCC
49538638 ACCCATGTGG
1 ACCCATGTGG
49538648 AAATAATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.19
Consensus pattern (52 bp):
ACCCATGTGGCTCACACGCCTTAGGCAATGAAGGGACACGCCCGTGTCCTCC
Found at i:49557280 original size:17 final size:18
Alignment explanation
Indices: 49557243--49557282 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
49557233 TCGTGTGGTG
* *
49557243 TGCCTGTGTGGGCTCACA
1 TGCCCGTGTGGCCTCACA
49557261 TGCCCGTGTGGCCT-ACA
1 TGCCCGTGTGGCCTCACA
49557278 TGCCC
1 TGCCC
49557283 AATTTGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.35, G:0.30, T:0.25
Consensus pattern (18 bp):
TGCCCGTGTGGCCTCACA
Found at i:49571426 original size:48 final size:47
Alignment explanation
Indices: 49571350--49571619 Score: 219
Period size: 44 Copynumber: 5.8 Consensus size: 47
49571340 CATATCGATA
* *
49571350 CCGATGCCATATCCCAGATATGGTCTTACACTGGTTCTCACACATCTGTG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGG-TCTCACACATCTGTG
*
49571400 CCGATGCATGTCCCAGACATGTCTT--AC---TCT-AGCACATCTCATAG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGTCTCA-CACATCT-GT-G
*
49571444 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACACATCCGTG
1 CCGATGCATGTCCCAGACATGTCTTACACTGG-TCTCACACATCTGTG
* * * *
49571492 CCGATACATGTCCTAGACATGTCTTACACTAG---CACATC-TCAT-AG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGTCTCACA-CATC-TGTG
* * * *
49571536 CCGATGTATGTCCCAGACATGTCTTACACTGG-CT--TATATCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGTCTCACACATCT-G-TG
*
49571582 CCGATGCATGTCCCAGACATGTCTGACACTGG-CTCACA
1 CCGATGCATGTCCCAGACATGTCTTACACTGGTCTCACA
49571620 TAACAGCAGT
Statistics
Matches: 180, Mismatches: 20, Indels: 42
0.74 0.08 0.17
Matches are distributed among these distances:
41 1 0.01
42 10 0.06
43 2 0.01
44 64 0.36
45 1 0.01
46 37 0.21
48 36 0.20
49 13 0.07
50 15 0.08
51 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (47 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGTCTCACACATCTGTG
Found at i:49571449 original size:44 final size:44
Alignment explanation
Indices: 49571399--49571611 Score: 234
Period size: 44 Copynumber: 4.7 Consensus size: 44
49571389 ACACATCTGT
*
49571399 GCCGATGCATGTCCCAGACATGTCTTACTCTAGCACATCTCATA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACATCTCATA
* *
49571443 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACA-CATCCGT-
1 GCCGATGCATGTCCCAGACATGTCTTACACTAG----CACATC-T-CATA
* *
49571491 GCCGATACATGTCCTAGACATGTCTTACACTAGCACATCTCATA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACATCTCATA
* * * *
49571535 GCCGATGTATGTCCCAGACATGTCTTACACTGGCTTATATCTCGA-G
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC--ACATCTC-ATA
*
49571581 GCCGATGCATGTCCCAGACATGTCTGACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
49571612 GGCTCACATA
Statistics
Matches: 143, Mismatches: 15, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
43 2 0.01
44 66 0.46
45 1 0.01
46 35 0.24
47 2 0.01
48 35 0.24
49 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACATCTCATA
Found at i:49571620 original size:92 final size:92
Alignment explanation
Indices: 49571350--49571611 Score: 352
Period size: 92 Copynumber: 2.8 Consensus size: 92
49571340 CATATCGATA
* * * * *
49571350 CCGATGCCATATCCCAGATATGGTCTTACACTGGTTCTCACACATCTGTGCCGATGCATGTCCCA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCACACATCCGGGCCGATGCATGTCCCA
*
49571415 GACATGTCTTACTCTAGCACATCTCATAG
64 GACATGTCTTACACTAGCACATCTCATAG
* * *
49571444 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACACATCCGTGCCGATACATGTCCTAGA
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACACATCCGGGCCGATGCATGTCCCAGA
49571509 CATGTCTTACACTAGCACATCTCATAG
66 CATGTCTTACACTAGCACATCTCATAG
* *
49571536 CCGATGTATGTCCCAGACATGTCTTACACTGGCT-T---ATATCTCGAGGCCGATGCATGTCCCA
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACACATC-CG-GGCCGATGCATGTCCCA
*
49571597 GACATGTCTGACACT
64 GACATGTCTTACACT
49571612 GGCTCACATA
Statistics
Matches: 153, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
88 4 0.03
89 2 0.01
90 28 0.18
91 1 0.01
92 100 0.65
93 12 0.08
94 6 0.04
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (92 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCACACATCCGGGCCGATGCATGTCCCAGA
CATGTCTTACACTAGCACATCTCATAG
Found at i:49584342 original size:3 final size:3
Alignment explanation
Indices: 49584334--49584364 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
49584324 AGATATTTAC
49584334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49584365 CAATTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49584589 original size:5 final size:5
Alignment explanation
Indices: 49584525--49584600 Score: 59
Period size: 5 Copynumber: 14.8 Consensus size: 5
49584515 AACAATAAAT
* * *
49584525 AAAAG -AAAG AAAA- ACAAG AAAAAG AAACAG AGAAG AAACG AAATAG
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAA-AG AAAAG AAAAG AAA-AG
49584571 -AAAG AATGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA--AAG AAAAG AAAAG AAAAG AAAA
49584601 AGGAGAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
4 9 0.16
5 34 0.60
6 9 0.16
7 5 0.09
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:49584596 original size:22 final size:21
Alignment explanation
Indices: 49584525--49584598 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 21
49584515 AACAATAAAT
*
49584525 AAAAGAAAGAAAAACAAGAAAAAG
1 AAAAG-AAGAAGAA-AAG-AAAAG
*
49584549 AAACAG-AGAAGAAACGAAATAG
1 AAA-AGAAGAAGAAAAGAAA-AG
49584571 -AAAGAATGAAGAAAAGAAAAG
1 AAAAGAA-GAAGAAAAGAAAAG
49584592 AAAAGAA
1 AAAAGAA
49584599 AAAGGAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 2 0.05
21 8 0.19
22 21 0.50
23 6 0.14
24 3 0.07
25 2 0.05
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.03
Consensus pattern (21 bp):
AAAAGAAGAAGAAAAGAAAAG
Found at i:49589624 original size:40 final size:40
Alignment explanation
Indices: 49589579--49589661 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
49589569 CTATGTTTAA
49589579 ATGTTTCATGAGATATGATGATGAGGTTTACCATGTCTGG
1 ATGTTTCATGAGATATGATGATGAGGTTTACCATGTCTGG
49589619 ATGTTTCATGAGATATGATGATGAGGTTTACCATGTCTGG
1 ATGTTTCATGAGATATGATGATGAGGTTTACCATGTCTGG
49589659 ATG
1 ATG
49589662 ATTGAAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (40 bp):
ATGTTTCATGAGATATGATGATGAGGTTTACCATGTCTGG
Found at i:49592352 original size:3 final size:3
Alignment explanation
Indices: 49592344--49592390 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
49592334 TAACTATAGC
49592344 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49592391 CAATTTCAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49595266 original size:24 final size:23
Alignment explanation
Indices: 49595239--49595304 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
49595229 AGTATAATGT
49595239 TATTTAAATGTTTTTTTATTAAGA
1 TATTTAAATGTTTTTTTATTAA-A
* * * *
49595263 TATTAAAATATTTGTTAATTAAA
1 TATTTAAATGTTTTTTTATTAAA
49595286 -ATTTATAATGATTTTTTTA
1 TATTTA-AATG-TTTTTTTA
49595305 ATTGAGAAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 24 0.75
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
TATTTAAATGTTTTTTTATTAAA
Found at i:49617773 original size:8 final size:8
Alignment explanation
Indices: 49617760--49617829 Score: 54
Period size: 8 Copynumber: 8.2 Consensus size: 8
49617750 ATATTTTCTC
49617760 AAAAATTT
1 AAAAATTT
49617768 AAAAATTACT
1 AAAAATT--T
*
49617778 AATAATTT
1 AAAAATTT
*
49617786 AATAAATTG
1 AA-AAATTT
49617795 AAAAA-TT
1 AAAAATTT
49617802 AAATAATTT
1 AAA-AATTT
49617811 AATAAAATTT
1 -A-AAAATTT
49617821 -AAAATTT
1 AAAAATTT
49617828 AA
1 AA
49617830 GAGGTCTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
7 11 0.22
8 16 0.32
9 8 0.16
10 13 0.26
11 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (8 bp):
AAAAATTT
Found at i:49617812 original size:25 final size:26
Alignment explanation
Indices: 49617762--49617816 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
49617752 ATTTTCTCAA
*
49617762 AAATTTAAAAATTACTAATAATTTAAT
1 AAATTGAAAAATTAC-AATAATTTAAT
49617789 AAATTGAAAAATTA-AATAATTTAAT
1 AAATTGAAAAATTACAATAATTTAAT
49617814 AAA
1 AAA
49617817 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.52
27 13 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATTGAAAAATTACAATAATTTAAT
Found at i:49617824 original size:25 final size:26
Alignment explanation
Indices: 49617761--49617826 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
49617751 TATTTTCTCA
49617761 AAAATTTAAAAATTACTAATAATTTAAT
1 AAAATTT-AAAATTAC-AATAATTTAAT
*
49617789 -AAATTGAAAAATTA-AATAATTTAAT
1 AAAATT-TAAAATTACAATAATTTAAT
49617814 AAAATTTAAAATT
1 AAAATTTAAAATT
49617827 TAAGAGGTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 17 0.50
26 5 0.15
27 12 0.35
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATTTAAAATTACAATAATTTAAT
Found at i:49617829 original size:17 final size:18
Alignment explanation
Indices: 49617761--49617822 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
49617751 TATTTTCTCA
*
49617761 AAAATTTAA-AAATTACT
1 AAAATTTAATAAATTAAT
*
49617778 AATAATTTAATAAATTGA-
1 AA-AATTTAATAAATTAAT
* *
49617796 AAAATTAAATAATTTAAT
1 AAAATTTAATAAATTAAT
49617814 AAAATTTAA
1 AAAATTTAA
49617823 AATTTAAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 14 0.39
18 17 0.47
19 5 0.14
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAATTTAATAAATTAAT
Found at i:49624981 original size:48 final size:48
Alignment explanation
Indices: 49624900--49625114 Score: 306
Period size: 48 Copynumber: 4.5 Consensus size: 48
49624890 AGTACCATGT
* * **
49624900 CATGTCCCCGACATGGTCTTACATGAATC-CACATATCATCACCGATGC
1 CATGTCCCAGACATGGTCTTACA-CAGGCACACATATCATCACCGATGC
* * * *
49624948 CATATCCTAGACATGGTCTTACACTGGCACACATATCATCGCCGATGC
1 CATGTCCCAGACATGGTCTTACACAGGCACACATATCATCACCGATGC
49624996 CATGTCCCAGACATGGTCTTACACAGGCACACATATCATCACCGATGC
1 CATGTCCCAGACATGGTCTTACACAGGCACACATATCATCACCGATGC
* * * *
49625044 CATGTCGCAAACATGGTCTTACACAGGCATATATATCATCACCGATGC
1 CATGTCCCAGACATGGTCTTACACAGGCACACATATCATCACCGATGC
49625092 CATGTCCCAGACATGGTCTTACA
1 CATGTCCCAGACATGGTCTTACA
49625115 TAGGATCTCA
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
47 1 0.01
48 147 0.99
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACAGGCACACATATCATCACCGATGC
Found at i:49643669 original size:42 final size:42
Alignment explanation
Indices: 49643575--49643731 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 42
49643565 ATGTGTGATT
* * **
49643575 TCGTGTAAGACCATATCTGGGATATGGCATTAATATGTGATT
1 TCGTGTAAGACCATATCTGGGATATGGCATCAATATGAGACA
* * * * *
49643617 TTGAGAAAGACCATGTCTGGGATATGGTATCAATATGAGACA
1 TCGTGTAAGACCATATCTGGGATATGGCATCAATATGAGACA
* * * *
49643659 TCGTGTAAGACCATAGCTGGGCTATCGGCATCGATATGTGATC-
1 TCGTGTAAGACCATATCTGGGATAT-GGCATCAATATGAGA-CA
* * *
49643702 CCATGTAAGGCCATATCTGGGATATGGCAT
1 TCGTGTAAGACCATATCTGGGATATGGCAT
49643732 TGGCATCTTA
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 57 0.63
43 32 0.36
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
TCGTGTAAGACCATATCTGGGATATGGCATCAATATGAGACA
Found at i:49648646 original size:18 final size:18
Alignment explanation
Indices: 49648623--49648675 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
49648613 TTCATTGAGA
49648623 GTTCATGGTGAAGAACTT
1 GTTCATGGTGAAGAACTT
49648641 GTTCAT--TG-AG-A---
1 GTTCATGGTGAAGAACTT
49648652 GTTCATGGTGAAGAACTT
1 GTTCATGGTGAAGAACTT
49648670 GTTCAT
1 GTTCAT
49648676 CGAGAATTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
11 6 0.21
13 2 0.07
14 3 0.11
15 3 0.11
16 2 0.07
18 12 0.43
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (18 bp):
GTTCATGGTGAAGAACTT
Found at i:49648647 original size:29 final size:29
Alignment explanation
Indices: 49648605--49648680 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
49648595 GAAGAGGTAG
49648605 AGAACTTGTTCATTGAGAGTTCATGGTGA
1 AGAACTTGTTCATTGAGAGTTCATGGTGA
49648634 AGAACTTGTTCATTGAGAGTTCATGGTGA
1 AGAACTTGTTCATTGAGAGTTCATGGTGA
*
49648663 AGAACTTGTTCATCGAGA
1 AGAACTTGTTCATTGAGA
49648681 ATTCGTTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (29 bp):
AGAACTTGTTCATTGAGAGTTCATGGTGA
Found at i:49649080 original size:47 final size:47
Alignment explanation
Indices: 49649011--49649104 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
49649001 TTATTGCTTT
* *
49649011 GCGATCGTTCTATGTTGCCATTATCGGCGTTAGTTTCTACACTAATC
1 GCGATCATTCTATGTTGCCATTATCGACGTTAGTTTCTACACTAATC
49649058 GCGATCATTCTATGTTGCCATTATCGACGTTAGTTTCTACACTAATC
1 GCGATCATTCTATGTTGCCATTATCGACGTTAGTTTCTACACTAATC
49649105 TAATCGAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (47 bp):
GCGATCATTCTATGTTGCCATTATCGACGTTAGTTTCTACACTAATC
Found at i:49649937 original size:12 final size:12
Alignment explanation
Indices: 49649920--49649944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49649910 ACTTAATCAT
49649920 TTTAATATTAAA
1 TTTAATATTAAA
49649932 TTTAATATTAAA
1 TTTAATATTAAA
49649944 T
1 T
49649945 CTTATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:49653285 original size:43 final size:43
Alignment explanation
Indices: 49653232--49653396 Score: 158
Period size: 43 Copynumber: 3.8 Consensus size: 43
49653222 GACAAGTACA
* *
49653232 ATGCCACTGTCCCAGACGTGGTCTTACATGTAATTCAATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCAATATCG
* * * **
49653275 ATGCCTCTGTCCCAGACAAGGTCTTATACG-AAAACAGATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCA-ATATCG
* *
49653317 ATGCCGA-TGTTCCAGACATAGTCTTACACGTAAATTTCAA-ATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGT-AA-TTCAATATCG
* *
49653361 ATGCCAGTGTCCCAGACATGGTCTTATACGATAATT
1 ATGCCACTGTCCCAGACATGGTCTTACACG-TAATT
49653397 TAGATCAATA
Statistics
Matches: 97, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
42 30 0.31
43 32 0.33
44 32 0.33
45 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCAATATCG
Found at i:49653397 original size:44 final size:42
Alignment explanation
Indices: 49653232--49653396 Score: 154
Period size: 44 Copynumber: 3.8 Consensus size: 42
49653222 GACAAGTACA
* *
49653232 ATGCCACTGTCCCAGACGTGGTCTTACATGTAATTCAATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCAA-ATCG
* * * ** *
49653275 ATGCCTCTGTCCCAGACAAGGTCTTATACG-AAAACAGATACG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCAAAT-CG
* *
49653317 ATGCCGA-TGTTCCAGACATAGTCTTACACGTAAATTTCAAATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGT-AA-TTCAAATCG
* *
49653361 ATGCCAGTGTCCCAGACATGGTCTTATACGATAATT
1 ATGCCACTGTCCCAGACATGGTCTTACACG-TAATT
49653397 TAGATCAATA
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.02
42 30 0.31
43 28 0.29
44 31 0.32
45 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAATTCAAATCG
Found at i:49681354 original size:39 final size:40
Alignment explanation
Indices: 49681246--49681470 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
49681236 TTGAATGATG
* * * *
49681246 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
49681286 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49681326 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
49681365 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49681405 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
49681446 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
49681471 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.20
40 118 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:49681488 original size:80 final size:80
Alignment explanation
Indices: 49681246--49681503 Score: 215
Period size: 80 Copynumber: 3.2 Consensus size: 80
49681236 TTGAATGATG
* * * * * * * * *
49681246 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGTAT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAA
** *
49681309 TTGTGCGAGAT-ACTAAT
64 TTGAACGAG-TGACTAAA
* *
49681326 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCAATT
** *
49681390 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
* * *
49681405 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCAAT
*
49681469 TGAACGAG-GAGCTATA
65 TGAACGAGTGA-CTAAA
* *
49681485 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
49681504 TACGTGATTT
Statistics
Matches: 151, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.01
79 72 0.48
80 75 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCAATT
GAACGAGTGACTAAA
Found at i:49701406 original size:23 final size:22
Alignment explanation
Indices: 49701355--49701406 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
49701345 CCTCGTCTTT
*
49701355 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
49701377 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
49701400 TTCTTTT
1 TTCTTTT
49701407 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:49706875 original size:35 final size:35
Alignment explanation
Indices: 49706835--49706985 Score: 144
Period size: 35 Copynumber: 4.3 Consensus size: 35
49706825 AATCTAACCA
*
49706835 AAACACACCAGATGCTCATAAGAGCCAATCCAT-CT
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATCCT
* * *
49706870 GAACACACCAATGCTCGTAATG-GCTAATCCCTCCT
1 AAACACACCAATGCTCATAA-GAGCTAATCCATCCT
* * * *
49706905 AAACACACCAATGCTCATAAAAGCTAATCCTTTCG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCT
* * * * * *
49706940 AAACACATCAGTGCTCATCAGAGCTAGTCCAACCG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCT
49706975 AAACACACCAA
1 AAACACACCAA
49706986 AACAGAAAGC
Statistics
Matches: 93, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
34 17 0.18
35 76 0.82
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.19
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATCCT
Found at i:49708720 original size:49 final size:49
Alignment explanation
Indices: 49708664--49708762 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
49708654 ATTATTGATG
49708664 TTTAATGATAGATTATGAGACCTTGTTGATAAATAAACAAGTTTTGTAA
1 TTTAATGATAGATTATGAGACCTTGTTGATAAATAAACAAGTTTTGTAA
49708713 TTTAATGATAGATTATGAGACCTTGTTGATAAATAAACAAGTTTTGTAA
1 TTTAATGATAGATTATGAGACCTTGTTGATAAATAAACAAGTTTTGTAA
49708762 T
1 T
49708763 GTGATTTTTG
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:0.38, C:0.06, G:0.16, T:0.39
Consensus pattern (49 bp):
TTTAATGATAGATTATGAGACCTTGTTGATAAATAAACAAGTTTTGTAA
Found at i:49723286 original size:7 final size:7
Alignment explanation
Indices: 49723274--49723316 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
49723264 GAATTAGTAT
49723274 TTTATTA
1 TTTATTA
49723281 TTTATTA
1 TTTATTA
49723288 TTTATTA
1 TTTATTA
49723295 TTTATTA
1 TTTATTA
*
49723302 TTTATAA
1 TTTATTA
49723309 TGTTATTA
1 T-TTATTA
49723317 AAGTGCTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:49725090 original size:47 final size:46
Alignment explanation
Indices: 49725019--49725293 Score: 168
Period size: 47 Copynumber: 5.8 Consensus size: 46
49725009 CGCCCATATT
*
49725019 ATGAGAGCCAGTGTAAGACTATGTCTGGGATATGGCATCGACATCCAG
1 ATGAGAGCTAGTGTAAGAC-ATGTCTGGGATATGGCATCGACAT-CAG
* * * * *
49725067 ACGAGGGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCAT-ATT
1 ATGAGAGCTAGTGTAAGACATGTCTGGGATATGGCATC-GACATCA-G
* * * *
49725113 ATGAGAGCCAATGTAAAACCATGTCTGGGATATGGCATCGGCACA-GAG
1 ATGAGAGCTAGTGTAAGA-CATGTCTGGGATATGGCATC-G-ACATCAG
* * * * * *
49725161 ATGAGTGCTAGAGTAAGACATGTCTGGGACAT-ACATCGGCCTTGACAG
1 ATGAGAGCTAGTGTAAGACATGTCTGGGATATGGCATC-GACAT--CAG
* * * *
49725209 A-GATAGCTAGTGTAAGACGTGTCTGGGACAT-GCATCAGCACGCAT-AT
1 ATGAGAGCTAGTGTAAGACATGTCTGGGATATGGCATC-G-A--CATCAG
* *
49725256 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGAGAGCTAGTGTAAGA-CATGTCTGGGATATGGCAT
49725294 TGGCAATGTA
Statistics
Matches: 175, Mismatches: 37, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
45 2 0.01
46 24 0.14
47 75 0.43
48 52 0.30
49 16 0.09
50 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (46 bp):
ATGAGAGCTAGTGTAAGACATGTCTGGGATATGGCATCGACATCAG
Found at i:49725143 original size:94 final size:94
Alignment explanation
Indices: 49724982--49725198 Score: 303
Period size: 94 Copynumber: 2.3 Consensus size: 94
49724972 TTTGTGCGCC
* * * * *
49724982 AGTGTAAGACATGTCTAGGACATGCTTCGCCCATATTATGAGAGCCAGTGTAAGACTATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGCCCATATTATGAGAGCCAATGTAAAACCATGTCTGG
49725047 GATATGGCATCGACATC-CAGACGAGGGCT
66 GATATGGCATCGACA-CACAGACGAGGGCT
49725076 AGTGTAAGACATGTCTGGGACATGCATCAG-CCATATTATGAGAGCCAATGTAAAACCATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCCATATTATGAGAGCCAATGTAAAACCATGTCTG
* * * *
49725140 GGATATGGCATCGGCACAGAGATGAGTGCT
65 GGATATGGCATCGACACACAGACGAGGGCT
* *
49725170 AGAGTAAGACATGTCTGGGACATACATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
49725199 GCCTTGACAG
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
93 2 0.02
94 107 0.97
95 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCCATATTATGAGAGCCAATGTAAAACCATGTCTGG
GATATGGCATCGACACACAGACGAGGGCT
Found at i:49725232 original size:94 final size:94
Alignment explanation
Indices: 49724982--49725288 Score: 275
Period size: 94 Copynumber: 3.2 Consensus size: 94
49724972 TTTGTGCGCC
* * * * *
49724982 AGTGTAAGACATGTCTAGGACATGCTTC-GCCCATATTATGAGAGCCAGTGTAAGACTATGTCTG
1 AGTGTAAGACATGTCTGGGACATACATCAG-CCATATGAAGAGAGCCAGTGTAAGAC-ATGTCTG
* * * *
49725046 GGATATGGCATCGACATC-CAGACGAGGGCT
64 GGATATGGCATCGGCACCACAGATGAGAGCT
* * * * *
49725076 AGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGAGCCAATGTAAAACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATACATCAGCCATATGAAGAGAGCCAGTGTAAGA-CATGTCTGG
* *
49725141 GATATGGCATCGGCA-CAGAGATGAGTGCT
65 GATATGGCATCGGCACCACAGATGAGAGCT
* * * *
49725170 AGAGTAAGACATGTCTGGGACATACATCGGCC-T-TGACAGAGATAGCTAGTGTAAGACGTGTCT
1 AGTGTAAGACATGTCTGGGACATACATCAGCCATATGA-AGAG--AGCCAGTGTAAGACATGTCT
* * * * *
49725233 GGGACAT-GCATCAGCACGCATATATGAGAGCC
63 GGGATATGGCATCGGCAC-CACAGATGAGAGCT
49725265 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGA-CATGTCTGGGACAT
49725289 GGCATTGGCA
Statistics
Matches: 180, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
92 2 0.01
93 13 0.07
94 121 0.67
95 30 0.17
96 14 0.08
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATACATCAGCCATATGAAGAGAGCCAGTGTAAGACATGTCTGGG
ATATGGCATCGGCACCACAGATGAGAGCT
Found at i:49730680 original size:178 final size:178
Alignment explanation
Indices: 49730420--49730794 Score: 642
Period size: 178 Copynumber: 2.1 Consensus size: 178
49730410 TTACTTAATT
*
49730420 AATTTAATCACAATTTACTTAATCTTATTTATCTACTAATAAAAAAAAGTGGATTCCATCATGAA
1 AATTTAAT-A-AAATTACTTAATCTTATTTATCTACTAATAAAAAAAAGTGGATTCCATCATGAA
* *
49730485 ATTCCACTATCCACTATTAACAATTTCTCTTTTGCTCTATTAGCTAATTAAAAATCTATAGCAAT
64 ATTCCACTATCCACTATTAACAATTGCTCTTTTGCTCTATTAGCTAATTAAAAATCTAAAGCAAT
49730550 TAAACTTTTACCATTTTTACGATTTAATCCTTATACTTTAATTAACTATC
129 TAAACTTTTACCATTTTTACGATTTAATCCTTATACTTTAATTAACTATC
* *
49730600 AATTTAATAAAATTACTTAATCTTATTTATCTACTAATCAAACAAAGTGGATTCCATCATGAAAT
1 AATTTAATAAAATTACTTAATCTTATTTATCTACTAATAAAAAAAAGTGGATTCCATCATGAAAT
* *
49730665 TCCACTATCCACTATTAACAATTGCTCTTTTGTTCTATTAGCTAATTAAAAATCTAAAGCGATTA
66 TCCACTATCCACTATTAACAATTGCTCTTTTGCTCTATTAGCTAATTAAAAATCTAAAGCAATTA
* *
49730730 AACTTTTACCATTTTTATGATTTAATCCTTATATTTTAATTAACTATC
131 AACTTTTACCATTTTTACGATTTAATCCTTATACTTTAATTAACTATC
*
49730778 AATTTAAAAAAATTACT
1 AATTTAATAAAATTACT
49730795 AGACCGAAAT
Statistics
Matches: 185, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
178 176 0.95
179 1 0.01
180 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.41
Consensus pattern (178 bp):
AATTTAATAAAATTACTTAATCTTATTTATCTACTAATAAAAAAAAGTGGATTCCATCATGAAAT
TCCACTATCCACTATTAACAATTGCTCTTTTGCTCTATTAGCTAATTAAAAATCTAAAGCAATTA
AACTTTTACCATTTTTACGATTTAATCCTTATACTTTAATTAACTATC
Found at i:49742942 original size:40 final size:40
Alignment explanation
Indices: 49742879--49743048 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
49742869 GGAAAATGCT
* * * *
49742879 GCAATAGGTAAAGCAGTACCGGTGTTTTTGATAAAAACGCA
1 GCAAAAGGT-AAGCAATAGCGGTGTTTATGATAAAAACGCA
* * *
49742920 ACAAAAGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCC
1 GCAAAAGGTAAGCAATAGCGGTGTTTATGATAAAAACGCA
*** * *
49742960 GCAAAAGGTAAGCAATAGCGACATTTATGGTAAAAACGCT
1 GCAAAAGGTAAGCAATAGCGGTGTTTATGATAAAAACGCA
*** * * *
49743000 GCAAAAGGTAAGCAATAGCGACATTTGTGTTAAAAACGCT
1 GCAAAAGGTAAGCAATAGCGGTGTTTATGATAAAAACGCA
49743040 GCAAAAGGT
1 GCAAAAGGT
49743049 TTTTTACTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
40 107 0.94
41 7 0.06
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (40 bp):
GCAAAAGGTAAGCAATAGCGGTGTTTATGATAAAAACGCA
Found at i:49743135 original size:15 final size:16
Alignment explanation
Indices: 49743115--49743145 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49743105 ACATACGAAT
49743115 TATTTTCTTT-CTTGA
1 TATTTTCTTTGCTTGA
49743130 TATTTTCTTTGCTTGA
1 TATTTTCTTTGCTTGA
49743146 AACCTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.65
Consensus pattern (16 bp):
TATTTTCTTTGCTTGA
Found at i:49743214 original size:46 final size:47
Alignment explanation
Indices: 49743132--49743252 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 47
49743122 TTTCTTGATA
* ** *
49743132 TTTTCTTTGCTTGAAACCTCAAAATCATTTCCCTTTTCTTTCTCGGAC
1 TTTT-TTTGCTTGAAACCACAAAATCACATCCCTTTTCTTTCTCAGAC
* *
49743180 TTTTTTTGCTTGAAACCAC-AAATCCCATCCCTTTTCTTTCTCAGTC
1 TTTTTTTGCTTGAAACCACAAAATCACATCCCTTTTCTTTCTCAGAC
* *
49743226 TTTTTGTTGCTCGAAAACCCCAAAATC
1 TTTTT-TTGCTTG-AAACCACAAAATC
49743253 CCGTCCTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
46 27 0.44
47 20 0.32
48 10 0.16
49 5 0.08
ACGTcount: A:0.21, C:0.28, G:0.08, T:0.42
Consensus pattern (47 bp):
TTTTTTTGCTTGAAACCACAAAATCACATCCCTTTTCTTTCTCAGAC
Found at i:49745878 original size:20 final size:20
Alignment explanation
Indices: 49745853--49745919 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
49745843 TGGAGGTAAA
49745853 TCCCCAACGGACCTGGACTC
1 TCCCCAACGGACCTGGACTC
** * * *
49745873 TCCCCATAAAGATTCTGAAAT-
1 TCCCCA-ACGGA-CCTGGACTC
49745894 TCCCCAACGGACCTGGACTC
1 TCCCCAACGGACCTGGACTC
49745914 TCCCCA
1 TCCCCA
49745920 TAAAGATTCT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 5 0.15
20 15 0.44
21 9 0.26
22 5 0.15
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.19
Consensus pattern (20 bp):
TCCCCAACGGACCTGGACTC
Found at i:49745898 original size:41 final size:41
Alignment explanation
Indices: 49745853--49745934 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
49745843 TGGAGGTAAA
49745853 TCCCCAACGGACCTGGACTCTCCCCATAAAGATTCTGAAAT
1 TCCCCAACGGACCTGGACTCTCCCCATAAAGATTCTGAAAT
49745894 TCCCCAACGGACCTGGACTCTCCCCATAAAGATTCTGAAAT
1 TCCCCAACGGACCTGGACTCTCCCCATAAAGATTCTGAAAT
49745935 AAATTGACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.34, G:0.15, T:0.22
Consensus pattern (41 bp):
TCCCCAACGGACCTGGACTCTCCCCATAAAGATTCTGAAAT
Found at i:49745899 original size:21 final size:22
Alignment explanation
Indices: 49745871--49745934 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
49745861 GGACCTGGAC
49745871 TCTCCCCATAAAGATTCTGAAA
1 TCTCCCCATAAAGATTCTGAAA
** * * *
49745893 T-TCCCCA-ACGGA-CCTGGAC
1 TCTCCCCATAAAGATTCTGAAA
49745912 TCTCCCCATAAAGATTCTGAAA
1 TCTCCCCATAAAGATTCTGAAA
49745934 T
1 T
49745935 AAATTGACCA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
19 5 0.17
20 9 0.31
21 9 0.31
22 6 0.21
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (22 bp):
TCTCCCCATAAAGATTCTGAAA
Found at i:49747649 original size:49 final size:50
Alignment explanation
Indices: 49747543--49747718 Score: 166
Period size: 50 Copynumber: 3.6 Consensus size: 50
49747533 TAATACGGAT
* * * * *
49747543 GCCATGTCTCAGACATGGTCTTACACTGGCTCATC-C--ATC-AAGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACT-ATCACAAATCGAGGCCGAC
* *
49747590 GCCATGTCCCAG-CTATAGTCTTACACTGACTATTA-AAATCGAGGCCGAC
1 GCCATGTCCCAGAC-ATGGTCTTACACTGACTATCACAAATCGAGGCCGAC
* * * * * *
49747639 GCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATCTATGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCGAGGCCGAC
*
49747689 GCCATGTCCTAGACATGGTCTTACACTGAC
1 GCCATGTCCCAGACATGGTCTTACACTGAC
49747719 ACCTCTATAT
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
46 3 0.03
47 26 0.25
48 3 0.03
49 34 0.32
50 39 0.37
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCGAGGCCGAC
Found at i:49747703 original size:50 final size:49
Alignment explanation
Indices: 49747540--49747948 Score: 232
Period size: 48 Copynumber: 8.6 Consensus size: 49
49747530 GTATAATACG
* * * *
49747540 GATGCCATGTCTCAGACATGGTCTTACACTGGCTCATC-C-ATC-AAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTC-TCACTATCTATGCC
* * * ** * *
49747587 GATGCCATGTCCCAG-CTATAGTCTTACACTGACTATTAAAATCGAGGCC
1 GATGCCATGTCCCAGAC-ATGGTCTTACACTGACTCTCACTATCTATGCC
* *
49747636 GACGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATCTATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAC-TATCTATGCC
* * * * *
49747686 GATGCCATGTCCTAGACATGGTCTTACACTGACAC-CTCTATATGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACTATCTATGCC
* * * * *
49747734 GATGCCATGTCCAAGACATGGTCGTATACTGA--CACA-TCTCGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACTATC-TATGCC
* * * * *
49747780 AATG-CATGTCTCAAACAT-GTCTTACACTGGCT-T-AC-ATCTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACTATCT--ATGCC
* * * * * * *
49747826 GATG-CATATCCCAAACAT-GTTTTACACT-AGCTCTC-GTCTCAATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCACTATCTATGCC
* * * *
49747872 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCA-TAATGT-GGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACT-ATCTATGCC
*
49747920 GATG-CATGTCCCAAACAT-GTCTTACACTG
1 GATGCCATGTCCCAGACATGGTCTTACACTG
49747949 GCACACAAAT
Statistics
Matches: 277, Mismatches: 62, Indels: 47
0.72 0.16 0.12
Matches are distributed among these distances:
43 1 0.00
44 12 0.04
45 12 0.04
46 58 0.21
47 55 0.20
48 63 0.23
49 37 0.13
50 39 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACTATCTATGCC
Found at i:49747831 original size:46 final size:46
Alignment explanation
Indices: 49747768--49747950 Score: 183
Period size: 46 Copynumber: 3.9 Consensus size: 46
49747758 TATACTGACA
* *
49747768 CATCTCGTA-GCCAATGCATGTCTCAAACATGTCTTACACTGGCT-T
1 CATCTCG-AGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCT
* * *
49747813 ACATCTCGAGGCCGATGCATATCCCAAACATGTTTTACACTAGCTCT
1 -CATCTCGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCT
* * * * * *
49747860 CGTCTCAATGCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCT
1 CATCTCGAGGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTCT
* *
49747908 CATAAT-GTGGCCGATGCATGTCCCAAACATGTCTTACACTGGC
1 CAT-CTCGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGC
49747951 ACACAAATAA
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
45 1 0.01
46 62 0.56
47 24 0.22
48 22 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATCTCGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTCT
Found at i:49747899 original size:48 final size:47
Alignment explanation
Indices: 49747540--49747910 Score: 178
Period size: 46 Copynumber: 7.8 Consensus size: 47
49747530 GTATAATACG
* *
49747540 GATGCCATGT-CTCAGACATGGTCTTACACTG-GCTCATCCATCAA-GTC
1 GATGCCATGTCCT-AGACATGGTCTTACACTGCTCTCAT-C-TCAATGCC
* * * * ** * *
49747587 GATGCCATGTCCCAG-CTATAGTCTTACACTGACTATTAAAATCGAGGCC
1 GATGCCATGTCCTAGAC-ATGGTCTTACACTG-CT-CTCATCTCAATGCC
* * * * *
49747636 GACGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATCTATGCC
1 GATGCCATGTCCTAGACATGGTCTTACACT-GCTCT--CATCTCAATGCC
*
49747686 GATGCCATGTCCTAGACATGGTCTTACACTGACAC-C-TCT-ATATGTGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTG-CTCTCATCTCA-A--TGCC
* * * * * *
49747734 GATGCCATGTCCAAGACATGGTCGTATACTG-ACACATCTC-GTAGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTGCTCTCATCTCAAT-GCC
* * * *
49747780 AATG-CATGT-CTCAAACAT-GTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCCATGTCCT-AGACATGGTCTTACACT-GCTCT-CATCTCAATGCC
* * * * * *
49747826 GATG-CATATCCCAAACAT-GTTTTACACTAGCTCTCGTCTCAATGCT
1 GATGCCATGTCCTAGACATGGTCTTACACT-GCTCTCATCTCAATGCC
49747872 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCAT
1 GATGCCATGTCCTAGACATGGTCTTACACT-GCTCTCAT
49747911 AATGTGGCCG
Statistics
Matches: 246, Mismatches: 51, Indels: 53
0.70 0.15 0.15
Matches are distributed among these distances:
44 9 0.04
45 12 0.05
46 58 0.24
47 40 0.16
48 56 0.23
49 30 0.12
50 41 0.17
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCTAGACATGGTCTTACACTGCTCTCATCTCAATGCC
Found at i:49758406 original size:50 final size:50
Alignment explanation
Indices: 49758284--49758532 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
49758274 GATAATAACA
* * * ** * *
49758284 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
49758335 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49758385 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49758435 TGCCCATGCCATGTCCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
49758490 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
49758533 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49758461 original size:100 final size:104
Alignment explanation
Indices: 49758283--49758532 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
49758273 TGATAATAAC
* **
49758283 ATGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
49758348 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
49758385 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
49758448 TCCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
49758490 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
49758533 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:49758648 original size:13 final size:13
Alignment explanation
Indices: 49758627--49758658 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49758617 GCTTGGATCA
*
49758627 TCATCAAATAAAT
1 TCATAAAATAAAT
49758640 TCATAAAATAAAT
1 TCATAAAATAAAT
49758653 TCATAA
1 TCATAA
49758659 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:49758906 original size:30 final size:30
Alignment explanation
Indices: 49758870--49758927 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49758860 CCTCGACTCT
*
49758870 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
49758900 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
49758928 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:49761458 original size:13 final size:13
Alignment explanation
Indices: 49761440--49761467 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49761430 GATAAAAGAG
49761440 CATATAGAATACC
1 CATATAGAATACC
49761453 CATATAGAATACC
1 CATATAGAATACC
49761466 CA
1 CA
49761468 GAAGAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:49764031 original size:50 final size:50
Alignment explanation
Indices: 49763907--49764155 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
49763897 GATAATAACA
* * ** * *
49763907 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
49763958 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49764008 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49764058 TGCCCATGCCATGTCCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
49764113 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
49764156 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49764086 original size:100 final size:104
Alignment explanation
Indices: 49763906--49764155 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
49763896 TGATAATAAC
**
49763906 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
49763971 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
49764008 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
49764071 TCCCAGGCATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
49764113 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
49764156 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:49764271 original size:13 final size:13
Alignment explanation
Indices: 49764250--49764281 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49764240 GCTTGGATCA
*
49764250 TCATCAAATAAAT
1 TCATAAAATAAAT
49764263 TCATAAAATAAAT
1 TCATAAAATAAAT
49764276 TCATAA
1 TCATAA
49764282 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:49764529 original size:30 final size:30
Alignment explanation
Indices: 49764493--49764550 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49764483 CCTCGACTCT
*
49764493 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
49764523 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
49764551 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:49766590 original size:26 final size:26
Alignment explanation
Indices: 49766561--49766613 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
49766551 TCAAACATGC
49766561 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
49766587 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
49766613 A
1 A
49766614 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:49768125 original size:26 final size:26
Alignment explanation
Indices: 49768089--49768172 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
49768079 CATGAAATTC
49768089 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
49768115 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
49768141 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
49768167 TTATCA
1 TTATCA
49768173 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:49769514 original size:13 final size:13
Alignment explanation
Indices: 49769496--49769521 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49769486 ATTGATTTGC
49769496 TTCAAATCAGTGT
1 TTCAAATCAGTGT
49769509 TTCAAATCAGTGT
1 TTCAAATCAGTGT
49769522 AAGTGAGCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTCAAATCAGTGT
Found at i:49777559 original size:13 final size:13
Alignment explanation
Indices: 49777541--49777567 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49777531 CATAATACAA
49777541 AGGACCTAAATCT
1 AGGACCTAAATCT
49777554 AGGACCTAAATCT
1 AGGACCTAAATCT
49777567 A
1 A
49777568 TGTCTGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
AGGACCTAAATCT
Found at i:49778220 original size:23 final size:23
Alignment explanation
Indices: 49778162--49778249 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
49778152 TTATTAACAT
* *
49778162 TGTTCGTGAACATATTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
49778186 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
49778209 TGTTCGTAAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
49778232 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
49778250 TGAATATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.60
24 18 0.34
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:49778221 original size:47 final size:46
Alignment explanation
Indices: 49778162--49778250 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
49778152 TTATTAACAT
* *
49778162 TGTTCGTGAACATATTCAATTATATGTT-CATGAACATGTTCGTTTAA
1 TGTTCGTAAACATATTCAATTA-A-GTTAAATGAACATGTTCGTTTAA
* *
49778209 TGTTCGTAAACATGTTCGATTAAGTTAAATGAACATGTTCGT
1 TGTTCGTAAACATATTCAATTAAGTTAAATGAACATGTTCGT
49778251 GAATATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 3 0.08
46 15 0.41
47 19 0.51
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (46 bp):
TGTTCGTAAACATATTCAATTAAGTTAAATGAACATGTTCGTTTAA
Found at i:49785476 original size:9 final size:10
Alignment explanation
Indices: 49785426--49785482 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 10
49785416 TATATTTTTA
*
49785426 AAAAAAATA-
1 AAAAAATTAT
49785435 AAAAAATTCA-
1 AAAAAATT-AT
*
49785445 AAAAAA-TCT
1 AAAAAATTAT
49785454 AAAAAATATAT
1 AAAAAAT-TAT
49785465 AAAAAATT-T
1 AAAAAATTAT
49785474 AAAAAATTA
1 AAAAAATTA
49785483 CAAATTTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 23 0.57
10 8 0.20
11 9 0.22
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:49796360 original size:70 final size:71
Alignment explanation
Indices: 49796231--49796362 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 71
49796221 AAGGTAAGCA
* * * * * *
49796231 AGAGATCTATTTGTGTAGCCTTCGGTAAGGCATGTATATTGTTAACTGGATAGGTAGATCACTGC
1 AGAGATCTATTTGTATAGCCTCCGGTAAGGCATGTATAATGCTAACTAGATAGGAAGATCACTGC
49796296 GAAAAT
66 GAAAAT
* * *
49796302 AGAGATTTA-TTGTATAGCCTCCGGTAGGGCA-GCTATAATGCTAACTAGATTGGAAGATCAC
1 AGAGATCTATTTGTATAGCCTCCGGTAAGGCATG-TATAATGCTAACTAGATAGGAAGATCAC
49796363 AAAATAAATC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
69 1 0.02
70 42 0.82
71 8 0.16
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (71 bp):
AGAGATCTATTTGTATAGCCTCCGGTAAGGCATGTATAATGCTAACTAGATAGGAAGATCACTGC
GAAAAT
Found at i:49796503 original size:26 final size:25
Alignment explanation
Indices: 49796463--49796541 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 25
49796453 ATGGTAAACA
*
49796463 CAAAACTCTTTGAAAAGCCTTTGTGG
1 CAAATCTCTTTG-AAAGCCTTTGTGG
49796489 CAAATC-CTTTAGAAAGCCTTTGTGG
1 CAAATCTCTTT-GAAAGCCTTTGTGG
* *
49796514 CTAACTCTCTCTGAAAGCCTTTGTGG
1 C-AAATCTCTTTGAAAGCCTTTGTGG
49796540 CA
1 CA
49796542 TGTTACCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 19 0.40
26 25 0.53
27 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
CAAATCTCTTTGAAAGCCTTTGTGG
Found at i:49799123 original size:25 final size:27
Alignment explanation
Indices: 49799075--49799124 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
49799065 TGTTATTATG
* *
49799075 TGTTGAATGATTGATTTTGCATAATAA
1 TGTTGAATGATTGATTATGAATAATAA
49799102 TGTTGAAT-A-TGATTATGAATAAT
1 TGTTGAATGATTGATTATGAATAAT
49799125 GTATGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 1 0.05
27 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (27 bp):
TGTTGAATGATTGATTATGAATAATAA
Found at i:49799316 original size:48 final size:48
Alignment explanation
Indices: 49799264--49799391 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 48
49799254 GGTGTGCCAA
* ** *
49799264 TGTAAGACCATGTTTGGAACATGGCATCGACAATGTTATGAGAGCTAG
1 TGTAAGACCATGTTTGGGACATGGCATCGACAATGAGACGAGAGCTAG
** ** *
49799312 TGTAAGACCATGTCAGGGACATGGCATCGGTATTGAGACGAGAGCTAG
1 TGTAAGACCATGTTTGGGACATGGCATCGACAATGAGACGAGAGCTAG
* *
49799360 TGTAACACTATGTTTGGGACATGGCATCGACA
1 TGTAAGACCATGTTTGGGACATGGCATCGACA
49799392 CTCTACCCCT
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGGACATGGCATCGACAATGAGACGAGAGCTAG
Found at i:49800226 original size:17 final size:17
Alignment explanation
Indices: 49800167--49800226 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
49800157 CACACGGGCA
* *
49800167 GACACACGTGCTTGTGT
1 GACACACGGGCGTGTGT
*
49800184 GACACACGAGCGTGTGT
1 GACACACGGGCGTGTGT
49800201 GACACACGGGCGTGTGT
1 GACACACGGGCGTGTGT
*
49800218 GACATACGG
1 GACACACGG
49800227 TCTGCCCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.35, T:0.20
Consensus pattern (17 bp):
GACACACGGGCGTGTGT
Found at i:49813220 original size:47 final size:47
Alignment explanation
Indices: 49813169--49813391 Score: 324
Period size: 47 Copynumber: 4.7 Consensus size: 47
49813159 TTAGGATTCT
* * *
49813169 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
49813216 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
49813263 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCGTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
49813310 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC-AAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA-TGGCCG
* * *
49813357 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
49813392 TCCCGAAGGG
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
46 3 0.02
47 158 0.98
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:49813566 original size:37 final size:37
Alignment explanation
Indices: 49813510--49813588 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
49813500 CCGAGCTCTA
* *
49813510 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
49813547 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
49813584 AAGAC
1 AAGAC
49813589 TTCGTAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:49815532 original size:40 final size:40
Alignment explanation
Indices: 49815442--49815625 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
49815432 TCGAATGATG
* * *
49815442 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AT
*
49815483 T-CGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
49815522 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
49815561 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
49815600 AACCGGGCTAAGTCCCGAAGAGCATT
1 -TCCGGGCTAAGTCCCGAAG-GCATT
49815626 CATGCTAGTG
Statistics
Matches: 124, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 39 0.31
40 71 0.57
41 14 0.11
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:49815646 original size:40 final size:40
Alignment explanation
Indices: 49815522--49815756 Score: 233
Period size: 40 Copynumber: 5.9 Consensus size: 40
49815512 AGTTACTAAT
** * * *
49815522 TCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
* ** * *
49815561 TCCGGGTTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
* *
49815601 ACCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
49815641 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * *
49815681 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
49815721 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
49815757 CGTGTATTCG
Statistics
Matches: 167, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
39 10 0.06
40 145 0.87
41 12 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:49818686 original size:47 final size:47
Alignment explanation
Indices: 49818635--49818857 Score: 324
Period size: 47 Copynumber: 4.7 Consensus size: 47
49818625 TTAGGATTCT
* * *
49818635 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
49818682 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
49818729 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCGTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
49818776 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC-AAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA-TGGCCG
* * *
49818823 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
49818858 TCCCGAAGGG
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
46 3 0.02
47 158 0.98
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:49819032 original size:37 final size:37
Alignment explanation
Indices: 49818976--49819054 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
49818966 CCGAGCTCTA
* * *
49818976 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
49819013 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
49819050 AAGAC
1 AAGAC
49819055 TTCGTAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:49822703 original size:25 final size:25
Alignment explanation
Indices: 49822675--49822725 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
49822665 AGACGTGCAA
*
49822675 TCAACTCCGCTTAATTACGACAAAT
1 TCAACTCCGCTTAATTACGAAAAAT
49822700 TCAACTCCGCTTAATTACGAAAAAT
1 TCAACTCCGCTTAATTACGAAAAAT
49822725 T
1 T
49822726 TACTCTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.29
Consensus pattern (25 bp):
TCAACTCCGCTTAATTACGAAAAAT
Found at i:49828004 original size:17 final size:18
Alignment explanation
Indices: 49827972--49828005 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49827962 CATATTGCGG
49827972 GCCCATGTAGGCCCACAC
1 GCCCATGTAGGCCCACAC
*
49827990 GCCCGTGTA-GCCCACA
1 GCCCATGTAGGCCCACA
49828006 TAGCCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.44, G:0.24, T:0.12
Consensus pattern (18 bp):
GCCCATGTAGGCCCACAC
Found at i:49832093 original size:27 final size:26
Alignment explanation
Indices: 49832076--49832145 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
49832066 ATATTAAGTC
49832076 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
* *
49832103 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
49832131 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
49832146 GTACAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:49832139 original size:28 final size:28
Alignment explanation
Indices: 49832076--49832170 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
49832066 ATATTAAGTC
*
49832076 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
49832103 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
49832131 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
49832160 CGCACACTTAG
1 CGCACACTTAG
49832171 CGCCAATCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.36
28 22 0.37
29 16 0.27
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.