Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 3 of 35
Found at i:395586 original size:64 final size:64
Alignment explanation
Indices: 395446--395595 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 64
395436 CAACCTTAGC
* *
395446 CCTTAAAGAGCAGGGTGCTTACCAACATCAATCCTTAAAGAGCAAGGCACTTACAAACCTCAAT
1 CCTTAAAGAGCAAGATGCTTACCAACATCAATCCTTAAAGAGCAAGGCACTTACAAACCTCAAT
* * * *
395510 -CTTCAAAGAGCAAGATGCTTACCAACCTTAGT-CTTCAAAGAGTAAGGCACTTACCAAA-CTCA
1 CCTT-AAAGAGCAAGATGCTTACCAACATCAATCCTT-AAAGAGCAAGGCACTTA-CAAACCTCA
*
395572 GT
63 AT
*
395574 CCTTAAAAAGCAAGATGCTTAC
1 CCTTAAAGAGCAAGATGCTTAC
395596 TTATTTCAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
63 6 0.08
64 61 0.82
65 7 0.09
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.22
Consensus pattern (64 bp):
CCTTAAAGAGCAAGATGCTTACCAACATCAATCCTTAAAGAGCAAGGCACTTACAAACCTCAAT
Found at i:396545 original size:22 final size:22
Alignment explanation
Indices: 396498--396547 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
396488 TAAAAAAGGG
* *
396498 AAAAAATTAAAAAATCCAAATC
1 AAAAAATCAAAAAATCAAAATC
396520 AAAAAATCAAAAAATCAAAAAT-
1 AAAAAATCAAAAAATC-AAAATC
396542 AAAAAA
1 AAAAAA
396548 GAGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAAATCAAAAAATCAAAATC
Found at i:396547 original size:7 final size:8
Alignment explanation
Indices: 396498--396540 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
396488 TAAAAAAGGG
*
396498 AAAAAATT
1 AAAAAATC
396506 AAAAAATC
1 AAAAAATC
*
396514 --CAAATC
1 AAAAAATC
396520 AAAAAATC
1 AAAAAATC
396528 AAAAAATC
1 AAAAAATC
396536 AAAAA
1 AAAAA
396541 TAAAAAAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
8 25 0.83
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAATC
Found at i:396547 original size:16 final size:16
Alignment explanation
Indices: 396515--396547 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
396505 TAAAAAATCC
*
396515 AAATCAAAAAATCAAA
1 AAATCAAAAAATAAAA
396531 AAATC-AAAAATAAAA
1 AAATCAAAAAATAAAA
396546 AA
1 AA
396548 GAGAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAATCAAAAAATAAAA
Found at i:398930 original size:41 final size:40
Alignment explanation
Indices: 398832--398937 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 40
398822 TAATCCTAGC
* *
398832 CAACCTCTTTTCATTTATTGACTTATCCATTTTGCCCTGGT
1 CAACC-CTTTTCATTTGTTGACTTATCCATTTTGCCCTGAT
* * **
398873 CAACCCCTTTTCATTTGTTGAGTTATCGATTTTTTCCTGAT
1 CAA-CCCTTTTCATTTGTTGACTTATCCATTTTGCCCTGAT
*
398914 CAACCCTTTTCTATTTGTTAACTT
1 CAACCCTTTTC-ATTTGTTGACTT
398938 GTTAGTTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 8 0.15
41 45 0.82
42 2 0.04
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (40 bp):
CAACCCTTTTCATTTGTTGACTTATCCATTTTGCCCTGAT
Found at i:398989 original size:41 final size:41
Alignment explanation
Indices: 398911--398990 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
398901 ATTTTTTCCT
* *
398911 GATCAACCCTTTTCTATTTGTTAACTTGTTAGTTTTGTCTC
1 GATCAACCCTTTTCTATTTGTTAACTTGTCAGCTTTGTCTC
*
398952 GATCAACCCTTTTCTCATTTGTTAACTT-TCGGCTTTGTC
1 GATCAACCCTTTTCT-ATTTGTTAACTTGTCAGCTTTGTC
398991 CCAATCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 23 0.66
42 12 0.34
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.49
Consensus pattern (41 bp):
GATCAACCCTTTTCTATTTGTTAACTTGTCAGCTTTGTCTC
Found at i:398998 original size:82 final size:82
Alignment explanation
Indices: 398871--399247 Score: 207
Period size: 82 Copynumber: 4.6 Consensus size: 82
398861 TTTTGCCCTG
* * * ** * ** *
398871 GTCAACCCCTTTTCATTTGTTGAGTTATCGATTTTTTCCTGATCAACCCTTTTCTATTTGTTAAC
1 GTCAA-CCTTTTTCATTTGTTAACTTATCGGCTTTGTCCCAATCAACCCTTTTCTATTTGTTGAC
*
398936 TTGTTAGTTTTGTCTCGA
65 TTGTCAGTTTTGTCTCGA
* *
398954 -TCAACCCTTTTCTCATTTGTTAACTT-TCGGCTTTGTCCCAATCAA---TTTGC-ATTTGCTGA
1 GTCAA-CCTTTT-TCATTTGTTAACTTATCGGCTTTGTCCCAATCAACCCTTTTCTATTTGTTGA
** *
399013 CTTGTTGGTTTTGT-TCTTA
64 CTTGTCAGTTTTGTCTC-GA
* * * * * * * *
399032 GTTAACCTCTTTTCATTTGTTGACTCATAGGTTTTGTCACAATCAACCTTTTTTTATCATATGTT
1 GTCAACCT-TTTTCATTTGTTAACTTATCGGCTTTGTCCCAATCAACCCTTTTCTAT--T-TGTT
* * * * *
399097 GACTTATCGGCTCTGTC-CTA
62 GACTTGTCAGTTTTGTCTCGA
* * * * * * * * *
399117 GTCAACTTTTTTTCATTTGTTAACTTGTTGACTTTGTCCTAGTCAACTTCTTATC-ATTTGTTGG
1 GTCAAC-CTTTTTCATTTGTTAACTTATCGGCTTTGTCCCAATCAAC-CCTTTTCTATTTGTTGA
* *
399181 CTTCTCAGTTTTGTCTTGA
64 CTTGTCAGTTTTGTCTCGA
* * *
399200 -TCAACCCTTTTTCATTTGTTGACTTATCGGCTTTATCCCATTCAACCC
1 GTCAA-CCTTTTTCATTTGTTAACTTATCGGCTTTGTCCCAATCAACCC
399248 CTTCTCATTC
Statistics
Matches: 220, Mismatches: 57, Indels: 36
0.70 0.18 0.12
Matches are distributed among these distances:
77 2 0.01
78 36 0.16
79 26 0.12
81 1 0.00
82 79 0.36
83 17 0.08
85 39 0.18
86 20 0.09
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (82 bp):
GTCAACCTTTTTCATTTGTTAACTTATCGGCTTTGTCCCAATCAACCCTTTTCTATTTGTTGACT
TGTCAGTTTTGTCTCGA
Found at i:399122 original size:44 final size:42
Alignment explanation
Indices: 399074--399163 Score: 101
Period size: 41 Copynumber: 2.1 Consensus size: 42
399064 TTTGTCACAA
* *
399074 TCAACCTTTTTTTATCATATGTTGACTTATCGGCTCTGTCCTAG
1 TCAACC-TTTTTT-TCATATGTTAACTTATCGACTCTGTCCTAG
* * * *
399118 TCAA-CTTTTTTTCATTTGTTAACTTGTTGACTTTGTCCTAG
1 TCAACCTTTTTTTCATATGTTAACTTATCGACTCTGTCCTAG
399159 TCAAC
1 TCAAC
399164 TTCTTATCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 1 0.03
44 4 0.10
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (42 bp):
TCAACCTTTTTTTCATATGTTAACTTATCGACTCTGTCCTAG
Found at i:399262 original size:123 final size:119
Alignment explanation
Indices: 398940--399301 Score: 311
Period size: 123 Copynumber: 2.9 Consensus size: 119
398930 GTTAACTTGT
* *
398940 TAGTTTTGTCTCGATCAACCCTTTTCTCATTTGTTAACTT-TCGGCTTTGTCCCAATCAA-TTTG
1 TAGTTTTGTCTCGATCAACCCTTTTATCATTTGTTGACTTATCGGCTTTGTCCCAATCAACTTT-
* * * * * *
399003 CATTTGCTGACTTGTTGGTTTTGTTCTTAGTTAACCTCTTTTCATTTGTTGACTCA
65 CATTTGTTAACTTGTTGATTTTG-TCCTAGTCAACTTCTTTTCATTTGTTGACTCA
* * * * * * *
399059 TAGGTTTTGTCACAATCAACCTTTTTTTATCATATGTTGACTTATCGGCTCTGTCCTAGTCAACT
1 TA-GTTTTGTCTCGATCAACC--CTTTTATCATTTGTTGACTTATCGGCTTTGTCCCAATCAAC-
* * *
399124 TTTTTTCATTTGTTAACTTGTTGACTTTGTCCTAGTCAACTTCTTATCATTTGTTGGCTTC-
62 ---TTTCATTTGTTAACTTGTTGATTTTGTCCTAGTCAACTTCTTTTCATTTGTTGAC-TCA
* * *
399185 TCAGTTTTGTCTTGATCAACCCTTTT-TCATTTGTTGACTTATCGGCTTTATCCCATTCAACCCC
1 T-AGTTTTGTCTCGATCAACCCTTTTATCATTTGTTGACTTATCGGCTTTGTCCCAATCAA---C
* * * * *
399249 TTCTCATTCGTTAACCTG-TAAGTTTTGTCCTAATCAACTTCTTTTAATTTGTT
62 TT-TCATTTGTTAACTTGTTGA-TTTTGTCCTAGTCAACTTCTTTTCATTTGTT
399302 CACCTATCAA
Statistics
Matches: 193, Mismatches: 34, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
119 2 0.01
120 16 0.08
122 20 0.10
123 85 0.44
124 4 0.02
126 41 0.21
127 22 0.11
128 3 0.02
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.48
Consensus pattern (119 bp):
TAGTTTTGTCTCGATCAACCCTTTTATCATTTGTTGACTTATCGGCTTTGTCCCAATCAACTTTC
ATTTGTTAACTTGTTGATTTTGTCCTAGTCAACTTCTTTTCATTTGTTGACTCA
Found at i:399580 original size:147 final size:146
Alignment explanation
Indices: 399269--399584 Score: 343
Period size: 147 Copynumber: 2.2 Consensus size: 146
399259 TTAACCTGTA
* * *
399269 AGTTTTGTCCTAATCAACT-TCTTTTAATTTGTTCACCTATCAATTTTGTTTCGGTTAACCCCTT
1 AGTTTTG-CCTCATCAACTCT-TTTTAATTTATTAACCTATCAATTTTGTTTCGGTTAACCCCTT
* * *
399333 TCATTTATTGACTATTCTGGTTTCACCCTAGTCAACCTTTTTCAACTTAGGTTTCATCCTAGTTA
64 TCATTCATCGACTATTCTAGTTTCACCCTAGTCAACCTTTTTCAACTTAGGTTTCATCCTAGTTA
* *
399398 TCCTTGTTTGACTACATC
129 TCCTTATTTGACCACATC
* ** * * * * * *
399416 ACTTTTGTTTCGGTCAACTCTTTTTAATTTATTAACTTGTCAGTTTTGTCTT-GGTTGACCCTTT
1 AGTTTTGCCTC-ATCAACTCTTTTTAATTTATTAACCTATCAATTTTGT-TTCGGTTAACCCCTT
* * * *
399480 TCATTCATCGACTATTCTAGTTTCACCTTCGTCAACCCTTTTT-GACTTAGGTTTTATCCTAGTT
64 TCATTCATCGACTATTCTAGTTTCACCCTAGTCAA-CCTTTTTCAACTTAGGTTTCATCCTAGTT
*
399544 ATCCTTATTTGACCATATC
128 ATCCTTATTTGACCACATC
*
399563 GGTTTTGCCCTCATCAAC-CTTT
1 AGTTTTG-CCTCATCAACTCTTT
399585 CAGACTAGGT
Statistics
Matches: 137, Mismatches: 27, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
146 5 0.04
147 120 0.88
148 12 0.09
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (146 bp):
AGTTTTGCCTCATCAACTCTTTTTAATTTATTAACCTATCAATTTTGTTTCGGTTAACCCCTTTC
ATTCATCGACTATTCTAGTTTCACCCTAGTCAACCTTTTTCAACTTAGGTTTCATCCTAGTTATC
CTTATTTGACCACATC
Found at i:400900 original size:18 final size:18
Alignment explanation
Indices: 400877--400931 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
400867 AATTATGAAC
400877 TTTAATTTTAATTTTTCT-
1 TTTAATTTTAATTTTT-TA
400895 TTTAATTTTAAATTTTTTA
1 TTTAATTTT-AATTTTTTA
* *
400914 TTTTATTTTATTTTTTTA
1 TTTAATTTTAATTTTTTA
400932 ACTAGTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTAATTTTAATTTTTTA
Found at i:410183 original size:53 final size:53
Alignment explanation
Indices: 410103--410209 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
410093 TCATCATAAT
*
410103 AGGGTGGCCGTAATGTGCCAATAAACCTGACGATCATTTCCTTTTCCGTCAAC
1 AGGGTGGCCGTAATGTGCCAATAAACCTGACGATCATTTCCTTTTCCATCAAC
410156 AGGGTGGCCGTAATGTGCCAATAAACCTGACGATCATTTCCTTTTCCATCAAC
1 AGGGTGGCCGTAATGTGCCAATAAACCTGACGATCATTTCCTTTTCCATCAAC
410209 A
1 A
410210 AAGGCTGAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (53 bp):
AGGGTGGCCGTAATGTGCCAATAAACCTGACGATCATTTCCTTTTCCATCAAC
Found at i:411875 original size:13 final size:13
Alignment explanation
Indices: 411857--411881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411847 ATGTTGCACA
411857 GTATCGATACATT
1 GTATCGATACATT
411870 GTATCGATACAT
1 GTATCGATACAT
411882 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:411894 original size:20 final size:21
Alignment explanation
Indices: 411869--411921 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
411859 ATCGATACAT
**
411869 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
411889 TGTATCGATACATGAAAAGAA
1 TGTATCGATACATGAAAAGAA
411910 TGTATCGATACA
1 TGTATCGATACA
411922 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:417390 original size:13 final size:13
Alignment explanation
Indices: 417372--417396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
417362 ATGTTGCACA
417372 GTATCGATACATT
1 GTATCGATACATT
417385 GTATCGATACAT
1 GTATCGATACAT
417397 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:417409 original size:20 final size:21
Alignment explanation
Indices: 417384--417432 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
417374 ATCGATACAT
**
417384 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
417404 TGTATCGATACATGAAAAGAA
1 TGTATCGATACATGAAAAGAA
417425 TGTATCGA
1 TGTATCGA
417433 ATCAAGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:418035 original size:34 final size:35
Alignment explanation
Indices: 417972--418038 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
417962 CTAAGTGATT
417972 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
418008 GAGAGGTTTCTATTTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
418039 TATTATAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:423697 original size:80 final size:79
Alignment explanation
Indices: 423554--423728 Score: 233
Period size: 80 Copynumber: 2.2 Consensus size: 79
423544 AATAAAATCA
* * * *
423554 GGGTTGGAGTATCCCCAATTATGAAAAATCGATGCTTTAGAAATAAGGCCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATCATGAAAAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTATCC
*
423619 CCGATGAAATAACG
66 CCGAGGAAATAACG
* * * *
423633 GGGTTGGAGTATCCCCAATCGTGAAAAAATCAATATTTTAGATATAAAGCCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCAATCATG-AAAAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTATC
** *
423698 CCCTCGGGAATAACG
65 CCCGAGGAAATAACG
423713 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
423729 GATGAAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
79 21 0.25
80 62 0.75
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCAATCATGAAAAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTATCC
CCGAGGAAATAACG
Found at i:423743 original size:28 final size:28
Alignment explanation
Indices: 423683--423754 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
423673 GATATAAAGC
** * *
423683 CGGGGTTGGAGTATCCCCTCGGGAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAAAAA
*
423711 CGGGGTTGGAGTATCCCCGATGAAAAAA
1 CGGGGTTGGAGTATCCCCGAGGAAAAAA
*
423739 TGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
423755 TCAATTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAAAAA
Found at i:423821 original size:51 final size:50
Alignment explanation
Indices: 423764--423911 Score: 165
Period size: 51 Copynumber: 2.9 Consensus size: 50
423754 CTCAATTGTT
* *
423764 AAAAATT-AGTGTTTCGGAAATAAAATCGGAGTTGGAGTATCCTCGATTACG
1 AAAAATTGA-TGTTT-GGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAG
** * *
423815 GTAAATTGATGCTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAG
1 AAAAATTGATG-TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAG
* *
423866 AAAAATTGATGTTTTGGAAATGAAACCGG-GATTGGAGTATCCCCGA
1 AAAAATTGATG-TTTGGAAATAAAATCGGAG-TTGGAGTATCCCCGA
423912 CATGAAAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
51 76 0.94
52 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (50 bp):
AAAAATTGATGTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAG
Found at i:425960 original size:20 final size:19
Alignment explanation
Indices: 425931--426005 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
425921 AAAAATGCCT
*
425931 AAATGTATCGATACATTGTA
1 AAATGTATCGATACAATG-A
*
425951 AAATGCATCGATACAATGA
1 AAATGTATCGATACAATGA
*
425970 GCAATGTATCGATACAATGCA
1 -AAATGTATCGATACAATG-A
*
425991 AAATGTATTGATACA
1 AAATGTATCGATACA
426006 TCTGGGTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (19 bp):
AAATGTATCGATACAATGA
Found at i:428126 original size:20 final size:21
Alignment explanation
Indices: 428103--428147 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
428093 CTAGGTATTG
428103 ATACCACA-CCTT-AGGTATCA
1 ATACCA-AGCCTTCAGGTATCA
*
428123 ATACCAAGCCTTCATGTATCA
1 ATACCAAGCCTTCAGGTATCA
428144 ATAC
1 ATAC
428148 TTGCTATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 10 0.45
21 11 0.50
ACGTcount: A:0.36, C:0.29, G:0.09, T:0.27
Consensus pattern (21 bp):
ATACCAAGCCTTCAGGTATCA
Found at i:428172 original size:112 final size:111
Alignment explanation
Indices: 428026--428263 Score: 368
Period size: 112 Copynumber: 2.1 Consensus size: 111
428016 CAATACTTGA
* * * * *
428026 GTATCAATACTTGCTGTCTAAAAATCAAATTTTAGCTACTGCTAAGGCATGTATCGATACAATCA
1 GTATCAATACTTGCTATCCAAAAATAAAAATTTAGCTACTGCCAAGGCATGTATCGATACAATCA
* * *
428091 CACTAGGTATTGATACCACACCTTAGGTATCAATACCAAGCCTTCAT
66 CACTAAGTATCGATACCACACCCTA-GTATCAATACCAAGCCTTCAT
*
428138 GTATCAATACTTGCTATCCAAAAATAAAAATTTAGCTACTGCCAAGGCTTGTATCGATACAATCA
1 GTATCAATACTTGCTATCCAAAAATAAAAATTTAGCTACTGCCAAGGCATGTATCGATACAATCA
428203 CACTAAGTATCGATACCACACCCTAGTATCAATACCAAGCCTTCAT
66 CACTAAGTATCGATACCACACCCTAGTATCAATACCAAGCCTTCAT
*
428249 GTATCGATACATTGC
1 GTATCAATAC-TTGC
428264 CTGGAAATTC
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
111 30 0.26
112 85 0.74
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (111 bp):
GTATCAATACTTGCTATCCAAAAATAAAAATTTAGCTACTGCCAAGGCATGTATCGATACAATCA
CACTAAGTATCGATACCACACCCTAGTATCAATACCAAGCCTTCAT
Found at i:428232 original size:19 final size:21
Alignment explanation
Indices: 428188--428239 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
428178 GCCAAGGCTT
*
428188 GTATCGATACAATCACACTAA
1 GTATCGATACCATCACACTAA
*
428209 GTATCGATACCA-CACCCT-A
1 GTATCGATACCATCACACTAA
*
428228 GTATCAATACCA
1 GTATCGATACCA
428240 AGCCTTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (21 bp):
GTATCGATACCATCACACTAA
Found at i:429220 original size:13 final size:13
Alignment explanation
Indices: 429202--429226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
429192 CATAAAATGT
429202 TGTATCGATACAA
1 TGTATCGATACAA
429215 TGTATCGATACA
1 TGTATCGATACA
429227 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:429224 original size:33 final size:33
Alignment explanation
Indices: 429182--429246 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
429172 TTCAACAATT
429182 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
429215 TGTATCGATACATATTTTTTTGTATCGATACA
1 TGTATCGATACATAAAATGTTGTATCGATACA
429247 TTTTAAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:429307 original size:13 final size:13
Alignment explanation
Indices: 429289--429316 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
429279 ATTACTCAAA
429289 TGTATCGATACAT
1 TGTATCGATACAT
429302 TGTATCGATACAT
1 TGTATCGATACAT
429315 TG
1 TG
429317 ATCTTTGTAT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:432734 original size:141 final size:140
Alignment explanation
Indices: 432475--433232 Score: 533
Period size: 141 Copynumber: 5.4 Consensus size: 140
432465 TTCTTTAAAA
* * * * * * *
432475 ACTAAAAAGATAAAAGGGTCCCACTAACTTATCTGGGCTTTGAAGAAAAAGAAAAAGTTTCTTGC
1 ACTAAAAAGATAAAA-GGTGCCACCAGCTTGTGTGGGCTTTG-A-AAAAAGAAAAAGTGTCCTGC
* * * ** * **
432540 TTTTTGAGGATTAAAAAGATAAAAGGTGCCACCAGCTTGTGTGGGCTTT--AAAAAAAAGGTGTC
63 TCTTTGAGAACTAAAAAGATAAAAGGTGCCATAAGCTTGTGTGGGTTTTGAAAAAAAAAGGCATC
*
432603 GTACTCTTTGAGG
128 GTGCTCTTTGAGG
* * **
432616 ACTAAAAAGATAAAGGGGTGCCACTAGCTTGTGTGGGCTTTGAAAAAAGAAAAAACGTCCTGCTC
1 ACTAAAAAGATAAA-AGGTGCCACCAGCTTGTGTGGGCTTTGAAAAAAGAAAAAGTGTCCTGCTC
* * * *
432681 TTTCAGAACTAAAAAGATAAAAGGTACCATAAGCTTGTGTGGGTTTTGAAAAAAAAAGACATCCT
65 TTTGAGAACTAAAAAGATAAAAGGTGCCATAAGCTTGTGTGGGTTTTGAAAAAAAAAGGCATCGT
* **
432746 GCTCTTTAAAA
130 GCTCTTTGAGG
* * * * * * * *
432757 ACTAAAAAAATAAAAAGTGCTACCAACTTCTGTAGGCTTT-----AA-AAAAAGTGTTCTTCTCT
1 ACTAAAAAGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAAAGAAAAAGTGTCCTGCTCT
* * * * * * * *
432816 TTAAGGACTTAAAAGATAAAAAGTGCCATTAGCTTTTGTGGGCTTTT---AAAAAAATGCATCAT
66 TTGAGAACTAAAAAGATAAAAGGTGCCATAAGCTTGTGTGGG-TTTTGAAAAAAAAAGGCATCGT
432878 GCTCTTTGAGG
130 GCTCTTTGAGG
* *
432889 ACTAGAAATAGA-AAAAGGTGCCACCAGCTTGTGTGGACTTTGAAGGAAAAGAAAAAGTGTCCAG
1 ACTA-AAA-AGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAA--AAAAGAAAAAGTGTCCTG
* * ** * *
432953 CTTTTTGACG-ACTAAAAAGATAAAAAGTGCCACCAGCTTATGTGGGGTTTGAAAAAAAAGAAAA
62 CTCTTTGA-GAACTAAAAAGATAAAAGGTGCCATAAGCTTGTGTGGGTTTTG---AAAAA-AAAA
**
433017 AACAT-GTTGCTCTTTGAGG
122 GGCATCG-TGCTCTTTGAGG
* * * **
433036 ACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAA-AAAAGGCATCCTGCTCT
1 ACTAAAAAGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAAAGAAAAAGTGTCCTGCTCT
* * * * * *
433100 TTGA-AGACTAAAAAGATCAAGGGCTACCTTCAA-CTTGTATGGGTTTTGAAGAAAAACAAAATG
66 TTGAGA-ACTAAAAAGATAAAAGG-TGCCAT-AAGCTTGTGTGGGTTTT---GAAAAA-AAAAGG
* * *
433163 CGTCTTGCTCTTTGAAG
124 CATCGTGCTCTTTGAGG
* * * * * *
433180 ACTAAAAAGATAAAAAGTGCCAACATCTTATATGGGCATTGAAAAAAAGAAAA
1 ACTAAAAAGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTG-AAAAAAGAAAA
433233 GGCATCCTGC
Statistics
Matches: 483, Mismatches: 100, Indels: 63
0.75 0.15 0.10
Matches are distributed among these distances:
132 24 0.05
133 26 0.05
134 50 0.10
135 6 0.01
139 57 0.12
140 25 0.05
141 116 0.24
142 1 0.00
143 30 0.06
144 76 0.16
145 9 0.02
146 39 0.08
147 24 0.05
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (140 bp):
ACTAAAAAGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAAAGAAAAAGTGTCCTGCTCT
TTGAGAACTAAAAAGATAAAAGGTGCCATAAGCTTGTGTGGGTTTTGAAAAAAAAAGGCATCGTG
CTCTTTGAGG
Found at i:432802 original size:69 final size:68
Alignment explanation
Indices: 432641--432803 Score: 159
Period size: 69 Copynumber: 2.3 Consensus size: 68
432631 GGGTGCCACT
* * * * * *
432641 AGCTTGTGTGGGCTTTGAAAAAAGAAAAAACGTCCTGCTCTTTCAGAACTAAAAAGATAAAAGGT
1 AGCTTCTGTAGGCTTT-AAAAAA-AAAAAACATCCTGCTCTTTAAAAACTAAAAAAATAAAAGGT
432706 ACCATA
64 ACCA-A
* * * * *
432712 AGCTTGTGTGGGTTTTGAAAAAAAAAGACATCCTGCTCTTTAAAAACTAAAAAAATAAAAAGTGC
1 AGCTTCTGTAGGCTTTAAAAAAAAAAAACATCCTGCTCTTTAAAAACTAAAAAAAT-AAAAG-G-
432777 TACC-A
63 TACCAA
432782 A-CTTCTGTAGGCTTTAAAAAAA
1 AGCTTCTGTAGGCTTTAAAAAAA
432804 GTGTTCTTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
69 46 0.59
70 12 0.15
71 16 0.21
72 4 0.05
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (68 bp):
AGCTTCTGTAGGCTTTAAAAAAAAAAAACATCCTGCTCTTTAAAAACTAAAAAAATAAAAGGTAC
CAA
Found at i:433004 original size:73 final size:73
Alignment explanation
Indices: 432877--433232 Score: 321
Period size: 73 Copynumber: 4.9 Consensus size: 73
432867 AAATGCATCA
* * * *
432877 TGCTCTTTGAGGACTAGAAATAGA-AAAAGGTGCCACCAGCTTGTGTGGACTTTGAAGGAAAAGA
1 TGCTCTTTGAAGACTA-AAA-AGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGA
432941 AAAAGTGTCC
64 AAAAGTGTCC
* * * * * *
432951 AGCTTTTTGACGACTAAAAAGATAAAAAGTGCCACCAGCTTATGTGGGGTTTGAAAAAAAAGAAA
1 TGCTCTTTGAAGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAG-AA
*
433016 AAACATGT--
65 AAA-GTGTCC
*
433024 TGCTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTG--GAAAAA-AAA
1 TGCTCTTTGAAGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAA
* **
433086 AGGCATCC
66 AAGTGTCC
* ** * ** * * * *
433094 TGCTCTTTGAAGACTAAAAAGATCAAGGGCTACCTTCAACTTGTATGGGTTTTGAAGAAAAACAA
1 TGCTCTTTGAAGACTAAAAAGATAAAAAG-TGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAA
* * *
433159 AATGCGTCT
65 AAAGTGTCC
* * * * *
433168 TGCTCTTTGAAGACTAAAAAGATAAAAAGTGCCAACATCTTATATGGGCATTGAA-AAAAAGAAA
1 TGCTCTTTGAAGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAA
433232 A
66 A
433233 GGCATCCTGC
Statistics
Matches: 229, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
68 1 0.00
69 4 0.02
70 25 0.11
71 23 0.10
72 12 0.05
73 109 0.48
74 52 0.23
75 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (73 bp):
TGCTCTTTGAAGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAA
AAGTGTCC
Found at i:433185 original size:144 final size:143
Alignment explanation
Indices: 432606--433243 Score: 411
Period size: 144 Copynumber: 4.5 Consensus size: 143
432596 AGGTGTCGTA
** * * **
432606 CTCTTTGAGGACTAAAAAGATAAAGGGGTGCCACTAGCTTGTGTGGGCTTTGAAAAAAGAAAAAA
1 CTCTTTGAGGACTAAAAAGATAAA-AAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAA-AAAAGG
* * * * * * *
432671 CGTCCTGCTCTTT-CAGAACTAAAAAGATAAAAGGTACCA-TAAGCTTGTGTGGGTTTTG-AAAA
64 CATCCTGCTCTTTGAAG-ACTAAAAAGATAAAAAGTACCACCAA-CTTATATGGGGTTTGAAAAA
* *
432733 AAA-AAGA--CATCCTG
127 AAACAAAATGCATCTTG
* ** * * * * *
432747 CTCTTTAAAAACTAAAAAAATAAAAAGTGCTACCAACTTCTGTAGGCTTT----AAAAAAAGTG-
1 CTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAAAAAAG-GC
* * * * ** * * * * *
432807 -TTCTTCTCTTT-AAGGACTTAAAAGATAAAAAGTGCCATTAGCTTTTGTGGGCTTT-----TAA
65 ATCCTGCTCTTTGAA-GACTAAAAAGATAAAAAGTACCACCAACTTATATGGGGTTTGAAAAAAA
*
432865 A-AAAATGCATCATG
129 ACAAAATGCATCTTG
* *
432879 CTCTTTGAGGACTAGAAATAGA-AAAAGGTGCCACCAGCTTGTGTGGACTTTGAAGGAAAAGAAA
1 CTCTTTGAGGACTA-AAA-AGATAAAAAGTGCCACCAGCTTGTGTGGGCTTT---GGAAAA-AAA
* * * * * *
432943 AAGTG--TCCAGCTTTTTGACGACTAAAAAGATAAAAAGTGCCACCAGCTTATGTGGGGTTTGAA
60 AAG-GCATCCTGCTCTTTGAAGACTAAAAAGATAAAAAGTACCACCAACTTATATGGGGTTTGAA
* ** *
433006 AAAAAAGAAAAAACATGTTG
124 AAAAAACAAAATGCATCTTG
433026 CTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAAAAAAGGCA
1 CTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAAAAAAGGCA
* ** ** * * *
433091 TCCTGCTCTTTGAAGACTAAAAAGATCAAGGGCTACCTTCAACTTGTATGGGTTTTGAAGAAAAA
66 TCCTGCTCTTTGAAGACTAAAAAGATAAAAAG-TACCACCAACTTATATGGGGTTTGAAAAAAAA
*
433156 CAAAATGCGTCTTG
130 CAAAATGCATCTTG
* * * * * * *
433170 CTCTTTGAAGACTAAAAAGATAAAAAGTGCCAACATCTTATATGGGCATTGAAAAAAAGAAAAGG
1 CTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTG-GAAAAA-AAAAGG
433235 CATCCTGCT
64 CATCCTGCT
433244 TGTGTAAGCT
Statistics
Matches: 391, Mismatches: 78, Indels: 51
0.75 0.15 0.10
Matches are distributed among these distances:
130 6 0.02
132 17 0.04
133 26 0.07
134 43 0.11
135 7 0.02
136 3 0.01
140 21 0.05
141 72 0.18
142 7 0.02
143 32 0.08
144 78 0.20
145 8 0.02
146 48 0.12
147 23 0.06
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (143 bp):
CTCTTTGAGGACTAAAAAGATAAAAAGTGCCACCAGCTTGTGTGGGCTTTGGAAAAAAAAAGGCA
TCCTGCTCTTTGAAGACTAAAAAGATAAAAAGTACCACCAACTTATATGGGGTTTGAAAAAAAAC
AAAATGCATCTTG
Found at i:434533 original size:19 final size:20
Alignment explanation
Indices: 434490--434534 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
434480 ATGTAAGCTG
* *
434490 ATTTTTGTTTTTTTTTTTCT
1 ATTTTTGTTGTTTTTTTGCT
*
434510 CTTTTT-TTGTTTTTTTGCT
1 ATTTTTGTTGTTTTTTTGCT
434529 ATTTTT
1 ATTTTT
434535 AAGAAAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.82
Consensus pattern (20 bp):
ATTTTTGTTGTTTTTTTGCT
Found at i:447566 original size:20 final size:20
Alignment explanation
Indices: 447541--447579 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
447531 TATCAAGCTT
447541 CTAATAAATGCATAAACATG
1 CTAATAAATGCATAAACATG
*
447561 CTAATAAATGCATGAACAT
1 CTAATAAATGCATAAACAT
447580 TCTTATGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (20 bp):
CTAATAAATGCATAAACATG
Found at i:448294 original size:21 final size:20
Alignment explanation
Indices: 448270--448320 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
448260 TCAAGGCCAT
*
448270 GTATCAATACAATCACATTAG
1 GTATCAATACAA-CACACTAG
* *
448291 GTATCAATACCACACCCTAG
1 GTATCAATACAACACACTAG
448311 GTATCAATAC
1 GTATCAATAC
448321 TAAGTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (20 bp):
GTATCAATACAACACACTAG
Found at i:448426 original size:112 final size:113
Alignment explanation
Indices: 448227--448432 Score: 299
Period size: 112 Copynumber: 1.8 Consensus size: 113
448217 GAGTATCAGC
* *
448227 ACTTGCTATCCAAAAATCGAATTTTAGCTACTATCAAGGCCATGTATCAATACAATCACATTAGG
1 ACTTGCTATCCAAAAATCAAATTTTAGCTACTATCAAGGCCATGTATCAATACAATCACACTAGG
448292 TATCAATACCACACCCTAGGTATCAATACTAAGTTTTCATGTATCGAT
66 TATCAATACCACACCCTAGGTATCAATACTAAGTTTTCATGTATCGAT
* * * *
448340 ACTTGCTGTCCAAAAATCAAATTTTAGCTACTA-CTAAGG-CTTGTATCGATATAATCACACTAG
1 ACTTGCTATCCAAAAATCAAATTTTAGCTACTATC-AAGGCCATGTATCAATACAATCACACTAG
** * *
448403 GTATCAATACCATTCCTTGGGTATCAATAC
65 GTATCAATACCACACCCTAGGTATCAATAC
448433 CAAGCCTTCA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 47 0.57
113 35 0.43
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (113 bp):
ACTTGCTATCCAAAAATCAAATTTTAGCTACTATCAAGGCCATGTATCAATACAATCACACTAGG
TATCAATACCACACCCTAGGTATCAATACTAAGTTTTCATGTATCGAT
Found at i:448440 original size:20 final size:20
Alignment explanation
Indices: 448402--448440 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
448392 AATCACACTA
**
448402 GGTATCAATACCATTCCTTG
1 GGTATCAATACCAAGCCTTG
448422 GGTATCAATACCAAGCCTT
1 GGTATCAATACCAAGCCTT
448441 CATTTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (20 bp):
GGTATCAATACCAAGCCTTG
Found at i:450188 original size:6 final size:6
Alignment explanation
Indices: 450177--450205 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
450167 TTGAACCAAT
450177 TATTTA TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTT
450206 GAGACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:452906 original size:31 final size:31
Alignment explanation
Indices: 452865--452942 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
452855 AACATTTTAT
*
452865 TGTATCGATACATTCTGGTTTTTGACCCAAA
1 TGTATCGATACATTCTGGGTTTTGACCCAAA
*
452896 TGTATTGATACATTCTGGGTTTTGACCCAAA
1 TGTATCGATACATTCTGGGTTTTGACCCAAA
*
452927 TGTATCAATACATTCT
1 TGTATCGATACATTCT
452943 TCAATGTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (31 bp):
TGTATCGATACATTCTGGGTTTTGACCCAAA
Found at i:455562 original size:28 final size:28
Alignment explanation
Indices: 455520--455650 Score: 163
Period size: 28 Copynumber: 4.7 Consensus size: 28
455510 TTTTCATCTC
* * *
455520 AGGGGAAACTCCAACCTTACCATTTTCG
1 AGGGGATACTCCAACCTCACCAATTTCG
* * *
455548 ACGGGATGCTCCAACCTCATCAATTTCG
1 AGGGGATACTCCAACCTCACCAATTTCG
* *
455576 AGGGGATACTCCAACCTTACCATTTTCG
1 AGGGGATACTCCAACCTCACCAATTTCG
* * *
455604 AGGGGATGCTCCAACCCCATCAATTTCG
1 AGGGGATACTCCAACCTCACCAATTTCG
455632 AGGGGATACTCCAACCTCA
1 AGGGGATACTCCAACCTCA
455651 TTTTTACTTC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 85 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (28 bp):
AGGGGATACTCCAACCTCACCAATTTCG
Found at i:455581 original size:56 final size:56
Alignment explanation
Indices: 455520--455648 Score: 231
Period size: 56 Copynumber: 2.3 Consensus size: 56
455510 TTTTCATCTC
* *
455520 AGGGGAAACTCCAACCTTACCATTTTCGACGGGATGCTCCAACCTCATCAATTTCG
1 AGGGGATACTCCAACCTTACCATTTTCGACGGGATGCTCCAACCCCATCAATTTCG
*
455576 AGGGGATACTCCAACCTTACCATTTTCGAGGGGATGCTCCAACCCCATCAATTTCG
1 AGGGGATACTCCAACCTTACCATTTTCGACGGGATGCTCCAACCCCATCAATTTCG
455632 AGGGGATACTCCAACCT
1 AGGGGATACTCCAACCT
455649 CATTTTTACT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (56 bp):
AGGGGATACTCCAACCTTACCATTTTCGACGGGATGCTCCAACCCCATCAATTTCG
Found at i:455745 original size:108 final size:109
Alignment explanation
Indices: 455577--455837 Score: 328
Period size: 109 Copynumber: 2.4 Consensus size: 109
455567 TCAATTTCGA
** * *
455577 GGGGATACTCCAACCTTACCATTTTCGAGGGGATGCTCCAACCCCATCAATTTCGAGGGGATACT
1 GGGGATACTCCAACCCCATCATTTTCGA-GGGATACTCCAACCCCATCAATTTCGAGGGGATACT
* * ** *
455642 CCAAC-CTCATTTTTACTTCTAAAACATTGAATTTCTTTTTCTTT
65 CCAACTCCCATTTTTACTTCTAAAACATTAAATTTCTTCATCTCT
* * *
455686 GGGGATACTCCAACCCCATCGTTTTTGAGGGATACTTCAACCCCATCAA-TTCTGAGGGGATACT
1 GGGGATACTCCAACCCCATCATTTTCGAGGGATACTCCAACCCCATCAATTTC-GAGGGGATACT
* *
455750 TCAACTCCCGTTTTTACTTCTAAAACATTAAATTTCTTCATCTCT
65 CCAACTCCCATTTTTACTTCTAAAACATTAAATTTCTTCATCTCT
* **
455795 AGGGATACAACAACCCCATCATTTTCGAAGGGATACTCCAACC
1 GGGGATACTCCAACCCCATCATTTTCG-AGGGATACTCCAACC
455838 TCGTTTTTAT
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
107 3 0.02
108 34 0.26
109 78 0.60
110 14 0.11
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (109 bp):
GGGGATACTCCAACCCCATCATTTTCGAGGGATACTCCAACCCCATCAATTTCGAGGGGATACTC
CAACTCCCATTTTTACTTCTAAAACATTAAATTTCTTCATCTCT
Found at i:455754 original size:28 final size:28
Alignment explanation
Indices: 455686--455754 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
455676 CTTTTTCTTT
* ** *
455686 GGGGATACTCCAACCCCATCGTTTTTGA
1 GGGGATACTTCAACCCCATCAATTCTGA
455714 -GGGATACTTCAACCCCATCAATTCTGA
1 GGGGATACTTCAACCCCATCAATTCTGA
455741 GGGGATACTTCAAC
1 GGGGATACTTCAAC
455755 TCCCGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (28 bp):
GGGGATACTTCAACCCCATCAATTCTGA
Found at i:455892 original size:81 final size:82
Alignment explanation
Indices: 455713--455892 Score: 215
Period size: 82 Copynumber: 2.2 Consensus size: 82
455703 ATCGTTTTTG
* * *
455713 AGGGATACTTCAACCCCATCAATTCTGAGGGGATACTTCAACTCCCGTTTTTACTTCTAAAACAT
1 AGGGATACTACAACCCCATCAATTCTGAAGGGATACTCCAACTCCCGTTTTTACTTCTAAAACAT
*
455778 TAAATTTCTTCATCTCT
66 TAAAATTCTTCATCTCT
* * * * *
455795 AGGGATACAACAACCCCATC-ATTTTCGAAGGGATACTCCAAC-CTCGTTTTTATTTTTCAAAAC
1 AGGGATACTACAACCCCATCAATTCT-GAAGGGATACTCCAACTCCCGTTTTTACTTCT-AAAAC
455858 ATTAAAATT-TTCATCTC-
64 ATTAAAATTCTTCATCTCT
*
455875 AGGGGATACTCCAACCCC
1 A-GGGATACTACAACCCC
455893 GATTTTCACC
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
80 1 0.01
81 38 0.45
82 45 0.54
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (82 bp):
AGGGATACTACAACCCCATCAATTCTGAAGGGATACTCCAACTCCCGTTTTTACTTCTAAAACAT
TAAAATTCTTCATCTCT
Found at i:457016 original size:26 final size:24
Alignment explanation
Indices: 456940--457027 Score: 63
Period size: 25 Copynumber: 3.6 Consensus size: 24
456930 CATACCTTAT
* *
456940 AAACAAATTTAAACTTCTACGAATAA
1 AAACAAA-TTAAACTTTTA-AAATAA
* ** *
456966 AAATAAATTATTC-CTTAAAAT-A
1 AAACAAATTAAACTTTTAAAATAA
456988 AAACAAATTTAAACTTTTATAAATAA
1 AAACAAA-TTAAACTTTTA-AAATAA
*
457014 AAATAAATTAAACT
1 AAACAAATTAAACT
457028 CGTATAATCA
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
22 7 0.15
23 7 0.15
24 5 0.11
25 15 0.32
26 13 0.28
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (24 bp):
AAACAAATTAAACTTTTAAAATAA
Found at i:457033 original size:25 final size:25
Alignment explanation
Indices: 456961--457034 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
456951 AACTTCTACG
**
456961 AATAAAAATAAATTATTC-CTTA-A
1 AATAAAAATAAATTAAACTCTTATA
* *
456984 AATAAAACA-AATTTAAACTTTTATA
1 AATAAAA-ATAAATTAAACTCTTATA
*
457009 AATAAAAATAAATTAAACTCGTATA
1 AATAAAAATAAATTAAACTCTTATA
457034 A
1 A
457035 TCATATCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 13 0.32
24 5 0.12
25 22 0.55
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.32
Consensus pattern (25 bp):
AATAAAAATAAATTAAACTCTTATA
Found at i:457342 original size:18 final size:19
Alignment explanation
Indices: 457307--457343 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
457297 CTTTTTAAAC
*
457307 TTTTATTTTAATTTAAAAT
1 TTTTATTTTAATTAAAAAT
457326 TTTTATTTT-ATTAAAAAT
1 TTTTATTTTAATTAAAAAT
457344 CAGTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATTTTAATTAAAAAT
Found at i:457487 original size:26 final size:28
Alignment explanation
Indices: 457453--457512 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
457443 TCAACACGAG
457453 TTTTT-AAA-TTTTAATTAAATTTAAT-
1 TTTTTAAAATTTTTAATTAAATTTAATA
*
457478 TTTTTAAAATTTTTAATTAAATTTTATA
1 TTTTTAAAATTTTTAATTAAATTTAATA
457506 TTTTTAA
1 TTTTTAA
457513 TTTTATCACG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 5 0.16
26 3 0.10
27 16 0.52
28 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTAAAATTTTTAATTAAATTTAATA
Found at i:459181 original size:33 final size:33
Alignment explanation
Indices: 459137--459201 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
459127 TACCACTGTT
* * *
459137 TGTATCGATACATGGGACATTGTATCGATACAA
1 TGTATCGATACATAGGAAAATGTATCGATACAA
* *
459170 TGTATCTATACATAGTAAAATGTATCGATACA
1 TGTATCGATACATAGGAAAATGTATCGATACA
459202 TTATGCCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGAAAATGTATCGATACAA
Found at i:460789 original size:3 final size:3
Alignment explanation
Indices: 460783--460823 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
460773 AACCACCAAG
*
460783 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
460824 AGTTGACTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:461284 original size:15 final size:16
Alignment explanation
Indices: 461250--461291 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
461240 GAATAAATCA
*
461250 AAAATTGTTGAAAATG
1 AAAATTATTGAAAATG
*
461266 -AAATTCTTGAAAA-G
1 AAAATTATTGAAAATG
461280 AAAATTATTGAA
1 AAAATTATTGAA
461292 CTAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (16 bp):
AAAATTATTGAAAATG
Found at i:465359 original size:12 final size:13
Alignment explanation
Indices: 465335--465372 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
465325 ACAAGGATCT
465335 TTGTATCGATACA
1 TTGTATCGATACA
465348 TTGTAT-GATACA
1 TTGTATCGATACA
465360 TTGTATCGATACA
1 TTGTATCGATACA
465373 AGGGTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:467254 original size:15 final size:15
Alignment explanation
Indices: 467234--467263 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
467224 GGATAAAGGG
467234 GGAGAAATTATTTTA
1 GGAGAAATTATTTTA
467249 GGAGAAATTATTTTA
1 GGAGAAATTATTTTA
467264 TAGAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
GGAGAAATTATTTTA
Found at i:467970 original size:21 final size:20
Alignment explanation
Indices: 467944--467982 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
467934 AGGTCAAAAC
467944 CCTAGAAAATATCGATACAAG
1 CCTAG-AAATATCGATACAAG
*
467965 CCTAGAAGTATCGATACA
1 CCTAGAAATATCGATACA
467983 TATTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
CCTAGAAATATCGATACAAG
Found at i:468080 original size:20 final size:20
Alignment explanation
Indices: 468034--468089 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
468024 TATCACTGTT
* * * *
468034 TGTATCGATACATGGCACAT
1 TGTATCGATACATAGTAAAA
*
468054 TGCATCGATACATAGTAAAA
1 TGTATCGATACATAGTAAAA
468074 TGTATCGATACATAGT
1 TGTATCGATACATAGT
468090 GCCCAATGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAGTAAAA
Found at i:475428 original size:166 final size:166
Alignment explanation
Indices: 475234--476204 Score: 854
Period size: 166 Copynumber: 5.8 Consensus size: 166
475224 TTTATGGGAG
* * * * ** *
475234 TTAAATAACAATATTAGATGAGTTTTAAAAATTTTAAACCAAGAAAAATCTCCCCGAAAAAATTT
1 TTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAAT-TCCCCAAAAAAATTT
* * * * *
475299 ACAGAGAAGAAAAT-TCG-ATTTCTCAAAAGAAAAAGGAATTTAAACAAAAAATTCCAAAACTCA
65 ACGGAGTAGAAAATAACGTATTTCTGAAAA-AAAAA-GAATTTAAAGAAAAAATTCCAAAACTCA
* *
475362 TGAAAATGAA-TAATTTTTCAAAACTAAATTAATATGAA
128 TGAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
* * * * *
475400 TTAAATGATAATGTTTTATGAATTTTAAAAATTAAAAATCGAGAAAAA-TCCACTC-GAAAAATT
1 TTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTCC-C-CAAAAAAATT
* * *
475463 TACGGAGTAGAAAATAACGTATTTC-GAAAAAAGGAA-AATTTCAAGAAAAAAATTCAAAAACTC
64 TACGGAGTAGAAAATAACGTATTTCTGAAAAAA-AAAGAATTTAAAG-AAAAAATTCCAAAACTC
* * * * * * *
475526 ATCAAAACGAATTAATTTATGAAAAATTATTTAATA-CAA
127 ATGAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
* * * * * * *
475565 -AAAAGTAATAATATTTGATGAAATTTAAAAATTGAGAACCGAGAAAAATTCCCTCAAAAAAAAT
1 TTAAA-TAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCC-CAAAAAAATT
* * * *
475629 TACGGAATAGAAAAT-ACTGTATTT-TGGAAAAAAAAAGAGTTTCAATGAAAAAAAT-CAAACAC
64 TACGGAGTAGAAAATAAC-GTATTTCT-GAAAAAAAAAGAATTT-AAAGAAAAAATTCCAAA-AC
*
475691 TCATTAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
125 TCATGAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
* * *
475733 TTAACTAATGAA-GTTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCTCAAAAAAATT
1 TTAAATAAT-AATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCC-CAAAAAAATT
* * ** * * * *
475797 TATGAAGTAGAAAATATTGTATTTC--AAAAAAATGAGAGTTTCAAGAAAAAAAT-CAAACACTC
64 TACGGAGTAGAAAATAACGTATTTCTGAAAAAAA-AAGAATTTAAAGAAAAAATTCCAAA-ACTC
* * *
475859 ATGAAAATGAATTAATTTTTTAAACCTGATTTCATATGAA
127 ATGAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
* * * *
475899 TCAAATAATGATGTTTGATGAATTTTAAAAATTAAAAAACAAG-AAAATTCCCCTCAAAGAAATT
1 TTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATT-CCC-CAAAAAAATT
* * * * *
475963 TACGAAGTAGAAAATAACGTATTTC-GAAAAAAAGAA-AATTTTAGGGAAAAATTCAAAAACTCA
64 TACGGAGTAGAAAATAACGTATTTCTGAAAAAAA-AAGAATTTAAAGAAAAAATTCCAAAACTCA
* * * *
476026 TGAAAATGAATAAATTTTTAAAAACTGATTTAACATGAA
128 TGAAAATGAATTAATTTTTTAAAACTAATTTAATATGAA
* * * * * * *
476065 ATAAATGATAATATTTGATGAAATTTAAAAATTGAAAACCGAGAAAAATTCTCTCAAAAAAATTT
1 TTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTC-CCCAAAAAAATTT
* * * * *
476130 ACGGAGTAGAAAACATCGTATTTC-GAAAAAAGGAAAG--TTTTAAGGAAAAA-TCAAAAACTCA
65 ACGGAGTAGAAAATAACGTATTTCTGAAAAAA--AAAGAATTTAAAGAAAAAATTCCAAAACTCA
476191 TGAAAATGAATTAA
128 TGAAAATGAATTAA
476205 CATGAAATAA
Statistics
Matches: 662, Mismatches: 112, Indels: 63
0.79 0.13 0.08
Matches are distributed among these distances:
164 13 0.02
165 121 0.18
166 369 0.56
167 84 0.13
168 71 0.11
169 4 0.01
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (166 bp):
TTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCCAAAAAAATTTA
CGGAGTAGAAAATAACGTATTTCTGAAAAAAAAAGAATTTAAAGAAAAAATTCCAAAACTCATGA
AAATGAATTAATTTTTTAAAACTAATTTAATATGAA
Found at i:476140 original size:332 final size:332
Alignment explanation
Indices: 475243--476204 Score: 1038
Period size: 332 Copynumber: 2.9 Consensus size: 332
475233 GTTAAATAAC
* ** ** * * * *
475243 AATATTAGATGAGTTTTAAAAATTTTAAACCAAGAAAAATCTCCC-CGAAAAAATTTACAGAGA-
1 AATATTTGATGAAATTTAAAAATTAAAAAACAAGAAAAAT-TCCCTCAAAAAAAATTACGGA-AT
* ** *
475306 AGAAAATTC-G-ATTTCTC-AAAAGAAAAAGGAATTT-AAACAAAAAATTCCAAAACTCATGAAA
64 AGAAAATACTGTATTT-TCGAAAA-AAAAA-GAATTTCAAGGAAAAAATTCAAAAACTCATGAAA
* * *
475367 ATGAATAATTTTTCAAAACTAAATTAATATGAATTAAATGATAATGTTTTATGAATTTTAAAAAT
126 ATGAATAATTTTTAAAAACTAATTTAATATGAATTAAATGATAATGTTTGATGAATTTTAAAAAT
* * *
475432 TAAAAATCGAGAAAAATCCACTC-GAAAAATTTACGGAGTAGAAAATAACGTATTTCGAAAAAAG
191 TAAAAACCGAGAAAAATCCACTCAAAAAAATTTACGGAGTAGAAAATATCGTATTTCGAAAAAAG
* * * *
475496 GAAAATTTCAAGAAAAAAATTCAAAAACTCATCAAAACGAATTAATTTATGAAAAATTATTTAAT
256 GAAAGTTTCAAGAAAAAAA-TCAAAAACTCATGAAAATGAATTAATTTATGAAAAATGATTTAAT
475561 ACAAAAAAGTAAT
320 ACAAAAAAGTAAT
* * * *
475574 AATATTTGATGAAATTTAAAAATTGAGAACCGAGAAAAATTCCCTCAAAAAAAATTACGGAATAG
1 AATATTTGATGAAATTTAAAAATTAAAAAACAAGAAAAATTCCCTCAAAAAAAATTACGGAATAG
* * * * * *
475639 AAAATACTGTATTTTGGAAAAAAAAAGAGTTTCAATGAAAAAAATCAAACACTCATTAAAATGAA
66 AAAATACTGTATTTTCGAAAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAA
* * *
475704 TTAATTTTTTAAAACTAATTTAATATGAATTAACTAATGAA-GTTTGATGAATTTTAAAAATTAA
131 -TAATTTTTAAAAACTAATTTAATATGAATTAAATGAT-AATGTTTGATGAATTTTAAAAATTAA
** * * * * * * *
475768 AAACTAAGAAAAATCCCCTCAAAAAAATTTATGAAGTAGAAAATATTGTATTTCAAAAAAATGAG
194 AAACCGAGAAAAATCCACTCAAAAAAATTTACGGAGTAGAAAATATCGTATTTCGAAAAAAGGAA
* * * ** * *
475833 AGTTTCAAGAAAAAAATCAAACACTCATGAAAATGAATTAATTTTTTAAACCTGATTTCATATGA
259 AGTTTCAAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTATGAAAAATGATTTAATA-CA
*
475898 ATCAAA-TAAT
323 A-AAAAGTAAT
* * * * *
475908 GATGTTTGATGAATTTTAAAAATTAAAAAACAAG-AAAATTCCCCTCAAAGAAATTTAC-GAAGT
1 AATATTTGATGAAATTTAAAAATTAAAAAACAAGAAAAATT-CCCTCAAAAAAAATTACGGAA-T
* *
475971 AGAAAATAAC-GTA-TTTCGAAAAAAAGAA-AATTT-TAGGGAAAAATTCAAAAACTCATGAAAA
64 AGAAAAT-ACTGTATTTTCGAAAAAAA-AAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAA
* * * * *
476032 TGAATAAATTTTTAAAAACTGATTTAACATGAAATAAATGATAATATTTGATGAAATTTAAAAAT
127 TGAAT-AATTTTTAAAAACTAATTTAATATGAATTAAATGATAATGTTTGATGAATTTTAAAAAT
* * * *
476097 TGAAAACCGAGAAAAATTCTCTCAAAAAAATTTACGGAGTAGAAAACATCGTATTTCGAAAAAAG
191 TAAAAACCGAGAAAAATCCACTCAAAAAAATTTACGGAGTAGAAAATATCGTATTTCGAAAAAAG
* *
476162 GAAAGTTTTAAG-GAAAAATCAAAAACTCATGAAAATGAATTAA
256 GAAAGTTTCAAGAAAAAAATCAAAAACTCATGAAAATGAATTAA
476205 CATGAAATAA
Statistics
Matches: 526, Mismatches: 88, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
330 5 0.01
331 91 0.17
332 171 0.33
333 140 0.27
334 114 0.22
335 5 0.01
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (332 bp):
AATATTTGATGAAATTTAAAAATTAAAAAACAAGAAAAATTCCCTCAAAAAAAATTACGGAATAG
AAAATACTGTATTTTCGAAAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAA
TAATTTTTAAAAACTAATTTAATATGAATTAAATGATAATGTTTGATGAATTTTAAAAATTAAAA
ACCGAGAAAAATCCACTCAAAAAAATTTACGGAGTAGAAAATATCGTATTTCGAAAAAAGGAAAG
TTTCAAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTATGAAAAATGATTTAATACAAAA
AAGTAAT
Found at i:476326 original size:146 final size:146
Alignment explanation
Indices: 476046--476336 Score: 342
Period size: 146 Copynumber: 2.0 Consensus size: 146
476036 TAAATTTTTA
* *
476046 AAAACTGATTTAACATGAAATAAATGATAATATTTGATGAAATTTAAAAATTGAAAACCGAGAAA
1 AAAACTGAATTAACATGAAATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCGAGAAA
* * * * ** *
476111 AATTCTCTCAAAAAAATTTACGGAGTAGAAAACATCGTATTTCGAAAAAAGGAAAGTTTTAAGGA
66 AATCCTCCCAAAAAAATTTACAGAGAAGAAAACA-CGTATTTCGAAAAAAGGAAAGTTCAAAAGA
476176 AAAATCAAAAACTCATG
130 AAAATCAAAAACTCATG
* * *
476193 AAAA-TGAATTAACATGAAATAAATGATAATATTTGATGAATTTTGAAAATTAAAAACTGATG-A
1 AAAACTGAATTAACATGAAATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCGA-GAA
* *
476256 AAATCCTCCCAAAAAAA-TTACAGAGAAGAAATTC-CGTATTTTGAGAAAATAGGAGAA-TTCCA
65 AAATCCTCCCAAAAAAATTTACAGAGAAGAAA-ACACGTATTTCGA-AAAA-AGGA-AAGTT-CA
*
476318 AAAG-AAAATCAATAACTCA
125 AAAGAAAAATCAAAAACTCA
476337 AAAAAATAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
144 9 0.07
145 16 0.13
146 88 0.72
147 10 0.08
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (146 bp):
AAAACTGAATTAACATGAAATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCGAGAAA
AATCCTCCCAAAAAAATTTACAGAGAAGAAAACACGTATTTCGAAAAAAGGAAAGTTCAAAAGAA
AAATCAAAAACTCATG
Found at i:476950 original size:19 final size:19
Alignment explanation
Indices: 476923--476979 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
476913 TTTATCGGTG
* *
476923 CATTATATCGATACATGCT
1 CATTGTATCGATACATGAT
* *
476942 CATTGTATCTATACATAAT
1 CATTGTATCGATACATGAT
476961 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
476980 AATTGATAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:477928 original size:13 final size:13
Alignment explanation
Indices: 477907--477941 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
477897 AATGTTCTAA
*
477907 GTATTGATACATT
1 GTATCGATACATT
*
477920 GTATCGATAGATT
1 GTATCGATACATT
477933 GTATCGATA
1 GTATCGATA
477942 TAGGGTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:480014 original size:27 final size:26
Alignment explanation
Indices: 479967--480022 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
479957 TCTTTTAATA
479967 AAAATCTGTTTCTAAATAAAAAAAAC
1 AAAATCTGTTTCTAAATAAAAAAAAC
*
479993 AAAATCTGTTTCTAAATAAAAACAAC
1 AAAATCTGTTTCTAAATAAAAAAAAC
480019 AAAA
1 AAAA
480023 GGGAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATCTGTTTCTAAATAAAAAAAAC
Found at i:480323 original size:63 final size:63
Alignment explanation
Indices: 480224--480353 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
480214 ATACAATCGA
480224 TAGGGAGTAAAGTGAACCAAATTTATTTTTTAAGTTTTGTTATATCAAAAAGGGGGAGATAGT
1 TAGGGAGTAAAGTGAACCAAATTTATTTTTTAAGTTTTGTTATATCAAAAAGGGGGAGATAGT
480287 TAGGGAGTAAAGTGAACCAAATTTATTTTTTAAGTTTTGTTATATCAAAAAGGGGGAGATAGT
1 TAGGGAGTAAAGTGAACCAAATTTATTTTTTAAGTTTTGTTATATCAAAAAGGGGGAGATAGT
480350 TAGG
1 TAGG
480354 ATCTTGGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (63 bp):
TAGGGAGTAAAGTGAACCAAATTTATTTTTTAAGTTTTGTTATATCAAAAAGGGGGAGATAGT
Found at i:480689 original size:19 final size:20
Alignment explanation
Indices: 480665--480720 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
480655 TGTATCGATA
480665 TATTGTATCGATACATACT-
1 TATTGTATCGATACATACTC
480684 TATTGTATCGATACATACTC
1 TATTGTATCGATACATACTC
* *
480704 AATTGCATCGATACATA
1 TATTGTATCGATACATA
480721 AAATTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
TATTGTATCGATACATACTC
Found at i:482460 original size:42 final size:40
Alignment explanation
Indices: 482350--482469 Score: 102
Period size: 42 Copynumber: 2.9 Consensus size: 40
482340 ATGTACTTGG
* * **
482350 GACTAAGCCGACAAGTAAACAAGAGATATAAAGTTGACCGG
1 GACTAAGCCGACAGGTAAACAAGGGATA-AAAGTTGACCAA
* *
482391 GACTAAACCGAC-GAGT--ACATAGAGGATAAAAGATTTACCCAA
1 GACTAAGCCGACAG-GTAAACA-AG-GGATAAAAG-TTGA-CCAA
482433 GACTAAGCCGACAGGTAAACAAGGGATAAACAGTTGA
1 GACTAAGCCGACAGGTAAACAAGGGATAAA-AGTTGA
482470 TCGAGGGATG
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
39 3 0.05
40 6 0.10
41 20 0.32
42 25 0.40
43 5 0.08
44 3 0.05
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (40 bp):
GACTAAGCCGACAGGTAAACAAGGGATAAAAGTTGACCAA
Found at i:482924 original size:47 final size:46
Alignment explanation
Indices: 482799--483495 Score: 380
Period size: 44 Copynumber: 15.2 Consensus size: 46
482789 CAGGCAAAGA
* * * * *
482799 TGAAAGGAGTTTAACTAGG-ACTAACGCTAATACAGTCAAACAACGG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA-GG
* * * * *
482845 TGAAAACAAAAGTTTAACCAGGTCCTAACGCCAATACAATCAAACAATGG
1 TG--AA-AAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA-GG
* *
482895 TGAAAAGAGTTTGACTAGGTCCTAACGCCAATACGGTCAAACAAGGG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAA-GG
* * * * * *
482942 TAAAAAGAGTTTAACCATG-ACTAATGCTAATACAGTCAAACAA-G
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
** * * **
482986 AAAAAAGAGTTTAACCAAGG--CTAATGCCAATACAGTCAAATGA-G
1 TGAAAAGAGTTTGA-CTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * * **
483030 AGAAAAGAGTTTGACAAGG-GCTAATGCCAATACAATCAAATGA-G
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * * *
483074 AGAAAAAAGTTTGACTAGGTCCTAATGCCAGTACAGTTAAACGA-G
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * *** * *
483119 AGAAAAGAGTTTGAGTAGG-GAAAATGCCAATACAGTTAAACGAGAG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAG-G
* ** *
483165 TAAAAAAGAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAA-A
1 T--GAAA-AGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * * * * * *
483213 AGAAAATATTTTGACCAAG-ACTAATGCTAATACAGTCAAACGA-G
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * * * * * ** *
483257 AGAAAAGAGTCTGACCAAG-ACTAATGCCAATATAGTTAAATGAGA
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * * *
483302 TGAGAAGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAATGATGG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAA-CAAGG
** * * * ** *
483349 TGAAAAGTCTTTGACCAGGTCTTAATGCCAATGCAGTCAAATGAGA
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
* * * *
483395 TGAGAAGAGTTTAACTAAGTCCTAACGCCAATACAGTCAAACAAGAG
1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAG-G
** * * *
483442 TGGAAAAG-GTTTGACTAGGTCCTAACACCAATAAAATCAAACGAGGG
1 T-GAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAAC-AAGG
483489 TGAAAAG
1 TGAAAAG
483496 GTTAACTAGA
Statistics
Matches: 519, Mismatches: 113, Indels: 38
0.77 0.17 0.06
Matches are distributed among these distances:
43 5 0.01
44 162 0.31
45 65 0.13
46 86 0.17
47 120 0.23
48 14 0.03
49 25 0.05
50 42 0.08
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (46 bp):
TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGG
Found at i:483239 original size:94 final size:91
Alignment explanation
Indices: 482897--483483 Score: 399
Period size: 89 Copynumber: 6.4 Consensus size: 91
482887 AACAATGGTG
* * * *
482897 AAAAGAGTTTGACTAGGTCCTAACGCCAATACGGTCAAACAAGGGTAAAAAGAGTTTAACCATGA
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGAG--AAAAGAGTTTGACCAAGA
*
482962 CTAATGCTAATACAGTCAAAC-A-AGAA
64 CTAATGCCAATACAGTCAAACGAGAGAA
* * * ** *
482988 AAAAGAGTTTAACCAAGG--CTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGA-CAAGGG
1 AAAAGAGTTTGA-CTAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACCAA-GA
* *
483050 CTAATGCCAATACAATCAAATGAGAG-A
64 CTAATGCCAATACAGTCAAACGAGAGAA
* * * * ** *
483077 AAAA-AGTTTGACTAGGTCCTAATGCCAGTACAGTTAAACGAGAGAAAAGAGTTTGAGTAGGGA-
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACCA-AGAC
* *
483140 AAATGCCAATACAGTTAAACGAGAGTAAA
65 TAATGCCAATACAGTCAAACGAGAG--AA
* * * *
483169 AAAGAGAGTTTGACTAGGTCCTAACACCAATACAGTCAAACAAAAGAAAATATTTTGACCAAGAC
1 AAA-AGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACCAAGAC
*
483234 TAATGCTAATACAGTCAAACGAGAG--
65 TAATGCCAATACAGTCAAACGAGAGAA
* * * * * * * ** * * *
483259 AAAAGAGTCTGACCAAG-ACTAATGCCAATATAGTTAAATGAGATGAGAAGAGTTTGACCAGGTC
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGA-GAAAAGAGTTTGACCAAG-A
* * **
483323 CTAATGCCAATATAGTCAAATGATG-GTG
64 CTAATGCCAATACAGTCAAACGA-GAGAA
** * * * * ** * * * *
483351 AAAAGTCTTTGACCAGGTCTTAATGCCAATGCAGTCAAATGAGATGAGAAGAGTTTAACTAAGTC
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGA-GAAAAGAGTTTGACCAAG-A
* * **
483416 CTAACGCCAATACAGTCAAACAAGAGTGG
64 CTAATGCCAATACAGTCAAACGAGAG-AA
* * *
483445 AAAAG-GTTTGACTAGGTCCTAACACCAATAAAATCAAAC
1 AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAAC
483484 GAGGGTGAAA
Statistics
Matches: 390, Mismatches: 84, Indels: 42
0.76 0.16 0.08
Matches are distributed among these distances:
87 6 0.02
88 54 0.14
89 87 0.22
90 49 0.13
91 12 0.03
92 22 0.06
93 87 0.22
94 73 0.19
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (91 bp):
AAAAGAGTTTGACTAGGTCCTAACGCCAATACAGTCAAACAAGAGAAAAGAGTTTGACCAAGACT
AATGCCAATACAGTCAAACGAGAGAA
Found at i:483406 original size:227 final size:226
Alignment explanation
Indices: 482852--483440 Score: 555
Period size: 227 Copynumber: 2.6 Consensus size: 226
482842 CGGTGAAAAC
* * * * * * * *
482852 AAAAGTTTAACCAGGTCCTAACGCCAATACAATCAAACAATGGTGAAAAGAGTTTGACTAGGTCC
1 AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGA--GAGAAAAGACTTTGACCAGG-CA
* * * * * * * * ** *
482917 TAACGCCAATACGGTCAAACAAGGGT-AAAA-AGAGTTTAACCATG-ACTAATGCTAATACAGTC
63 AAATGCCAATACAGTCAAACGAGAGTAAAAAGAGAGTTTAACTAAGTCCTAACACCAATACAGTC
* * *
482979 AAACAAGAAAAAAGAGTTTAACCAAGGCTAATGCCAATACAGTCAAATGAGAGAAAAGAGTTTGA
128 AAACAAGAAAAAAGAGTTTAACCAAGACTAATGCCAATACAGTCAAACGAGAGAAAAGAGTCTGA
*
483044 CAAGGGCTAATGCCAATACAATCAAATGAGAGAA
193 CAAGGACTAATGCCAATACAATCAAATGAGAGAA
* * * * ** *
483078 AAAAGTTTGACTAGGTCCTAATGCCAGTACAGTTAAACGAGAGAAAAGAGTTTGAGTAGGGAAAA
1 AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGAGAAAAGACTTTGACCAGGCAAAA
* * *
483143 TGCCAATACAGTTAAACGAGAGTAAAAAAGAGAGTTTGACTAGGTCCTAACACCAATACAGTCAA
66 TGCCAATACAGTCAAACGAGAGT-AAAAAGAGAGTTTAACTAAGTCCTAACACCAATACAGTCAA
* * * *
483208 ACAA-AAGAAAATATTTTGACCAAGACTAATGCTAATACAGTCAAACGAGAGAAAAGAGTCTGAC
130 ACAAGAA-AAAAGAGTTTAACCAAGACTAATGCCAATACAGTCAAACGAGAGAAAAGAGTCTGA-
* * * *
483272 CAA-GACTAATGCCAATATAGTTAAATGAGATGAG
193 CAAGGACTAATGCCAATACAATCAAATGAGA-GAA
* * * * * *
483306 AAGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAATGATGGTGAAAAGTCTTTGACCAGGTCT
1 AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGA--GAGAAAAGACTTTGACCAGG-CA
* * * * * *
483371 TAATGCCAATGCAGTCAAATGAGA-T-GAGA-AGAGTTTAACTAAGTCCTAACGCCAATACAGTC
63 AAATGCCAATACAGTCAAACGAGAGTAAAAAGAGAGTTTAACTAAGTCCTAACACCAATACAGTC
483433 AAACAAGA
128 AAACAAGA
483441 GTGGAAAAGG
Statistics
Matches: 294, Mismatches: 58, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
223 20 0.07
224 18 0.06
225 4 0.01
226 46 0.16
227 128 0.44
228 42 0.14
230 16 0.05
231 20 0.07
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (226 bp):
AAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGAGAAAAGACTTTGACCAGGCAAAA
TGCCAATACAGTCAAACGAGAGTAAAAAGAGAGTTTAACTAAGTCCTAACACCAATACAGTCAAA
CAAGAAAAAAGAGTTTAACCAAGACTAATGCCAATACAGTCAAACGAGAGAAAAGAGTCTGACAA
GGACTAATGCCAATACAATCAAATGAGAGAA
Found at i:483482 original size:93 final size:93
Alignment explanation
Indices: 483294--483482 Score: 211
Period size: 93 Copynumber: 2.0 Consensus size: 93
483284 CAATATAGTT
* * * * * *
483294 AAATGAGATGAGAAGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAATGATGGTGAAAAGTCT
1 AAATGAGATGAGAAGAGTTTAACCAAGTCCTAACGCCAATACAGTCAAATCAAGGTGAAAAGTCT
* ** ** *
483359 TTGACCAGGTCTTAATGCCAATGCAGTC
66 TTGACCAGGTCCTAACACCAATAAAATC
*
483387 AAATGAGATGAGAAGAGTTTAACTAAGTCCTAACGCCAATACAGTCAAA-CAAGAGTGGAAAAG-
1 AAATGAGATGAGAAGAGTTTAACCAAGTCCTAACGCCAATACAGTCAAATCAAG-GT-GAAAAGT
* *
483450 GTTTGACTAGGTCCTAACACCAATAAAATC
64 CTTTGACCAGGTCCTAACACCAATAAAATC
483480 AAA
1 AAA
483483 CGAGGGTGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
92 2 0.03
93 71 0.90
94 6 0.08
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (93 bp):
AAATGAGATGAGAAGAGTTTAACCAAGTCCTAACGCCAATACAGTCAAATCAAGGTGAAAAGTCT
TTGACCAGGTCCTAACACCAATAAAATC
Found at i:485090 original size:13 final size:13
Alignment explanation
Indices: 485072--485097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
485062 TACACCAAGT
485072 ATGTATCGATACA
1 ATGTATCGATACA
485085 ATGTATCGATACA
1 ATGTATCGATACA
485098 CAAAAACTTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:490800 original size:13 final size:13
Alignment explanation
Indices: 490782--490807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490772 TACACCAAGT
490782 ATGTATCGATACA
1 ATGTATCGATACA
490795 ATGTATCGATACA
1 ATGTATCGATACA
490808 CAAAAACTTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:492019 original size:25 final size:24
Alignment explanation
Indices: 491986--492036 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
491976 AATATGCCTC
491986 TTTTCC-TTTGTCTTTTTCTTGATTT
1 TTTTCCTTTTG-CTTTTTCTTG-TTT
* *
492011 TTTTTCTTTTGCTTTTTTTTGTTT
1 TTTTCCTTTTGCTTTTTCTTGTTT
492035 TT
1 TT
492037 GAAAGCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 14 0.61
26 4 0.17
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (24 bp):
TTTTCCTTTTGCTTTTTCTTGTTT
Found at i:492809 original size:13 final size:13
Alignment explanation
Indices: 492791--492816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
492781 AATTTTTTGG
492791 TGTATCGATACAA
1 TGTATCGATACAA
492804 TGTATCGATACAA
1 TGTATCGATACAA
492817 GTTTGGCTAC
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:494886 original size:21 final size:20
Alignment explanation
Indices: 494862--494904 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
494852 GGCTAGTGTG
*
494862 GGGACTACCCGGTTGCGACCT
1 GGGACT-CCCGGTCGCGACCT
* *
494883 GGGAGTGCCGGTCGCGACCT
1 GGGACTCCCGGTCGCGACCT
494903 GG
1 GG
494905 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTCCCGGTCGCGACCT
Found at i:495201 original size:21 final size:21
Alignment explanation
Indices: 495177--495223 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
495167 TTTGAAGCCG
495177 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
495197 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
495218 ATTTTG
1 ATTTTG
495224 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:495363 original size:13 final size:13
Alignment explanation
Indices: 495345--495383 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
495335 ATAATCCCCC
* *
495345 TGTATCAATACAG
1 TGTATCGATACAA
495358 TGTATCGATACAA
1 TGTATCGATACAA
495371 TGTATCGATACAA
1 TGTATCGATACAA
495384 AGAAAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:495562 original size:13 final size:14
Alignment explanation
Indices: 495544--495583 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
495534 AATAAAAACA
495544 CAAAATCATTCA-T
1 CAAAATCATTCATT
495557 CAAAATCATTCATTT
1 CAAAATCATTCA-TT
*
495572 CAACATCATTCA
1 CAAAATCATTCA
495584 ACACAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (14 bp):
CAAAATCATTCATT
Found at i:495594 original size:15 final size:15
Alignment explanation
Indices: 495540--495594 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
495530 AAATAATAAA
495540 AACACAAAATCATTC
1 AACACAAAATCATTC
*
495555 -A-TCAAAATCATTC
1 AACACAAAATCATTC
*** *
495568 ATTTCAACATCATTC
1 AACACAAAATCATTC
495583 AACACAAAATCA
1 AACACAAAATCA
495595 CAAAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 19 0.61
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (15 bp):
AACACAAAATCATTC
Found at i:501563 original size:13 final size:13
Alignment explanation
Indices: 501545--501570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501535 AATTTTTTGG
501545 TGTATCGATACAT
1 TGTATCGATACAT
501558 TGTATCGATACAT
1 TGTATCGATACAT
501571 ACTTAGTGTA
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):
TGTATCGATACAT
Found at i:502808 original size:16 final size:17
Alignment explanation
Indices: 502787--502820 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
502777 AAGATTTGGG
*
502787 TACAAAAA-TTTATGGT
1 TACAAAAAGTCTATGGT
502803 TACAAAAAGTCTATGGT
1 TACAAAAAGTCTATGGT
502820 T
1 T
502821 GAAAGTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TACAAAAAGTCTATGGT
Found at i:505608 original size:33 final size:33
Alignment explanation
Indices: 505571--505637 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
505561 TTCAACGATT
505571 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
505604 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
505637 T
1 T
505638 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:505609 original size:13 final size:13
Alignment explanation
Indices: 505591--505615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
505581 CATAAAATGT
505591 TGTATCGATACAA
1 TGTATCGATACAA
505604 TGTATCGATACA
1 TGTATCGATACA
505616 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:505804 original size:52 final size:52
Alignment explanation
Indices: 505711--505834 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
505701 CACTGATCTT
*
505711 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
505762 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
505814 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
505835 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:511225 original size:154 final size:155
Alignment explanation
Indices: 510877--511236 Score: 404
Period size: 155 Copynumber: 2.3 Consensus size: 155
510867 CTAAGTTCAA
* * * ** *
510877 GAAAAATTACGAAAATGCCTCTAGGGGATACCTTCGACATAAAAGTACAAAATACCTCTAAAGGA
1 GAAAAATTAAGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCAATACCCCTAAAGGA
* *
510942 CTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAACACCCATCTTCGGCATAAAAGCAGACC
66 CTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAACACCCACCTTCGGCATAAAAGCAGACC
* * * * * *
511007 TGGTTATAACCTAGGACTTTGCTCT
131 CGATGACAACCTAGGACTTGGCTAT
* ** *
511032 -ACAAAATTAAAAAAATGCCCCTAAAGGATACCTTCGACGTGAAAGTATCCCAATACCCCTAAAG
1 GA-AAAATTAAGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTA-CCCAATACCCCTAAAG
** * * * * *
511096 GACTTAAAAAGGA-TA-ATTTAGAGATGAACTTATCCTAAATATCTACCTTCGGCATAAAA-CGG
64 GACTTAAAAAGGACTATA-AAAGAGATGAACCTATCCTAAACACCCACCTTCGGCATAAAAGCAG
* *
511158 ACCCGATGACAGCCTAGGACTTGGTTAT
128 ACCCGATGACAACCTAGGACTTGGCTAT
* *
511186 GAAAAATTATGAAAATGCCCCTAGGGGATACCTTTGACGTAAAAGTACCCA
1 GAAAAATTAAGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCA
511237 GTATCCTTAA
Statistics
Matches: 168, Mismatches: 33, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
153 4 0.02
154 63 0.38
155 75 0.45
156 26 0.15
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (155 bp):
GAAAAATTAAGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCAATACCCCTAAAGGA
CTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAACACCCACCTTCGGCATAAAAGCAGACC
CGATGACAACCTAGGACTTGGCTAT
Found at i:512762 original size:13 final size:13
Alignment explanation
Indices: 512744--512777 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
512734 TCACTATTTT
*
512744 TCTTTTTTTTCTC
1 TCTTTTCTTTCTC
512757 TCTTTTCTTTCTC
1 TCTTTTCTTTCTC
512770 T-TTTTCTT
1 TCTTTTCTT
512778 CTCACTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTCTTTCTC
Found at i:512785 original size:13 final size:13
Alignment explanation
Indices: 512744--512785 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
512734 TCACTATTTT
*
512744 TCTTTTTTTTCTC
1 TCTTTTTCTTCTC
512757 TC-TTTTCTT-TC
1 TCTTTTTCTTCTC
512768 TCTTTTTCTTCTC
1 TCTTTTTCTTCTC
*
512781 ACTTT
1 TCTTT
512786 GCTAGCTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 4 0.16
12 13 0.52
13 8 0.32
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTTCTTCTC
Found at i:513359 original size:165 final size:164
Alignment explanation
Indices: 513167--513840 Score: 605
Period size: 165 Copynumber: 4.0 Consensus size: 164
513157 AATACTATAA
** * *
513167 GAATTTTAAAAATTTTAAACTAAG-AAAAT-CCCTCAGAAAAAATTTACGGAGAAAAAAACTCTA
1 GAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTC-GAAAAAATTTACGGAGAAAAAAACTCCA
* * *
513230 TTTCTCGAAAAAAAAG-GAATTTCAACAAAAAATCCAAAACTCATGAAAATGAATTAAATTTTCC
65 TTT-TCGAAAAAAAAGAGAATTTCAAGAAAAAATCAAAAACTCATGAAAATGAATT-AATTTTCT
* *
513294 AAAAATGATTTAATATGAATCAAATGATGATGTTTGAT
128 AAAAATGATTTAATATGAAT-AAATGATAATATTTGAT
* * *
513332 GAATTCTAAAAATTGAAAACCAAGAAAAATCCCCTCCAAAAAATTTACGGAG-TAAAAACTCACA
1 GAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGAAAAAAACTC-C-
* * *
513396 AATTTCGAAAAAAAA-AGCAAATTTCAAGGAAAAAATTTAAAAACTCATGAAAATAAATTAATTT
64 ATTTTCGAAAAAAAAGAG--AATTTCAA-GAAAAAA-TCAAAAACTCATGAAAATGAATTAATTT
* *
513460 TCTAATACAT-ATTTAATATGAAGTAAATGATAATATTTTAT
125 TCTAA-AAATGATTTAATATGAA-TAAATGATAATATTTGAT
* * * *** * *
513501 GAAATGTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGTGGAAAACACCGT
1 GAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGAAAAAAACTCCAT
* * * * * *
513566 ATT-GAAGAAAAGGAGAGTTTTAAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTAA
66 TTTCGAAAAAAAAGAGAATTTCAAG-AAAAAATCAAAAACTCATGAAAATGAATTAATTTTCTAA
*
513630 AACTGATTTAATATGAAATAAATGATAATATTTGAT
130 AAATGATTTAATATG-AATAAATGATAATATTTGAT
* * * * *
513666 GAATTTTAAAAATTAAAAACTGATG-AAAATCCTCC-C-AAAAAAATTACGGAGAATAAAACTCC
1 GAATTTTAAAAATTGAAAAC-CAAGAAAAATCC-CCTCGAAAAAATTTACGGAGAAAAAAACTCC
* * * * ** * **
513728 GTTTTTCGAAAAAAATGAGAGAATTTCAA-AAGAAAATCTACAACTAAAAAAAATAAAAAGAATT
64 -ATTTTCGAAAAAAA--AGAGAATTTCAAGAA-AAAATCAAAAACTCATGAAAAT-GAATTAATT
* * ** * *
513792 TTTTAAAACTGATTTAATGGGAATTAAATGATAATATTTAAA
124 TTCTAAAAATGATTTAATATGAA-TAAATGATAATATTTGAT
513834 GAATTTT
1 GAATTTT
513841 GACGTTTGAA
Statistics
Matches: 418, Mismatches: 66, Indels: 47
0.79 0.12 0.09
Matches are distributed among these distances:
164 22 0.05
165 114 0.27
166 59 0.14
167 34 0.08
168 69 0.17
169 90 0.22
170 30 0.07
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (164 bp):
GAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGAAAAAAACTCCAT
TTTCGAAAAAAAAGAGAATTTCAAGAAAAAATCAAAAACTCATGAAAATGAATTAATTTTCTAAA
AATGATTTAATATGAATAAATGATAATATTTGAT
Found at i:514323 original size:20 final size:20
Alignment explanation
Indices: 514298--514350 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
514288 AAAACCCTTA
514298 AAAGTATCGATACGCAATTC
1 AAAGTATCGATACGCAATTC
514318 AAAGTATCGATACGCAATTC
1 AAAGTATCGATACGCAATTC
514338 AAAGTATCGATAC
1 AAAGTATCGATAC
514351 ATGTTGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (20 bp):
AAAGTATCGATACGCAATTC
Found at i:514461 original size:13 final size:13
Alignment explanation
Indices: 514443--514468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514433 TACACCAAGT
514443 ATGTATCGATACA
1 ATGTATCGATACA
514456 ATGTATCGATACA
1 ATGTATCGATACA
514469 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:514466 original size:32 final size:33
Alignment explanation
Indices: 514425--514488 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
514415 TAGCCAAACT
* **
514425 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
514457 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
514489 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:520955 original size:31 final size:31
Alignment explanation
Indices: 520917--521043 Score: 184
Period size: 31 Copynumber: 4.1 Consensus size: 31
520907 GCAAATAGTA
* * *
520917 TTGCATCAACAAAGTTCAAAGACTATAATAT
1 TTGCATCAGCAAAGTTCGAAGGCTATAATAT
*
520948 TTGCATCAGCAAGGTTCGAAGGCTATAATAT
1 TTGCATCAGCAAAGTTCGAAGGCTATAATAT
* *
520979 TTGCATCAGCAAGGTTCGAAGGCTATGATAT
1 TTGCATCAGCAAAGTTCGAAGGCTATAATAT
*
521010 TTGCATCAGC-AAGTTTGAAGGCTATAATAT
1 TTGCATCAGCAAAGTTCGAAGGCTATAATAT
521040 TTGC
1 TTGC
521044 CTCATTGAGG
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 21 0.24
31 67 0.76
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (31 bp):
TTGCATCAGCAAAGTTCGAAGGCTATAATAT
Found at i:521055 original size:61 final size:62
Alignment explanation
Indices: 520917--521061 Score: 193
Period size: 62 Copynumber: 2.4 Consensus size: 62
520907 GCAAATAGTA
* *
520917 TTGCATCAACAAAGTTCAAAGACTATAATATTTGCATCAGCAAGGTTCGAAGGCTATAATAT
1 TTGCATCAGCAAGGTTCAAAGACTATAATATTTGCATCAGCAAGGTTCGAAGGCTATAATAT
* * * *
520979 TTGCATCAGCAAGGTTCGAAGGCTATGATATTTGCATCAGCAA-GTTTGAAGGCTATAATAT
1 TTGCATCAGCAAGGTTCAAAGACTATAATATTTGCATCAGCAAGGTTCGAAGGCTATAATAT
* ***
521040 TTGCCTCATTGAGGTTCAAAGA
1 TTGCATCAGCAAGGTTCAAAGA
521062 TGTGGCTAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 33 0.46
62 38 0.54
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (62 bp):
TTGCATCAGCAAGGTTCAAAGACTATAATATTTGCATCAGCAAGGTTCGAAGGCTATAATAT
Found at i:522259 original size:21 final size:22
Alignment explanation
Indices: 522222--522262 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
522212 TATAAGATTT
*
522222 TAATTTTTTATTTTTTAAAAAA
1 TAATTATTTATTTTTTAAAAAA
522244 TAATTATTTA-TTTTTAAAA
1 TAATTATTTATTTTTTAAAA
522263 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTATTTATTTTTTAAAAAA
Found at i:525246 original size:21 final size:21
Alignment explanation
Indices: 525216--525256 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
525206 TCCAAAAAAC
525216 TTTTTTTTAGG-ATAAAATAG
1 TTTTTTTTAGGAATAAAATAG
525236 TTTTCTTTTAGGAATAAAATA
1 TTTT-TTTTAGGAATAAAATA
525257 ATAGTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (21 bp):
TTTTTTTTAGGAATAAAATAG
Found at i:526124 original size:13 final size:13
Alignment explanation
Indices: 526106--526132 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
526096 TACATTGAAC
526106 ATGTATCGATACA
1 ATGTATCGATACA
526119 ATGTATCGATACA
1 ATGTATCGATACA
526132 A
1 A
526133 AGCATAATGT
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:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:530403 original size:34 final size:34
Alignment explanation
Indices: 530362--530429 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
530352 AATCTTACAA
*
530362 CCCTATCTTTTCATAGGCTAAAATAGAACCTCTT
1 CCCTATCTTTTCACAGGCTAAAATAGAACCTCTT
*
530396 CCCTATCTTTTCACAGGCTAAGATAGAACCTCTT
1 CCCTATCTTTTCACAGGCTAAAATAGAACCTCTT
530430 AATCATTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (34 bp):
CCCTATCTTTTCACAGGCTAAAATAGAACCTCTT
Found at i:531236 original size:20 final size:19
Alignment explanation
Indices: 531190--531245 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
531180 TTGTATCGAT
**
531190 ACATTGTATTGATACATGT
1 ACATTGTATTGATACATAC
*
531209 TCATTGTATTGATACATAC
1 ACATTGTATTGATACATAC
*
531228 ACAATTGTATCGATACAT
1 AC-ATTGTATTGATACAT
531246 GAAGCTGGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
ACATTGTATTGATACATAC
Found at i:532902 original size:15 final size:15
Alignment explanation
Indices: 532882--532916 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
532872 ATCCATCAAA
532882 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
532897 GATGATGATGATAAT
1 GATGATGAAGATAAT
532912 GATGA
1 GATGA
532917 AGTTGACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:538233 original size:13 final size:13
Alignment explanation
Indices: 538215--538240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538205 ACGAAGATCC
538215 ATGTATCGATACA
1 ATGTATCGATACA
538228 ATGTATCGATACA
1 ATGTATCGATACA
538241 TTGAGTAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:538300 original size:13 final size:13
Alignment explanation
Indices: 538278--538335 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
538268 GGCAGTAGCT
*
538278 TTGTAGCGATACA
1 TTGTATCGATACA
538291 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
538307 TTTATGTATCGATACA
1 --T-TGTATCGATACA
538323 TTGTATCGATACA
1 TTGTATCGATACA
538336 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:538316 original size:19 final size:18
Alignment explanation
Indices: 538292--538354 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
538282 AGCGATACAT
538292 TGTATCGATACAACATTTA
1 TGTATCGATACAACA-TTA
538311 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
538324 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
538343 TGTATCGATACA
1 TGTATCGATACA
538355 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:538325 original size:32 final size:32
Alignment explanation
Indices: 538279--538354 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
538269 GCAGTAGCTT
* *
538279 TGTAGCGATACATTGTATCGATACAACATTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
538311 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
538343 TGTATCGATACA
1 TGTATCGATACA
538355 GTTACTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:538614 original size:13 final size:13
Alignment explanation
Indices: 538596--538659 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
538586 ACAATATTCT
538596 TTGTATCGATACA
1 TTGTATCGATACA
538609 TTGTATCGATACA
1 TTGTATCGATACA
* *
538622 ATGTATCGATATA
1 TTGTATCGATACA
*
538635 TTGTATCAATACA
1 TTGTATCGATACA
*
538648 ATGTATCGATAC
1 TTGTATCGATAC
538660 GTGGGTTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:538637 original size:26 final size:26
Alignment explanation
Indices: 538597--538659 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
538587 CAATATTCTT
*
538597 TGTATCGATACATTGTATCGATACAA
1 TGTATCGATACATTGTATCAATACAA
*
538623 TGTATCGATATATTGTATCAATACAA
1 TGTATCGATACATTGTATCAATACAA
538649 TGTATCGATAC
1 TGTATCGATAC
538660 GTGGGTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (26 bp):
TGTATCGATACATTGTATCAATACAA
Found at i:541330 original size:20 final size:19
Alignment explanation
Indices: 541305--541376 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
541295 ACCCTTGAAA
541305 GTATCGATACATATCCAGAT
1 GTATCGATACATAT-CAGAT
**
541325 GTATCGATACATCATGC-TTT
1 GTATCGATACAT-AT-CAGAT
541345 GTATCGATACATA-CAGAACT
1 GTATCGATACATATCAG-A-T
541365 GTATCGATACAT
1 GTATCGATACAT
541377 GAAACTAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 1 0.02
19 1 0.02
20 38 0.88
21 3 0.07
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACATATCAGAT
Found at i:541445 original size:13 final size:13
Alignment explanation
Indices: 541427--541451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541417 CATGGCACAT
541427 TGTATCGATACAA
1 TGTATCGATACAA
541440 TGTATCGATACA
1 TGTATCGATACA
541452 TGAATAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:542280 original size:20 final size:21
Alignment explanation
Indices: 542240--542280 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
542230 TCTAAACATG
*
542240 TATCTATACAATCACAAGGTT
1 TATCGATACAATCACAAGGTT
*
542261 TATCGATACAAT-AGAAGGTT
1 TATCGATACAATCACAAGGTT
542281 AGCTACTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (21 bp):
TATCGATACAATCACAAGGTT
Found at i:546324 original size:34 final size:34
Alignment explanation
Indices: 546285--546386 Score: 159
Period size: 34 Copynumber: 3.0 Consensus size: 34
546275 AACCTCACAA
546285 CCTTATCTTTTTACAGGCTAAGATAGAACCTCTT
1 CCTTATCTTTTTACAGGCTAAGATAGAACCTCTT
* *
546319 CCTTATCTTTTCACAAGCTAAGATAGAACCTCTT
1 CCTTATCTTTTTACAGGCTAAGATAGAACCTCTT
* *
546353 CCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CCTTATCTTTTT-ACAGGCTAAGATAGAACCTCT
546387 CAATCACTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
34 42 0.69
35 19 0.31
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (34 bp):
CCTTATCTTTTTACAGGCTAAGATAGAACCTCTT
Found at i:546973 original size:33 final size:33
Alignment explanation
Indices: 546931--546994 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
546921 AATTCCACAG
546931 TGTATCGATA-TAAAGCAATTTGTATCGATACGA
1 TGTATCGATACT-AAGCAATTTGTATCGATACGA
*
546964 TGTATCGATACTTAGCAATTTGTATCGATAC
1 TGTATCGATACTAAGCAATTTGTATCGATAC
546995 ATCTGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACTAAGCAATTTGTATCGATACGA
Found at i:548838 original size:105 final size:106
Alignment explanation
Indices: 548693--548925 Score: 296
Period size: 105 Copynumber: 2.2 Consensus size: 106
548683 TTTAGCAACA
* * * * * *
548693 ATAATTAACGTATGATAAATTTTTTACGTAATGTTGTTATTTAATATTGAATTCTCCAATTATAT
1 ATAATTAAAGTATGAT-AATTTTTTACATAATGTTATTATTTAACATTGAATTATCCAAATATAT
548758 ATTATTTAGAATAAATTTG-GGAGTTTCAAAATTTAAAAGA-T
65 ATTATTTAGAATAAA-TTGAGGAGTTTCAAAATTTAAAAGAGT
* *
548799 ATAATTAAAGTATGATAATTTTCTTACAT-ATGTTATTATTTAACATTTAATTATTCAAATATAT
1 ATAATTAAAGTATGATAATTTT-TTACATAATGTTATTATTTAACATTGAATTATCCAAATATAT
* * *
548863 ATTATTTATAGTAAATTGAGGAGTTTCAAATTTTAAAAGAGT
65 ATTATTTAGAATAAATTGAGGAGTTTCAAAATTTAAAAGAGT
548905 -TAATT-AAGATATGATAATTTT
1 ATAATTAAAG-TATGATAATTTT
548926 ATTTTAATAA
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
104 6 0.05
105 85 0.76
106 21 0.19
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (106 bp):
ATAATTAAAGTATGATAATTTTTTACATAATGTTATTATTTAACATTGAATTATCCAAATATATA
TTATTTAGAATAAATTGAGGAGTTTCAAAATTTAAAAGAGT
Found at i:549846 original size:13 final size:13
Alignment explanation
Indices: 549805--549857 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
549795 CCGTTTGAAG
549805 CAATGTATCGATA
1 CAATGTATCGATA
549818 CAA--T-TC-AT-
1 CAATGTATCGATA
549826 C-ATGTATCGATA
1 CAATGTATCGATA
*
549838 CATTGTATCGATA
1 CAATGTATCGATA
549851 CAATGTA
1 CAATGTA
549858 CCATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:549850 original size:33 final size:33
Alignment explanation
Indices: 549808--549872 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
549798 TTTGAAGCAA
*
549808 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
549841 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
549873 AACAGTGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:550589 original size:38 final size:37
Alignment explanation
Indices: 550529--550624 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 37
550519 ATAATCGATT
*
550529 AAAAAGATTTTCTCCCCATTGATTAAAATTTATTTTC
1 AAAAAGATTTTCTCCCCATTGATAAAAATTTATTTTC
*
550566 AAAATAGATTTTCTCCCCCTTGATAAAAATTTATTTTC
1 AAAA-AGATTTTCTCCCCATTGATAAAAATTTATTTTC
550604 AAAACA-ATATTTCTCCCCATT
1 AAAA-AGAT-TTTCTCCCCATT
550625 TTTGTTATAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 6 0.11
38 47 0.89
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAAAGATTTTCTCCCCATTGATAAAAATTTATTTTC
Found at i:551394 original size:22 final size:21
Alignment explanation
Indices: 551359--551408 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
551349 TTTGTTGATG
*
551359 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
551379 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
551400 AATTTGAAG
1 ATTTTGAAG
551409 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:551405 original size:21 final size:22
Alignment explanation
Indices: 551366--551408 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
551356 ATGATTTTGA
* *
551366 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
551388 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
551409 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:551535 original size:13 final size:13
Alignment explanation
Indices: 551517--551542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
551507 TAGTAACCCT
551517 TGTATCGATACAA
1 TGTATCGATACAA
551530 TGTATCGATACAA
1 TGTATCGATACAA
551543 AGAATATTAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:558848 original size:19 final size:19
Alignment explanation
Indices: 558792--558848 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
558782 CTGCCAGTTT
**
558792 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
* *
558813 CATGTATCAATATAATGAA
1 CATGTATCGATACAATGAA
558832 CATGTATCGATACAATG
1 CATGTATCGATACAATG
558849 TATCGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:558851 original size:13 final size:13
Alignment explanation
Indices: 558833--558859 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
558823 TATAATGAAC
558833 ATGTATCGATACA
1 ATGTATCGATACA
558846 ATGTATCGATACA
1 ATGTATCGATACA
558859 A
1 A
558860 AGCAGCATGT
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:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:561384 original size:13 final size:13
Alignment explanation
Indices: 561366--561391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
561356 AAATAGTATC
561366 CAATGTATCGATA
1 CAATGTATCGATA
561379 CAATGTATCGATA
1 CAATGTATCGATA
561392 TAAGGAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:569114 original size:26 final size:26
Alignment explanation
Indices: 569068--569125 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
569058 TATAAAATTT
569068 ATAAAA-AATACTAAATAAAAATAAA
1 ATAAAATAATACTAAATAAAAATAAA
* * *
569093 ATAAAATAATAGTAAATGAAAATGAA
1 ATAAAATAATACTAAATAAAAATAAA
*
569119 TTAAAAT
1 ATAAAAT
569126 GAAAATAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (26 bp):
ATAAAATAATACTAAATAAAAATAAA
Found at i:572940 original size:23 final size:22
Alignment explanation
Indices: 572873--572924 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
572863 CTGTTTCCTT
572873 TCTAGCCATGTGCACCCTCCCA
1 TCTAGCCATGTGCACCCTCCCA
572895 TCTAGCCATGTGCACCCTCCCA
1 TCTAGCCATGTGCACCCTCCCA
572917 TCTAGCCA
1 TCTAGCCA
572925 AATTGCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.44, G:0.13, T:0.23
Consensus pattern (22 bp):
TCTAGCCATGTGCACCCTCCCA
Found at i:579177 original size:2 final size:2
Alignment explanation
Indices: 579170--579207 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
579160 AATAAGTTGA
579170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
579208 GTTTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.