Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold277
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: 582610
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 2 of 4
Found at i:187679 original size:15 final size:15
Alignment explanation
Indices: 187659--187689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
187649 TAAAAATGTC
*
187659 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
187674 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
187689 C
1 C
187690 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:189750 original size:13 final size:13
Alignment explanation
Indices: 189732--189769 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
189722 CATTTTTCTT
189732 TGTATCGATACAA
1 TGTATCGATACAA
*
189745 TGTATCGATACAC
1 TGTATCGATACAA
189758 TGTATCGATACA
1 TGTATCGATACA
189770 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:191671 original size:39 final size:40
Alignment explanation
Indices: 191614--191694 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 40
191604 TTTAATAAAA
*
191614 GGGGAGAATGCGTAAATTTGCTAAAATTA-TCTTA-TTAAG
1 GGGGAGAATGCATAAATTTGCTAAAATTACT-TTAGTTAAG
* * *
191653 GGGGAGAATGTATGAATTTGTTAAAATTACTTTAGTTAAG
1 GGGGAGAATGCATAAATTTGCTAAAATTACTTTAGTTAAG
191693 GG
1 GG
191695 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (40 bp):
GGGGAGAATGCATAAATTTGCTAAAATTACTTTAGTTAAG
Found at i:192344 original size:13 final size:13
Alignment explanation
Indices: 192326--192351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
192316 TACACAAAGT
192326 ATGTATCGATACA
1 ATGTATCGATACA
192339 ATGTATCGATACA
1 ATGTATCGATACA
192352 CAAAAAAATT
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:192370 original size:34 final size:32
Alignment explanation
Indices: 192308--192372 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
192298 TAGCCAAACT
**
192308 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
192340 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
192373 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:193726 original size:28 final size:28
Alignment explanation
Indices: 193676--193730 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
193666 ATCTTATCAG
* *
193676 ATTGCTAGAGTTATCAGCTTTAGAGCAA
1 ATTGCTAGAGTCATCAGCCTTAGAGCAA
*
193704 ATTGCTAGAGTCATCGGCCTTAGAGCA
1 ATTGCTAGAGTCATCAGCCTTAGAGCA
193731 TATAAACTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (28 bp):
ATTGCTAGAGTCATCAGCCTTAGAGCAA
Found at i:193964 original size:54 final size:54
Alignment explanation
Indices: 193900--194077 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 54
193890 TCGCCATTAT
* ** *
193900 GGCATCATTATCAATGATGTTAGGTCACCCTTATCAAATTTTGATCACCACCAA
1 GGCATCATTATCAATGATGTTAAGTCACCCTTATCAAATTTTGATTGCCACAAA
* * ** * * * *
193954 GGCATCATTATTAGTGACATCAAGTCACCCTTATTAAATTCTGATTGCCATAAA
1 GGCATCATTATCAATGATGTTAAGTCACCCTTATCAAATTTTGATTGCCACAAA
* * * *
194008 GGCATCATTATCAGTGATGCTAAGTCACCTTTATCAAATTTCGATTGCCACAAA
1 GGCATCATTATCAATGATGTTAAGTCACCCTTATCAAATTTTGATTGCCACAAA
*
194062 AGCATCA-TATCAATGA
1 GGCATCATTATCAATGA
194078 CACCAAGTCA
Statistics
Matches: 100, Mismatches: 24, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
53 8 0.08
54 92 0.92
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (54 bp):
GGCATCATTATCAATGATGTTAAGTCACCCTTATCAAATTTTGATTGCCACAAA
Found at i:194067 original size:108 final size:107
Alignment explanation
Indices: 193900--194106 Score: 270
Period size: 108 Copynumber: 1.9 Consensus size: 107
193890 TCGCCATTAT
* * * * *
193900 GGCATCATTATCAATGATGTTAGGTCACCCTTATCAAATTTTGATCACCACCAAGGCATCATTAT
1 GGCATCATTATCAATGATGCTAAGTCACCCTTATCAAATTTCGATCACCACAAAAGCATCA-TAT
* * * *
193965 TAGTGACATCAAGTCACCCTTATTAAATTCTGATTGCCATAAA
65 CAATGACACCAAGTCACCCTTATCAAATTCTGATTGCCATAAA
* * **
194008 GGCATCATTATCAGTGATGCTAAGTCACCTTTATCAAATTTCGATTGCCACAAAAGCATCATATC
1 GGCATCATTATCAATGATGCTAAGTCACCCTTATCAAATTTCGATCACCACAAAAGCATCATATC
* *
194073 AATGACACCAAGTCACGCTTATCACATTCTGATT
66 AATGACACCAAGTCACCCTTATCAAATTCTGATT
194107 ACCACCACGG
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
107 32 0.38
108 52 0.62
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (107 bp):
GGCATCATTATCAATGATGCTAAGTCACCCTTATCAAATTTCGATCACCACAAAAGCATCATATC
AATGACACCAAGTCACCCTTATCAAATTCTGATTGCCATAAA
Found at i:195591 original size:13 final size:13
Alignment explanation
Indices: 195573--195597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195563 CATAAAGTGT
195573 TGTATCGATACAA
1 TGTATCGATACAA
195586 TGTATCGATACA
1 TGTATCGATACA
195598 TAAGTTTTGT
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:195613 original size:32 final size:33
Alignment explanation
Indices: 195553--195618 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
195543 TTCAACGATT
195553 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
195586 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
195618 T
1 T
195619 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:195677 original size:13 final size:13
Alignment explanation
Indices: 195659--195683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195649 ATTACTCAAA
195659 TGTATCGATACAT
1 TGTATCGATACAT
195672 TGTATCGATACA
1 TGTATCGATACA
195684 CTGATCTTTG
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):
TGTATCGATACAT
Found at i:203153 original size:6 final size:6
Alignment explanation
Indices: 203128--203168 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
203118 GACTAGACAA
* * *
203128 GGCACT GGCAGT GACAGT GGCAGT GGCAGC GGCAGT GGCAG
1 GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCAG
203169 AGCCACCCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.46, T:0.12
Consensus pattern (6 bp):
GGCAGT
Found at i:204307 original size:2 final size:2
Alignment explanation
Indices: 204268--204297 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
204258 TAGATCAAAC
204268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204298 GCTCATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:204764 original size:16 final size:15
Alignment explanation
Indices: 204722--204765 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
204712 TTTTATTAAA
204722 AAAATAATTTTTTTAT
1 AAAAT-ATTTTTTTAT
204738 AATTAA-ATTTTTTTAT
1 AA--AATATTTTTTTAT
204754 AAAATATTTTTT
1 AAAATATTTTTT
204766 AAATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.08
15 7 0.28
16 14 0.56
18 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAATATTTTTTTAT
Found at i:207023 original size:3 final size:3
Alignment explanation
Indices: 207015--207054 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
207005 CCACTCAAAG
207015 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
207055 AAAGATGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:209482 original size:78 final size:79
Alignment explanation
Indices: 209364--209569 Score: 234
Period size: 79 Copynumber: 2.6 Consensus size: 79
209354 GAGATAATAA
* * * * * * * *
209364 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTAGAGTATCCCCGGTTGTGAGAAATCGAT-G
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAG
*
209428 CTTAGAAAAAAAAT
66 CTTAGAAAAAAAAC
* * * *
209442 CGGGATTGGAGTATCCCCTCGAAAATAACGGAGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAG
* * * *
209507 TTTGGAAATAAAGC
66 CTTAGAAAAAAAAC
* *
209521 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
209570 GAAATAACGA
Statistics
Matches: 105, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
78 52 0.50
79 53 0.50
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAG
CTTAGAAAAAAAAC
Found at i:209561 original size:28 final size:28
Alignment explanation
Indices: 209521--209592 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
209511 GAAATAAAGC
** *
209521 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
209549 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
209577 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
209593 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:209654 original size:80 final size:82
Alignment explanation
Indices: 209553--209730 Score: 279
Period size: 80 Copynumber: 2.2 Consensus size: 82
209543 AAGTAACGGG
* *
209553 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGACTGTGAA-AAATTGGT-ATTT
1 GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGATTT
209616 TTGGAAATAAAATCGGA
66 TTGGAAATAAAATCGGA
** * * *
209633 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTT
1 GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGATTT
209698 TTGGAAATAAAATCGGA
66 TTGGAAATAAAATCGGA
209715 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
209731 TTATAGAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 45 0.52
81 8 0.09
82 34 0.39
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (82 bp):
GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGATTT
TTGGAAATAAAATCGGA
Found at i:209776 original size:51 final size:50
Alignment explanation
Indices: 209661--209998 Score: 188
Period size: 51 Copynumber: 6.4 Consensus size: 50
209651 AAATAACGGG
* * *
209661 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTAGTG---TTTGAAAATAAAACCGGA
*
209715 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTAGTGT-TTGAAAATAAAACC-GGA
* **
209767 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTGA-AAATAAAACCGGA
* ** * * * * *
209818 GTTGGAGTATCCCC--TCG-GAAATAA-CGGGGTTGGAGTATCCCCGATGATTAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AATTAGTGTTTGA--A-----AAT-A-AAACCGGA
* * *
209873 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTAGTG---TTTGAAAATAAAACCGGA
* * *
209927 GTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTAGTG-TTTGAAAATAAAACCGGA
* *
209978 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
209999 GAGAATTGAT
Statistics
Matches: 223, Mismatches: 34, Indels: 56
0.71 0.11 0.18
Matches are distributed among these distances:
48 9 0.04
49 2 0.01
50 3 0.01
51 70 0.31
52 35 0.16
53 21 0.09
54 46 0.21
55 20 0.09
56 2 0.01
57 2 0.01
58 5 0.02
59 4 0.02
60 1 0.00
62 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTGAAAATAAAACCGGA
Found at i:209823 original size:52 final size:49
Alignment explanation
Indices: 209661--209831 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 49
209651 AAATAACGGG
* *
209661 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGG--ATAAAACCGGA
* * *
209715 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTG--GATAAAACC-GGA
209767 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTT-G-GATAAAACCGGA
209818 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
209832 TCGGAAATAA
Statistics
Matches: 100, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
51 32 0.32
52 37 0.37
53 11 0.11
54 20 0.20
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGATAAAACCGGA
Found at i:209858 original size:28 final size:27
Alignment explanation
Indices: 209818--209888 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
209808 TAAAACCGGA
**
209818 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
209846 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
209873 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
209889 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:212373 original size:13 final size:13
Alignment explanation
Indices: 212355--212380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
212345 ACAAAGATCC
212355 ATGTATCGATACA
1 ATGTATCGATACA
212368 ATGTATCGATACA
1 ATGTATCGATACA
212381 CAGAAAAATG
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:212376 original size:33 final size:33
Alignment explanation
Indices: 212334--212400 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
212324 AAAATTTCCA
***
212334 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
212367 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
212400 A
1 A
212401 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:212444 original size:19 final size:18
Alignment explanation
Indices: 212420--212487 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
212410 CAGTAGCTAA
212420 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
212439 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
212454 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
212471 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
212488 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:212460 original size:13 final size:13
Alignment explanation
Indices: 212442--212466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212432 ACAATACTTA
212442 TGTATCGATACAT
1 TGTATCGATACAT
212455 TGTATCGATACA
1 TGTATCGATACA
212467 AAACTTATGT
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):
TGTATCGATACAT
Found at i:212464 original size:32 final size:32
Alignment explanation
Indices: 212423--212485 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
212413 TAGCTAATTA
*
212423 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
212455 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
212486 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:214503 original size:23 final size:23
Alignment explanation
Indices: 214458--214504 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
214448 ATTAGTTATA
* **
214458 AAATTTATAATTAACAATGTTTT
1 AAATATATAATTAACAAAATTTT
*
214481 AAATATATGATTAACAAAATTTT
1 AAATATATAATTAACAAAATTTT
214504 A
1 A
214505 GTACTTGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATATATAATTAACAAAATTTT
Found at i:214759 original size:20 final size:22
Alignment explanation
Indices: 214719--214760 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
214709 ATATAGTTTT
214719 CAATAAAAAATAAATTTAATTA
1 CAATAAAAAATAAATTTAATTA
*
214741 CAATAATAAA-AAA-TTAATTA
1 CAATAAAAAATAAATTTAATTA
214761 ATACTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
CAATAAAAAATAAATTTAATTA
Found at i:214862 original size:30 final size:29
Alignment explanation
Indices: 214826--214882 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
214816 TAAACTATAG
*
214826 AAATCAAACTATATTACATAATATATAAAT
1 AAATCAAACTAAATTACATAATA-ATAAAT
*
214856 AAATCAAACTAAATTACATGATAATAA
1 AAATCAAACTAAATTACATAATAATAA
214883 TAACAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.30
Consensus pattern (29 bp):
AAATCAAACTAAATTACATAATAATAAAT
Found at i:215751 original size:5 final size:5
Alignment explanation
Indices: 215741--215779 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
215731 ATTTAGATGG
215741 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATT
215780 CGGCAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:218917 original size:12 final size:12
Alignment explanation
Indices: 218891--218930 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
218881 GTTGATATTT
*
218891 TGGCT-GAAATA
1 TGGCTAGAAGTA
218902 TGGCTAGAAGTA
1 TGGCTAGAAGTA
218914 TGGCTAGAAGTA
1 TGGCTAGAAGTA
218926 TGGCT
1 TGGCT
218931 GAAAAATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.28
Consensus pattern (12 bp):
TGGCTAGAAGTA
Found at i:219456 original size:20 final size:19
Alignment explanation
Indices: 219411--219467 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
219401 CAAAACCCAG
219411 AATGTATCGATACAAAGCA
1 AATGTATCGATACAAAGCA
*
219430 AATTGTATCGATACATCTAG-A
1 AA-TGTATCGATACA--AAGCA
*
219451 AATGTATAGATACAAAG
1 AATGTATCGATACAAAG
219468 TAGATAGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.72
21 3 0.09
22 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (19 bp):
AATGTATCGATACAAAGCA
Found at i:220079 original size:22 final size:21
Alignment explanation
Indices: 220024--220080 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
220014 CTTTTTTTAT
*
220024 TTAATAATATTAATTATATAA
1 TTAATAATATTAAATATATAA
*
220045 --AATAATCTT--ATATATAA
1 TTAATAATATTAAATATATAA
220062 TTAATAATATATAAATATA
1 TTAATAATAT-TAAATATA
220081 AATAGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
17 7 0.25
19 15 0.54
20 1 0.04
22 5 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAATAATATTAAATATATAA
Found at i:220717 original size:29 final size:29
Alignment explanation
Indices: 220675--220733 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
220665 ATGAAGATAT
220675 GTGAATTTAGTATGACAAAATTAAACTTG
1 GTGAATTTAGTATGACAAAATTAAACTTG
**
220704 GTGAATTTAGTATGACAATGTTAAACTTG
1 GTGAATTTAGTATGACAAAATTAAACTTG
220733 G
1 G
220734 CTAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
GTGAATTTAGTATGACAAAATTAAACTTG
Found at i:222595 original size:20 final size:20
Alignment explanation
Indices: 222570--222626 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
222560 ATTGCCAGTT
*
222570 TTATGTGTCGATACAATTCA
1 TTATGTATCGATACAATTCA
222590 TTATGTATCGATACAATTCA
1 TTATGTATCGATACAATTCA
*
222610 TGATGTATCGATACAAT
1 TTATGTATCGATACAAT
222627 GAACATGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
TTATGTATCGATACAATTCA
Found at i:222641 original size:19 final size:18
Alignment explanation
Indices: 222612--222668 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
222602 ACAATTCATG
222612 ATGTATCGATACAATGAAC
1 ATGTATCGATAC-ATGAAC
**
222631 ATGTAGT-GATACTATTCAC
1 ATGTA-TCGATAC-ATGAAC
222650 ATGTATCGATACATGAAC
1 ATGTATCGATACATGAAC
222668 A
1 A
222669 GTGATGAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.19
19 24 0.77
20 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (18 bp):
ATGTATCGATACATGAAC
Found at i:224942 original size:64 final size:64
Alignment explanation
Indices: 224868--224995 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
224858 CTTTGACACC
224868 TCTAAAAGGGTCTTGTCCATGGGCTCCTAAGGCTCATCATACTTCATGGTTGCCAAGTTAATGT
1 TCTAAAAGGGTCTTGTCCATGGGCTCCTAAGGCTCATCATACTTCATGGTTGCCAAGTTAATGT
224932 TCTAAAAGGGTCTTGTCCATGGGCTCCTAAGGCTCATCATACTTCATGGTTGCCAAGTTAATGT
1 TCTAAAAGGGTCTTGTCCATGGGCTCCTAAGGCTCATCATACTTCATGGTTGCCAAGTTAATGT
224996 CTTCATCCTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (64 bp):
TCTAAAAGGGTCTTGTCCATGGGCTCCTAAGGCTCATCATACTTCATGGTTGCCAAGTTAATGT
Found at i:234239 original size:16 final size:18
Alignment explanation
Indices: 234203--234241 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
234193 ATAAATAAAT
*
234203 ATTTTGATATTAATTCAA
1 ATTTTGATATTAATCCAA
234221 ATTTT-ATATTAA-CCAA
1 ATTTTGATATTAATCCAA
234237 ATTTT
1 ATTTT
234242 TTATGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTGATATTAATCCAA
Found at i:234786 original size:30 final size:31
Alignment explanation
Indices: 234729--234786 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
234719 ATTTTATAAA
**
234729 AAATTTATTTATTTTTATAATTTTAAAATAT
1 AAATTTATTTATTTTTATAATAATAAAATAT
234760 AAATTTATTGT-TTTTTA-AATAATAAAA
1 AAATTTATT-TATTTTTATAATAATAAAA
234787 GTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.33
31 15 0.62
32 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
AAATTTATTTATTTTTATAATAATAAAATAT
Found at i:235022 original size:21 final size:22
Alignment explanation
Indices: 234993--235035 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
234983 AAATCAATAA
234993 AACTGAAAT-TATTATTATTTTT
1 AACTGAAATATATT-TTATTTTT
235015 AACT-AAATATATTTTATTTTT
1 AACTGAAATATATTTTATTTTT
235036 GCAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
AACTGAAATATATTTTATTTTT
Found at i:239732 original size:13 final size:13
Alignment explanation
Indices: 239714--239766 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
239704 ATACATTGCT
239714 CATTGTATCGATA
1 CATTGTATCGATA
239727 CATTGTATCGATA
1 CATTGTATCGATA
*
239740 TATTG---C--T-
1 CATTGTATCGATA
239747 CATTGTATCGATA
1 CATTGTATCGATA
239760 CATTGTA
1 CATTGTA
239767 AAATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 4 0.12
8 1 0.03
10 2 0.06
12 1 0.03
13 24 0.75
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:239745 original size:33 final size:33
Alignment explanation
Indices: 239694--239766 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
239684 ATACATTTTG
*
239694 CATTCTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
*
239727 CATTGTATCGATATATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
239760 CATTGTA
1 CATTGTA
239767 AAATGTATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:239750 original size:20 final size:20
Alignment explanation
Indices: 239694--239783 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
239684 ATACATTTTG
*
239694 CATTCTATCGATACATTGCT
1 CATTGTATCGATACATTGCT
239714 CATTGTATCGAT--A-----
1 CATTGTATCGATACATTGCT
*
239727 CATTGTATCGATATATTGCT
1 CATTGTATCGATACATTGCT
239747 CATTGTATCGATACATTG-T
1 CATTGTATCGATACATTGCT
* *
239766 AAAATGTATCGATACATT
1 -CATTGTATCGATACATT
239784 CAGGCATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.21
15 1 0.02
18 1 0.02
19 1 0.02
20 43 0.74
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:242183 original size:28 final size:28
Alignment explanation
Indices: 242136--242207 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
242126 TCACAATCGA
**
242136 GGATACTCCAACCCTATTA-TTTC-ATTAG
1 GGATACTCCAACCCCGTTATTTTCGA--AG
*
242164 GGATACTCCAACCCCGTTATTTTCGAGG
1 GGATACTCCAACCCCGTTATTTTCGAAG
242192 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
242208 GCTTTATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTTCGAAG
Found at i:242247 original size:79 final size:77
Alignment explanation
Indices: 242164--242498 Score: 284
Period size: 79 Copynumber: 4.2 Consensus size: 77
242154 ATTTCATTAG
*
242164 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTAA
1 GGATACTCCAACCCCGTTATTTTCGA-GGGATACTCCAACCCCGGCTTTATTTCTAAAACATTAA
*
242229 TTTCTCATAATTGA
65 TTT-TCATAATCGA
* * * *
242243 GGATACTCCAACCCCGTTATTTTCGCAGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCAA
1 GGATACTCCAACCCCGTTATTTTCG-AGGGATACTCCAACCCCGGCTTTATTTCTAAAACATTAA
242308 TTTTTCATAATCG-
65 -TTTTCATAATCGA
** * * ** *
242321 GAGATACTTTAATCTCGTTATTTTTTAGGGATACTCCAATCCCAGG-TCTTATTT-TCAAAACAT
1 G-GATACTCCAACCCCGTTATTTTCGAGGGATACTCCAA-CCCCGGCT-TTATTTCT-AAAACAT
* *
242384 TGATTTTCCACAATCGA
62 TAATTTT-CATAATCGA
* * * * ** *
242401 GGATACTCCAACCTCATTATTTTTGAGGGGATACTCCAGCCCCGATTTTA-TTCTCAAAAC-GTA
1 GGATACTCCAACCCCGTTATTTTCGA-GGGATACTCCAACCCCGGCTTTATTTCT-AAAACATTA
* *
242464 GATTTCCTATAATCAGG
64 -ATTTTC-ATAATC-GA
*
242481 GGATACTCCAGCCCCGTT
1 GGATACTCCAACCCCGTT
242499 GTCATCTCTA
Statistics
Matches: 208, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
78 23 0.11
79 152 0.73
80 33 0.16
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (77 bp):
GGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAACCCCGGCTTTATTTCTAAAACATTAAT
TTTCATAATCGA
Found at i:242273 original size:107 final size:107
Alignment explanation
Indices: 242083--242284 Score: 282
Period size: 107 Copynumber: 1.9 Consensus size: 107
242073 TTTTCATCTC
*
242083 GGGGATACTCCAACCCCGGTTTCATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTCATTTCCAAAATACCAATTTCTCACAATCGAGGATACTCCAAC
* **
242148 CCTATTATTTCATTAGGGATACTCCAACCCCGTTATTTTCGA
66 CCCATTATTTCAGCAGGGATACTCCAACCCCGTTATTTTCGA
* ** * *
242190 GGGGATACTCCAACCCCGGCTTT-ATTTCTAAAATATTAATTTCTCATAATTGAGGATACTCCAA
1 GGGGATACTCCAACCCCGG-TTTCATTTCCAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
242254 CCCCGTTATTTTC-GCAGGGATACTCCAACCC
65 CCCCATTA-TTTCAGCAGGGATACTCCAACCC
242285 TGGCCTTATT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 76 0.92
108 7 0.08
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGGTTTCATTTCCAAAATACCAATTTCTCACAATCGAGGATACTCCAAC
CCCATTATTTCAGCAGGGATACTCCAACCCCGTTATTTTCGA
Found at i:254874 original size:1 final size:1
Alignment explanation
Indices: 254870--254953 Score: 60
Period size: 1 Copynumber: 84.0 Consensus size: 1
254860 ATTCTTTTTC
* * * * * * * * *
254870 AAAAAAAAAAACAACAAAAAAACAAAAAAACAAAAAAACAAGAAAACAAAAAAAAAACAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
254935 AGAAAAAGAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
254954 GAAGAATCTG
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:254893 original size:8 final size:8
Alignment explanation
Indices: 254869--254940 Score: 94
Period size: 8 Copynumber: 9.0 Consensus size: 8
254859 CATTCTTTTT
254869 CAAAAAAA
1 CAAAAAAA
*
254877 -AAAACAA
1 CAAAAAAA
254884 CAAAAAAA
1 CAAAAAAA
254892 CAAAAAAA
1 CAAAAAAA
254900 CAAAAAAA
1 CAAAAAAA
*
254908 CAAGAAAA
1 CAAAAAAA
254916 CAAAAAAA
1 CAAAAAAA
254924 -AAACAAAA
1 CAAA-AAAA
254932 CAAAGAAAA
1 CAAA-AAAA
254941 AGAGAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
7 9 0.16
8 40 0.71
9 7 0.12
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:254904 original size:24 final size:23
Alignment explanation
Indices: 254869--254953 Score: 100
Period size: 24 Copynumber: 3.7 Consensus size: 23
254859 CATTCTTTTT
*
254869 CAAAAAAAAAAACAACAAAAAAA
1 CAAAAAAAAAAAAAACAAAAAAA
*
254892 CAAAAAAACAAAAAAACAAGAAAA
1 CAAAAAAA-AAAAAAACAAAAAAA
*
254916 CAAAAAAAAAACAAAACAAAGAAA
1 CAAAAAAAAAA-AAAACAAAAAAA
* *
254940 -AAGAGAAAAAAAAA
1 CAAAAAAAAAAAAAA
254954 GAAGAATCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
22 4 0.07
23 19 0.35
24 31 0.57
ACGTcount: A:0.85, C:0.11, G:0.05, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAAAAAAACAAAAAAA
Found at i:254915 original size:27 final size:27
Alignment explanation
Indices: 254870--254953 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
254860 ATTCTTTTTC
254870 AAAA-AAAAAAACAACAAAA-AAACAAA
1 AAAACAAAAAAACAACAAAACAAA-AAA
*
254896 AAAACAAAAAAACAAGAAAACAAAAAA
1 AAAACAAAAAAACAACAAAACAAAAAA
* *
254923 AAAACAAAACAAAGAA-AAAGAGAAAAAA
1 AAAACAAAA-AAACAACAAA-ACAAAAAA
254951 AAA
1 AAA
254954 GAAGAATCTG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 4 0.08
27 29 0.57
28 18 0.35
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (27 bp):
AAAACAAAAAAACAACAAAACAAAAAA
Found at i:256208 original size:61 final size:60
Alignment explanation
Indices: 255928--256251 Score: 395
Period size: 55 Copynumber: 5.5 Consensus size: 60
255918 TTCACTTTTT
* *
255928 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTAGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACG-CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
255989 AGTCCTCAAAGAGCAGGACG-----CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
256044 AGTCCTCAAAGAGCA-GA----ATGCCTTTCAAAGCCCACACAAGTTGATGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
256099 AGTCCTCAAAGAGTAGGACGCCTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
256159 AGTCCTCAAAGAGCAGGATGCTTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCC
1 AGTCCTCAAAGAGCAGGACGCTTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
256219 TAGTCTTCAAAGAGCAGGACGCTCTCTCCTTTC
1 -AGTCCTCAAAGAGCAGGACGCT-TTTCCTTTC
256252 GCCCTTTAGT
Statistics
Matches: 235, Mismatches: 14, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
54 5 0.02
55 92 0.39
56 2 0.01
59 4 0.02
60 55 0.23
61 76 0.32
62 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:256441 original size:210 final size:212
Alignment explanation
Indices: 256064--256450 Score: 636
Period size: 210 Copynumber: 1.8 Consensus size: 212
256054 GAGCAGAATG
*
256064 CCTTTCAAAGCCCACACAAGTTGATGGCATTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCTTT
1 CCTTTCAAAGCCCACACAAGTTGATGGCATTTTTCAGTCCTCAAAGAGCAGGACGCC---TCTTT
* *
256129 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTCAAA
63 CAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATGCTTTCTCCTTTCAAA
* * *
256194 GCCCACACAAGTTGGTGGCACTTCCTAGTCTTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTT
128 GCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTT
256259 AGTCCTTAAAGAGTAAGACA
193 AGTCCTTAAAGAGTAAGACA
* *
256279 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACG-C-CTTTCA
1 CCTTTCAAAGCCCACACAAGTTGATGGCATTTTTC-AGTCCTCAAAGAGCAGGACGCCTCTTTCA
*
256341 AAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATGCTTTCTTCTTTCAAAGC
65 AAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATGCTTTCTCCTTTCAAAGC
256406 CCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGC
130 CCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGC
256451 CTTTTAAAGC
Statistics
Matches: 162, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
210 110 0.68
214 6 0.04
215 46 0.28
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (212 bp):
CCTTTCAAAGCCCACACAAGTTGATGGCATTTTTCAGTCCTCAAAGAGCAGGACGCCTCTTTCAA
AACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATGCTTTCTCCTTTCAAAGCC
CACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGT
CCTTAAAGAGTAAGACA
Found at i:256489 original size:116 final size:114
Alignment explanation
Indices: 256280--256619 Score: 464
Period size: 116 Copynumber: 2.9 Consensus size: 114
256270 AGTAAGACAC
* * * * *
256280 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAATCCTCAAAGAGCAGGACGCCTTTTAAAGC
* *
256345 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATGCTTTCTT
65 CCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAAGATGCCTTC-T
*
256396 CTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCTTTTAAAGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAATCCTCAAAGAGCAGGACGCCTTTTAAAGC
*
256461 CCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGATGCCTTCT
65 CCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAAGATGCCTTCT
*
256511 CATTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAATCCTCAAAGAGTAGGACGCCTTTTTTTT
1 C-TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAATCCTCAAAGAGCAGGACGCC-----TTT
* **
256576 TCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAG
59 T-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAG
256620 TAGGACGCCT
Statistics
Matches: 200, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
115 4 0.02
116 151 0.75
117 3 0.01
121 4 0.02
122 38 0.19
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (114 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAATCCTCAAAGAGCAGGACGCCTTTTAAAGCC
CACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAAGATGCCTTCT
Found at i:256628 original size:61 final size:59
Alignment explanation
Indices: 256281--256632 Score: 398
Period size: 61 Copynumber: 6.0 Consensus size: 59
256271 GTAAGACACC
* *
256281 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCC----
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
256336 TTTCAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGATG-CTTTCT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTT-T
* *
256395 TCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCC----
1 T-TTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
256452 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGATGCCTTCTCA
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTT-T-T
* * *
256513 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAATCCTCAAAGAGTAGGACGCCTTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCC-TTTT
* ** *
256573 TTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGACGCCTTTT
1 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
256633 CCTTTTCTCC
Statistics
Matches: 254, Mismatches: 27, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
54 1 0.00
55 96 0.38
56 3 0.01
57 1 0.00
59 1 0.00
60 10 0.04
61 139 0.55
62 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (59 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:257230 original size:20 final size:20
Alignment explanation
Indices: 257205--257352 Score: 102
Period size: 20 Copynumber: 7.8 Consensus size: 20
257195 TTTTCACAAT
257205 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
** * *
257225 TTGTATTAATACAATGA-GCAA
1 TTGTATCGATAC-ATTATTC-A
257246 TT-TATCGATACATT-TTGCA
1 TTGTATCGATACATTATT-CA
*
257265 TTGTATCGATACATTACTCA
1 TTGTATCGATACATTATTCA
257285 TTGTATCG----A-TA--CA
1 TTGTATCGATACATTATTCA
**
257298 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTATTCA
257318 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTATT-CA
* *
257338 ATGTATCAATACATT
1 TTGTATCGATACATT
257353 CAGGCATTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
13 10 0.10
15 2 0.02
16 1 0.01
17 1 0.01
18 1 0.01
19 6 0.06
20 73 0.72
21 7 0.07
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:257292 original size:40 final size:39
Alignment explanation
Indices: 257205--257352 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 39
257195 TTTTCACAAT
* * *
257205 TTGTATCGATACATTATTCATTGTATTAATACAATGAGC-AA
1 TTGTATCGATACATT-TTCATTGTATCAATAC-ATTA-CTCA
*
257246 TT-TATCGATACATTTTGCATTGTATCGATACATTACTCA
1 TTGTATCGATACATTTT-CATTGTATCAATACATTACTCA
* *
257285 TTGTATCGAT--A----CATTGTATCGATACATTGCTCA
1 TTGTATCGATACATTTTCATTGTATCAATACATTACTCA
*
257318 TTGTATCGATACATTTTACAATGTATCAATACATT
1 TTGTATCGATACATTTT-CATTGTATCAATACATT
257353 CAGGCATTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
33 31 0.34
35 1 0.01
38 2 0.02
39 8 0.09
40 46 0.51
41 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (39 bp):
TTGTATCGATACATTTTCATTGTATCAATACATTACTCA
Found at i:257305 original size:33 final size:33
Alignment explanation
Indices: 257263--257332 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
257253 ATACATTTTG
257263 CATTGTATCGATACATTACTCATTGTATCGATA
1 CATTGTATCGATACATTACTCATTGTATCGATA
*
257296 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTACTCATTGTATCGATA
257329 CATT
1 CATT
257333 TTACAATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTACTCATTGTATCGATA
Found at i:257332 original size:13 final size:13
Alignment explanation
Indices: 257283--257313 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
257273 ATACATTACT
257283 CATTGTATCGATA
1 CATTGTATCGATA
257296 CATTGTATCGATA
1 CATTGTATCGATA
257309 CATTG
1 CATTG
257314 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:257343 original size:53 final size:53
Alignment explanation
Indices: 257248--257352 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
257238 ATGAGCAATT
* * *
257248 TATCGATACATTTTGCATTGTATCGATACATTACTCATTGTATCGATACATTG
1 TATCGATACATTCTGCATTGTATCGATACATTACTCAATGTATCAATACATTG
*
257301 TATCGATACATTGCT-CATTGTATCGATACATT-TTACAATGTATCAATACATT
1 TATCGATACATT-CTGCATTGTATCGATACATTACT-CAATGTATCAATACATT
257353 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 1 0.02
53 44 0.96
54 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (53 bp):
TATCGATACATTCTGCATTGTATCGATACATTACTCAATGTATCAATACATTG
Found at i:259762 original size:28 final size:27
Alignment explanation
Indices: 259703--259774 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
259693 TTTACAATCG
* *
259703 GGGATACTCCAACCCTGTTATTTCATTG
1 GGGATACTCCAACCCCGTTATTTCA-TA
259731 GGGATACTCCAACCCCGTTATTTTCGA-A
1 GGGATACTCCAACCCCGTTA-TTTC-ATA
259759 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
259775 AGCTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTCATA
Found at i:259843 original size:107 final size:106
Alignment explanation
Indices: 259652--259852 Score: 244
Period size: 107 Copynumber: 1.9 Consensus size: 106
259642 TTTCATCTCG
* ** *
259652 GGGATACTCCAACCCCGGTTTCATTTCCAAAATACCAATTTTTTACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGCTTTCATTTCCAAAATACCAATTTTCCACAATCAGGGATACTCCAACC
** * *
259717 CTGTTATTTCATTGGGGATACTCCAACCCCGTTATTTTCGAA
66 CCATTATTT-ATCGAGGATACTCCAACCCCGTTATTTTCGAA
* ** *
259759 GGGATACTCCAACCCCAGCTTT-ATTTCTAAAATATTAATTTTCCATAATCAGGGATACTCCAAC
1 GGGATACTCCAACCCC-GCTTTCATTTCCAAAATACCAATTTTCCACAATCAGGGATACTCCAAC
259823 CCCATTATTT-TCGCAAGGATACTCCAACCC
65 CCCATTATTTATCG--AGGATACTCCAACCC
259853 TGGCCTTATT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
105 2 0.03
107 73 0.92
108 4 0.05
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (106 bp):
GGGATACTCCAACCCCGCTTTCATTTCCAAAATACCAATTTTCCACAATCAGGGATACTCCAACC
CCATTATTTATCGAGGATACTCCAACCCCGTTATTTTCGAA
Found at i:259966 original size:78 final size:79
Alignment explanation
Indices: 259730--260065 Score: 330
Period size: 79 Copynumber: 4.3 Consensus size: 79
259720 TTATTTCATT
* *
259730 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAG-CTT-TATTTCTAAAATA
1 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTCTTAT-TTTCTAAAACA
259793 TTAATTTTCCATAATC
65 -TAATTTTCCATAATC
* * * * *
259809 AGGGATACTCCAACCCCATTATTTTCGCAA-GGATACTCCAACCCTGGCCTTA-TTTCTAAAGCA
1 GGGGATACTCCAACCCCGTTATTTTCG-AAGGGATACTCCAACCCCGGTCTTATTTTCTAAAACA
*
259872 TCAATTTTTCATAATC
65 T-AATTTTCCATAATC
* * *
259888 GGGGATACTCTAATCCCGTTGTTTTCG-AGGGATACTCCAACCCCGGTCTTATTTTC-AAAACAC
1 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTCTTATTTTCTAAAACA-
* *
259951 TGATTTTCCACAATC
65 TAATTTTCCATAATC
* * * * * * *
259966 GAGGATACTCCAACCTCGTTATTTTC-AAGGGGATACTCCAGCCCCGATTTTATTCTC-AAAACG
1 GGGGATACTCCAACCCCGTTATTTTCGAA-GGGATACTCCAACCCCGGTCTTATTTTCTAAAACA
*
260029 TCGA-TTTCCTATAATC
65 T-AATTTTCC-ATAATC
*
260045 AGGGGATACTCCAGCCCCGTT
1 -GGGGATACTCCAACCCCGTT
260066 GTCATCTCTA
Statistics
Matches: 213, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.00
78 65 0.31
79 125 0.59
80 22 0.10
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGTCTTATTTTCTAAAACAT
AATTTTCCATAATC
Found at i:260019 original size:157 final size:157
Alignment explanation
Indices: 259730--260065 Score: 362
Period size: 157 Copynumber: 2.1 Consensus size: 157
259720 TTATTTCATT
* *
259730 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCTTTATTTCTAAAACACT
* * *
259795 AATTTTCCATAATCAGGGATACTCCAACCCCATTATTTTCGCAAGGATACTCCAACCCTGGCCTT
66 AATTTTCCACAATCAGGGATACTCCAACCCCATTATTTTC-CAAGGATACTCCAACCCCGACCTT
259860 ATTTCTAAAGCATCAATTTTTCATAATC
130 ATTTCTAAAGCATCAATTTTTCATAATC
* * * *
259888 GGGGATACTCTAATCCCGTTGTTTTCG-AGGGATACTCCAACCCC-GGTCTTATTT-TCAAAACA
1 GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCT-TTATTTCT-AAAACA
* * * *
259950 CTGATTTTCCACAATC-GAGGATACTCCAACCTCGTTATTTT-CAAGGGGATACTCCAGCCCCGA
64 CTAATTTTCCACAATCAG-GGATACTCCAACCCCATTATTTTCCAA--GGATACTCCAACCCCGA
** * * * *
260013 TTTTA-TTCTCAAAACGTCGA-TTTCCTATAATC
126 CCTTATTTCT-AAAGCATCAATTTTTC-ATAATC
*
260045 AGGGGATACTCCAGCCCCGTT
1 -GGGGATACTCCAACCCCGTT
260066 GTCATCTCTA
Statistics
Matches: 148, Mismatches: 22, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
155 3 0.02
156 12 0.08
157 92 0.62
158 41 0.28
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (157 bp):
GGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCTTTATTTCTAAAACACT
AATTTTCCACAATCAGGGATACTCCAACCCCATTATTTTCCAAGGATACTCCAACCCCGACCTTA
TTTCTAAAGCATCAATTTTTCATAATC
Found at i:265232 original size:21 final size:21
Alignment explanation
Indices: 265208--265267 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
265198 CTTTGGTTAT
* *
265208 AAAACTACATT-TTTTATCCA
1 AAAAATACATTCTTTCATCCA
*
265228 AAAAATGCATTCTTTCATCCA
1 AAAAATACATTCTTTCATCCA
** * *
265249 ACTAATGCATTATTTCATC
1 AAAAATACATTCTTTCATC
265268 TAAATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAATACATTCTTTCATCCA
Found at i:269938 original size:20 final size:20
Alignment explanation
Indices: 269913--269989 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
269903 GTAAAAAGAC
*
269913 AGAATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
* *
269933 AGAATGTATCAATACATTCA
1 AGAATGTATCGATACATTGA
*
269953 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
269973 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
269990 CTGGGTACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:272484 original size:13 final size:13
Alignment explanation
Indices: 272466--272490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272456 CATGGCATAT
272466 TGTATCGATACAA
1 TGTATCGATACAA
272479 TGTATCGATACA
1 TGTATCGATACA
272491 TGAAGAATTG
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:281061 original size:13 final size:13
Alignment explanation
Indices: 281043--281069 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
281033 ACATTATGCT
281043 TTGTATCGATACA
1 TTGTATCGATACA
281056 TTGTATCGATACA
1 TTGTATCGATACA
281069 T
1 T
281070 GCACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:284922 original size:3 final size:3
Alignment explanation
Indices: 284914--284942 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
284904 TTATCAAGCA
284914 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
284943 AGACGTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:286921 original size:15 final size:16
Alignment explanation
Indices: 286901--286934 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
286891 TCAATCTTAA
286901 GTTTGGATT-TTTTAG
1 GTTTGGATTATTTTAG
286916 GTTTGGATTATTTTAG
1 GTTTGGATTATTTTAG
286932 GTT
1 GTT
286935 CAGGCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (16 bp):
GTTTGGATTATTTTAG
Found at i:288519 original size:12 final size:12
Alignment explanation
Indices: 288504--288528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
288494 TTAAATCAAT
288504 ATTTAATATTTA
1 ATTTAATATTTA
288516 ATTTAATATTTA
1 ATTTAATATTTA
288528 A
1 A
288529 AAATTAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAATATTTA
Found at i:291406 original size:24 final size:24
Alignment explanation
Indices: 291374--291421 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
291364 GCAGAGAGCC
*
291374 ATTGTTGTGCCATTGGACTGGTGA
1 ATTGTTGTGCCATGGGACTGGTGA
* *
291398 ATTGTTGTGTCATGGGATTGGTGA
1 ATTGTTGTGCCATGGGACTGGTGA
291422 GTTGAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (24 bp):
ATTGTTGTGCCATGGGACTGGTGA
Found at i:291452 original size:20 final size:19
Alignment explanation
Indices: 291414--291452 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
291404 GTGTCATGGG
* *
291414 ATTGGTGAGTTGAAACAAA
1 ATTGGAGAGTTAAAACAAA
291433 ATTGGAGAGTTAATAACAAA
1 ATTGGAGAGTTAA-AACAAA
291453 GCTTTTACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (19 bp):
ATTGGAGAGTTAAAACAAA
Found at i:291816 original size:21 final size:21
Alignment explanation
Indices: 291777--291817 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
291767 AATAGTAAAC
*
291777 ATAAAATTAATTATTATAATA
1 ATAAAATTAATAATTATAATA
291798 ATAAAATTAA-AATTAATAAT
1 ATAAAATTAATAATT-ATAAT
291818 GAAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATTAATAATTATAATA
Found at i:293920 original size:19 final size:19
Alignment explanation
Indices: 293896--293932 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
293886 AACTTTTTAA
293896 TAAATAAAAATTTTTAAAT
1 TAAATAAAAATTTTTAAAT
*
293915 TAAATAAAATTTTTTAAA
1 TAAATAAAAATTTTTAAA
293933 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATAAAAATTTTTAAAT
Found at i:294257 original size:26 final size:25
Alignment explanation
Indices: 294219--294293 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 25
294209 TAATTATACG
*
294219 AGTTTAAACTTATTTTTATTTGTAAA
1 AGTTTAAATTTATTTTTATTT-TAAA
294245 AGTTTAAATTTA-TTTTATTTT-AA
1 AGTTTAAATTTATTTTTATTTTAAA
* *
294268 AGTAT-GATTTATTTTTATTTATAAA
1 AGTTTAAATTTATTTTTATTT-TAAA
294293 A
1 A
294294 TTAATTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.12
23 14 0.33
24 2 0.05
25 11 0.26
26 11 0.26
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (25 bp):
AGTTTAAATTTATTTTTATTTTAAA
Found at i:294300 original size:23 final size:22
Alignment explanation
Indices: 294228--294301 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 22
294218 GAGTTTAAAC
294228 TTATTTTTATTTGTAAAAGTTTAAAT
1 TTATTTTTATTT-TAAAA--TT-AAT
* *
294254 TTA-TTTTATTTTAAAGTATGAT
1 TTATTTTTATTTTAAAAT-TAAT
294276 TTATTTTTATTTATAAAATTAAT
1 TTATTTTTATTT-TAAAATTAAT
294299 TTA
1 TTA
294302 ATTCTTAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 6 0.15
23 15 0.37
24 9 0.22
25 8 0.20
26 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
TTATTTTTATTTTAAAATTAAT
Found at i:294496 original size:72 final size:71
Alignment explanation
Indices: 294420--295272 Score: 648
Period size: 72 Copynumber: 11.8 Consensus size: 71
294410 TGAAAAAGTG
* * *
294420 TTTTTGATATAATTATACAAGTTTAAATTTTTAAGATATAATTTATTTTTATTTTTATAAGTTTA
1 TTTTTGATATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTA
294485 AATTTGCTTTTT
66 AA------TTTT
* ** * * *
294497 TTTTTG-TTTAATTATTTAAGTTTAAATATTT-AGGTTATTATTTATTTTTATTTGTAGAAATTT
1 TTTTTGATATAATTATACAAGTTTAAATTTTTAAGG-TATAATTTATTTTTATTTGTAGAAGTTT
294560 AAATTTGT
65 AAATTT-T
* * * *
294568 TTTTTAAGTATGATTATACAAGTTTAAATTTTTAATGTATAATTTATTTTTAGTTT-TA-AATTT
1 TTTTTGA-TATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTA-TTTGTAGAAGTT
*
294631 TAAATTTA
64 TAAATTTT
* * * *
294639 TTTTTGGTATGATTATACAAGTTTAAATTTTTTTAAGGTATAATTTATTTTTATTTATAGAAATT
1 TTTTTGATATAATTATACAAGTTTAAA--TTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTT
294704 TAAATTTAT
64 TAAATTT-T
**
294713 TTTTTAGATATAATTATATGAGTTT-AATTTTTAAGGTAT-A---A--TTTATTTGTAGAAGTTT
1 TTTTT-GATATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTT
*
294771 AAATTAT
65 AAATTTT
* * * * * * *
294778 TTTTT-ATTTGATTATA-AGACTTTAAAGTTTTAAGTTATAATTTATCTTTATTTTTAGAAGTTT
1 TTTTTGATATAATTATACA-AGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTT
294841 AAATTTAT
65 AAATTT-T
* * ** * * *
294849 TTTTGGGTATAATTATATGATTTTAAATTTTTAAGGTATAA-TT-TTTTTATTTATAGCAGTTTA
1 TTTTTGATATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTA
*
294912 AGTTTAT
66 AATTT-T
* * * ** * * *
294919 TTCTTGAGTATGATTATACGAGTTTAAATTTTTAAAATATGATTTATTTTTATTTGAAGAACTTT
1 TTTTTGA-TATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTT
294984 AAATTTAT
65 AAATTT-T
* * * * * * *
294992 TTTTTGGTTTGATTATACGAGTTTAAATTTTTTAAAGTAT-TTTTATTTTTATTTATAGAAGTTT
1 TTTTTGATATAATTATACAAGTTTAAA-TTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTT
295056 AAATCTATT
65 AAAT-T-TT
* * ** * * * *
295065 TTTTAGGTATGTTTATATACAAGTTTAAACTTTTAAAGATATGATTTATTTTTATTTGTAGAACT
1 TTTTTGATAT-AAT-TATACAAGTTTAAA-TTTTTAAGGTATAATTTATTTTTATTTGTAGAAGT
295130 TTAAATTTGT
63 TTAAATTT-T
** * * * *
295140 TTGCT-AGTTTTATTATACAAGTTTAAATTTTTTAAGGTAT-TTTTATTTTTATTTGTATAAGTT
1 TTTTTGA-TATAATTATACAAGTTTAAA-TTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTT
295203 TAAATTTAT
64 TAAATTT-T
* **
295212 TTTTTAGGT-TAATTATAGGAG-TTAATATTTTTTTTAAGGTATAATTTATTTTTATTTGTAG
1 TTTTT-GATATAATTATACAAGTTTAA-A---TTTTTAAGGTATAATTTATTTTTATTTGTAG
295273 GATTAGTTTG
Statistics
Matches: 630, Mismatches: 106, Indels: 82
0.77 0.13 0.10
Matches are distributed among these distances:
63 13 0.02
64 12 0.02
65 7 0.01
66 20 0.03
68 2 0.00
70 71 0.11
71 54 0.09
72 161 0.26
73 120 0.19
74 30 0.05
75 61 0.10
76 73 0.12
77 6 0.01
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (71 bp):
TTTTTGATATAATTATACAAGTTTAAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTA
AATTTT
Found at i:295135 original size:148 final size:145
Alignment explanation
Indices: 294420--295272 Score: 767
Period size: 148 Copynumber: 5.9 Consensus size: 145
294410 TGAAAAAGTG
* * * * *
294420 TTTTTGATATAATTATACAAGTTTAAATTTTTAAGATATAATTTATTTTTATTTTTATAAGTTTA
1 TTTTTGGTATAATTATACGAGTTTAAATTTTTAAGGTAT-ATTTATTTTTATTTATAGAAGTTTA
* ** * * ** * * * *
294485 AATTTGCTTTTTTTTTTGTTTAATTATTTAAGTTTAAATATTT-AGGTTATTATTTATTTTTATT
65 AA-TT--TATTTTTTAGGTATGATTATACAAGTTTAAATTTTTAAAGATATAATTTATTTTTATT
*
294549 TGTAGAAATTTAAATTTGT
127 TGTAGAAATTTAAATTTAT
* * * * *
294568 TTTTTAAGTATGATTATACAAGTTTAAATTTTTAATGTATAATTTATTTTTAGTTT-TA-AATTT
1 TTTTT-GGTATAATTATACGAGTTTAAATTTTTAAGGTAT-ATTTATTTTTA-TTTATAGAAGTT
* *
294631 TAAATTTA-TTTTT-GGTATGATTATACAAGTTTAAATTTTTTTAAGGTATAATTTATTTTTATT
63 TAAATTTATTTTTTAGGTATGATTATACAAGTTTAAA-TTTTTAAAGATATAATTTATTTTTATT
*
294694 TATAGAAATTTAAATTTAT
127 TGTAGAAATTTAAATTTAT
* * *
294713 TTTTTAGATATAATTATATGAGTTT-AATTTTTAAGGTATA---A--TTTATTTGTAGAAGTTTA
1 TTTTT-GGTATAATTATACGAGTTTAAATTTTTAAGGTATATTTATTTTTATTTATAGAAGTTTA
* * * * * *
294772 AA-TTATTTTTTA--TTTGATTATA-AGACTTTAAAGTTTT-AAGTTATAATTTATCTTTATTTT
65 AATTTATTTTTTAGGTATGATTATACA-AGTTTAAATTTTTAAAGATATAATTTATTTTTATTTG
*
294832 TAGAAGTTTAAATTTAT
129 TAGAAATTTAAATTTAT
* * * * *
294849 TTTTGGGTATAATTATATGATTTTAAATTTTTAAGGTATAATT-TTTTTATTTATAGCAGTTTAA
1 TTTTTGGTATAATTATACGAGTTTAAATTTTTAAGGTATATTTATTTTTATTTATAGAAGTTTAA
* * * * *
294913 GTTTATTTCTT-GAGTATGATTATACGAGTTTAAATTTTTAAA-ATATGATTTATTTTTATTTGA
66 ATTTATTTTTTAG-GTATGATTATACAAGTTTAAATTTTTAAAGATATAATTTATTTTTATTTGT
*
294976 AGAACTTTAAATTTAT
130 AGAAATTTAAATTTAT
* * * *
294992 TTTTTGGTTTGATTATACGAGTTTAAATTTTTTAAAGTATTTTTATTTTTATTTATAGAAGTTTA
1 TTTTTGGTATAATTATACGAGTTTAAA-TTTTTAAGGTATATTTATTTTTATTTATAGAAGTTTA
* * * *
295057 AATCTATTTTTTAGGTATGTTTATATACAAGTTTAAACTTTTAAAGATATGATTTATTTTTATTT
65 AATTTATTTTTTAGGTATG-AT-TATACAAGTTTAAATTTTTAAAGATATAATTTATTTTTATTT
* *
295122 GTAGAACTTTAAATTTGT
128 GTAGAAATTTAAATTTAT
** * * * * * * *
295140 TTGCTAGTTTTATTATACAAGTTTAAATTTTTTAAGGTATTTTTATTTTTATTTGTATAAGTTTA
1 TTTTTGGTATAATTATACGAGTTTAAA-TTTTTAAGGTATATTTATTTTTATTTATAGAAGTTTA
* ** * *
295205 AATTTATTTTTTAGGT-TAATTATAGGAG-TTAATATTTTTTTTAAGGTATAATTTATTTTTATT
65 AATTTATTTTTTAGGTATGATTATACAAGTTTAA-A--TTTTTAAAGATATAATTTATTTTTATT
295268 TGTAG
127 TGTAG
295273 GATTAGTTTG
Statistics
Matches: 592, Mismatches: 83, Indels: 61
0.80 0.11 0.08
Matches are distributed among these distances:
135 17 0.03
136 55 0.09
137 8 0.01
138 25 0.04
139 13 0.02
140 18 0.03
141 8 0.01
143 91 0.15
144 41 0.07
145 96 0.16
146 3 0.01
147 51 0.09
148 120 0.20
149 43 0.07
150 3 0.01
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (145 bp):
TTTTTGGTATAATTATACGAGTTTAAATTTTTAAGGTATATTTATTTTTATTTATAGAAGTTTAA
ATTTATTTTTTAGGTATGATTATACAAGTTTAAATTTTTAAAGATATAATTTATTTTTATTTGTA
GAAATTTAAATTTAT
Found at i:295183 original size:351 final size:345
Alignment explanation
Indices: 294541--295184 Score: 732
Period size: 351 Copynumber: 1.8 Consensus size: 345
294531 TTATTATTTA
* * * **
294541 TTTTTATTTGTAGAAATTTAAATTTGTTTTTTAAGTATGATTATACAAGTTTAAATTTTTAATGT
1 TTTTTATTTATAGAAATTTAAATTTATTTCTTAAGTATGATTATACAAGTTTAAATTTTTAAAAT
* *
294606 ATAATTTATTTTTAGTTTTAAATTTTAAATTTATTTTTGGTATGATTATACAAGTTTAAATTTTT
66 ATAATTTATTTTTAGTTTAAAACTTTAAATTTATTTTTGGTATGATTATACAAGTTTAAATTTTT
* * *
294671 TTAAGGTATAATTTATTTTTATTTATAGAAATTTAAATTTATTTTTTAGATATAATTATATGAGT
131 TTAAAGTATAATTTATTTTTATTTATAGAAATTTAAATCTATTTTTTAGATATAATTATATAAGT
* * * *
294736 TTAATTTTTAAGGTATAATTTATTTGTAGAAGTTTAAATTATTTTTTATTTGATTATAAGACTTT
196 TTAATTTTAAAGATATAATTTATTTGTAGAACTTTAAATTATTTTCTATTTGATTAT-A-AC--T
* ***
294801 AAAGTTTTAAGTTATAATTTATCTTTATTTTTAGAAGTTTAAATTTATTTTTGGGTATAATTATA
257 -AAGTTTTAAATTAT-ATTTATAGGTATTTTTAGAAGTTTAAATTTATTTTTGGGTATAATTATA
294866 TGATTTTAAATTTTTAAGGTATAATT
320 TGATTTTAAATTTTTAAGGTATAATT
* * * * *
294892 TTTTTATTTATAGCAGTTTAAGTTTATTTCTTGAGTATGATTATACGAGTTTAAATTTTTAAAAT
1 TTTTTATTTATAGAAATTTAAATTTATTTCTTAAGTATGATTATACAAGTTTAAATTTTTAAAAT
* * *
294957 ATGATTTATTTTTA-TTTGAAGAACTTTAAATTTATTTTTTGGTTTGATTATACGAGTTTAAA-T
66 ATAATTTATTTTTAGTTT-AA-AACTTTAAATTTA-TTTTTGGTATGATTATACAAGTTTAAATT
* * * **
295020 TTTTTAAAGTAT-TTTTATTTTTATTTATAGAAGTTTAAATCTATTTTTTAGGTATGTTTATATA
128 TTTTTAAAGTATAATTTATTTTTATTTATAGAAATTTAAATCTATTTTTTAGATATAATTATAT-
295084 CAAGTTTAAACTTTTAAAGATATGATTTATTTTTATTTGTAGAACTTTAAATT-TGTTTGCTAGT
192 -AAGTTT-AA-TTTTAAAGATAT-A---A--TTTATTTGTAGAACTTTAAATTAT-TTT-CTA-T
*
295148 TTTATTAT-AC-AAG-TTTAAATT-T-TTTA-AGGTATTTTTA
245 TTGATTATAACTAAGTTTTAAATTATATTTATAGGTATTTTTA
295185 TTTTTATTTG
Statistics
Matches: 245, Mismatches: 32, Indels: 32
0.79 0.10 0.10
Matches are distributed among these distances:
350 3 0.01
351 122 0.50
352 28 0.11
353 30 0.12
354 3 0.01
355 17 0.07
356 4 0.02
359 1 0.00
360 3 0.01
361 24 0.10
362 2 0.01
363 8 0.03
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (345 bp):
TTTTTATTTATAGAAATTTAAATTTATTTCTTAAGTATGATTATACAAGTTTAAATTTTTAAAAT
ATAATTTATTTTTAGTTTAAAACTTTAAATTTATTTTTGGTATGATTATACAAGTTTAAATTTTT
TTAAAGTATAATTTATTTTTATTTATAGAAATTTAAATCTATTTTTTAGATATAATTATATAAGT
TTAATTTTAAAGATATAATTTATTTGTAGAACTTTAAATTATTTTCTATTTGATTATAACTAAGT
TTTAAATTATATTTATAGGTATTTTTAGAAGTTTAAATTTATTTTTGGGTATAATTATATGATTT
TAAATTTTTAAGGTATAATT
Found at i:299016 original size:111 final size:111
Alignment explanation
Indices: 298875--299088 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 111
298865 GTTCTTATTG
** * ** *
298875 TTAAACCTTTTCATGAAGTTAGTTGTAATATGTCAAATACAATACACTGAATAAGCATTTGGATG
1 TTAAACCTTTTCATGAAGTTAGCAGCAATATGTCAAATACAATACACCAAATAAGCATTTGGAGG
* * *
298940 ATTTCATGCACTACCTAAGCATCTGATTACAGCTTTAATCTTGTTA
66 ATTCCATGCACTACCTAAACATCTAATTACAGCTTTAATCTTGTTA
* ** *
298986 TTAAACCTTTTCATGAAGTTAGCAGCAATATGTCGAATGTAATACACCAAATAATCATTTGGAGG
1 TTAAACCTTTTCATGAAGTTAGCAGCAATATGTCAAATACAATACACCAAATAAGCATTTGGAGG
* *
299051 ATTCCATGCACTACCTAAATATCTAATTATAGCTTTAA
66 ATTCCATGCACTACCTAAACATCTAATTACAGCTTTAA
299089 CGGATTTATG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
111 88 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (111 bp):
TTAAACCTTTTCATGAAGTTAGCAGCAATATGTCAAATACAATACACCAAATAAGCATTTGGAGG
ATTCCATGCACTACCTAAACATCTAATTACAGCTTTAATCTTGTTA
Found at i:301369 original size:11 final size:11
Alignment explanation
Indices: 301353--301378 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
301343 GAACAACTGA
301353 TTTTTTAAATT
1 TTTTTTAAATT
301364 TTTTTTAAATT
1 TTTTTTAAATT
301375 TTTT
1 TTTT
301379 AGGTTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:304803 original size:25 final size:25
Alignment explanation
Indices: 304752--304810 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
304742 TTATTAATTT
* *
304752 ATTTTGAATAAAAATATAAATTTTA
1 ATTTTTAATAAAAATATAAATTATA
*
304777 ATTTTTAATATAAATAT-AATTAATA
1 ATTTTTAATAAAAATATAAATT-ATA
304802 ATTTTTAAT
1 ATTTTTAAT
304811 TATTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTTTAATAAAAATATAAATTATA
Found at i:304859 original size:28 final size:26
Alignment explanation
Indices: 304791--304859 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 26
304781 TTAATATAAA
304791 TATAATTAATAATTTTTAATTATTATT
1 TATAATTAAT-ATTTTTAATTATTATT
304818 TA-ACATTAATATATTTTTAATT-TATATTT
1 TATA-ATT-A-ATATTTTTAATTAT-TA-TT
304847 TATAATTGAATAT
1 TATAATT-AATAT
304860 AAATATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 17 0.49
29 10 0.29
30 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (26 bp):
TATAATTAATATTTTTAATTATTATT
Found at i:304872 original size:36 final size:35
Alignment explanation
Indices: 304783--304875 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 35
304773 TTTAATTTTT
* * * *
304783 AATATAAATATAATTAATAATTTTTAATTATTATTT
1 AATATAAATATAATT-TTAATTTATAATTATAATTG
* * * *
304819 AACATTAATATATTTTTAATTTATATTTTATAATTG
1 AATATAAATATAATTTTAATTTATA-ATTATAATTG
304855 AATATAAATATAATTTTAATT
1 AATATAAATATAATTTTAATT
304876 ATTTATCATT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 8 0.18
36 37 0.82
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (35 bp):
AATATAAATATAATTTTAATTTATAATTATAATTG
Found at i:304938 original size:16 final size:15
Alignment explanation
Indices: 304906--304935 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
304896 TTTTAATCTA
304906 ATTTTTTTAATAATT
1 ATTTTTTTAATAATT
*
304921 ATTTTTTTTATAATT
1 ATTTTTTTAATAATT
304936 TATCTTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTTAATAATT
Found at i:308575 original size:62 final size:58
Alignment explanation
Indices: 308454--308585 Score: 158
Period size: 62 Copynumber: 2.2 Consensus size: 58
308444 TTTTCTTTCT
* * **
308454 CTTCACGTTGCTGCTTTTTCTAGCTGCTGCCATTGCTTTAAGTTGCTGTCTCTATTCA
1 CTTCACGTTGCTACTTTTTCTAGCTGCTACCATTGCTTTAAGTTGCTACCTCTATTCA
* *
308512 CTTCACGTTGCTACTTCTTTC-AGCTGCTTACCAATTCTGCTTTGAGTTGCTACCTCTCTTCA
1 CTTCACGTTGCTACTT-TTTCTAGCTGC-TACC-A-T-TGCTTTAAGTTGCTACCTCTATTCA
308574 CTTCACGTTGCT
1 CTTCACGTTGCT
308586 GCAGCTTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 21 0.33
59 7 0.11
60 1 0.02
61 1 0.02
62 33 0.52
ACGTcount: A:0.13, C:0.29, G:0.15, T:0.43
Consensus pattern (58 bp):
CTTCACGTTGCTACTTTTTCTAGCTGCTACCATTGCTTTAAGTTGCTACCTCTATTCA
Found at i:308622 original size:35 final size:34
Alignment explanation
Indices: 308583--308656 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
308573 ACTTCACGTT
*
308583 GCTGCAGCTTTCTTTTCTATTTTTTTCCTTTCGCA
1 GCTGCAGCTTTCTTTTCTATGTTTTT-CTTTCGCA
* * * *
308618 GCTGCTGTTTTCTTTTTTGTGTTTTTCTTTCGCA
1 GCTGCAGCTTTCTTTTCTATGTTTTTCTTTCGCA
308652 GCTGC
1 GCTGC
308657 TGTTTTGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.05, C:0.23, G:0.16, T:0.55
Consensus pattern (34 bp):
GCTGCAGCTTTCTTTTCTATGTTTTTCTTTCGCA
Found at i:308678 original size:35 final size:35
Alignment explanation
Indices: 308604--308678 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 35
308594 CTTTTCTATT
*
308604 TTTTTCCTTTCGCAGCTGCTGTTTTCTTTTTTGTG
1 TTTTTCCTTTCGCAGCTGCTGTTTTCTTTTTTGTC
* *
308639 TTTTT-CTTTCGCAGCTGCTGTTTTGTATTTTTTTC
1 TTTTTCCTTTCGCAGCTGCTGTTTTCT-TTTTTGTC
308674 TTTTT
1 TTTTT
308679 TTCGTTTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 20 0.56
35 16 0.44
ACGTcount: A:0.04, C:0.17, G:0.15, T:0.64
Consensus pattern (35 bp):
TTTTTCCTTTCGCAGCTGCTGTTTTCTTTTTTGTC
Found at i:308680 original size:37 final size:34
Alignment explanation
Indices: 308591--308681 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 34
308581 TTGCTGCAGC
* *
308591 TTTCTTTTCTATTTTTTTCCTTTCGCAGCTGCTGT
1 TTTCTTTTTTCTTTTTTT-CTTTCGCAGCTGCTGT
* *
308626 TTTCTTTTTTGTGTTTTTCTTTCGCAGCTGCTGTT
1 TTTCTTTTTTCTTTTTTTCTTTCGCAGCTGCTG-T
*
308661 TTGTATTTTTTTCTTTTTTTC
1 TT-T-CTTTTTTCTTTTTTTC
308682 GTTTTGCCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 15 0.32
35 18 0.38
36 1 0.02
37 13 0.28
ACGTcount: A:0.04, C:0.18, G:0.12, T:0.66
Consensus pattern (34 bp):
TTTCTTTTTTCTTTTTTTCTTTCGCAGCTGCTGT
Found at i:310847 original size:76 final size:75
Alignment explanation
Indices: 310721--310869 Score: 165
Period size: 76 Copynumber: 2.0 Consensus size: 75
310711 GCCAACAAAA
* * * * * * *
310721 GATAAAAAGATTTACCCGGGACTAAGCTGATAGGTACACAAGGGATGAAAGATTGATTGGGAGT-
1 GATAAAAAGATTTACCCGGGACTAAGCCGACAAGTAAACAAGAGAAGAAAG-TTGATCGGGA-TC
310785 GAATCAACAATG
64 GAATCAACAATG
** * * *
310797 GATAAAAAGATTTACTTGGGAGTAAGCCGACAAGTAAATAAGAGAAGAAAGTTGATCGTGATCGA
1 GATAAAAAGATTTACCCGGGACTAAGCCGACAAGTAAACAAGAGAAGAAAGTTGATCGGGATCGA
310862 ATCAACAA
66 ATCAACAA
310870 GTCAACAGAG
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
74 1 0.02
75 18 0.30
76 41 0.68
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (75 bp):
GATAAAAAGATTTACCCGGGACTAAGCCGACAAGTAAACAAGAGAAGAAAGTTGATCGGGATCGA
ATCAACAATG
Found at i:311247 original size:168 final size:167
Alignment explanation
Indices: 311030--311645 Score: 646
Period size: 168 Copynumber: 3.7 Consensus size: 167
311020 GTCAACAATT
* * *
311030 GATAAAAGATTTACCTGGGACTAAGCCAATAGGTAAACAAAGGATAAAGAAGTTGATCGGGATTG
1 GATAAAAGATTTACCCGGGACTAGGCCAATGGGTAAACAAAGGATAAAGAAGTTGATCGGGATTG
* * * * * *
311095 GATCGACTAGTCAATAAAAGATAAAAGAAAGTACTTGGGACCAAGCCAACAAATGAATGAAGGAT
66 GACCGACAAGTCAACAAAAGATAAAAGAAAGTACCTAGGACCAAGCCGACAAATGAATGAAGGAT
* * **
311160 AAAAAGTTAACCGAGATTAAATCGATGAGTCAATGAGG
131 AAAAAGTTGACCGGGATTAAA-CGACAAGTCAATGAGG
* * * * * *
311198 GATAAAGGATTTACCCGGGATTGGGCCAATGGGTAAACAAAAGATAAAGAAGTTGA-CTAGTATT
1 GATAAAAGATTTACCCGGGACTAGGCCAATGGGTAAACAAAGGATAAAGAAGTTGATC-GGGATT
* * * ** *
311262 AGACCCACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGACCAAGTTGACAGATGAATGAAGGA
65 GGACCGACAAGTCAACAAAAGATAAAAGAAAGTACCTAGGACCAAGCCGACAAATGAATGAAGGA
* *
311327 TAAAAAGTGGACTGGGATTAAACCGACAAGTCAATGAGG
130 TAAAAAGTTGACCGGGATTAAA-CGACAAGTCAATGAGG
* * * * * *
311366 GATAAAGGATTTAGCCGGG---A---C--TGGGT---CGAAGGGTAAACAAGTTGATTGGGATTG
1 GATAAAAGATTTACCCGGGACTAGGCCAATGGGTAAACAAAGGATAAAGAAGTTGATCGGGATTG
** * * * **
311420 GAATGACAAGTTAACAAAAGATAAAAGGAAGTACCTAGGACCAAGTCGACAGGTGAATGAAGGAT
66 GACCGACAAGTCAACAAAAGATAAAAGAAAGTACCTAGGACCAAGCCGACAAATGAATGAAGGAT
* * *
311485 AAAAAGTTGATCGGGATTAAACTGACAAGTCAACGAAG
131 AAAAAGTTGACCGGGATTAAAC-GACAAGTCAATGAGG
* * *
311523 GATAAAAGATTTACCCGGGACTAGGCTATTGGGTAAACAAAGGATAAAGAAGTTGATCGAGATTG
1 GATAAAAGATTTACCCGGGACTAGGCCAATGGGTAAACAAAGGATAAAGAAGTTGATCGGGATTG
* * * *
311588 GACCAACAAGTCAACAAAAGAGAAAATAAAGTACC-AGGGACCAAGCCGACAAGTGAAT
66 GACCGACAAGTCAACAAAAGATAAAAGAAAGTACCTA-GGACCAAGCCGACAAATGAAT
311646 AATGGATGAA
Statistics
Matches: 367, Mismatches: 66, Indels: 30
0.79 0.14 0.06
Matches are distributed among these distances:
156 1 0.00
157 126 0.34
160 6 0.02
162 1 0.00
165 5 0.01
167 2 0.01
168 226 0.62
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.18
Consensus pattern (167 bp):
GATAAAAGATTTACCCGGGACTAGGCCAATGGGTAAACAAAGGATAAAGAAGTTGATCGGGATTG
GACCGACAAGTCAACAAAAGATAAAAGAAAGTACCTAGGACCAAGCCGACAAATGAATGAAGGAT
AAAAAGTTGACCGGGATTAAACGACAAGTCAATGAGG
Found at i:311358 original size:84 final size:84
Alignment explanation
Indices: 311240--311530 Score: 218
Period size: 84 Copynumber: 3.6 Consensus size: 84
311230 GTAAACAAAA
* * * * *
311240 GATAAAGAAGTTGACTAGTATTAGACCCACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGACC
1 GATAAACAAGTTGACTGGGATTAAACCGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGACC
*
311305 AAGTTGACAGATGAATGAAG
66 AAGTCGACAG-TGAATGAAG
* ** ** *
311325 GATAAA-AAGTGGACTGGGATTAAACCGACAAGTCAATGAGGGAT-AAAGG-A-T--TTA-G-CC
1 GATAAACAAGTTGACTGGGATTAAACCGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGACC
* **
311382 --G-GGAC--TGGGTCGAAG
66 AAGTCGACAGTGAAT-GAAG
* * * * *
311397 GGTAAACAAGTTGATTGGGATTGGAA-TGACAAGTTAACAAAAGATAAAAGGAAGTACCTAGGAC
1 GATAAACAAGTTGACTGGGATT-AAACCGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGAC
311461 CAAGTCGACAGGTGAATGAAG
65 CAAGTCGACA-GTGAATGAAG
* * *
311482 GATAAA-AAGTTGA-TCGGGATTAAACTGACAAGTCAACGAAGGATAAAAG
1 GATAAACAAGTTGACT-GGGATTAAACCGACAAGTCAACAAAAGATAAAAG
311531 ATTTACCCGG
Statistics
Matches: 156, Mismatches: 32, Indels: 37
0.69 0.14 0.16
Matches are distributed among these distances:
71 3 0.02
72 9 0.06
73 26 0.17
74 10 0.06
75 2 0.01
76 1 0.01
77 2 0.01
78 3 0.02
79 3 0.02
80 2 0.01
81 1 0.01
82 2 0.01
83 11 0.07
84 63 0.40
85 15 0.10
86 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.18
Consensus pattern (84 bp):
GATAAACAAGTTGACTGGGATTAAACCGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGGACC
AAGTCGACAGTGAATGAAG
Found at i:311501 original size:157 final size:155
Alignment explanation
Indices: 311069--311562 Score: 495
Period size: 157 Copynumber: 3.1 Consensus size: 155
311059 TAGGTAAACA
* * * * * * * *
311069 AAGGATAAAGAAGTTGATCGGGATTGG-ATCGACTAGTCAATAAAAGATAAAAGAAAGTACTTGG
1 AAGGGTAAACAAGTTGATTGGGATTGGAAT-GACAAGTCAACAAAAGATAAAAGGAAGTACCTAG
* * * * * * **
311133 GACCAAGCCAACAAATGAATGAAGGATAAAAAGTTAACCGAGATTAAATCGATGAGTCAATGAGG
65 GACCAAGTCGACAGATGAATGAAGGATAAAAAGTTGA-CGGGATTAAACCGACAAGTCAATGAGG
*
311198 GATAAAGGATTTACCCGGGATTGGGCC
129 GATAAAGGATTTACCCGGGACTGGGCC
* * * ***
311225 AATGGGTAAACAAAAGATAAAGAAGTTGACTAGTATTAGACCCACAAGTCAACAAAAGATAAAAG
1 AA-GGGTAAAC--AAG-T--TG-A-TTG----GGATTGGAATGACAAGTCAACAAAAGATAAAAG
* *
311290 GAAGTACCTAGGACCAAGTTGACAGATGAATGAAGGATAAAAAGTGGACTGGGATTAAACCGACA
54 GAAGTACCTAGGACCAAGTCGACAGATGAATGAAGGATAAAAAGTTGAC-GGGATTAAACCGACA
* *
311355 AGTCAATGAGGGATAAAGGATTTAGCCGGGACTGGGTCG
118 AGTCAATGAGGGATAAAGGATTTACCCGGGACTGGG-CC
*
311394 AAGGGTAAACAAGTTGATTGGGATTGGAATGACAAGTTAACAAAAGATAAAAGGAAGTACCTAGG
1 AAGGGTAAACAAGTTGATTGGGATTGGAATGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGG
* * * *
311459 ACCAAGTCGACAGGTGAATGAAGGATAAAAAGTTGATCGGGATTAAACTGACAAGTCAACGAAGG
66 ACCAAGTCGACAGATGAATGAAGGATAAAAAGTTGA-CGGGATTAAACCGACAAGTCAATGAGGG
* * *
311524 ATAAAAGATTTACCCGGGACTAGGCT
130 ATAAAGGATTTACCCGGGACTGGGCC
*
311550 ATTGGGTAAACAA
1 A-AGGGTAAACAA
311563 AGGATAAAGA
Statistics
Matches: 276, Mismatches: 45, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
156 4 0.01
157 133 0.48
158 1 0.00
159 3 0.01
160 1 0.00
161 3 0.01
162 2 0.01
163 2 0.01
164 2 0.01
165 1 0.00
166 3 0.01
167 1 0.00
168 117 0.42
169 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (155 bp):
AAGGGTAAACAAGTTGATTGGGATTGGAATGACAAGTCAACAAAAGATAAAAGGAAGTACCTAGG
ACCAAGTCGACAGATGAATGAAGGATAAAAAGTTGACGGGATTAAACCGACAAGTCAATGAGGGA
TAAAGGATTTACCCGGGACTGGGCC
Found at i:311807 original size:43 final size:42
Alignment explanation
Indices: 311759--311849 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
311749 CCCGGGACTG
*
311759 AGCCGATGGCCAAATAAAGAGAT-AAAGAAGTCTCCTGGGTCTA
1 AGCCGATGGCCAAACAAA-AGATGAAA-AAGTCTCCTGGGTCTA
** * * *
311802 AGCCGATGGGTAGACGAAAGATGAAAAAGTCTTCTGGGTCTA
1 AGCCGATGGCCAAACAAAAGATGAAAAAGTCTCCTGGGTCTA
311844 AGCCGA
1 AGCCGA
311850 CGGGCAGATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 25 0.61
43 16 0.39
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.19
Consensus pattern (42 bp):
AGCCGATGGCCAAACAAAAGATGAAAAAGTCTCCTGGGTCTA
Found at i:311867 original size:42 final size:42
Alignment explanation
Indices: 311786--312447 Score: 239
Period size: 42 Copynumber: 15.7 Consensus size: 42
311776 AGAGATAAAG
* * * * ***
311786 AAGTCTCCTGGGTCTAAGCCGATGGGTAGACGAAAGATGAAA
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
311828 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* ** * * * * *
311870 AAGTC-TCTCGAGTCTAAGTTGACAGACAGACGGTTGATAAAA
1 AAGTCTTCT-GGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* ** * * * * ** *
311912 GAAGTCTCCCAGGTCTAAACCGATGGGAAAACAGTGGATGAAG
1 -AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* * * * *** *
311955 AAGTCTCCTAGGT-TAAAGTCGATGGGCAGATAAAGGGT-AAA
1 AAGTCTTCTGGGTCT-AAGCCGACGGGCAGATGGTGGATGAAA
*** * * * *
311996 GAAGT-TTCCCAAGTCTAAACCGATGGGCAGACGGTTGAT-AAA
1 -AAGTCTT-CTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* ** *** *
312038 GAAGTC-TCTCGAGTCTAAGCCGATAGGCAGATGAAAGATGAAG
1 -AAGTCTTCT-GGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* * * * * ** *
312081 AAGT-TTACCGAGTCTAAGCCAAAGGGTAGACAGTGGATGAAG
1 AAGTCTT-CTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
** * * * *
312123 AAGTC-TCTCAAGTCTAAGCCGAAGGGCAGATAGTAGATGAAG
1 AAGTCTTCT-GGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* *
312165 AAGTCTCCCGGGTCTAAGCCGACGGGCAGATGGTGGAT-AAA
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* *** * * * ***
312206 GAAGTCTCCCAAGTCTAAGCCAACAGGTAGATGAAAGATGAAA
1 -AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
*** *
312249 AAGT-TTCCTGGGTCTAAGCCGACGGGCAGATGAAAGATGAAG
1 AAGTCTT-CTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* *** * * * *
312291 AAGTCTCCCAAGTCTAAGCCGATGGGCATACGGTGGATGAAG
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* * * * * * * *
312333 AAGTCTCCAGGGTTTAAGCTGACGGGCACATGGTTGTTAAAGA
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAA-A
* * * *
312376 AAGTCTTCCGGGTCTAAGTCGACGAGCAGATGGTGGATGAAG
1 AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
* *
312418 AAGTC-TCTTGGGTCAAAGCCGATGGGCAGA
1 AAGTCTTC-TGGGTCTAAGCCGACGGGCAGA
312448 CAAAGGGTAA
Statistics
Matches: 460, Mismatches: 139, Indels: 42
0.72 0.22 0.07
Matches are distributed among these distances:
41 14 0.03
42 381 0.83
43 64 0.14
44 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (42 bp):
AAGTCTTCTGGGTCTAAGCCGACGGGCAGATGGTGGATGAAA
Found at i:312246 original size:126 final size:124
Alignment explanation
Indices: 311994--312340 Score: 356
Period size: 126 Copynumber: 2.8 Consensus size: 124
311984 ATAAAGGGTA
* * * * * *
311994 AAGAAGTTTCCCAAGTCTAAACCGATGGGCAGACGGTTGATAAAGAAGTCTCTCGAGTCTAAGCC
1 AAGAAGTTT-CCAAGTCTAAGCCGAAGGGCAGA-TGTAGATGAAGAAGTCTCCCGAGTCTAAGCC
* *** * * * **
312059 GATAGGCAGATGAAAGATGAAGAAGTTTACCGAGTCTAAGCCAAAGGGTAGACAGTGGATG
64 GATGGGCAGATGGTGGATGAAGAAGTCTCCCAAGTCTAAGCCAAAGGGTAGACAGAAGATG
* *
312120 AAGAAGTCTCTCAAGTCTAAGCCGAAGGGCAGATAGTAGATGAAGAAGTCTCCCGGGTCTAAGCC
1 AAGAAGTTTC-CAAGTCTAAGCCGAAGGGCAGAT-GTAGATGAAGAAGTCTCCCGAGTCTAAGCC
* * *
312185 GACGGGCAGATGGTGGATAAAGAAGTCTCCCAAGTCTAAGCCAACA-GGTAGA-TGAAAGATG
64 GATGGGCAGATGGTGGATGAAGAAGTCTCCCAAGTCTAAGCCAA-AGGGTAGACAG-AAGATG
* ** * * *
312246 AAAAAGTTTCCTGGGTCTAAGCCGACGGGCAGATGAAAGATGAAGAAGTCTCCCAAGTCTAAGCC
1 AAGAAGTTTCC-AAGTCTAAGCCGAAGGGCAGATG-TAGATGAAGAAGTCTCCCGAGTCTAAGCC
* *
312311 GATGGGCATACGGTGGATGAAGAAGTCTCC
64 GATGGGCAGATGGTGGATGAAGAAGTCTCC
312341 AGGGTTTAAG
Statistics
Matches: 183, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
125 4 0.02
126 178 0.97
127 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (124 bp):
AAGAAGTTTCCAAGTCTAAGCCGAAGGGCAGATGTAGATGAAGAAGTCTCCCGAGTCTAAGCCGA
TGGGCAGATGGTGGATGAAGAAGTCTCCCAAGTCTAAGCCAAAGGGTAGACAGAAGATG
Found at i:312376 original size:84 final size:84
Alignment explanation
Indices: 311778--312447 Score: 389
Period size: 84 Copynumber: 8.0 Consensus size: 84
311768 CCAAATAAAG
*** * * * ** * * *
311778 AGATAAAGAAGTCTCCTGGGTCTAAGCCGATGGGTAGACGAAAGATGAAAAAGTCTTCTGGGTCT
1 AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTCT
311843 AAGCCGACGGGCAGATGGT
66 AAGCCGACGGGCAGATGGT
* * * ** * * * * *
311862 GGATGAAA-AAGTCTCTCGAGTCTAAGTTGACAGACAGACGGTTGATAAAAGAAGTCTCCCA-GG
1 AGAT-AAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGAT-GAAGAAGTCT-CCAGGG
* * * * **
311925 TCTAAACCGATGGGAAAACAGT
63 TCTAAGCCGACGGGCAGATGGT
* * * * * * ** * * * *
311947 GGATGAAGAAGTCTCCTAGGT-TAAAGTCGATGGGCAGAT-AAAGGGTAAAGAAGTTTCCCA-AG
1 AGATAAAGAAGTCTCCCAAGTCT-AAGCCGACGGGCAGATGGTA-GATGAAGAAGTCT-CCAGGG
* * *
312009 TCTAAACCGATGGGCAGACGGT
63 TCTAAGCCGACGGGCAGATGGT
* * * ** ** * *
312031 TGATAAAGAAGTCTCTCGAGTCTAAGCCGATAGGCAGATGAAAGATGAAGAAGTTTACC-GAGTC
1 AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCT-CCAGGGTC
* * * **
312095 TAAGCCAAAGGGTAGACAGT
65 TAAGCCGACGGGCAGATGGT
* * * * * *
312115 GGATGAAGAAGTCTCTCAAGTCTAAGCCGAAGGGCAGATAGTAGATGAAGAAGTCTCCCGGGTCT
1 AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTCT
312180 AAGCCGACGGGCAGATGGT
66 AAGCCGACGGGCAGATGGT
* * * * ** * * *
312199 GGATAAAGAAGTCTCCCAAGTCTAAGCCAACAGGTAGATGAAAGATGAAAAAGTTTCCTGGGTCT
1 AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTCT
**
312264 AAGCCGACGGGCAGATGAA
66 AAGCCGACGGGCAGATGGT
* * * * * *
312283 AGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCATACGGTGGATGAAGAAGTCTCCAGGGTTT
1 AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTCT
* *
312348 AAGCTGACGGGCACATGGT
66 AAGCCGACGGGCAGATGGT
* * * ** * * * **
312367 TGTTAAAGAAAGTCTTCCGGGTCTAAGTCGACGAGCAGATGGTGGATGAAGAAGTCTCTTGGGTC
1 AGATAAAG-AAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTC
* *
312432 AAAGCCGATGGGCAGA
65 TAAGCCGACGGGCAGA
312448 CAAAGGGTAA
Statistics
Matches: 451, Mismatches: 124, Indels: 21
0.76 0.21 0.04
Matches are distributed among these distances:
83 2 0.00
84 332 0.74
85 116 0.26
86 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (84 bp):
AGATAAAGAAGTCTCCCAAGTCTAAGCCGACGGGCAGATGGTAGATGAAGAAGTCTCCAGGGTCT
AAGCCGACGGGCAGATGGT
Found at i:312501 original size:85 final size:85
Alignment explanation
Indices: 312412--312618 Score: 236
Period size: 85 Copynumber: 2.4 Consensus size: 85
312402 CAGATGGTGG
*
312412 ATGAAGAAGTCTCTTGGGTCAAAGCCGATGGGCAGACAAAGGGTAAAAAAGTCTCCCGCGTCTGA
1 ATGAAGAAGTCTCTTGGGTCAAAGCCGATGGGCAGACAAAAGGTAAAAAAGTCTCCCGCGTCTGA
* *
312477 GCCAATGGGTAGACTTAAGA
66 GCCAACGGGCAGACTTAAGA
** * * * * *
312497 ATGAAGAAGTCTAC-TAAGTCAAAGTCGATGAGAAGACAAAAGGTAAAGAAGTCTCCCGGGTCTG
1 ATGAAGAAGTCT-CTTGGGTCAAAGCCGATGGGCAGACAAAAGGTAAAAAAGTCTCCCGCGTCTG
* * *
312561 AGCCGACGGGCATACTTAAGG
65 AGCCAACGGGCAGACTTAAGA
* * * **
312582 GTGAAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGAC
1 ATGAAGAAGTCTCTTGGGTCAAAGCCGATGGGCAGAC
312619 TTAAGTGTGA
Statistics
Matches: 97, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
84 1 0.01
85 95 0.98
86 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.18
Consensus pattern (85 bp):
ATGAAGAAGTCTCTTGGGTCAAAGCCGATGGGCAGACAAAAGGTAAAAAAGTCTCCCGCGTCTGA
GCCAACGGGCAGACTTAAGA
Found at i:312608 original size:43 final size:43
Alignment explanation
Indices: 312542--312675 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 43
312532 ACAAAAGGTA
* * * *
312542 AAGAAGTCTCCCGGGTCTGAGCCGACGGGCATACTTAAGGGTG
1 AAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGACTTAAGGGTG
*
312585 AAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGACTTAAGTGTG
1 AAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGACTTAAGGGTG
* * * * * * * **
312628 AGGAAGTTTTTCGGATCAAAGCCGACAAGTAGACTTAAAAGTG
1 AAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGACTTAAGGGTG
312671 AAGAA
1 AAGAA
312676 AGTTTGACCA
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (43 bp):
AAGAAGTCTCTCGGGTCTAAGCCGACAGGCAGACTTAAGGGTG
Found at i:312789 original size:48 final size:48
Alignment explanation
Indices: 312752--313161 Score: 437
Period size: 48 Copynumber: 8.6 Consensus size: 48
312742 GCTAATATAA
* *
312752 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAATACCAATACAA
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* * *
312800 TCAAACAAGGGATGAAAAGAGTTTGATTAGGCCCTAACACCAATACAA
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* *** *
312848 TCAAACGAGGGAAGATTTGAGTTTGACTAGGCCCTAACACCAATGCAG
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* * * *
312896 TTAAACAAGGGATGAAAAAAGTTTGACTAGGCCCTAACATCAATACAG
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* *** * **
312944 TCAAACGAGGGAAGATTTGAGTTTGACCAGGCCCTAATGCCAATACAG
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* *** *
312992 TCAAATGAGGGAAT-ATTTGAGTTTGACTAGGCCCTAACACTAATACAG
1 TCAAACGAGGG-ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* * *
313040 TCAAACGAGAGAAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAG
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* * *** * **
313088 TCAAATGAGGGAAGATTTGAGTTTGACTAGGTCCTAACGTCAATACAG
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
* **
313136 TCAAACAAATG-TGAAAAGAGTTTGAC
1 TCAAACGAGGGATGAAAAGAGTTTGAC
313162 CAGATACAGT
Statistics
Matches: 298, Mismatches: 62, Indels: 5
0.82 0.17 0.01
Matches are distributed among these distances:
47 12 0.04
48 285 0.96
49 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (48 bp):
TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAG
Found at i:312940 original size:144 final size:144
Alignment explanation
Indices: 312752--313141 Score: 483
Period size: 144 Copynumber: 2.7 Consensus size: 144
312742 GCTAATATAA
* * *
312752 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAATACCAATACAATCAAACAAGGGATGAAA
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACAAGGGAAGAAA
**
312817 AGAGTTTGATTAGGCCCTAACACCAATACAATCAAACGAGGGAAGATTTGAGTTTGACTAGGCCC
66 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAACGAGGGAAGATTTGAGTTTGACTAGGCCC
*
312882 TAACACCAATGCAG
131 TAACACCAATACAG
* * * * * **
312896 TTAAACAAGGGATGAAAAAAGTTTGACTAGGCCCTAACATCAATACAGTCAAACGAGGGAAGATT
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACAAGGGAAGAAA
* ** * * *
312961 TGAGTTTGACCAGGCCCTAATGCCAATACAGTCAAATGAGGGAATATTTGAGTTTGACTAGGCCC
66 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAACGAGGGAAGATTTGAGTTTGACTAGGCCC
*
313026 TAACACTAATACAG
131 TAACACCAATACAG
* * * ** **
313040 TCAAACGAGAGAAGAAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGAAGATT
1 TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACAAGGGAAGAAA
* * * ** *
313105 TGAGTTTGACTAGGTCCTAACGTCAATACAGTCAAAC
66 AGAGTTTGACCAGGCCCTAACACCAATACAATCAAAC
313142 AAATGTGAAA
Statistics
Matches: 213, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
144 213 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (144 bp):
TCAAACGAGGGATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACAAGGGAAGAAA
AGAGTTTGACCAGGCCCTAACACCAATACAATCAAACGAGGGAAGATTTGAGTTTGACTAGGCCC
TAACACCAATACAG
Found at i:313416 original size:22 final size:22
Alignment explanation
Indices: 313388--313433 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
313378 TAGATAAAAA
* *
313388 GGATATGATTGGGGAATGTGTG
1 GGATATGATTGGGAAATATGTG
313410 GGATATGATTGGGAAATATGTG
1 GGATATGATTGGGAAATATGTG
313432 GG
1 GG
313434 CTACAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.30
Consensus pattern (22 bp):
GGATATGATTGGGAAATATGTG
Found at i:313614 original size:91 final size:88
Alignment explanation
Indices: 313409--313663 Score: 269
Period size: 91 Copynumber: 2.8 Consensus size: 88
313399 GGGAATGTGT
* * *
313409 GGGATATGATTGGGAAATATGTGGGCTACAACTTGCCCGTAAGAAAATCAGGCTTTGTGATGCAT
1 GGGATATGATTGGG--ATATGTGGGCTACACCTTGCCC-CAAGGAAATCAGGCTTTGTGATGCAT
* ** * *
313474 CACTTACCATCTAGTGGTTAGATGAAG
63 CA-ATACCATCTAACGGTTAAAAGAAG
* * * *
313501 GAGATATAATTAGGGATATGTGGGCTGCACCTTGCCCCAAAGGAAATCAGGCTTTATGATGCATC
1 GGGATATGATT-GGGATATGTGGGCTACACCTTGCCCC-AAGGAAATCAGGCTTTGTGATGCATC
313566 AATACCATCTAACGGTTGAAAA-AGAG
64 AATACCATCTAACGGTT-AAAAGA-AG
* * * * *
313592 GGGATACGATTGGGAGTGTGTGGGCTACACCTTGCCCCATGGAAATTAGACTTTGTGATGCATCA
1 GGGATATGATTGGGA-TATGTGGGCTACACCTTGCCCCAAGGAAATCAGGCTTTGTGATGCATCA
313657 ATACCAT
65 ATACCAT
313664 TTAGGGGTTA
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
90 48 0.35
91 77 0.56
92 9 0.07
93 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (88 bp):
GGGATATGATTGGGATATGTGGGCTACACCTTGCCCCAAGGAAATCAGGCTTTGTGATGCATCAA
TACCATCTAACGGTTAAAAGAAG
Found at i:315432 original size:20 final size:20
Alignment explanation
Indices: 315409--315469 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
315399 TATTTCCTCA
315409 TCTTTTTTTTTTCATTTTTC
1 TCTTTTTTTTTTCATTTTTC
* *
315429 TC-TTTTTTTTGCACTTTTTT
1 TCTTTTTTTTTTCA-TTTTTC
315449 TCATTTATTTTTTTCATTTTT
1 TC-TTT-TTTTTTTCATTTTT
315470 TATTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.29
20 9 0.26
22 7 0.21
23 8 0.24
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.77
Consensus pattern (20 bp):
TCTTTTTTTTTTCATTTTTC
Found at i:315459 original size:13 final size:13
Alignment explanation
Indices: 315443--315467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315433 TTTTTTGCAC
315443 TTTTTTTCATTTA
1 TTTTTTTCATTTA
315456 TTTTTTTCATTT
1 TTTTTTTCATTT
315468 TTTATTTATT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTCATTTA
Found at i:315460 original size:42 final size:39
Alignment explanation
Indices: 315414--315494 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 39
315404 CCTCATCTTT
*
315414 TTTTTTTCATTTTTCTCTTT-TTTTTGCACTTTTTTTCATTTA
1 TTTTTTTCATTTTT-TATTTATTTTTG--CTTTTTTT-ATTTA
315456 TTTTTTTCATTTTTTATTTATTTTTGCTTTTTTTATTTA
1 TTTTTTTCATTTTTTATTTATTTTTGCTTTTTTTATTTA
315495 GAAGAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 5 0.14
40 8 0.22
41 4 0.11
42 20 0.54
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (39 bp):
TTTTTTTCATTTTTTATTTATTTTTGCTTTTTTTATTTA
Found at i:315474 original size:20 final size:20
Alignment explanation
Indices: 315433--315494 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
315423 TTTTTCTCTT
315433 TTTTTTGCACTTTTTTTCATTTA
1 TTTTTTGCA--TTTTTT-ATTTA
*
315456 TTTTTTTCATTTTTTATTTA
1 TTTTTTGCATTTTTTATTTA
*
315476 -TTTTTGCTTTTTTTATTTA
1 TTTTTTGCATTTTTTATTTA
315495 GAAGAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.47
20 5 0.14
21 6 0.17
23 8 0.22
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTGCATTTTTTATTTA
Found at i:316341 original size:23 final size:23
Alignment explanation
Indices: 316315--316358 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
316305 TGAGGAACCA
316315 TTCAAATGATCATGATTTATGCG
1 TTCAAATGATCATGATTTATGCG
316338 TTCAAATGATCATGATTTATG
1 TTCAAATGATCATGATTTATG
316359 ATAATAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (23 bp):
TTCAAATGATCATGATTTATGCG
Found at i:320911 original size:4 final size:4
Alignment explanation
Indices: 320902--320939 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
320892 AATAATAATG
320902 AAAT AAAT AAAT AAAT AAAT -AAT AAAT -AAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
320940 TGAGTTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:320922 original size:30 final size:30
Alignment explanation
Indices: 320883--320939 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
320873 GTACCACACG
320883 TAAAAAAATAAT-AATAATGAAATAAATAAA
1 TAAAAAAATAATAAATAAT-AAATAAATAAA
*
320913 TAAATAAATAATAAATAATAAATAAAT
1 TAAAAAAATAATAAATAATAAATAAAT
320940 TGAGTTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (30 bp):
TAAAAAAATAATAAATAATAAATAAATAAA
Found at i:320927 original size:7 final size:7
Alignment explanation
Indices: 320888--320937 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
320878 ACACGTAAAA
320888 AAATAAT
1 AAATAAT
320895 -AATAAT
1 AAATAAT
320901 GAAATAAAT
1 -AAAT-AAT
320910 AAATAAAT
1 AAAT-AAT
320918 AAATAAT
1 AAATAAT
320925 AAATAAT
1 AAATAAT
320932 AAATAA
1 AAATAA
320938 ATTGAGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.15
7 16 0.40
8 15 0.38
9 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:321777 original size:20 final size:21
Alignment explanation
Indices: 321752--321790 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
321742 TGACATGACT
*
321752 TTATTTTTA-AAATAAAAAAA
1 TTATTTTAATAAATAAAAAAA
321772 TTATTTTAATAAATAAAAA
1 TTATTTTAATAAATAAAAA
321791 TCAAATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATTTTAATAAATAAAAAAA
Found at i:321895 original size:22 final size:23
Alignment explanation
Indices: 321847--321897 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
321837 AATTTTAAAG
*
321847 TATATGCACATATAATCATTTTGC
1 TATATGCACATATAAT-ATTTTAC
*
321871 TATATGCACATATTAT-TTTTAC
1 TATATGCACATATAATATTTTAC
321893 TATAT
1 TATAT
321898 TTGTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
24 15 0.60
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (23 bp):
TATATGCACATATAATATTTTAC
Found at i:322994 original size:16 final size:16
Alignment explanation
Indices: 322959--323019 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
322949 TTTGATCCCA
322959 TTAATCATTTAAAAATT
1 TTAAT-ATTTAAAAATT
322976 TT-ATATTTAAAATATT
1 TTAATATTTAAAA-ATT
*
322992 TTAATA-TTAATAA-T
1 TTAATATTTAAAAATT
*
323006 TT-ATTTTTAAAAAT
1 TTAATATTTAAAAAT
323020 AAATTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 9 0.24
16 12 0.32
17 5 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATTTAAAAATT
Found at i:323596 original size:73 final size:74
Alignment explanation
Indices: 323442--323745 Score: 278
Period size: 73 Copynumber: 4.2 Consensus size: 74
323432 ATTAAGATCA
* * * * *
323442 ATTTATTTTTATTTATAAAAGTTTAAATATA-TTTTTT-GTTTCATTATACGAGTTTAAA-CTTT
1 ATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTTTGATTATACAAGTTTAAATTTTT
*
323504 TAAGATATT
66 TAAGATATG
* * *
323513 ATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTATAATTATATAAGTTTAAA-TTTT
1 ATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTTTGATTATACAAGTTTAAATTTTT
*
323577 TAAGATGTG
66 TAAGATATG
* * * * * *
323586 ATTTTATTTTAATTTGTAGAAGTATAAA--TATGTTTTCTAGTTTGATTATACGAGTTTAAAATT
1 A-TTTATTTTTATTTGTAAAAGTTTAAATTTAT-TTTTTTGGTTTGATTATACAAGTTT-AAATT
323649 TTTTAA-ACTATG
63 TTTTAAGA-TATG
* * *
323661 A-TTA----TATTTGTAGAAGTTTAAATTTATTTTTTAGG-TTGATTATA-AGAGTTAAAATTTT
1 ATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTTTGATTATACA-AGTTTAAATTTT
*
323719 TTAAGGTAT-
65 TTAAGATATG
323728 ATTTATTTTTATTTGTAA
1 ATTTATTTTTATTTGTAA
323746 GATTAGTTTG
Statistics
Matches: 189, Mismatches: 28, Indels: 31
0.76 0.11 0.12
Matches are distributed among these distances:
67 1 0.01
68 17 0.09
69 29 0.15
70 5 0.03
71 32 0.17
72 17 0.09
73 50 0.26
74 27 0.14
75 11 0.06
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (74 bp):
ATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTTTGATTATACAAGTTTAAATTTTT
TAAGATATG
Found at i:323672 original size:143 final size:143
Alignment explanation
Indices: 323442--323745 Score: 352
Period size: 143 Copynumber: 2.1 Consensus size: 143
323432 ATTAAGATCA
* * *
323442 ATTTATTTTTATTTATAAAAGTTTAAATATATTTTTTGTTTCATTATACGAGTTTAAACTTTTAA
1 ATTTATTTTTATTTGTAAAAGTATAAATATATTTTTAGTTTCATTATACGAGTTTAAACTTTTAA
* * * * *
323507 GATATTATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTTGGTATAATTATATA-AGTTTA
66 GATACTATTGATTTATATTTGTAAAAGTTTAAATTTATTTTTTAGGT-TAATTATA-AGAGTTAA
323571 AA-TTTTTAAGATGTGAT
129 AATTTTTTAAG--GT-AT
* * * * *
323588 -TTTATTTTAATTTGTAGAAGTATAAATATGTTTTCTAGTTTGATTATACGAGTTTAAAATTTTT
1 ATTTATTTTTATTTGTAAAAGTATAAATATATTTT-TAGTTTCATTATACGAGTTT-AAACTTTT
* * *
323652 TA-A-ACTA-TGA-TTATATTTGTAGAAGTTTAAATTTATTTTTTAGGTTGATTATAAGAGTTAA
64 AAGATACTATTGATTTATATTTGTAAAAGTTTAAATTTATTTTTTAGGTTAATTATAAGAGTTAA
323713 AATTTTTTAAGGTAT
129 AATTTTTTAAGGTAT
323728 ATTTATTTTTATTTGTAA
1 ATTTATTTTTATTTGTAA
323746 GATTAGTTTG
Statistics
Matches: 135, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
140 2 0.01
141 18 0.13
142 14 0.10
143 40 0.30
144 2 0.01
145 32 0.24
146 19 0.14
147 8 0.06
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (143 bp):
ATTTATTTTTATTTGTAAAAGTATAAATATATTTTTAGTTTCATTATACGAGTTTAAACTTTTAA
GATACTATTGATTTATATTTGTAAAAGTTTAAATTTATTTTTTAGGTTAATTATAAGAGTTAAAA
TTTTTTAAGGTAT
Found at i:326049 original size:20 final size:21
Alignment explanation
Indices: 326007--326060 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
325997 TTCTATAATT
* *
326007 TGTATTAATACATCAAGTTAA
1 TGTATCAATACATCAAGTGAA
326028 TGTATCAATACAT-AAGTGAA
1 TGTATCAATACATCAAGTGAA
*
326048 TGTATCGATACAT
1 TGTATCAATACAT
326061 GCAATGTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCAATACATCAAGTGAA
Found at i:329709 original size:27 final size:26
Alignment explanation
Indices: 329679--329737 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
329669 TTTTTTCAAT
* * *
329679 AATAATGTAAAAAAATATATTTTGAGA
1 AATAATGT-AAAAAACATAGTTTAAGA
*
329706 AATATTTGTAAAAAACATAGTTTAAGA
1 AATA-ATGTAAAAAACATAGTTTAAGA
329733 AATAA
1 AATAA
329738 AAAAATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (26 bp):
AATAATGTAAAAAACATAGTTTAAGA
Found at i:334913 original size:51 final size:51
Alignment explanation
Indices: 334753--334923 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
334743 GAAATAACGA
* * *
334753 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
334805 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
334858 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
334909 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
334924 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:334969 original size:27 final size:28
Alignment explanation
Indices: 334906--334981 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
334896 AAAATAAAGT
*
334906 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
334934 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
334961 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
334982 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Done.