Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 2 of 276
Found at i:266535 original size:27 final size:27
Alignment explanation
Indices: 266505--266778 Score: 234
Period size: 27 Copynumber: 9.9 Consensus size: 27
266495 CAAAATTACC
*
266505 GAAATACCCTTGTAGGGTAGAAATGCT
1 GAAATACCCTTGTAGGGTAGAAATACT
* *
266532 GAAATACCTTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAAATACT
* * *
266559 AAAATTCCCCTGTAGGGTAGAAATACTGAAAT
1 GAAATACCCTTGTAGGGTAGAAATAC-----T
266591 ACCGAAATACCCTTGTAGGGTAGAAATA-T
1 ---GAAATACCCTTGTAGGGTAGAAATACT
* * *
266620 CGAAATACCCCTATAGGGTAGAATTACT
1 -GAAATACCCTTGTAGGGTAGAAATACT
* * * *
266648 AAAATACCCCTGTAGGGTAGAATTATT
1 GAAATACCCTTGTAGGGTAGAAATACT
266675 GAAATACCCTTGTAGGGTAGAAATACCT
1 GAAATACCCTTGTAGGGTAGAAATA-CT
* *
266703 -AAATGCCCTTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAAATACT
* *
266729 GAAATACTCC-TGTAAGGTAGAATTA-T
1 GAAATAC-CCTTGTAGGGTAGAAATACT
* *
266755 CAAGATACCCTTGTGGGGTA-AAAT
1 GAA-ATACCCTTGTAGGGTAGAAAT
266779 GGTAGGTGTT
Statistics
Matches: 204, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
26 10 0.05
27 167 0.82
28 4 0.02
29 1 0.00
35 22 0.11
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAAATACT
Found at i:266601 original size:62 final size:62
Alignment explanation
Indices: 266532--266655 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 62
266522 TAGAAATGCT
* * * *
266532 GAAATACCTTTGTAGGGTAGAAATACCAAAATTCCCCTGTAGGGTAGAAATACTGAAATACC
1 GAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATAGGGTAGAAATACTAAAATACC
* * *
266594 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTATAGGGTAGAATTACTAAAATACC
1 GAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATAGGGTAGAAATACTAAAATACC
266656 CCTGTAGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (62 bp):
GAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATAGGGTAGAAATACTAAAATACC
Found at i:266608 original size:35 final size:35
Alignment explanation
Indices: 266551--266628 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
266541 TTGTAGGGTA
*
266551 GAAATACCAAAATTCCCCTGTAGGGTAGAAATA-C
1 GAAATACCAAAATACCCCTGTAGGGTAGAAATATC
* *
266585 TGAAATACCGAAATACCCTTGTAGGGTAGAAATATC
1 -GAAATACCAAAATACCCCTGTAGGGTAGAAATATC
266621 GAAATACC
1 GAAATACC
266629 CCTATAGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (35 bp):
GAAATACCAAAATACCCCTGTAGGGTAGAAATATC
Found at i:266652 original size:89 final size:84
Alignment explanation
Indices: 266501--266778 Score: 302
Period size: 81 Copynumber: 3.3 Consensus size: 84
266491 TTTACAAAAT
* * * * * *
266501 TACCGAAATACCCTTGTAGGGTAGAAATGCTGAAATACCTTTGTAGGGTAGAAATACCAAAATTC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACTAAAATAC
266566 CCCTGTAGGGTAGAAATACTGAAA
66 CCCTGTAGGGTAGAAAT--T---A
* * *
266590 TACCGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTATAGGGTAGAATTACTAAAATAC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACTAAAATAC
266655 CCCTGTAGGGTAG-AATTA
66 CCCTGTAGGGTAGAAATTA
* * * *
266673 T--TGAAATACCCTTGTAGGGTAGAAATACCTAAATGCCCTTGTAGGGTAGAATTACTGAAATAC
1 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACTAAAATAC
* *
266736 TCCTGTAAGGTAG-AATTA
66 CCCTGTAGGGTAGAAATTA
*
266754 T--C-AAGATACCCTTGTGGGGTA-AAAT
1 TACCGAA-ATACCCTTGTAGGGTAGAAAT
266779 GGTAGGTGTT
Statistics
Matches: 168, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
80 6 0.04
81 87 0.52
83 2 0.01
86 1 0.01
88 3 0.02
89 69 0.41
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (84 bp):
TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACTAAAATAC
CCCTGTAGGGTAGAAATTA
Found at i:267059 original size:27 final size:26
Alignment explanation
Indices: 267015--267066 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
267005 CTCGCTGCAA
*
267015 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
267042 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
267067 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:267188 original size:98 final size:98
Alignment explanation
Indices: 267019--267567 Score: 1073
Period size: 98 Copynumber: 5.6 Consensus size: 98
267009 CTGCAATCTG
*
267019 GTGGCCTCGCCACATATATCTGT-TCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAAT
1 GTGGCCTAGCCACA-ATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAAT
267083 CTGGTGGCTTCGCCACATATATATATCTGTTCTA
65 CTGGTGGCTTCGCCACATATATATATCTGTTCTA
267117 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
267182 TGGTGGCTTCGCCACATATATATATCTGTTCTA
66 TGGTGGCTTCGCCACATATATATATCTGTTCTA
267215 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
267280 TGGTGGCTTCGCCACATATATATATCTGTTCTA
66 TGGTGGCTTCGCCACATATATATATCTGTTCTA
267313 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
267378 TGGTGGCTTCGCCACATATATATATCTGTTCTA
66 TGGTGGCTTCGCCACATATATATATCTGTTCTA
267411 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
267476 TGGTGGCTTCGCCACATATATATATCTGTTCTA
66 TGGTGGCTTCGCCACATATATATATCTGTTCTA
267509 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCT
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCT
267568 CTAAATTCTG
Statistics
Matches: 449, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
97 8 0.02
98 441 0.98
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (98 bp):
GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGCAATC
TGGTGGCTTCGCCACATATATATATCTGTTCTA
Found at i:267706 original size:25 final size:25
Alignment explanation
Indices: 267678--267735 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
267668 CATTCACATT
* *
267678 CTGATTCTGATTTTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
267703 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
267728 CTGATTCT
1 CTGATTCT
267736 TGCTCTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:268086 original size:37 final size:37
Alignment explanation
Indices: 267703--268068 Score: 662
Period size: 37 Copynumber: 9.9 Consensus size: 37
267693 TTACCTGATA
267703 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267740 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267777 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267814 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267851 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267888 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267925 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
267962 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
*
267999 CTGATTCTGATTCTGTTACCTAATTCTGATTC-TGATT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCTTG-CT
* * * * *
268036 TTGATTTTGATTCTGTCACCTGATTCTAATTCT
1 CTGATTCTGATTCTGTTACCTAATTCTGATTCT
268069 GATTCTAATT
Statistics
Matches: 321, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
36 2 0.01
37 319 0.99
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTCTGTTACCTAATTCTGATTCTTGCT
Found at i:276604 original size:43 final size:43
Alignment explanation
Indices: 276484--276654 Score: 152
Period size: 43 Copynumber: 4.0 Consensus size: 43
276474 AGCTCATACA
* **
276484 ATGCCAACGTCCCAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGATATGGTCTTACACATAAATCAAATAT-G
** * *
276527 ATGCCATTGTCCCAAATA-GAGTCTTACAC-GAAATCAAATATG
1 ATGCCAACGTCCCAGATATG-GTCTTACACATAAATCAAATATG
* * **
276569 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCATAAGCTG
1 ATGCCAACGTCCCAGATATGGTCTTACACATAAATCA-AATATG
* ** *
276613 ATGCCAACGTCCCAGATGTTTTCTTACACA-AAATCACATATG
1 ATGCCAACGTCCCAGATATGGTCTTACACATAAATCAAATATG
276655 GAAATCCTAT
Statistics
Matches: 103, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
42 29 0.28
43 45 0.44
44 29 0.28
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATATGGTCTTACACATAAATCAAATATG
Found at i:280224 original size:46 final size:46
Alignment explanation
Indices: 280117--280370 Score: 243
Period size: 46 Copynumber: 5.5 Consensus size: 46
280107 ATGGCAATGC
* * *
280117 CATGTCCCAGACATGTCTTACACTAGC--ACATGTC-ATAGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGA-AGCCGATG
*
280161 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAATCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAAGCCGATG
* * ** *
280207 CATGTCCCAGACATGTCTTAAACTGGCTTACATCTCGAGGGTGTTG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAAGCCGATG
* * * *
280253 CATGTCCCAAACATGTCTTACACTAGCTCT-CGTCTC-AATGCCGATAC
1 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAA-GCCGAT-G
* **
280300 CATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAAGCCGATG
*
280347 CATGTCCCAGACATATCTTACACT
1 CATGTCCCAGACATGTCTTACACT
280371 AGCACACACA
Statistics
Matches: 174, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
44 26 0.15
45 1 0.01
46 94 0.54
47 29 0.17
48 23 0.13
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAAGCCGATG
Found at i:286651 original size:48 final size:47
Alignment explanation
Indices: 286523--286690 Score: 161
Period size: 47 Copynumber: 3.6 Consensus size: 47
286513 GGTATCATGG
* * * *
286523 CGATGCATTATCCCAGACATGTCTTACACTAG--CACATCTC-GTAGC
1 CGATGCA-TGTCCCAGACATGTCTTACACTGGCTCTCATCTCAATAGC
* * *
286568 CGATGCATGTCCTAGACATGACTTACATTGGCTCTCATCTCAAT-GC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAATAGC
*
286614 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA--T-AATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAA--TAGC
*
286662 GGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
286691 AGCACACACA
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
44 19 0.18
45 9 0.09
46 25 0.24
47 29 0.28
48 22 0.21
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAATAGC
Found at i:288239 original size:67 final size:67
Alignment explanation
Indices: 288156--288289 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
288146 GGTTTAGTTT
*
288156 CTAGTTTCTAGTTCTTTTTAGAATTAGGATTTATTTTTACTTATTTTCATTTTTGTTCA-TCGGA
1 CTAGTTTCTAGTTCTTTTTAGAATTAGGATTTATTTCTACTTATTTTCATTTTTGTTCACT-GGA
288220 AGA
65 AGA
288223 CTAGTTTCTAGTTCTTTTTAGAATTAGGATTTATTTCTACTTATTTTCATTTTTGTTCACTGGAA
1 CTAGTTTCTAGTTCTTTTTAGAATTAGGATTTATTTCTACTTATTTTCATTTTTGTTCACTGGAA
288288 GA
66 GA
288290 GCTGATTTGT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 64 0.98
68 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.53
Consensus pattern (67 bp):
CTAGTTTCTAGTTCTTTTTAGAATTAGGATTTATTTCTACTTATTTTCATTTTTGTTCACTGGAA
GA
Found at i:293870 original size:39 final size:40
Alignment explanation
Indices: 293825--293935 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
293815 CGGGGTTTAG
* * *
293825 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
293864 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
293904 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
293936 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:293895 original size:40 final size:40
Alignment explanation
Indices: 293848--293992 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
293838 CTCGCACAAG
* * * * *
293848 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
293888 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
293928 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
*
293969 GCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
293993 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.65
41 26 0.29
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:295221 original size:38 final size:38
Alignment explanation
Indices: 295179--295254 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
295169 CAAGAACTCC
*
295179 TTCCTCCTTCCTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
295217 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
295255 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:298224 original size:49 final size:49
Alignment explanation
Indices: 298152--298248 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
298142 CTCGTAGTGA
* *
298152 CCGTACCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTG
1 CCGTACCTCGTTCTGAAAGCAGTTTTGGGTATATCCGAATCTCGAATTG
*
298201 CCGTATCTCGTTCTGAAAGCAGTTTTGGGTATATCCGAATCTCGAATT
1 CCGTACCTCGTTCTGAAAGCAGTTTTGGGTATATCCGAATCTCGAATT
298249 CGCAACTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.34
Consensus pattern (49 bp):
CCGTACCTCGTTCTGAAAGCAGTTTTGGGTATATCCGAATCTCGAATTG
Found at i:299863 original size:18 final size:18
Alignment explanation
Indices: 299821--299863 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
299811 GCACATTCCG
*
299821 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
299839 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
299857 AAGTATG
1 AAGTATG
299864 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:300327 original size:28 final size:28
Alignment explanation
Indices: 300259--300356 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
300249 GTTGATCTCG
* * * *
300259 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
300288 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
300316 GCACTAAGTGTGAGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
300343 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
300357 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.37
28 21 0.34
29 18 0.29
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:300370 original size:29 final size:27
Alignment explanation
Indices: 300287--300370 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
300277 TAAATTGTAC
* * *
300287 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGAGA-CTTAATTATAT
* *
300315 AGCACTAAGTGTGAGAGTTGATTATAT
1 AGCACTAAGTGTGAGACTTAATTATAT
* *
300342 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTG-AGACTTAAT-TATAT
300371 TTTTGAATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 22 0.46
28 21 0.44
29 5 0.10
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGAGACTTAATTATAT
Found at i:301106 original size:31 final size:31
Alignment explanation
Indices: 301071--301135 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
301061 TTCGATTTTC
301071 TTTTTATGCCATATGTCATGGCTGATTAATT
1 TTTTTATGCCATATGTCATGGCTGATTAATT
301102 TTTTTATGCCATATGTCATGGCTGATTAATT
1 TTTTTATGCCATATGTCATGGCTGATTAATT
301133 TTT
1 TTT
301136 GGTGTTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTTTATGCCATATGTCATGGCTGATTAATT
Found at i:304737 original size:56 final size:56
Alignment explanation
Indices: 304531--304705 Score: 278
Period size: 56 Copynumber: 3.1 Consensus size: 56
304521 AGGCTTCAAT
* * * *
304531 GTAAGACCACGTTTAATATGTTGGTATCGATATGTGATTCTGATATATGTCTGCAA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
* *
304587 GTAAGACCACGTTTAATACGTTGTCATCTATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
* *
304643 GTAAGACCACATTCAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
304699 GTAAGAC
1 GTAAGAC
304706 ATTGTTTGGG
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 109 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (56 bp):
GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
Found at i:312598 original size:63 final size:65
Alignment explanation
Indices: 312464--312598 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 65
312454 TATGAACTTG
*
312464 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTGGGATAATTTAGTGATGCATGAGTTAAAGT
1 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTGGGATAA--TAGTGATGCATAAGTTAAAGT
312529 TC
64 TC
* * *
312531 ATTTAATA-ATGCTTCTATTAATTAAACTAGTTGCT-GGATTAA-A-TGATGCATAAGTGT-TAG
1 ATTTAATAGATGCTTCT-TTAAATAAACTAGTTACTGGGA-TAATAGTGATGCATAAGT-TAAAG
312591 TTC
63 TTC
312594 ATTTA
1 ATTTA
312599 TTTAAGTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
63 21 0.34
64 2 0.03
66 11 0.18
67 27 0.44
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (65 bp):
ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTGGGATAATAGTGATGCATAAGTTAAAGTTC
Found at i:314123 original size:29 final size:29
Alignment explanation
Indices: 314083--314180 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
314073 GGCCCGATCT
* *
314083 CATTTATATGGCCTATCAGGCCCAATTCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* *
314112 CATTCATATGGCCCATCAGGCCTAATTCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* * *
314141 TATTCATAT-GCCAATTAGGCCCAAATCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* *
314169 CCTTTATATGGC
1 CATTCATATGGC
314181 TCGTTAGGTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 21 0.37
29 36 0.63
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CATTCATATGGCCAATCAGGCCCAATTCA
Found at i:319213 original size:18 final size:19
Alignment explanation
Indices: 319177--319225 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
319167 CCTGCCCAGG
319177 ACCCCTTGGTGGCATCTGACC
1 ACCCCTTGGTGG-A-CTGACC
*
319198 ACCCCTTGGTGG-CTGAGC
1 ACCCCTTGGTGGACTGACC
319216 ACCACCTTGG
1 ACC-CCTTGG
319226 CCCACTACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
21 12 0.46
ACGTcount: A:0.14, C:0.37, G:0.27, T:0.22
Consensus pattern (19 bp):
ACCCCTTGGTGGACTGACC
Found at i:321854 original size:29 final size:27
Alignment explanation
Indices: 321795--321887 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 27
321785 TGACCCACTT
*
321795 GGCCCAATCTCATTTATATGG-TCCATCA
1 GGCCCAAT-TCATTTATATGGCT-CATTA
321823 GGCCCAATTCATATTCATATGGCTCATTA
1 GGCCCAATTCAT-TT-ATATGGCTCATTA
* * *
321852 GGCCCAAATCACCTTTATATGGCCCGTTA
1 GGCCCAATTCA--TTTATATGGCTCATTA
321881 GGCCCAA
1 GGCCCAA
321888 ATAAACTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.07
28 10 0.18
29 38 0.68
30 3 0.05
31 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (27 bp):
GGCCCAATTCATTTATATGGCTCATTA
Found at i:328271 original size:56 final size:56
Alignment explanation
Indices: 328204--328437 Score: 360
Period size: 56 Copynumber: 4.2 Consensus size: 56
328194 TTGTGATCAT
* *
328204 GAGTAAGACCACATTTAATACGTTGGCATTGATATGTGATTCTGATATATGTGTGC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* * *
328260 GAGTAAGACCACGTTTAATACGTTGGCATTGATATGTGATTCTGATATATATGTGT
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* * *
328316 GAGTAAGACGACGCTTAAAACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* * * *
328372 GAGTAAGACCACGTTTAATGCATTAGCATCGATATGTGATTCTGATATATGTGTGT
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
328428 GAGTAAGACC
1 GAGTAAGACC
328438 CTGTTTGGGA
Statistics
Matches: 162, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 162 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (56 bp):
GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
Found at i:337713 original size:44 final size:45
Alignment explanation
Indices: 337642--337857 Score: 154
Period size: 46 Copynumber: 4.7 Consensus size: 45
337632 GCATAACTGT
*
337642 GCCGATGCCATGT-CCAGACATGGTCTTACACTGAC-ACATTTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACTACATCTCG-AG
* *
337687 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGAC-TACATCTCGAG
* * * * *
337733 GCCGATGAATGTCCCAAACATGTCTTACACTAGCACT-CGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-ACTACATCTCGAG
* * * * * * *
337779 ACCGATGCCATGCCCCAGACATGGTCTTACAATGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACT-ACAT-CTCGAG
* *
337827 GCTGGTGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
337858 AGCTCACGAT
Statistics
Matches: 136, Mismatches: 24, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
44 17 0.12
45 16 0.12
46 59 0.43
47 27 0.20
48 16 0.12
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACTACATCTCGAG
Found at i:341803 original size:13 final size:13
Alignment explanation
Indices: 341787--341830 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
341777 GGACACATTA
*
341787 CCGTGTCACATGG
1 CCGTGTCGCATGG
341800 CCGTGTCGCAT-G
1 CCGTGTCGCATGG
*
341812 CCATGTCGCATGG
1 CCGTGTCGCATGG
*
341825 TCGTGT
1 CCGTGT
341831 GTCACACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.11, C:0.30, G:0.32, T:0.27
Consensus pattern (13 bp):
CCGTGTCGCATGG
Found at i:343851 original size:137 final size:138
Alignment explanation
Indices: 343593--343859 Score: 322
Period size: 137 Copynumber: 1.9 Consensus size: 138
343583 AAATGGGCAC
** * * * *
343593 CTCACACAAGTTGACGGTCAGAGTGTAAGCTACACGATGCTATTCACACAAGCTAATAAGTATCT
1 CTCACACAAGTTGACGGTCAGAACGTAAGCTACACGATGCCACTCACACAAGATAATAAGTATCC
* * ** * *
343658 ATAACTAATGTCAAACCACAGCCATTGGTAGGAAATTCAAGACCAGGACCCGAAACATGGTAACC
66 ACAACAAATGTCAAACCACAGCCATCAGTAGGAAATTCAAGACCAGCACCCAAAACATGGTAACC
343723 TAGGTCTA
131 TAGGTCTA
* * * *
343731 CTCACACAAGTTGACGGTCGGAACGT-AGCTACACGATGCCACTCACAGAAGATGATGAGTATCC
1 CTCACACAAGTTGACGGTCAGAACGTAAGCTACACGATGCCACTCACACAAGATAATAAGTATCC
** * * *
343795 ACAACAAATGTCGAAA-CTTAGCCATCAGTAGGACATTCAGGGCCAGCACCCAAAACATGGTAAC
66 ACAACAAATGTC-AAACCACAGCCATCAGTAGGAAATTCAAGACCAGCACCCAAAACATGGTAAC
343859 C
130 C
343860 CTAATGACAT
Statistics
Matches: 107, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 81 0.76
138 26 0.24
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (138 bp):
CTCACACAAGTTGACGGTCAGAACGTAAGCTACACGATGCCACTCACACAAGATAATAAGTATCC
ACAACAAATGTCAAACCACAGCCATCAGTAGGAAATTCAAGACCAGCACCCAAAACATGGTAACC
TAGGTCTA
Found at i:349876 original size:40 final size:40
Alignment explanation
Indices: 349789--349976 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
349779 TCCAAACACA
* *
349789 AATGCCTTCGGGACTTAGCCTGGATATAAC-ACCAGTACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
* * ** * *
349828 AGTACCTTCGAAACTTGGCCCGGATATAATAACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
* *
349868 AATGCCTTCAGGACTTAGCCCGGATATAACAACCAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
*
349908 AATGCCTTCGGGACTTAACCCGGATATAACAACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
*
349948 AATGCCTTCGGGACTTAACCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
349977 TCCTCAACTA
Statistics
Matches: 129, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
39 23 0.18
40 106 0.82
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
Found at i:357287 original size:27 final size:27
Alignment explanation
Indices: 357257--357870 Score: 895
Period size: 27 Copynumber: 22.7 Consensus size: 27
357247 TACTGAAATG
* * * *
357257 CCCTCAATTTGTAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
357284 CCCTTGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357311 CCATCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
357338 CCTTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357365 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357392 CCATCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357419 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357446 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357473 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357500 CTCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357527 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357554 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357581 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357608 CTCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357635 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357662 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357689 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357716 CTCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
357743 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
357770 CCCTCGATTTATAGAATTACCGTGTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * **
357797 CTCTCAATTTACAGAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
357824 CCCTCGATTTACAGAACTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
357851 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTATAGAATTAC
357871 TAAAATACCC
Statistics
Matches: 531, Mismatches: 56, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 531 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:357879 original size:27 final size:27
Alignment explanation
Indices: 357849--358056 Score: 158
Period size: 27 Copynumber: 7.7 Consensus size: 27
357839 ACTACCGTTT
* *
357849 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
357876 TACCCT-TAGTTTACAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
*
357903 TACCCTGGA-TTAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * *
357930 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* *
357957 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
** *
357984 TACCC-CTGGCTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * *
358011 TACCC-CTGATTTATGAAATTATCGAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* *
358038 TACTCTCGATTTGTAAAAT
1 TACCCTCGATTTATAAAAT
358057 ATCGAAATAC
Statistics
Matches: 150, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
26 4 0.03
27 142 0.95
28 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:358040 original size:81 final size:82
Alignment explanation
Indices: 357851--358031 Score: 267
Period size: 81 Copynumber: 2.2 Consensus size: 82
357841 TACCGTTTTA
* * **
357851 CCCTCGATTTACAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATA-CCCTGGATTA
1 CCCT-GATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATTA
357915 GTAAAATTACCAAAATAC
65 GTAAAATTACCAAAATAC
* * *
357933 CCCTGGTTTGTAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGCTT-G
1 CCCTGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATTAG
357997 TAAAATTACCAAAATAC
66 TAAAATTACCAAAATAC
*
358014 CCCTGATTTATGAAATTA
1 CCCTGATTTATAAAATTA
358032 TCGAAATACT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 76 0.86
82 12 0.14
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (82 bp):
CCCTGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATTAG
TAAAATTACCAAAATAC
Found at i:358051 original size:81 final size:82
Alignment explanation
Indices: 357851--358098 Score: 256
Period size: 81 Copynumber: 3.1 Consensus size: 82
357841 TACCGTTTTA
* ** **
357851 CCCTCGATTTACAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATA-CCCTGGATTA
1 CCCT-GATTTATAAAATTACTAAAATACCCCGAGTTTGTAAAATTACCAAAATACCCCTGGATTA
357915 GTAAAATTACCAAAATAC
65 GTAAAATTACCAAAATAC
* * * *
357933 CCCTGGTTTGTAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGCTT-G
1 CCCTGATTTATAAAATTACTAAAATACCCCGAGTTTGTAAAATTACCAAAATACCCCTGGATTAG
357997 TAAAATTACCAAAATAC
66 TAAAATTACCAAAATAC
* * * * * * **
358014 CCCTGATTTATGAAATTA-TCGAAATACTCTCGA-TTTGTAAAA-TATCGAAATACCCCTGTACG
1 CCCTGATTTATAAAATTACT-AAAATAC-CCCGAGTTTGTAAAATTACCAAAATACCCCTGGATT
* *
358076 A-TAGAATTACCGAAATAC
64 AGTAAAATTACCAAAATAC
358094 CCCTG
1 CCCTG
358099 TAAGGTCGAA
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
80 35 0.25
81 91 0.65
82 15 0.11
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (82 bp):
CCCTGATTTATAAAATTACTAAAATACCCCGAGTTTGTAAAATTACCAAAATACCCCTGGATTAG
TAAAATTACCAAAATAC
Found at i:358052 original size:54 final size:54
Alignment explanation
Indices: 357851--358098 Score: 220
Period size: 54 Copynumber: 4.6 Consensus size: 54
357841 TACCGTTTTA
* * * * **
357851 CCCTCGATTTACAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATA-
1 CCCT-GATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATAC
*
357905 CCCTGGA-TTAGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATAC
1 CCCT-GATTTA-TAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATAC
* *
357960 CCCT-AGTTTGTAAAATTACCAAAATACCCCTGGCTTGTAAAATTACCAAAATAC
1 CCCTGA-TTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATAC
* * * * * * *
358014 CCCTGATTTATGAAATTATCGAAATA-CTCTCGATTTGTAAAA-TATCGAAATAC
1 CCCTGATTTATAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATAC
** * *
358067 CCCTG-TACGATAGAATTACCGAAATACCCCTG
1 CCCTGAT-TTATAAAATTACCAAAATACCCCTG
358099 TAAGGTCGAA
Statistics
Matches: 160, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 36 0.22
54 116 0.73
55 7 0.04
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (54 bp):
CCCTGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATAC
Found at i:358097 original size:27 final size:27
Alignment explanation
Indices: 358059--358301 Score: 326
Period size: 27 Copynumber: 9.0 Consensus size: 27
358049 TGTAAAATAT
* *
358059 CGAAATACCCCTGTACGATAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
358086 CGAAATACCCCTGTAAGGTCGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
358113 C-AAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
** *
358139 TAAAATAACCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
358166 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
358193 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
358220 CGAAATACCCTTGTAAGGTAAAAATAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
358247 CAAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
358274 CGAGATACCCTTGTGGGGTAAAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
358301 C
1 C
358302 ATTTTGCCCT
Statistics
Matches: 189, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 23 0.12
27 166 0.88
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:358311 original size:27 final size:27
Alignment explanation
Indices: 358281--358344 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
358271 TACCGAGATA
*
358281 CCCTTGTGGGGTAAAATTACCATTTTG
1 CCCTTGTGGGGTAAAATGACCATTTTG
* * *
358308 CCCTTAG-GGTGTTAAATGACTATTTTG
1 CCCTT-GTGGGGTAAAATGACCATTTTG
*
358335 CCCTTATGGG
1 CCCTTGTGGG
358345 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (27 bp):
CCCTTGTGGGGTAAAATGACCATTTTG
Found at i:358542 original size:25 final size:25
Alignment explanation
Indices: 358504--358573 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
358494 AGGAAGTGCT
* *
358504 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
358529 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
358554 AAAAGAGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
358574 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:358780 original size:42 final size:42
Alignment explanation
Indices: 358721--358812 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
358711 TAGTCTCCCC
*
358721 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
358763 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
358805 AAATGGGC
1 AAATGGGC
358813 CTAAGGGCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:358874 original size:31 final size:32
Alignment explanation
Indices: 358836--358919 Score: 138
Period size: 31 Copynumber: 2.7 Consensus size: 32
358826 TGTTTACAGT
*
358836 AAAGGCTTCAGCCCAGTGATATGATTTAT-GA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGGA
358867 AAAGGCTTCGGCCCAGTGATATGATTTATGGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGGA
358899 AAA-GCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
358920 TCAAGACTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 5 0.10
31 41 0.80
32 5 0.10
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGGA
Found at i:360521 original size:17 final size:17
Alignment explanation
Indices: 360462--360521 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
360452 GAGACAGCCA
* * *
360462 CCATACATGCACTTAAG
1 CCATTCATGCATTTAAT
360479 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TAAT
*
360496 -CATCCCATGCATTTAAT
1 CCAT-TCATGCATTTAAT
360513 CCATTCATG
1 CCATTCATG
360522 GACTAGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 26 0.76
18 4 0.12
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTAAT
Found at i:360952 original size:30 final size:30
Alignment explanation
Indices: 360918--361014 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
360908 TAAACTAAAA
360918 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
360948 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
360978 TGAGCTAA-CGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGC-TTTAGCTCGTGAGCT-AAAGT
361008 TGAGCTA
1 TGAGCTA
361015 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:369442 original size:71 final size:71
Alignment explanation
Indices: 369321--369462 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
369311 CTCCTTCACC
*
369321 TCACGAGCTAGGATACGTATCGGTTCTTCTTCATAGCTCATATCGACTTGAATTTCAACCTCTGA
1 TCACGAGCTAGGATACGCATCGGTTCTTCTTCATAGCTCATATCGACTTGAATTTCAACCTCTGA
369386 TGGGCT
66 TGGGCT
*
369392 TCACGAGCTAGGATACGCATCGGTTCTTCTTCATAGCTCATATCGTCTTGAATTTCAACCTCTGA
1 TCACGAGCTAGGATACGCATCGGTTCTTCTTCATAGCTCATATCGACTTGAATTTCAACCTCTGA
369457 TGGGCT
66 TGGGCT
369463 AATTATGTGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (71 bp):
TCACGAGCTAGGATACGCATCGGTTCTTCTTCATAGCTCATATCGACTTGAATTTCAACCTCTGA
TGGGCT
Found at i:374327 original size:150 final size:150
Alignment explanation
Indices: 374056--374352 Score: 567
Period size: 150 Copynumber: 2.0 Consensus size: 150
374046 ACCCGAGTCC
*
374056 GACACCGGAGTCGAACACGAGGTGTTAAGAAACTTTGAAAAATTTCCAGACACTGCCCAATCTGT
1 GACACCGGAGTCGAACACGAGGTGTTAACAAACTTTGAAAAATTTCCAGACACTGCCCAATCTGT
374121 GTACTAGTCGCTTTAAAAATCATATCTTGAGATTCACAACTCGAAAATCAGTTTCGTGATTTTTC
66 GTACTAGTCGCTTTAAAAATCATATCTTGAGATTCACAACTCGAAAATCAGTTTCGTGATTTTTC
*
374186 CCTGAAACTATACTCATATT
131 CCTGAAACTAGACTCATATT
374206 GACACCGGAGTCGAACACGAGGTGTTAACAAACTTTGAAAAATTTCCAGACACTGCCCAATCTGT
1 GACACCGGAGTCGAACACGAGGTGTTAACAAACTTTGAAAAATTTCCAGACACTGCCCAATCTGT
*
374271 GTACTAGTCGCTTTAAAAATCATATCTTGAGCTTCACAACTCGAAAATCAGTTTCGTGATTTTTC
66 GTACTAGTCGCTTTAAAAATCATATCTTGAGATTCACAACTCGAAAATCAGTTTCGTGATTTTTC
374336 CCTGAAACTAGACTCAT
131 CCTGAAACTAGACTCAT
374353 GTCCCCACCT
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 144 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (150 bp):
GACACCGGAGTCGAACACGAGGTGTTAACAAACTTTGAAAAATTTCCAGACACTGCCCAATCTGT
GTACTAGTCGCTTTAAAAATCATATCTTGAGATTCACAACTCGAAAATCAGTTTCGTGATTTTTC
CCTGAAACTAGACTCATATT
Found at i:378226 original size:49 final size:47
Alignment explanation
Indices: 378154--378374 Score: 163
Period size: 49 Copynumber: 4.7 Consensus size: 47
378144 GGGATAAGTT
378154 GCTGATGCCATGTCCCAGACATGGTCTTACACTATCTATCATCACCGAG
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTATCTATCATCACCGAG
* *
378203 GCTGATGCCATGTCCCAGACATGGTCTTATACCAGCTCTCGTAT-AT-A-CG-T
1 GCTGATG-CATGTCCCAGACAT-GTC-T-TA-CA-CTATC-TATCATCACCGAG
* * * **
378253 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-A-CAACTCTTA-
1 GCTGATGCATGTCCCAGACATGTCTTACACTATCTATCATCACCGAG
* ** * **
378297 GCCGATGTGTGTCCCAGACACGTCTTACACT-TGCTATCATCGTCGAG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAT-CTATCATCACCGAG
378344 GCTGATGCATG-CCCTAGACATGTCTTACACT
1 GCTGATGCATGTCCC-AGACATGTCTTACACT
378375 GGCACTCGTC
Statistics
Matches: 136, Mismatches: 22, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
42 2 0.01
44 31 0.23
45 3 0.02
46 9 0.07
47 24 0.18
48 3 0.02
49 40 0.29
50 8 0.06
51 4 0.03
52 3 0.02
53 6 0.04
54 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTATCTATCATCACCGAG
Found at i:380267 original size:39 final size:39
Alignment explanation
Indices: 380212--380288 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
380202 ATGCAGAACA
*
380212 CATATTAATGATGTTCAAACTATGACATAATTAAAGACT
1 CATATTAATGAAGTTCAAACTATGACATAATTAAAGACT
*
380251 CATATTAATTAAGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGAAGTTCAAACTATGACATAATTAAAGAC
380289 ACAAACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (39 bp):
CATATTAATGAAGTTCAAACTATGACATAATTAAAGACT
Found at i:383025 original size:47 final size:44
Alignment explanation
Indices: 382951--383124 Score: 170
Period size: 46 Copynumber: 3.8 Consensus size: 44
382941 GTCACCTGTG
*
382951 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGA
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCG---ACATTAAGA
*
382998 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGA
1 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTAAGA
* * **
383043 TGAGTTCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
1 TGAG--CTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGA
* * * *
383089 CGTAAGCCAGTGTAAGACATGTTTGGGACCTGCATC
1 --TGAGCTAGTGTAAGACATGTCTGGGACATGCATC
383125 AACTAAGAGA
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
45 8 0.07
46 54 0.50
47 28 0.26
48 19 0.17
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (44 bp):
TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGA
Found at i:383055 original size:48 final size:44
Alignment explanation
Indices: 382952--383079 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 44
382942 TCACCTGTGT
*
382952 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCG--CACATTAAGA
*
382998 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG-ACATTAAGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGCACATTAAGA
383043 TGAGTTCTAGTGTAAGACATGTCTGGGACATGCATCG
1 -GAG--CTAGTGTAAGACATGTCTGGGACATGCATCG
383080 GCCTCGAGAC
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
45 8 0.11
46 22 0.30
47 28 0.38
48 16 0.22
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGCACATTAAGA
Found at i:388510 original size:46 final size:46
Alignment explanation
Indices: 388359--388531 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 46
388349 TCACTTGTGT
* * * *
388359 GAGCTAGTGTAAGACATGTCTAGGACATGCATCAGCC-ACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTTCA-GATGA
* * * *
388405 GAGCCAATGTAAGACCATGTCTGGGACATGATATCAGCATTCAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACATG-CATCAGCCTTCAGATGA
* * *
388453 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTGAGATGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTTCAGATG-A
388500 -AGCCAGTGTAAGACATGTCTGGGACATGCATC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC
388532 GGCTACAAGA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
46 54 0.51
47 30 0.28
48 20 0.19
49 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTTCAGATGA
Found at i:391076 original size:23 final size:23
Alignment explanation
Indices: 391046--391092 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
391036 TTATAGTGTC
391046 ACCAAGCTAGCTCGAGGATCGGA
1 ACCAAGCTAGCTCGAGGATCGGA
*
391069 ACCAAGCTAGCTCGAGTATCGGA
1 ACCAAGCTAGCTCGAGGATCGGA
391092 A
1 A
391093 GACATCGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.28, T:0.15
Consensus pattern (23 bp):
ACCAAGCTAGCTCGAGGATCGGA
Found at i:393198 original size:40 final size:40
Alignment explanation
Indices: 393139--393283 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
393129 CTCACACAAG
* * * * *
393139 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* *
393179 GCCTTGGGGACTTAGCCCGGATACAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
393219 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
393260 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
393284 CATTCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 55 0.62
41 27 0.31
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:398243 original size:40 final size:40
Alignment explanation
Indices: 398188--398329 Score: 207
Period size: 40 Copynumber: 3.6 Consensus size: 40
398178 TATTCGAATG
398188 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
398228 ATATCCGGGCTAAGTCCCGAAGTCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
398268 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
398308 ATATCC-GGCTAAATCCAGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
398330 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 13 0.14
40 77 0.84
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:401243 original size:27 final size:26
Alignment explanation
Indices: 401200--401314 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 26
401190 AGCATGGTTG
*
401200 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
401226 CCCGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
401253 CCAGAACAGATATT-TGTAGC-GTAGCCA
1 CCAGAACAGATATTGTG-A-CAG-AGCCA
* * *
401280 CCAGAAACAGATGTTTGTGGCATAGCCA
1 CCAG-AACAGAT-ATTGTGACAGAGCCA
401308 CCAGAAC
1 CCAGAAC
401315 GCTTCCTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.03
26 14 0.19
27 36 0.49
28 17 0.23
29 2 0.03
30 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:401296 original size:28 final size:28
Alignment explanation
Indices: 401232--401313 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
401222 GTCACCCGAT
* *
401232 ACAGATA-TTGTGGCAGAGCCACCAG-A
1 ACAGATATTTGTAGCATAGCCACCAGAA
*
401258 ACAGATATTTGTAGCGTAGCCACCAGAA
1 ACAGATATTTGTAGCATAGCCACCAGAA
* *
401286 ACAGATGTTTGTGGCATAGCCACCAGAA
1 ACAGATATTTGTAGCATAGCCACCAGAA
401314 CGCTTCCTCC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.15
27 15 0.31
28 26 0.54
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (28 bp):
ACAGATATTTGTAGCATAGCCACCAGAA
Found at i:401601 original size:19 final size:19
Alignment explanation
Indices: 401577--401624 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
401567 TGGGCCCGTT
401577 GGCCCATTAACCCGATTTC
1 GGCCCATTAACCCGATTTC
401596 GGCCCATTAACCCGATTTC
1 GGCCCATTAACCCGATTTC
401615 GGCCCATTAA
1 GGCCCATTAA
401625 GCCCAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (19 bp):
GGCCCATTAACCCGATTTC
Found at i:409441 original size:27 final size:26
Alignment explanation
Indices: 409405--409519 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 26
409395 AGCATGGCTG
*
409405 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
*
409431 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* *
409458 CCAGAATAGATATTTGTGGC-GTAGCCA
1 CCAGAACAGATA-TTGTGACAG-AGCCA
* * * *
409485 CCAGAAATAGATGTTTGTGGCATAGCCA
1 CCAG-AACAGAT-ATTGTGACAGAGCCA
409513 CCAGAAC
1 CCAGAAC
409520 GCTTCCTCCA
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.16
27 42 0.55
28 23 0.30
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:409502 original size:28 final size:28
Alignment explanation
Indices: 409429--409518 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 28
409419 GTGACAGAGT
* *
409429 CACCAGATACAGATA-TTGTGGCAG-AGC
1 CACCAGAAATAGATATTTGTGGC-GTAGC
409456 CACCAG-AATAGATATTTGTGGCGTAGC
1 CACCAGAAATAGATATTTGTGGCGTAGC
* *
409483 CACCAGAAATAGATGTTTGTGGCATAGC
1 CACCAGAAATAGATATTTGTGGCGTAGC
409511 CACCAGAA
1 CACCAGAA
409519 CGCTTCCTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.12
27 22 0.39
28 27 0.48
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAAATAGATATTTGTGGCGTAGC
Found at i:409709 original size:27 final size:27
Alignment explanation
Indices: 409679--409829 Score: 72
Period size: 27 Copynumber: 5.1 Consensus size: 27
409669 TCATACTTAG
409679 GGGTATTCTAGTAAATTTACTATTTTA
1 GGGTATTCTAGTAAATTTACTATTTTA
* * * * *
409706 GGGTTTTC-ATGCACATTACAACCATTAACTTA
1 GGGTATTCTA-GTAAATT--TACTATT---TTA
409738 GGGGTATTCTAGTAAATTTACTATTTTA
1 -GGGTATTCTAGTAAATTTACTATTTTA
* * * * *
409766 GGGTTTTC-ATGCACATTACAACCATTAACTTA
1 GGGTATTCTA-GTAAATT--TACTATT---TTA
409798 GGGGTATTCTAGTAAATTTACTATTTTA
1 -GGGTATTCTAGTAAATTTACTATTTTA
409826 GGGT
1 GGGT
409830 TTTCATTCAC
Statistics
Matches: 88, Mismatches: 20, Indels: 32
0.63 0.14 0.23
Matches are distributed among these distances:
26 2 0.02
27 28 0.32
28 6 0.07
29 10 0.11
31 10 0.11
32 6 0.07
33 24 0.27
34 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (27 bp):
GGGTATTCTAGTAAATTTACTATTTTA
Found at i:409746 original size:60 final size:60
Alignment explanation
Indices: 409673--409854 Score: 346
Period size: 60 Copynumber: 3.0 Consensus size: 60
409663 TTATTTTCAT
409673 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
1 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
409733 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
1 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
* *
409793 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATTCACATTACAACTATTA
1 ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
409853 AC
1 AC
409855 GTATTAACAG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 120 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (60 bp):
ACTTAGGGGTATTCTAGTAAATTTACTATTTTAGGGTTTTCATGCACATTACAACCATTA
Found at i:414129 original size:47 final size:47
Alignment explanation
Indices: 414076--414190 Score: 176
Period size: 47 Copynumber: 2.4 Consensus size: 47
414066 CCAAAAGTGC
*
414076 AAACAAGCTGCCAAGACAAATAATTATGGCCAAGCCACTAGAATCGT
1 AAACAAGCTGCCAAAACAAATAATTATGGCCAAGCCACTAGAATCGT
* * * *
414123 AGACAAGCTACCAAAACGAATAATTATGGTCAAGCCACTAGAATCGT
1 AAACAAGCTGCCAAAACAAATAATTATGGCCAAGCCACTAGAATCGT
*
414170 AAACAAGCTGCCAAAGCAAAT
1 AAACAAGCTGCCAAAACAAAT
414191 GTGTGGTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (47 bp):
AAACAAGCTGCCAAAACAAATAATTATGGCCAAGCCACTAGAATCGT
Found at i:418068 original size:34 final size:34
Alignment explanation
Indices: 418030--418095 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
418020 AGTACATTTT
418030 CTATCATCAAACATCAAAACACACAATTTCATTA
1 CTATCATCAAACATCAAAACACACAATTTCATTA
*
418064 CTATCATCAAACATCAAAACACACATTTTCAT
1 CTATCATCAAACATCAAAACACACAATTTCAT
418096 CAATTGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (34 bp):
CTATCATCAAACATCAAAACACACAATTTCATTA
Found at i:421980 original size:699 final size:698
Alignment explanation
Indices: 420569--422378 Score: 2406
Period size: 699 Copynumber: 2.6 Consensus size: 698
420559 CAACATGAAC
* *
420569 TGGGTCTACCACAACATTTTGTTGCTTACCCTTTTCAAATTTAGTATATTCTTTAGATGACTCCG
1 TGGGTCTACCATAACATTTTGTTGCTTACCTTTTTCAAATTTAGTATATTCTTTAGATGACTCCG
* * *
420634 GGATCTTTACTTTGTTGTTATTCAAGTTTTCCTTTTCTACCGTGGCATCTTAAGAACCATCATCA
66 GGATCTTTACTTAGTTGTTATTCAAGTTTTCCTTTTCTACTGTGGCATCTTGAGAACCATCATCA
* *
420699 AGCTGAGTTCCGCTTTTAAGAGTGATGGCCTTACGCTACTCCTT-CCTTGTGATCTTGACTTCTC
131 AGCTGAGTTCCACTTTTAAGAGTGATGGCCTTACACTACTCCTTCCCTTGTGATCTTGACTTCTC
* * *
420763 AGTATCACCAGGCAATGCCCGTTATAGTCTCAAATTCAAAGCGTTTGTTATTTTCCTACCTAAGT
196 AGTATCACCAGGCAATGCCCGTTGTGGTCTCAAATTCAAAGCATTTGTTATTTTCCTACCTAAGT
* ** * *
420828 CTTAAGAGCTTAGAGAGATGTAACCTAACTCTAAATTACAGCATCATTCTTGGCCATATACT-CT
261 CTTAAGAGCTCAGAGAGACATAGCCTAACTCTAAATTACAGCATCATTCTTGGCCATATATTCCT
* * * *
420892 TTCAGCAAAGCTTCAATAGATGATGATGATGATGAAACTAATGCC-AACATAG--G-----TTGA
326 TT-AGCAAAGCTTCAATAGATGATGAT--T-ATGAAA-TTATGCCTGACATTGCTGACATTTTGC
* * * * *****
420949 GTATAAC-TAGG-CGATGCATTGATAGCATTTTTTCTTATCGTATTGGTGAAATTCCCCACACCA
386 CT-TAACATAGGTTGA-GTA-T-A-ACCAGGCGGTCTTATCGTATTGGTGAAATTCCCCACACCA
** * * *
421012 TACCTTTAGCCAAGCTTTAATAGATGATGATGATAAAACCGATGCCTAACCTTGCTAGACATTTT
446 TACCTGCAACAAAGCTTCAATAGATGATGATGATAAAACCGATGCCTAACCTTGCTAGACATTTT
* * * * *
421077 GCCTCAACATATGTTAAGTATAACTAGGTGGTACATTGATGGCATTCTATCTTATCGTATTGGTG
511 GCCTCAACATAGGTTAAGTATAACCAGGCGATACATTGATGGCATTCTATCTAATCGTATTGGTG
*
421142 AAATTCCCCACAACTTGATTAATCCAACTAAAGTTTGGATGTCTCTTCCACCCAACATTATACGT
576 AAATTCCCCACAACTTGATTAATCCAACTAAAGTTTGAATGTCTCTTCCACCCAACATTATACGT
* *
421207 GTTGGAATAGGGGTTATTGTTCTGGTTGAAATTACCCATGTAGCACACAAATGCTACA
641 GTTGGAATAGGGATTATTGTTCTAGTTGAAATTACCCATGTAGCACACAAATGCTACA
* *
421265 TGGGTCTACCATAACATTTTGTTGCTTACCTTTTTCAAATTTAGTATATTCTTTAAATGACT-CT
1 TGGGTCTACCATAACATTTTGTTGCTTACCTTTTTCAAATTTAGTATATTCTTTAGATGACTCCG
* * *
421329 AGATCTTTACTTGGTTGTTATGCAAGTTTTCCTTTTCTACTGTGGCATCTTGAGAACCATCATCA
66 GGATCTTTACTTAGTTGTTATTCAAGTTTTCCTTTTCTACTGTGGCATCTTGAGAACCATCATCA
*
421394 AGCTGAGTTCCACTTTTAAGAGTGATGGGCTTACACTACTCCTTCCCTTGTGATCTTGACTTCTC
131 AGCTGAGTTCCACTTTTAAGAGTGATGGCCTTACACTACTCCTTCCCTTGTGATCTTGACTTCTC
421459 AGTATCACCAGGCAATGCCCGTTGTGGTCTCAAATTCAAAGCATTTGTTATTTTCCTACCTAAGT
196 AGTATCACCAGGCAATGCCCGTTGTGGTCTCAAATTCAAAGCATTTGTTATTTTCCTACCTAAGT
421524 CTTAAGAGCTCAGAGAGACATAGCCTAACTCTAAATTACAGCATCATTCTTGGCCATATATTCCT
261 CTTAAGAGCTCAGAGAGACATAGCCTAACTCTAAATTACAGCATCATTCTTGGCCATATATTCCT
*
421589 TTAGCAAAGCTTCAATAGATGATGATTATGAAATTATTGCCTGACCTTGCTGAACATTTTGCCTT
326 TTAGCAAAGCTTCAATAGATGATGATTATGAAATTA-TGCCTGACATTGCTG-ACATTTTGCCTT
* *
421654 AACATAGGTTGAGTATAACCAGGCGGTCTTATTGTATTGGTGAAA-TCCCCTACACCATTCCTGC
389 AACATAGGTTGAGTATAACCAGGCGGTCTTATCGTATTGGTGAAATTCCCC-ACACCATACCTGC
* * **
421718 AACAAAGCTTCAATAGATGATGATGATAAAATCGATGCCTAACCTTGCTGGACATTTTGCCTTGA
453 AACAAAGCTTCAATAGATGATGATGATAAAACCGATGCCTAACCTTGCTAGACATTTTGCCTCAA
* * *
421783 CATAGGTTGAGTATAACCAGGCGATGCATTGATGGCATTCTATCTAATTGTATTGGTGAAATTCC
518 CATAGGTTAAGTATAACCAGGCGATACATTGATGGCATTCTATCTAATCGTATTGGTGAAATTCC
* * * * *
421848 CTATACCTTTATTATTCCAACTAAAGTTTGAATGT-TGCTTCCACCCAACATTATACGTGTTGGA
583 CCACAACTTGATTAATCCAACTAAAGTTTGAATGTCT-CTTCCACCCAACATTATACGTGTTGGA
* *
421912 ATCGGGATTATTGTTCTAGTTGAAATTACCTATGTAGCACACAAATGCTACA
647 ATAGGGATTATTGTTCTAGTTGAAATTACCCATGTAGCACACAAATGCTACA
*
421964 TGGGTCTACCATAACATTTTGTTACTTACCTTTTTCAAATTTAGTGA-ATTCTTTAGATGACTCC
1 TGGGTCTACCATAACATTTTGTTGCTTACCTTTTTCAAATTTAGT-ATATTCTTTAGATGACTCC
* * *
422028 GGGATCTTTACCTAGTTGTTATTCAAGTTTTCCTCTTCTA-TCATGGCATCTTGAGAACCATCAT
65 GGGATCTTTACTTAGTTGTTATTCAAGTTTTCCTTTTCTACT-GTGGCATCTTGAGAACCATCAT
* * * * *
422092 CAAGTTGAGTTCTACTTCTAAGAGTGATGGCCTGACACTACT-CTCTCCCTTGTGATCTTGAATT
129 CAAGCTGAGTTCCACTTTTAAGAGTGATGGCCTTACACTACTCCT-TCCCTTGTGATCTTGACTT
* * * * * * *
422156 TTCGGTATCACTAGGCAATGCCCCTTGTGGTCTCGAATTCAAA--ATGTTCATTATTTTCCCCAC
193 CTCAGTATCACCAGGCAATGCCCGTTGTGGTCTCAAATTCAAAGCAT-TT-GTTATTTT-CCTAC
* * * * * *
422219 CTGAGTCTTAAGAGCTCGGAGAGACATAGCCTGACTCAAAATTATAGCATCATTCTTGGCCACAT
255 CTAAGTCTTAAGAGCTCAGAGAGACATAGCCTAACTCTAAATTACAGCATCATTCTTGGCCATAT
* * * * * *
422284 ATTCCTTCAGTAAAGCTTTAATAGATGATG---ATGAAACTGATGCCTGACTTTACTGGACATTT
320 ATTCCTTTAGCAAAGCTTCAATAGATGATGATTATGAAA-TTATGCCTGACATTGCT-GACATTT
* * *
422346 TGCCTCAACATAGGTTGGGTATAACTAGGCGGT
383 TGCCTTAACATAGGTTGAGTATAACCAGGCGGT
422379 GCATTAATGG
Statistics
Matches: 989, Mismatches: 100, Indels: 48
0.87 0.09 0.04
Matches are distributed among these distances:
692 2 0.00
693 10 0.01
694 5 0.01
695 102 0.10
696 223 0.23
697 4 0.00
698 62 0.06
699 316 0.32
700 158 0.16
701 95 0.10
702 10 0.01
703 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (698 bp):
TGGGTCTACCATAACATTTTGTTGCTTACCTTTTTCAAATTTAGTATATTCTTTAGATGACTCCG
GGATCTTTACTTAGTTGTTATTCAAGTTTTCCTTTTCTACTGTGGCATCTTGAGAACCATCATCA
AGCTGAGTTCCACTTTTAAGAGTGATGGCCTTACACTACTCCTTCCCTTGTGATCTTGACTTCTC
AGTATCACCAGGCAATGCCCGTTGTGGTCTCAAATTCAAAGCATTTGTTATTTTCCTACCTAAGT
CTTAAGAGCTCAGAGAGACATAGCCTAACTCTAAATTACAGCATCATTCTTGGCCATATATTCCT
TTAGCAAAGCTTCAATAGATGATGATTATGAAATTATGCCTGACATTGCTGACATTTTGCCTTAA
CATAGGTTGAGTATAACCAGGCGGTCTTATCGTATTGGTGAAATTCCCCACACCATACCTGCAAC
AAAGCTTCAATAGATGATGATGATAAAACCGATGCCTAACCTTGCTAGACATTTTGCCTCAACAT
AGGTTAAGTATAACCAGGCGATACATTGATGGCATTCTATCTAATCGTATTGGTGAAATTCCCCA
CAACTTGATTAATCCAACTAAAGTTTGAATGTCTCTTCCACCCAACATTATACGTGTTGGAATAG
GGATTATTGTTCTAGTTGAAATTACCCATGTAGCACACAAATGCTACA
Found at i:423436 original size:24 final size:25
Alignment explanation
Indices: 423404--423453 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
423394 TTGATGATAG
423404 ATTATGAATGTTTGTTGTG-AATAT
1 ATTATGAATGTTTGTTGTGAAATAT
*
423428 ATTATGAATTTTTGTTGTGAAATAT
1 ATTATGAATGTTTGTTGTGAAATAT
423453 A
1 A
423454 CAAGTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (25 bp):
ATTATGAATGTTTGTTGTGAAATAT
Found at i:423461 original size:21 final size:24
Alignment explanation
Indices: 423414--423461 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
423404 ATTATGAATG
* *
423414 TTTGTTGTGAATATATTATGAATT
1 TTTGTTGTGAATATATTATCAAGT
423438 TTTGTTGTGAA-ATA-TA-CAAGT
1 TTTGTTGTGAATATATTATCAAGT
423459 TTT
1 TTT
423462 ATTAAGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 3 0.14
24 11 0.50
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTGTTGTGAATATATTATCAAGT
Found at i:431841 original size:15 final size:15
Alignment explanation
Indices: 431823--431853 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
431813 TCGAGTTTAT
431823 TTCATACGAGCTTAC
1 TTCATACGAGCTTAC
431838 TTCATACGAGCTTAC
1 TTCATACGAGCTTAC
431853 T
1 T
431854 AAGCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (15 bp):
TTCATACGAGCTTAC
Found at i:433265 original size:40 final size:39
Alignment explanation
Indices: 433213--433330 Score: 134
Period size: 39 Copynumber: 3.0 Consensus size: 39
433203 TCCAATTTCT
* *
433213 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
1 AGCACTAAGCCTGCGGGATTTAACCCGGATAT-TAATACC
* * *
433253 AGCACTAGGCCTGC-GGACTATAATTCCGGATA-TAATACC
1 AGCACTAAGCCTGCGGGA-TTTAA-CCCGGATATTAATACC
*
433292 AGCATTAAGCCTGCGGGATTTAACCCGGATA-TAATACC
1 AGCACTAAGCCTGCGGGATTTAACCCGGATATTAATACC
433330 A
1 A
433331 CATAAATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
38 15 0.23
39 25 0.38
40 19 0.29
41 7 0.11
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (39 bp):
AGCACTAAGCCTGCGGGATTTAACCCGGATATTAATACC
Found at i:436371 original size:15 final size:15
Alignment explanation
Indices: 436351--436382 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
436341 AAACTTGTAG
*
436351 AAGTTAAATATAACT
1 AAGTTAAATAAAACT
436366 AAGTTAAATAAAACT
1 AAGTTAAATAAAACT
436381 AA
1 AA
436383 TGGAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (15 bp):
AAGTTAAATAAAACT
Found at i:441743 original size:20 final size:20
Alignment explanation
Indices: 441704--441743 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
441694 AAACTTCTTC
* *
441704 ACTTACTCACTTACTCAAAT
1 ACTTACTCACTTAATAAAAT
*
441724 ACTTACTTACTTAATAAAAT
1 ACTTACTCACTTAATAAAAT
441744 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
ACTTACTCACTTAATAAAAT
Found at i:442116 original size:55 final size:54
Alignment explanation
Indices: 441997--442182 Score: 236
Period size: 55 Copynumber: 3.4 Consensus size: 54
441987 GACATGTCTC
441997 GACATGGT-TTACATGGTATCCTTGCCTTAT-GAACTCACCAATGT-CATGCCTT
1 GACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAAT-TCCATGCCTT
* * * *
442049 GGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAATTCCATGTCTT
1 GACATGGTCTTACATGGTATCC-TTGCCTTATAG-AACTCACCAATTCCATGCCTT
* * *
442104 GACATGGTCTTACATGGTATCCTTGCCTTAGAAAACTTACCAATTTCCATGCCTT
1 GACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAA-TTCCATGCCTT
*
442159 GGCATGGTCTTACATGGTATCCTT
1 GACATGGTCTTACATGGTATCCTT
442183 AAACCCTAAT
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
52 9 0.08
53 18 0.16
54 10 0.09
55 76 0.66
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
GACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCACCAATTCCATGCCTT
Found at i:445047 original size:35 final size:34
Alignment explanation
Indices: 444978--445070 Score: 123
Period size: 35 Copynumber: 2.7 Consensus size: 34
444968 GTTGATATTA
*
444978 TGATTCACTTGTTAAGCATGCCATATACTAATTC
1 TGATTCACATGTTAAGCATGCCATATACTAATTC
* *
445012 TGATTCGCATGTTAAGCATGCCACTATACTGATTC
1 TGATTCACATGTTAAGCATGCCA-TATACTAATTC
* * *
445047 TAATTCACATGTAAAACATGCCAT
1 TGATTCACATGTTAAGCATGCCAT
445071 TGTGTTCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 22 0.43
35 29 0.57
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (34 bp):
TGATTCACATGTTAAGCATGCCATATACTAATTC
Found at i:445359 original size:49 final size:48
Alignment explanation
Indices: 445249--445369 Score: 136
Period size: 49 Copynumber: 2.5 Consensus size: 48
445239 ATATCTACAA
* * * * * *
445249 ATCTAGTGGCTTGACCATAATATTCTGTATCTGGCATTTGATTGCATT
1 ATCTGGTGGCTTGTCCACAATATTCTGTATCTAGCACTTGACTGCATT
445297 ATCTGGAT-GCTTGTCCACAATATTCTGTATCTAGCAACTTGACTGCATT
1 ATCTGG-TGGCTTGTCCACAATATTCTGTATCTAGC-ACTTGACTGCATT
* * *
445346 ATTTGGTGGCTTGTCAACATTATT
1 ATCTGGTGGCTTGTCCACAATATT
445370 GGTGTAGTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 30 0.49
49 31 0.51
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (48 bp):
ATCTGGTGGCTTGTCCACAATATTCTGTATCTAGCACTTGACTGCATT
Found at i:453144 original size:62 final size:62
Alignment explanation
Indices: 453029--453146 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
453019 AATAAACCTA
* *
453029 TTAAGGTAACGGCACTAAGTGTGCGATACATCACAAGACTGTGCCACTAAGTGTGCAAGACG
1 TTAAGGTAACGACACTAAGTGTGCGATACATCACAAGAATGTGCCACTAAGTGTGCAAGACG
* * * * *
453091 TTAATGTAACGACACTAAGTGTGCGATACGTTACAAGGAAT-TGGCACTGAGTGTGC
1 TTAAGGTAACGACACTAAGTGTGCGATACATCACAA-GAATGTGCCACTAAGTGTGC
453147 GAGTTTACAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 45 0.94
63 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (62 bp):
TTAAGGTAACGACACTAAGTGTGCGATACATCACAAGAATGTGCCACTAAGTGTGCAAGACG
Found at i:456912 original size:16 final size:16
Alignment explanation
Indices: 456888--456922 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
456878 CAACCCACTT
*
456888 TTTTTGCTTTTCAGCC
1 TTTTGGCTTTTCAGCC
456904 TTTTGGCTTTTCAGCC
1 TTTTGGCTTTTCAGCC
456920 TTT
1 TTT
456923 GCAGTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.14, T:0.57
Consensus pattern (16 bp):
TTTTGGCTTTTCAGCC
Found at i:463211 original size:20 final size:21
Alignment explanation
Indices: 463167--463211 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
463157 TGATTTCGTA
*
463167 CTTTGGCCCATTTTCTCCATT
1 CTTTGGCCCAGTTTCTCCATT
463188 -TTTGGCCC-GTTTCT-CATT
1 CTTTGGCCCAGTTTCTCCATT
463206 CCTTTG
1 -CTTTG
463212 TCTCTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 12 0.57
ACGTcount: A:0.07, C:0.31, G:0.13, T:0.49
Consensus pattern (21 bp):
CTTTGGCCCAGTTTCTCCATT
Found at i:469194 original size:25 final size:25
Alignment explanation
Indices: 469155--469249 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
469145 TCATGTACAT
*
469155 GTATGCTCATATGAGCTGTGAATCG
1 GTATGCTCACATGAGCTGTGAATCG
*
469180 GTATGCTCACTTGAGCTGT-AGATCG
1 GTATGCTCACATGAGCTGTGA-ATCG
* * ** * * *
469205 TTATGCTCTCACAAGCTATAAATTG
1 GTATGCTCACATGAGCTGTGAATCG
469230 GTATGCTCACATGAGCTGTG
1 GTATGCTCACATGAGCTGTG
469250 GAGTATCCGC
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (25 bp):
GTATGCTCACATGAGCTGTGAATCG
Found at i:471998 original size:46 final size:45
Alignment explanation
Indices: 471938--472113 Score: 149
Period size: 46 Copynumber: 3.8 Consensus size: 45
471928 TGGTTGAGCA
*
471938 TCCGAACTCATTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
471984 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCATTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * * *
472031 TCCGAGCCCATTGAGTTGAGTCCGAGTTCACTTGTGGATACGAACG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
472077 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
472114 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 63 0.62
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:472094 original size:93 final size:93
Alignment explanation
Indices: 471935--472105 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
471925 GGATGGTTGA
* * * * *
471935 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACCCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
*
472000 TGAGTCTGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
472028 GCATCCGAGCCCATTGAGTTGAGTCCGAGTTCACTTGTGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACCCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
472093 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
472106 ACTTATGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACCCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:484424 original size:18 final size:18
Alignment explanation
Indices: 484390--484424 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
484380 ACATGCCCTC
*
484390 ATAATCACTTATCACATA
1 ATAATCACTTATAACATA
*
484408 ATAATCACTTTTAACAT
1 ATAATCACTTATAACAT
484425 GTTAAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATCACTTATAACATA
Found at i:486337 original size:42 final size:43
Alignment explanation
Indices: 486253--486352 Score: 175
Period size: 42 Copynumber: 2.3 Consensus size: 43
486243 AACACTAAGG
*
486253 GACACATGGCCGTGTAACCTAACCGTGTGTCACACACGACTAA
1 GACACATGCCCGTGTAACCTAACCGTGTGTCACACACGACTAA
486296 GACACATGCCCGTGTAACCTAACC-TGTGTCACACACGACTAA
1 GACACATGCCCGTGTAACCTAACCGTGTGTCACACACGACTAA
*
486338 AACACATGCCCGTGT
1 GACACATGCCCGTGT
486353 GGACAAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 32 0.58
43 23 0.42
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (43 bp):
GACACATGCCCGTGTAACCTAACCGTGTGTCACACACGACTAA
Found at i:490132 original size:39 final size:40
Alignment explanation
Indices: 490037--490298 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
490027 TTGAATGATG
*
490037 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
490075 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
490116 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
490155 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
490194 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
490233 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
490272 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
490299 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:511733 original size:30 final size:30
Alignment explanation
Indices: 511699--511759 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
511689 TCTTTAACTC
511699 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
511729 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
511759 A
1 A
511760 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:518863 original size:27 final size:27
Alignment explanation
Indices: 518829--519006 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
518819 GAAATTGTAC
518829 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
518856 TGCACTAAGTGTGCGAAATGAGTATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
518882 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
518910 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
518938 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
518965 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
518992 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
519007 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:518947 original size:82 final size:81
Alignment explanation
Indices: 518830--518985 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
518820 AAATTGTACA
* *
518830 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAGTATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGTA-GCACTAAGTG
518894 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
518911 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGTAGCACTAAGTG
*
518976 TGCGAGTTGA
65 TGCGAATTGA
518986 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:518997 original size:82 final size:81
Alignment explanation
Indices: 518826--519006 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
518816 GATGAAATTG
* *
518826 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAGTATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGATGCACTAA
518891 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
518907 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGAT-GCACT
* **
518971 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
518989 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
519007 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAGTACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:521253 original size:13 final size:13
Alignment explanation
Indices: 521235--521260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
521225 GGATCTTTTG
521235 GAGTTCAACTATA
1 GAGTTCAACTATA
521248 GAGTTCAACTATA
1 GAGTTCAACTATA
521261 AATAAAAGCA
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):
GAGTTCAACTATA
Found at i:524322 original size:13 final size:13
Alignment explanation
Indices: 524304--524328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524294 GGTTAACTTG
524304 TATATATATGATA
1 TATATATATGATA
524317 TATATATATGAT
1 TATATATATGAT
524329 TTAAAATGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TATATATATGATA
Found at i:525624 original size:31 final size:31
Alignment explanation
Indices: 525588--525646 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
525578 GAAAAGTCAG
525588 TTTAATTGGTATTTATTTGGTAATGCATCGT
1 TTTAATTGGTATTTATTTGGTAATGCATCGT
525619 TTTAATTGGTATTTATTTGGTAATGCAT
1 TTTAATTGGTATTTATTTGGTAATGCAT
525647 TGTAACCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.53
Consensus pattern (31 bp):
TTTAATTGGTATTTATTTGGTAATGCATCGT
Found at i:527271 original size:15 final size:15
Alignment explanation
Indices: 527251--527282 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
527241 AGCTAAAAAA
*
527251 TGATATGAGGTCGTG
1 TGATATGAGGCCGTG
527266 TGATATGAGGCCGTG
1 TGATATGAGGCCGTG
527281 TG
1 TG
527283 CGAGGGACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.09, G:0.41, T:0.31
Consensus pattern (15 bp):
TGATATGAGGCCGTG
Found at i:529988 original size:137 final size:138
Alignment explanation
Indices: 529741--530013 Score: 370
Period size: 137 Copynumber: 2.0 Consensus size: 138
529731 CTATAAAATG
*** * *
529741 GGTCTGCTCACACAAGCTAACGGTTGGAATGTAAGCTACACGATGCTGCTCACACAAGCTGATGA
1 GGTCTGCTCACACAAGCTAACGGTCAAAATGTAAGCTACACAATGCTGCTCACACAAGCTAATGA
* ** * * ***
529806 GTATCCACAACTAATGCTGGACCTCAGCCATCGGTAGGACATTCAGGACCAGCACTTGAAACATG
66 GTATCCACAACAAATGCCAGACCTCAACCATCGATAGGACATTCAGGACCAGCACCCAAAACATG
529871 GTAACCTA
131 GTAACCTA
*
529879 GGTCTGCTCACACAAGCTGACGGTCAAAATGT-AGCTACACAATG-TCGCTCACACAAGCTAATG
1 GGTCTGCTCACACAAGCTAACGGTCAAAATGTAAGCTACACAATGCT-GCTCACACAAGCTAATG
** *
529942 AGTATCTGCAACAAATGCCAGACCTCAACCATCGATAGGACATTCAGGACCATCACCCAAAACAT
65 AGTATCCACAACAAATGCCAGACCTCAACCATCGATAGGACATTCAGGACCAGCACCCAAAACAT
530007 GGTAACC
130 GGTAACC
530014 CTAATGACAT
Statistics
Matches: 117, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
136 1 0.01
137 88 0.75
138 28 0.24
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (138 bp):
GGTCTGCTCACACAAGCTAACGGTCAAAATGTAAGCTACACAATGCTGCTCACACAAGCTAATGA
GTATCCACAACAAATGCCAGACCTCAACCATCGATAGGACATTCAGGACCAGCACCCAAAACATG
GTAACCTA
Found at i:536484 original size:30 final size:30
Alignment explanation
Indices: 536450--536506 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
536440 AAGACTAAGT
536450 ATATAATATATATCATAAAACGAAAAAAGA
1 ATATAATATATATCATAAAACGAAAAAAGA
*
536480 ATATAATATATATCATAAAACTAAAAA
1 ATATAATATATATCATAAAACGAAAAA
536507 GATAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (30 bp):
ATATAATATATATCATAAAACGAAAAAAGA
Found at i:542887 original size:26 final size:25
Alignment explanation
Indices: 542852--542911 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
542842 AATAAATTTT
*
542852 TATTTTATTTTTAAAAATTATTAAAA
1 TATTATATTTTT-AAAATTATTAAAA
*
542878 TATTATATTTTTAATATTATTAAAA
1 TATTATATTTTTAAAATTATTAAAA
*
542903 -AATATATTT
1 TATTATATTT
542912 AATTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 8 0.26
25 12 0.39
26 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATATTTTTAAAATTATTAAAA
Found at i:543145 original size:19 final size:20
Alignment explanation
Indices: 543112--543153 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
543102 TCATCTTATT
*
543112 TTATTAATATAATTTTATAA
1 TTATTAATATAATTTTAAAA
*
543132 TTATTAA-ATTATTTTAAAA
1 TTATTAATATAATTTTAAAA
543151 TTA
1 TTA
543154 ATTTTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAATATAATTTTAAAA
Found at i:550346 original size:23 final size:21
Alignment explanation
Indices: 550294--550389 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
550284 CCTAATCAGT
** * *
550294 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
550315 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
550336 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
550357 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
550378 AAATACGACACA
1 --ATACGACACA
550390 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:550354 original size:42 final size:43
Alignment explanation
Indices: 550294--550399 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
550284 CCTAATCAGT
*
550294 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
550336 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
550380 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
550400 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:550797 original size:15 final size:15
Alignment explanation
Indices: 550772--550829 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
550762 TCATGTATAT
550772 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
550788 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
550803 AATAATTTCAATCAA
1 TATAAATTCAATCAA
550818 TATAAATTCAAT
1 TATAAATTCAAT
550830 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:566013 original size:46 final size:46
Alignment explanation
Indices: 565957--566124 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
565947 TGGTTGAGCA
565957 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
566003 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* *
566048 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
566095 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA
566125 TTTAGGGGCG
Statistics
Matches: 104, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 1 0.01
46 84 0.81
47 1 0.01
49 4 0.04
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:566113 original size:92 final size:92
Alignment explanation
Indices: 565956--566123 Score: 300
Period size: 92 Copynumber: 1.8 Consensus size: 92
565946 ATGGTTGAGC
* *
565956 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGTTG
566021 AGTCCGAGTTCGTGAGATGTAACTAGG
66 AGTCCGAGTTCGTGAGATGTAACTAGG
* *
566048 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGTTG
566113 AGTCCGAGTTC
66 AGTCCGAGTTC
566124 ATTTAGGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (92 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCGTGAGATGTAACTAGG
Found at i:570137 original size:29 final size:29
Alignment explanation
Indices: 570094--570160 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
570084 TCAATGGCCT
* *
570094 ATATCTTTATAA-TTTTAAAGGATAAAAAC
1 ATATTTTTATAATTTTTAAA-GACAAAAAC
* * *
570123 ATATTTTTATTATTTTTAAAGACCAAAAT
1 ATATTTTTATAATTTTTAAAGACAAAAAC
570152 ATATTTTTA
1 ATATTTTTA
570161 CCATTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (29 bp):
ATATTTTTATAATTTTTAAAGACAAAAAC
Found at i:570681 original size:107 final size:107
Alignment explanation
Indices: 570550--570765 Score: 346
Period size: 108 Copynumber: 2.0 Consensus size: 107
570540 AAAGGTAAGC
*
570550 AATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAATAAATCAAT-T-TATAAAAAATAAAATAAAA
1 AATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAAAA
*
570613 AATTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
66 AA-TTTTTAGCATAGCAAAACGGCGTCATTTTGCTCAAAATGA
* * *
570656 AATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAATAAA
1 AATAGCGGC-GTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAAA
*
570721 AAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGA
65 AAATTTTTAGCATAGCAAAACGGCGTCATTTTGCTCAAAATGA
570764 AA
1 AA
570766 AATTTTTTGC
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
106 9 0.09
107 31 0.31
108 41 0.41
109 20 0.20
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (107 bp):
AATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAAAA
AATTTTTAGCATAGCAAAACGGCGTCATTTTGCTCAAAATGA
Found at i:570719 original size:195 final size:194
Alignment explanation
Indices: 570359--570721 Score: 606
Period size: 195 Copynumber: 1.9 Consensus size: 194
570349 ATATTCTTAT
*
570359 CGGCGTTTTTTAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAATTTT
1 CGGCGTTTTTAAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAATTTT
* *
570424 TTAGCATAACAAAACGGTGTCATTTTGCTGAAAATGAAATAGCGGCTTTTTTTTTATAAAAAACG
66 TTAGCATAACAAAACGGCGTCATTTTGCTGAAAATGAAATAGCGGC--TATTTTTATAAAAAACG
*
570489 CCGCAAAAAACAAATCAATATATAAATAAAAAATAAAATAAAAACGCCGCTAAAGGTAAGCAATA
129 CCGCAAAAAACAAATCAATATATAAAAAAAAAATAAAATAAAAACGCCGCTAAAGGTAAGCAATA
570554 G
194 G
570555 CGGCG-TTTTAAAAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTT
1 CGGCGTTTTTAAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAT-AAAAATTT
*
570618 TTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGAAATAGCGGC-ATTTTTATAAAAAACGC
65 TTTAGCATAACAAAACGGCGTCATTTTGCTGAAAATGAAATAGCGGCTATTTTTATAAAAAACGC
570682 CGCAAAAAACAAATCAATATATATATAAAATAAAATAAAA
130 CGCAAAAAACAAATCAATATATA-A-AAAA-AAAATAAAA
570722 AATTTTTAGC
Statistics
Matches: 158, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
192 39 0.25
193 1 0.01
194 15 0.09
195 98 0.62
196 5 0.03
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (194 bp):
CGGCGTTTTTAAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAATTTT
TTAGCATAACAAAACGGCGTCATTTTGCTGAAAATGAAATAGCGGCTATTTTTATAAAAAACGCC
GCAAAAAACAAATCAATATATAAAAAAAAAATAAAATAAAAACGCCGCTAAAGGTAAGCAATAG
Found at i:570959 original size:107 final size:109
Alignment explanation
Indices: 570810--571005 Score: 315
Period size: 108 Copynumber: 1.8 Consensus size: 109
570800 AAAGGTAAGC
* * *
570810 AATAGCGGCGTTTTTTAAAAAAAACGCCGCAAAAAATAAATCAATTTATA-AAAAAATAAAATAA
1 AATAGCGGCGATTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAA
**
570874 AATTTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
66 AAAATTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
* *
570918 AATAGCGGC-ATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAATAA
1 AATAGCGGCGATTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAA
570982 AAAATTTTTAGCATAGCAAAACGG
66 AAAATTTTTAGCATAGCAAAACGG
571006 NNNNNNNNNN
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 36 0.45
108 44 0.55
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (109 bp):
AATAGCGGCGATTTTTAAAAAAAACGCCGCAAAAAACAAATCAATATATATAAAAAATAAAATAA
AAAATTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
Found at i:570989 original size:262 final size:260
Alignment explanation
Indices: 570526--571005 Score: 917
Period size: 262 Copynumber: 1.8 Consensus size: 260
570516 AAAAAATAAA
570526 ATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAATAAATCA
1 ATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAATAAATCA
570591 ATTTATAAAAAATAAAATAAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
66 ATTTATAAAAAATAAAATAAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
570656 AATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAATAAA
131 AATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAATAAA
570721 AAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAATTTTTTGCGGCGTTTCTC
196 AAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAATTTTTTGCGGCGTTTCTC
570786 ATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTAAAAAAAACGCCGCAAAAAATAAAT
1 ATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCG--TTTTAAAAAAAACGCCGCAAAAAATAAAT
*
570851 CAATTTATAAAAAAATAAAAT-AAAATTTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAA
64 CAATTTAT-AAAAAATAAAATAAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAA
570915 TGAAATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAAT
128 TGAAATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAAT
570980 AAAAAATTTTTAGCATAGCAAAACGG
193 AAAAAATTTTTAGCATAGCAAAACGG
571006 NNNNNNNNNN
Statistics
Matches: 216, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
260 34 0.16
262 170 0.79
263 12 0.06
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (260 bp):
ATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTAAAAAAAACGCCGCAAAAAATAAATCA
ATTTATAAAAAATAAAATAAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGCTGAAAATGA
AATAGCGGCATTTTTATAAAAAACGCCGCAAAAAACAAATCAATATATATATAAAATAAAATAAA
AAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAATTTTTTGCGGCGTTTCTC
Found at i:576502 original size:44 final size:44
Alignment explanation
Indices: 576454--576577 Score: 101
Period size: 44 Copynumber: 3.0 Consensus size: 44
576444 CATTTAATTA
576454 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
1 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
* * **
576498 ATTATC-ATTCATAA--A-A-CA-AACAATCATTTA---AT--TA-
1 ATTATCTA-TCTTAATCATATCATACCCCT-ATTTAGCCATAATAC
*
576532 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCGTAATAC
1 ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
576576 AT
1 AT
576578 CCCATTACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 28
0.61 0.10 0.30
Matches are distributed among these distances:
34 11 0.19
35 3 0.05
36 1 0.02
37 3 0.05
38 7 0.12
39 6 0.11
40 7 0.12
41 2 0.04
42 1 0.02
43 3 0.05
44 13 0.23
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (44 bp):
ATTATCTATCTTAATCATATCATACCCCTATTTAGCCATAATAC
Found at i:576509 original size:78 final size:78
Alignment explanation
Indices: 576419--576577 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 78
576409 TTCAACATTT
576419 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
1 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
576484 TTTAGCCATAATA
66 TTTAGCCATAATA
576497 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
1 CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
*
576562 TTTAGCCGTAATA
66 TTTAGCCATAATA
576575 CAT
1 CAT
576578 CCCATTACAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (78 bp):
CATTATCATTCATAAAACAAACAATCATTTAATTAATTATCTATCTTAATCATATCATACCCCTA
TTTAGCCATAATA
Found at i:578041 original size:16 final size:17
Alignment explanation
Indices: 578020--578053 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
578010 AAAATTTAAT
578020 AAAAGTCCATTTA-AAA
1 AAAAGTCCATTTACAAA
*
578036 AAAAGTTCATTTACAAA
1 AAAAGTCCATTTACAAA
578053 A
1 A
578054 TACAAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAGTCCATTTACAAA
Found at i:578098 original size:17 final size:18
Alignment explanation
Indices: 578069--578103 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
578059 GCCCAAATAC
578069 AAAAACCTAAAAGCCTAA
1 AAAAACCTAAAAGCCTAA
578087 AAAAACCT-AAAGCCTAA
1 AAAAACCTAAAAGCCTAA
578104 TGGCCCACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAACCTAAAAGCCTAA
Found at i:578315 original size:14 final size:16
Alignment explanation
Indices: 578293--578329 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
578283 AAAGAAAAAA
*
578293 AACAAAAGCAGA-AAC
1 AACAGAAGCAGAGAAC
578308 -ACAGAAGCAGAGAAC
1 AACAGAAGCAGAGAAC
578323 AACAGAA
1 AACAGAA
578330 CAAAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (16 bp):
AACAGAAGCAGAGAAC
Found at i:593482 original size:19 final size:20
Alignment explanation
Indices: 593460--593507 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
593450 AATTATATTG
*
593460 AATTGAAAAAAATAT-AGTT
1 AATTGAAAAAAATATGAATT
*
593479 AATT-AATTAAAATATGAATT
1 AATTGAA-AAAAATATGAATT
593499 AATTGAAAA
1 AATTGAAAA
593508 CTAGAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTGAAAAAAATATGAATT
Found at i:593938 original size:18 final size:18
Alignment explanation
Indices: 593885--593952 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
593875 AAAGATCGAC
*
593885 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-TTGAT
* *
593904 TGTTACTGTATATTTGAT
1 TGTTACTGAATAATTGAT
*
593922 T-TTCACTGAATAATTGAC
1 TGTT-ACTGAATAATTGAT
*
593940 TGTTACTGGATAA
1 TGTTACTGAATAA
593953 CCGATCAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.05
18 25 0.62
19 13 0.32
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:598862 original size:20 final size:18
Alignment explanation
Indices: 598834--598877 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
598824 ATAGAGGTAA
*
598834 TAAAGTGTACATAATAATAT
1 TAAAATGTACA-AATAA-AT
*
598854 TAAAATGTATAAATAAAT
1 TAAAATGTACAAATAAAT
598872 TAAAAT
1 TAAAAT
598878 AAAAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 5 0.23
20 9 0.41
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (18 bp):
TAAAATGTACAAATAAAT
Found at i:602985 original size:18 final size:17
Alignment explanation
Indices: 602962--602999 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
602952 TAGTTCCATC
*
602962 TTATTTTTTTTTTCAATT
1 TTATTTTATTTTT-AATT
602980 TTATTTTATTTTTAATT
1 TTATTTTATTTTTAATT
602997 TTA
1 TTA
603000 ACTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTATTTTTAATT
Found at i:602991 original size:17 final size:17
Alignment explanation
Indices: 602966--602999 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
602956 TCCATCTTAT
*
602966 TTTTTTTTTCAATTTTA
1 TTTTATTTTCAATTTTA
*
602983 TTTTATTTTTAATTTTA
1 TTTTATTTTCAATTTTA
603000 ACTTTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTCAATTTTA
Found at i:608791 original size:16 final size:17
Alignment explanation
Indices: 608765--608797 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
608755 ATTTTTCATG
*
608765 TTATTATTAAATCATTC
1 TTATTATTAAAGCATTC
608782 TTATTA-TAAAGCATTC
1 TTATTATTAAAGCATTC
608798 ACACGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATTATTAAAGCATTC
Found at i:612753 original size:29 final size:29
Alignment explanation
Indices: 612691--612810 Score: 152
Period size: 29 Copynumber: 4.2 Consensus size: 29
612681 TACATATATG
* * *
612691 CATATGGCCCACTGGGCCC-AATCTCATT
1 CATATGGCCCATTAGGCCCAAATCACATT
* *
612719 CATATGGCCCATTAGTCTCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
*
612748 CGTATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
* * *
612777 CATATGGCCCATTATGCCAAAACCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
612806 CATAT
1 CATAT
612811 TCATGCTTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 15 0.19
29 64 0.81
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAAATCACATT
Found at i:617280 original size:13 final size:13
Alignment explanation
Indices: 617262--617290 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
617252 AACAAAATAG
617262 GAAATAAAAGAAA
1 GAAATAAAAGAAA
617275 GAAATAAAAGAAA
1 GAAATAAAAGAAA
617288 GAA
1 GAA
617291 GAGAAGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
GAAATAAAAGAAA
Found at i:621813 original size:55 final size:55
Alignment explanation
Indices: 621748--621857 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
621738 AAAATCTATA
*
621748 AAAGAATGTAAATGTTTTAGTTG-TGGAAAAATAGGATATAGCTAAATATTGTAGG
1 AAAGAATGTAAATGTTTTAGTTGCT-GAAAAATAGGATACAGCTAAATATTGTAGG
* *
621803 AAAGAATGTAAATGTTTTAGTTGCTGAAGAATAGGATGCAGCTAAATATTGTAGG
1 AAAGAATGTAAATGTTTTAGTTGCTGAAAAATAGGATACAGCTAAATATTGTAGG
621858 GAAAAAAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 50 0.98
56 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (55 bp):
AAAGAATGTAAATGTTTTAGTTGCTGAAAAATAGGATACAGCTAAATATTGTAGG
Found at i:623206 original size:18 final size:18
Alignment explanation
Indices: 623183--623248 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
623173 AAAATGTGAG
* *
623183 AAATGATGTTCGCATTTT
1 AAATGATGTTCACATTTC
623201 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
623219 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
623237 AAATGATGTTCA
1 AAATGATGTTCA
623249 AATTGATGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:623772 original size:72 final size:71
Alignment explanation
Indices: 623672--623843 Score: 229
Period size: 72 Copynumber: 2.4 Consensus size: 71
623662 AATAAAAATC
* * * *
623672 CTAAACTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 CTAAATTACTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
623737 TCTAT-
66 TCTATA
* * * *
623742 GTGTAATCTACTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGTTATTGAATTTATGTTCTACT
1 CT-AAAT-TACTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACT
*
623807 TATTTATA
64 TATCTATA
*
623815 CTAAATTAGTTTTATCAATAGTTGTTTAT
1 CTAAATTACTTTTATCAATAGTTGTTTAT
623844 ATATGATTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.27
72 61 0.71
73 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (71 bp):
CTAAATTACTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
TCTATA
Found at i:625888 original size:13 final size:13
Alignment explanation
Indices: 625864--625898 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
625854 CTTAAAATTT
*
625864 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
625877 TTAAAAGCACTTC
1 TCAAAAGCACTTC
625890 TCAAAAGCA
1 TCAAAAGCA
625899 TTTCCAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:629180 original size:46 final size:48
Alignment explanation
Indices: 629108--629210 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
629098 GACATGACAG
* * * * *
629108 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGACATTGGA
*
629154 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGACATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGACATTGGA
629202 GACAGGAAT
1 GACAGGAAT
629211 AATTCATGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 27 0.55
47 1 0.02
48 21 0.43
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGACATTGGA
Done.