Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 15 of 103
Found at i:5718748 original size:50 final size:49
Alignment explanation
Indices: 5718598--5718888 Score: 239
Period size: 49 Copynumber: 5.9 Consensus size: 49
5718588 ACAAGTCTAG
* * * * *
5718598 GTCTCTAAATCATTTGTTCAAGATCAAGTCGCAAGACCCTTAAAGCGAA
1 GTCTCTAAATCATTCGTTCAAGATCAAGTTGTAAGACCTTTGAAGCGAA
* ** ** *
5718647 GTCT-TCAAATCATTCATTCAAGATTGAGTCATAAGACCTTTGAAACGAA
1 GTCTCT-AAATCATTCGTTCAAGATCAAGTTGTAAGACCTTTGAAGCGAA
* * *
5718696 GTCTCTAAATCATTTGTTCAAAATCAAGTTGTTAAGACCTTTGAAGTGAA
1 GTCTCTAAATCATTCGTTCAAGATCAAGTTG-TAAGACCTTTGAAGCGAA
* * *
5718746 GTCTCCAAATCATTCGTTCAAGATCAAGTTGTAGGACCTTTGAAGTGAA
1 GTCTCTAAATCATTCGTTCAAGATCAAGTTGTAAGACCTTTGAAGCGAA
* * * * * ** *
5718795 G--TCTACATCGTTCATTCAAGATCAAGTCGTCAAAACCCATGAAGCAAA
1 GTCTCTAAATCATTCGTTCAAGATCAAGTTGT-AAGACCTTTGAAGCGAA
** * * *
5718843 GTCT-TCAAATTGTTCGTTCAATATTAAGTCGTCAAGACCTTTGAAG
1 GTCTCT-AAATCATTCGTTCAAGATCAAGTTGT-AAGACCTTTGAAG
5718889 TTGAAATACC
Statistics
Matches: 194, Mismatches: 41, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
47 24 0.12
48 13 0.07
49 79 0.41
50 78 0.40
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (49 bp):
GTCTCTAAATCATTCGTTCAAGATCAAGTTGTAAGACCTTTGAAGCGAA
Found at i:5718784 original size:99 final size:98
Alignment explanation
Indices: 5718598--5718887 Score: 260
Period size: 97 Copynumber: 2.9 Consensus size: 98
5718588 ACAAGTCTAG
* *
5718598 GTCTCTAAATCATTTGTTCAAGATCAAGTCGCAAGACCCTTAAAGCGAAGTCTTCAAATCATTCA
1 GTCTCTAAATCATTTGTTCAAAATCAAGTCGCAAGACCCTTAAAGCGAAGTCTCCAAATCATTCA
**
5718663 TTCAAGATTGAGTCATAAGACCTTTGAAACGAA
66 TTCAAGATCAAGTCATAAGACCTTTGAAACGAA
* * * * *
5718696 GTCTCTAAATCATTTGTTCAAAATCAAGTTGTTAAGACCTTTGAAGTGAAGTCTCCAAATCATTC
1 GTCTCTAAATCATTTGTTCAAAATCAAGTCG-CAAGACCCTTAAAGCGAAGTCTCCAAATCATTC
* ** * **
5718761 GTTCAAGATCAAGTTGTAGGACCTTTGAAGTGAA
65 ATTCAAGATCAAGTCATAAGACCTTTGAAACGAA
* * ** * * * * * * **
5718795 G--TCTACATCGTTCATTCAAGATCAAGTCGTCAAAACCCATGAAGCAAAGTCTTCAAATTGTTC
1 GTCTCTAAATCATTTGTTCAAAATCAAGTCG-CAAGACCCTTAAAGCGAAGTCTCCAAATCATTC
* * * *
5718858 GTTCAATATTAAGTCGTCAAGACCTTTGAA
65 ATTCAAGATCAAGTCAT-AAGACCTTTGAA
5718888 GTTGAAATAC
Statistics
Matches: 156, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
97 61 0.39
98 40 0.26
99 55 0.35
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (98 bp):
GTCTCTAAATCATTTGTTCAAAATCAAGTCGCAAGACCCTTAAAGCGAAGTCTCCAAATCATTCA
TTCAAGATCAAGTCATAAGACCTTTGAAACGAA
Found at i:5719149 original size:19 final size:19
Alignment explanation
Indices: 5719125--5719169 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5719115 CCAAGGAGAC
5719125 AAAATAAAATTTT-TAGAAT
1 AAAATAAAATTTTAT-GAAT
* *
5719144 AAAATAATATTTTATTAAT
1 AAAATAAAATTTTATGAAT
5719163 AAAATAA
1 AAAATAA
5719170 TATTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAAAATTTTATGAAT
Found at i:5719739 original size:2 final size:2
Alignment explanation
Indices: 5719732--5719759 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5719722 AGAAAGAATA
5719732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5719760 GTAATTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5719856 original size:27 final size:29
Alignment explanation
Indices: 5719820--5719896 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
5719810 AGGGAGAGTA
*
5719820 AAAGAGAAACAAAGAAGAAA-C-G-GAGAG
1 AAAGAAAAACAAA-AAGAAACCGGCGAGAG
*
5719847 AAAGAAAAACAAAAAGAAAACCGTGCGTGAG
1 AAAGAAAAACAAAAAG-AAACCG-GCGAGAG
5719878 AAAGAAAAACAAAAAGAAA
1 AAAGAAAAACAAAAAGAAA
5719897 AGAAAGCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 3 0.07
27 15 0.35
28 1 0.02
30 4 0.09
31 20 0.47
ACGTcount: A:0.66, C:0.09, G:0.22, T:0.03
Consensus pattern (29 bp):
AAAGAAAAACAAAAAGAAACCGGCGAGAG
Found at i:5720375 original size:5 final size:5
Alignment explanation
Indices: 5720357--5720408 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
5720347 ATGGTGGAAG
* *
5720357 AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAATA ACAAGA AAGGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA AAAGA
5720406 AAA
1 AAA
5720409 TGGGCATGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
4 8 0.19
5 30 0.71
6 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:5720435 original size:27 final size:26
Alignment explanation
Indices: 5720394--5720474 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
5720384 AAAAGAAAAT
* * *
5720394 AACAAGAAAGGAAAATGGGCATGGCCC
1 AACAAG-AAGAAAAATGGACATGGTCC
5720421 AACAAGCAAGAAAAATGGACATGGTCC
1 AACAAG-AAGAAAAATGGACATGGTCC
* *
5720448 AATAA-AGGAAAAATGGACATGGTCC
1 AACAAGAAGAAAAATGGACATGGTCC
5720473 AA
1 AA
5720475 TAAAGGAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 21 0.44
27 27 0.56
ACGTcount: A:0.48, C:0.16, G:0.25, T:0.11
Consensus pattern (26 bp):
AACAAGAAGAAAAATGGACATGGTCC
Found at i:5720464 original size:25 final size:25
Alignment explanation
Indices: 5720430--5720514 Score: 111
Period size: 25 Copynumber: 3.4 Consensus size: 25
5720420 CAACAAGCAA
5720430 GAAAAATGGACATGGTCCAATAAAG
1 GAAAAATGGACATGGTCCAATAAAG
5720455 GAAAAATGGACATGGTCCAATAAAG
1 GAAAAATGGACATGGTCCAATAAAG
* *
5720480 GAAGAAT-GAGCATGGTTCAATTAAA-
1 GAAAAATGGA-CATGGTCCAA-TAAAG
*
5720505 AAAAAATGGA
1 GAAAAATGGA
5720515 AGAAGTCCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
24 2 0.04
25 45 0.85
26 6 0.11
ACGTcount: A:0.49, C:0.09, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAAAATGGACATGGTCCAATAAAG
Found at i:5722593 original size:50 final size:49
Alignment explanation
Indices: 5722500--5722652 Score: 157
Period size: 50 Copynumber: 3.1 Consensus size: 49
5722490 GGTCATGACA
* * * *
5722500 GAAGCGAAGTCTCCAAATTGTTCATTCAATATTAAGTCATCAAGACCCTT
1 GAAGAGAAGTCTCCAAATCGTTCATTCAAGATAAAGTCATCAAGA-CCTT
* * **
5722550 GAAGAGAAGTCTCCAAATCATTCATTCAAGATCAAGTTGTCAAGACCTT
1 GAAGAGAAGTCTCCAAATCGTTCATTCAAGATAAAGTCATCAAGACCTT
* * *
5722599 TACA-ATGAAGTCTCTAAATCGTTCGTTCAAGATAAAGTCAT-AAGACCTTT
1 GA-AGA-GAAGTCTCCAAATCGTTCATTCAAGATAAAGTCATCAAGACC-TT
5722649 GAAG
1 GAAG
5722653 CGAATTCAAG
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
49 13 0.15
50 71 0.85
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (49 bp):
GAAGAGAAGTCTCCAAATCGTTCATTCAAGATAAAGTCATCAAGACCTT
Found at i:5723873 original size:20 final size:20
Alignment explanation
Indices: 5723848--5723907 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
5723838 TTTTAGACCA
*
5723848 AATGTATCGATACAGTTTGG
1 AATGTATCGATACATTTTGG
* **
5723868 AATGTATGGATACATTTTAA
1 AATGTATCGATACATTTTGG
*
5723888 AATGTATCCATACATTTTGG
1 AATGTATCGATACATTTTGG
5723908 GCAAAACCAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTTTGG
Found at i:5724072 original size:21 final size:21
Alignment explanation
Indices: 5724046--5724121 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
5724036 TGCAAGGGAG
* *
5724046 GTTTAAAACTAATTTAAACAA
1 GTTTAAAAATAATTCAAACAA
*
5724067 GTTTAAAAATGATTCAAACAA
1 GTTTAAAAATAATTCAAACAA
* * *
5724088 GGTTCAAAAATCATTCAAGCAA
1 -GTTTAAAAATAATTCAAACAA
*
5724110 TTTTAAAAATAA
1 GTTTAAAAATAA
5724122 CTTTGCGATA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 27 0.60
22 18 0.40
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (21 bp):
GTTTAAAAATAATTCAAACAA
Found at i:5724096 original size:22 final size:21
Alignment explanation
Indices: 5724061--5724119 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
5724051 AAACTAATTT
* *
5724061 AAACAAGTTTAAAAATGATTC
1 AAACAAGTTCAAAAATCATTC
5724082 AAACAAGGTTCAAAAATCATTC
1 AAACAA-GTTCAAAAATCATTC
* * *
5724104 AAGCAATTTTAAAAAT
1 AAACAAGTTCAAAAAT
5724120 AACTTTGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (21 bp):
AAACAAGTTCAAAAATCATTC
Found at i:5728534 original size:31 final size:31
Alignment explanation
Indices: 5728499--5728557 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5728489 TCCACTATGA
* * *
5728499 AAAATACTTTTTAAGGCTCAAGCATAACCTT
1 AAAATACCTTTCAAGGATCAAGCATAACCTT
*
5728530 AAAATGCCTTTCAAGGATCAAGCATAAC
1 AAAATACCTTTCAAGGATCAAGCATAAC
5728558 TTTCCAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (31 bp):
AAAATACCTTTCAAGGATCAAGCATAACCTT
Found at i:5729044 original size:20 final size:20
Alignment explanation
Indices: 5729019--5729058 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5729009 TTCTAAACCA
*
5729019 AATGTATCGATACATTTTGG
1 AATGTATCCATACATTTTGG
5729039 AATGTATCCATACATTTTGG
1 AATGTATCCATACATTTTGG
5729059 GCAGAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
AATGTATCCATACATTTTGG
Found at i:5729241 original size:21 final size:22
Alignment explanation
Indices: 5729198--5729256 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5729188 TGCAAGGGAG
*
5729198 GTTT-AAAACTAATTTAAACAA
1 GTTTAAAAACTAATTCAAACAA
*
5729219 GTTTAAAAACT-ATTCAAATAA
1 GTTTAAAAACTAATTCAAACAA
* *
5729240 GTTCAAAAA-TCATTCAA
1 GTTTAAAAACTAATTCAA
5729257 GAAATTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 26 0.79
22 6 0.18
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (22 bp):
GTTTAAAAACTAATTCAAACAA
Found at i:5729290 original size:21 final size:21
Alignment explanation
Indices: 5729224--5729291 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
5729214 AACAAGTTTA
*
5729224 AAAACT-ATTCAA-ATAAGTTC
1 AAAACTCATTCAAGA-AATTTC
*
5729244 AAAAATCATTCAAGAAATTTC
1 AAAACTCATTCAAGAAATTTC
* * *
5729265 AAAACTCATTGAAGTAATTTT
1 AAAACTCATTCAAGAAATTTC
5729286 AAAACT
1 AAAACT
5729292 TTTCACATGG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.12
21 34 0.85
22 1 0.03
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (21 bp):
AAAACTCATTCAAGAAATTTC
Found at i:5729391 original size:21 final size:21
Alignment explanation
Indices: 5729346--5729413 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
5729336 GTTTAAAAAC
* * **
5729346 TCATTCAAACAACTTCAAAAA
1 TCATTCAAATAAGTTCAAAGT
* * *
5729367 TCATTTAAATAAGTTTATAGT
1 TCATTCAAATAAGTTCAAAGT
5729388 TCATTCAAATAAGTTCAAAGT
1 TCATTCAAATAAGTTCAAAGT
5729409 TCATT
1 TCATT
5729414 GAAGCAATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.37
Consensus pattern (21 bp):
TCATTCAAATAAGTTCAAAGT
Found at i:5735302 original size:3 final size:3
Alignment explanation
Indices: 5735294--5735337 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5735284 TGTAACCTCA
5735294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5735338 AAGAGAGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5738402 original size:2 final size:2
Alignment explanation
Indices: 5738395--5738419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5738385 TAAGACAGAT
5738395 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5738420 AATAGACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5744002 original size:10 final size:10
Alignment explanation
Indices: 5743989--5744030 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
5743979 AAAGTACAAA
5743989 AAATTTATTT
1 AAATTTATTT
5743999 AAATTTATTT
1 AAATTTATTT
* *
5744009 AAA-TAATTA
1 AAATTTATTT
*
5744018 AAATTTTTTT
1 AAATTTATTT
5744028 AAA
1 AAA
5744031 ATATTATGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATTTATTT
Found at i:5744036 original size:19 final size:18
Alignment explanation
Indices: 5743994--5744036 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5743984 ACAAAAAATT
*
5743994 TATTTAAATTTATTTAAA
1 TATTAAAATTTATTTAAA
*
5744012 TAATTAAAATTTTTTTAAAA
1 T-ATTAAAATTTATTT-AAA
5744032 TATTA
1 TATTA
5744037 TGTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTAAAATTTATTTAAA
Found at i:5745266 original size:18 final size:19
Alignment explanation
Indices: 5745224--5745266 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5745214 TTGGAGCTTT
5745224 TTTTTTAAAAAAAAAATAC
1 TTTTTTAAAAAAAAAATAC
* *
5745243 TCTTTT-AAAAAAAATTAC
1 TTTTTTAAAAAAAAAATAC
5745261 TTTTTT
1 TTTTTT
5745267 TGTACGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTTTAAAAAAAAAATAC
Found at i:5746175 original size:27 final size:28
Alignment explanation
Indices: 5746127--5746183 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
5746117 AATTTTGTTA
**
5746127 TAATTAAAATTTTTTTCATTATTTTAAT
1 TAATTAAAATTTTAATCATTATTTTAAT
*
5746155 TAATTAAAATTTTAAT-ATTATTTTCAT
1 TAATTAAAATTTTAATCATTATTTTAAT
5746182 TA
1 TA
5746184 TAATTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TAATTAAAATTTTAATCATTATTTTAAT
Found at i:5748066 original size:26 final size:26
Alignment explanation
Indices: 5748030--5748081 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5748020 CTAAAAGTCA
5748030 ATTTTAAAATGTCAAGGGTTTGGCAG
1 ATTTTAAAATGTCAAGGGTTTGGCAG
5748056 ATTTTAAAATGTCAAGGGTTTGGCAG
1 ATTTTAAAATGTCAAGGGTTTGGCAG
5748082 CAAGTTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.35
Consensus pattern (26 bp):
ATTTTAAAATGTCAAGGGTTTGGCAG
Found at i:5748264 original size:19 final size:20
Alignment explanation
Indices: 5748226--5748276 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5748216 TGGGGGCAAA
*
5748226 AAAAAATCCCTAGCGGTAGCC
1 AAAAAA-CCCTAGCGCTAGCC
5748247 AAAAAACCCTAGC-CTAGCC
1 AAAAAACCCTAGCGCTAGCC
* *
5748266 GAAAAGCCCTA
1 AAAAAACCCTA
5748277 AAAACCTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 14 0.52
20 7 0.26
21 6 0.22
ACGTcount: A:0.41, C:0.31, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAAAACCCTAGCGCTAGCC
Found at i:5751488 original size:19 final size:19
Alignment explanation
Indices: 5751461--5751497 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5751451 CCATTTGACT
5751461 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
*
5751480 TATTTGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
5751498 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:5751594 original size:27 final size:27
Alignment explanation
Indices: 5751543--5751595 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 27
5751533 TTGGAGTATA
5751543 GGGGCGAAATGGTAATTTTACCACCCCG
1 GGGGCGAAATGGTAATTTTA-CACCCCG
5751571 GGGGC-AAATCGGTAAATTTT-CACCC
1 GGGGCGAAAT-GGT-AATTTTACACCC
5751596 TCGACATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
27 9 0.39
28 8 0.35
29 6 0.26
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (27 bp):
GGGGCGAAATGGTAATTTTACACCCCG
Found at i:5752756 original size:13 final size:13
Alignment explanation
Indices: 5752738--5752762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5752728 GGAGAAATTG
5752738 TGATTTTATAAAA
1 TGATTTTATAAAA
5752751 TGATTTTATAAA
1 TGATTTTATAAA
5752763 TTTTCTAAAA
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):
TGATTTTATAAAA
Found at i:5762223 original size:13 final size:13
Alignment explanation
Indices: 5762205--5762229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5762195 TTCCAGAAAA
5762205 TTTATAAAATCAT
1 TTTATAAAATCAT
5762218 TTTATAAAATCA
1 TTTATAAAATCA
5762230 CAATTTTTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5763634 original size:19 final size:19
Alignment explanation
Indices: 5763610--5763647 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5763600 CTACCAAACC
*
5763610 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5763629 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5763648 AGTTAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5768443 original size:35 final size:35
Alignment explanation
Indices: 5768404--5768475 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5768394 CTCTTATGCC
5768404 AATGTAACTCAAAAAGTGGTATATAAATTCATCAA
1 AATGTAACTCAAAAAGTGGTATATAAATTCATCAA
* * *
5768439 AATGTAACTTAGAAAGTGGTATGTAAATTCATCAA
1 AATGTAACTCAAAAAGTGGTATATAAATTCATCAA
5768474 AA
1 AA
5768476 AAGAGATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (35 bp):
AATGTAACTCAAAAAGTGGTATATAAATTCATCAA
Found at i:5769157 original size:24 final size:24
Alignment explanation
Indices: 5769129--5769176 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5769119 ACTATGCCTA
5769129 AAAAAAAGGAGAACA-AAAAAGAAAG
1 AAAAAAAGG-GAA-AGAAAAAGAAAG
5769154 AAAAAAAGGGAAAGAAAAAGAAA
1 AAAAAAAGGGAAAGAAAAAGAAA
5769177 AAAGAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 12 0.55
25 9 0.41
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAAAAGGGAAAGAAAAAGAAAG
Found at i:5769171 original size:25 final size:25
Alignment explanation
Indices: 5769128--5769176 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5769118 TACTATGCCT
5769128 AAAAAAAAGGAGAACAAAAAAGAAAG
1 AAAAAAAAGGAGAAC-AAAAAGAAAG
* *
5769154 AAAAAAAGGGA-AAGAAAAAGAAA
1 AAAAAAAAGGAGAACAAAAAGAAA
5769177 AAAGAGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGGAGAACAAAAAGAAAG
Found at i:5770102 original size:34 final size:34
Alignment explanation
Indices: 5770059--5770124 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5770049 AATTGATTTA
*
5770059 AAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTTC
1 AAAGTTGTGGAGCCTCAGATGAGAAGTTGTTTTC
**
5770093 AAAGTTGTGGAGCCTTGGATGAGAAGTTGTTT
1 AAAGTTGTGGAGCCTCAGATGAGAAGTTGTTT
5770125 ATCTTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (34 bp):
AAAGTTGTGGAGCCTCAGATGAGAAGTTGTTTTC
Found at i:5770150 original size:53 final size:53
Alignment explanation
Indices: 5770088--5770283 Score: 261
Period size: 53 Copynumber: 3.7 Consensus size: 53
5770078 TGAGGAGTTG
* * *
5770088 TTTTCAAAGTTGTGGAGCCTTGGATGAGAAGTTGTTTATCTTTTTCAAAATTG
1 TTTTTAAAGTTGTGGAGCCTTAGATGAGAAGTTGTTTATCTTTTTCAAAATTA
* *
5770141 TTTTTAAAGTTGTGGAGCATTGGATGA-AGAGTTGTTTATCTTTTTCAAAATTA
1 TTTTTAAAGTTGTGGAGCCTTAGATGAGA-AGTTGTTTATCTTTTTCAAAATTA
* * * * *
5770194 TTTTTAAAGTTATGGAGTCTCAAATGAGGAA-TTGTTTATCTTTTTCAAGATTA
1 TTTTTAAAGTTGTGGAGCCTTAGATGA-GAAGTTGTTTATCTTTTTCAAAATTA
*
5770247 TTTTTAAAGTTGTGGAGCCTTAGATGAGGAGTTGTTT
1 TTTTTAAAGTTGTGGAGCCTTAGATGAGAAGTTGTTT
5770284 TTAAAGTTCT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
52 3 0.02
53 119 0.96
54 1 0.01
55 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (53 bp):
TTTTTAAAGTTGTGGAGCCTTAGATGAGAAGTTGTTTATCTTTTTCAAAATTA
Found at i:5770173 original size:87 final size:85
Alignment explanation
Indices: 5770003--5770177 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 85
5769993 TGTTAAATTA
*
5770003 TTTTTAAAGTTGTAGAGCCTCGGATGAAGAGTTGTTTATTTTTTCAAATTGATTTAAAAGTTGTG
1 TTTTCAAAGTTGTAGAGCCTCGGATGAAGAGTTGTTTATTTTTTCAAATTGATTTAAAAGTTGTG
* *
5770068 GAGCCTCAGATGAGGAGTTG
66 GAGCATCAGATGAAGAGTTG
* * * *
5770088 TTTTCAAAGTTGTGGAGCCTTGGATG-AGAAGTTGTTTATCTTTTTCAAAATTGTTTTTAAAGTT
1 TTTTCAAAGTTGTAGAGCCTCGGATGAAG-AGTTGTTTAT-TTTTTC-AAATTGATTTAAAAGTT
**
5770152 GTGGAGCATTGGATGAAGAGTTG
63 GTGGAGCATCAGATGAAGAGTTG
5770175 TTT
1 TTT
5770178 ATCTTTTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
84 2 0.03
85 33 0.42
86 6 0.08
87 37 0.47
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (85 bp):
TTTTCAAAGTTGTAGAGCCTCGGATGAAGAGTTGTTTATTTTTTCAAATTGATTTAAAAGTTGTG
GAGCATCAGATGAAGAGTTG
Found at i:5770290 original size:34 final size:34
Alignment explanation
Indices: 5770247--5770317 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
5770237 TTCAAGATTA
* **
5770247 TTTTTAAAGTTGTGGAGCCTTAGATGAGGAGTTG
1 TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTG
5770281 TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTG
1 TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTG
5770315 TTT
1 TTT
5770318 ATCTTTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (34 bp):
TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTG
Found at i:5770297 original size:87 final size:87
Alignment explanation
Indices: 5770194--5770370 Score: 273
Period size: 87 Copynumber: 2.0 Consensus size: 87
5770184 TTCAAAATTA
* * *
5770194 TTTTTAAAGTTATGGAGTCTCAAATGAGGAATTGTTTATCTTTTTCAAGATTATTTTTAAAGTTG
1 TTTTTAAAGTTATGGAGCCCCAAATGAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTG
* * *
5770259 TGGAGCCTTAGATGAGGAGTTG
66 TGGAGCCTCAAATAAGGAGTTG
* * *
5770281 TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAGTTG
1 TTTTTAAAGTTATGGAGCCCCAAATGAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTG
5770346 TGGAGCCTCAAATAAGGAGTTG
66 TGGAGCCTCAAATAAGGAGTTG
5770368 TTT
1 TTT
5770371 ATCTTTTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (87 bp):
TTTTTAAAGTTATGGAGCCCCAAATGAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTG
TGGAGCCTCAAATAAGGAGTTG
Found at i:5770324 original size:193 final size:190
Alignment explanation
Indices: 5769997--5770473 Score: 634
Period size: 193 Copynumber: 2.5 Consensus size: 190
5769987 CCTATTTGTT
* * * * *
5769997 AAATTATTTTTAAAGTTGTAGAGCCTCGGATGAAGAGTTGTTTATTTTTTCAAATTGATTTAAAA
1 AAATTATTTTTAAAGTTGTGGAGTCTCGGATGAGGAATTGTTTATTTTTTCAAATT-ATTTTAAA
* ***
5770062 GTTGTGGAGCCTCAGATGAGGAGTTGTTTTCAAAGTTGTGGAGCCTTGGATGAGAAGTTGTTTAT
65 GTTGTGGAGCCTCAGATGAGGAGTTGTTTTCAAAGTTCTGGAGCCCCAGATGAGAAGTTGTTTAT
* ***
5770127 CTTTTTCAAAATTGTTTTTAAAGTTGTGGAGCATTGGATGAA-GAGTTGTTTATCTTTTTCA
130 CTTTTTCAAAATTATTTTTAAAGTTGTGGAGCATCAAAT-AAGGAGTTGTTTATCTTTTTCA
* **
5770188 AAATTATTTTTAAAGTTATGGAGTCTCAAATGAGGAATTGTTTATCTTTTTCAAGATTATTTTTA
1 AAATTATTTTTAAAGTTGTGGAGTCTCGGATGAGGAATTGTTTAT-TTTTTCAA-ATTA-TTTTA
* * *
5770253 AAGTTGTGGAGCCTTAGATGAGGAGTTGTTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTGTTT
63 AAGTTGTGGAGCCTCAGATGAGGAGTTGTTTTCAAAGTTCTGGAGCCCCAGATGAGAAGTTGTTT
*
5770318 ATCTTTTTCAAAATTATTTTTAAAGTTGTGGAGCCTCAAATAAGGAGTTGTTTATCTTTTTCA
128 ATCTTTTTCAAAATTATTTTTAAAGTTGTGGAGCATCAAATAAGGAGTTGTTTATCTTTTTCA
* * * *
5770381 AAATTATTTTTAAAGTTGTGGAGTCTTGGTTGAGGAATTATTTA-TTTTTCAAATTGGTTTTAAA
1 AAATTATTTTTAAAGTTGTGGAGTCTCGGATGAGGAATTGTTTATTTTTTCAAATT-ATTTTAAA
* * * *
5770445 GTTATGGAGACTCGGATGAAGAGTTGTTT
65 GTTGTGGAGCCTCAGATGAGGAGTTGTTT
5770474 ATTTTTCAAA
Statistics
Matches: 249, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
190 34 0.14
191 46 0.18
192 11 0.04
193 158 0.63
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (190 bp):
AAATTATTTTTAAAGTTGTGGAGTCTCGGATGAGGAATTGTTTATTTTTTCAAATTATTTTAAAG
TTGTGGAGCCTCAGATGAGGAGTTGTTTTCAAAGTTCTGGAGCCCCAGATGAGAAGTTGTTTATC
TTTTTCAAAATTATTTTTAAAGTTGTGGAGCATCAAATAAGGAGTTGTTTATCTTTTTCA
Found at i:5770343 original size:53 final size:50
Alignment explanation
Indices: 5770281--5770573 Score: 268
Period size: 50 Copynumber: 5.7 Consensus size: 50
5770271 TGAGGAGTTG
* *
5770281 TTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTGTTTATCTTTTTCAAAATTA
1 TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTA--TTTTTC-AAATTA
* *
5770334 TTTTTAAAGTTGTGGAGCCTCAAATAAGGAGTTGTTTATCTTTTTCAAAATTA
1 TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTA--TTTTTC-AAATTA
* ** * * * *
5770387 TTTTTAAAGTTGTGGAGTCTTGGTTGAGGAATTATTTATTTTTCAAATTG
1 TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTATTTTTCAAATTA
* * * * *
5770437 GTTTTAAAGTTATGGAGACTCGGATGAAGAGTTGTTTATTTTTCAAATTGA
1 TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTATTTTTCAAATT-A
* * ** * *
5770488 -CTTTAAACTTGTAAAACCTCGGATGAGGAGTTGTTTATTTTTCAAATTGA
1 TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTATTTTTCAAATT-A
* *
5770538 --TTTAAAGGTTATGGAGCCTCAGATGATGAGTTGTTT
1 TTTTTAAA-GTTGTGGAGCCTCAGATGAGGAGTTGTTT
5770574 TTAAAGTTAT
Statistics
Matches: 201, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 6 0.03
50 110 0.55
51 6 0.03
53 79 0.39
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (50 bp):
TTTTTAAAGTTGTGGAGCCTCAGATGAGGAGTTGTTTATTTTTCAAATTA
Found at i:5770416 original size:140 final size:140
Alignment explanation
Indices: 5770138--5770403 Score: 433
Period size: 140 Copynumber: 1.9 Consensus size: 140
5770128 TTTTTCAAAA
* ***
5770138 TTGTTTTTAAAGTTGTGGAGCATTGGATGAAGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAG
1 TTGTTTTTAAAGTTCTGGAGCACCAGATGAAGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAG
* * *
5770203 TTATGGAGTCTCAAATGAGGAATTGTTTATCTTTTTCAAGATTATTTTTAAAGTTGTGGAGCCTT
66 TTATGGAGCCTCAAATAAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTGTGGAGCCTT
5770268 AGATGAGGAG
131 AGATGAGGAG
* *
5770278 TTGTTTTTAAAGTTCTGGAGCCCCAGATGAGGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAG
1 TTGTTTTTAAAGTTCTGGAGCACCAGATGAAGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAG
* *
5770343 TTGTGGAGCCTCAAATAAGGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAGTTGTGGAG
66 TTATGGAGCCTCAAATAAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTGTGGAG
5770404 TCTTGGTTGA
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
140 115 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (140 bp):
TTGTTTTTAAAGTTCTGGAGCACCAGATGAAGAGTTGTTTATCTTTTTCAAAATTATTTTTAAAG
TTATGGAGCCTCAAATAAGGAATTGTTTATCTTTTTCAAAATTATTTTTAAAGTTGTGGAGCCTT
AGATGAGGAG
Found at i:5772756 original size:2 final size:2
Alignment explanation
Indices: 5772749--5772775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5772739 TGTTTCTTAA
5772749 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5772776 GACAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5787764 original size:15 final size:14
Alignment explanation
Indices: 5787740--5787774 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5787730 TTAATAGATG
5787740 TTAATTAGTTTACT
1 TTAATTAGTTTACT
*
5787754 TTAAGTTAGTTTAGT
1 TTAA-TTAGTTTACT
5787769 TTAATT
1 TTAATT
5787775 TTATGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (14 bp):
TTAATTAGTTTACT
Found at i:5788092 original size:21 final size:21
Alignment explanation
Indices: 5788066--5788109 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5788056 AAGCTAGATT
5788066 ACTGTAGGTCTACACGAGACA
1 ACTGTAGGTCTACACGAGACA
5788087 ACTGTAGGTCTACACGAGACA
1 ACTGTAGGTCTACACGAGACA
5788108 AC
1 AC
5788110 ATGTGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (21 bp):
ACTGTAGGTCTACACGAGACA
Found at i:5794015 original size:17 final size:18
Alignment explanation
Indices: 5793970--5794015 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5793960 AAAATTATTA
5793970 ATTATAATATATAT-ATC
1 ATTATAATATATATAATC
5793987 ATTAT--T-TATATAATC
1 ATTATAATATATATAATC
5794002 -TTATAATATATATA
1 ATTATAATATATATA
5794016 CTTAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 1 0.04
17 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATAATATATATAATC
Found at i:5799346 original size:40 final size:40
Alignment explanation
Indices: 5799289--5799494 Score: 225
Period size: 40 Copynumber: 5.0 Consensus size: 40
5799279 TTCTTTATAC
* * *
5799289 GCATTACGTGACTGAATATATGTTGAGCGTTGCGTGACAA
1 GCATTACGTGACTGAATATTTGTTGAGCATTGTGTGACAA
* * *
5799329 GTATTACGTGACTGAATATATGTTGAGCGTTGTGTGACAA
1 GCATTACGTGACTGAATATTTGTTGAGCATTGTGTGACAA
*
5799369 GTATTACGTGACTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATA
1 GCATTACGTGACTGAATATTTGTTGAGCATTGTGTGA---C---A-A
* *
5799416 GGCATTACGTGACTTAATATTTGTTGAGCTTTGTGTGACAA
1 -GCATTACGTGACTGAATATTTGTTGAGCATTGTGTGACAA
* *
5799457 GCGTTACGT-AGCTGAATATTTGTTGAGCATTGCGTGAC
1 GCATTACGTGA-CTGAATATTTGTTGAGCATTGTGTGAC
5799495 CTGTTTGTAG
Statistics
Matches: 146, Mismatches: 11, Indels: 18
0.83 0.06 0.10
Matches are distributed among these distances:
39 1 0.01
40 105 0.72
41 1 0.01
42 1 0.01
43 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 34 0.23
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (40 bp):
GCATTACGTGACTGAATATTTGTTGAGCATTGTGTGACAA
Found at i:5799406 original size:128 final size:128
Alignment explanation
Indices: 5799243--5799494 Score: 371
Period size: 128 Copynumber: 2.0 Consensus size: 128
5799233 TTTATTTGGC
* *
5799243 ATTAGGTGCCTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATACGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATACGCATTACGTGACTGAATAT
* * *
5799308 ATGTTGAGCGTTGCGTGACAAGTATTACGT-GACTGAATATATGTTGAGCGTTGTGTGACAAGT
66 ATGTTGAGCGTTGCGTGACAAGCATTACGTAG-CTGAATATATGTTGAGCATTGCGTGACAAGT
* * *
5799371 ATTACGTGACTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATAGGCATTACGTGACTTAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATACGCATTACGTGACTGAATAT
* * * * *
5799436 TTGTTGAGCTTTGTGTGACAAGCGTTACGTAGCTGAATATTTGTTGAGCATTGCGTGAC
66 ATGTTGAGCGTTGCGTGACAAGCATTACGTAGCTGAATATATGTTGAGCATTGCGTGAC
5799495 CTGTTTGTAG
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
128 109 0.99
129 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (128 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATACGCATTACGTGACTGAATAT
ATGTTGAGCGTTGCGTGACAAGCATTACGTAGCTGAATATATGTTGAGCATTGCGTGACAAGT
Found at i:5799480 original size:88 final size:88
Alignment explanation
Indices: 5799331--5799518 Score: 270
Period size: 88 Copynumber: 2.1 Consensus size: 88
5799321 CGTGACAAGT
* *
5799331 ATTACGTGACTGAATATATGTTGAGCGTTGTGTGACAAGTATTACGTGACTGAATATTTGTTGAG
1 ATTACGTGACTTAATATATGTTGAGCGTTGTGTGACAAGCATTACGTGACTGAATATTTGTTGAG
* **
5799396 CATTGTGTGAGTTCTTTATAGGC
66 CATTGCGTGACCTCTTTATAGGC
* * *
5799419 ATTACGTGACTTAATATTTGTTGAGCTTTGTGTGACAAGCGTTACGT-AGCTGAATATTTGTTGA
1 ATTACGTGACTTAATATATGTTGAGCGTTGTGTGACAAGCATTACGTGA-CTGAATATTTGTTGA
* *
5799483 GCATTGCGTGACCTGTTTGTAGGC
65 GCATTGCGTGACCTCTTTATAGGC
5799507 ATTACGTGACTT
1 ATTACGTGACTT
5799519 TAGCTACCTA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 1 0.01
88 88 0.99
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (88 bp):
ATTACGTGACTTAATATATGTTGAGCGTTGTGTGACAAGCATTACGTGACTGAATATTTGTTGAG
CATTGCGTGACCTCTTTATAGGC
Found at i:5801055 original size:110 final size:111
Alignment explanation
Indices: 5800878--5801537 Score: 921
Period size: 118 Copynumber: 5.8 Consensus size: 111
5800868 GGTGGGTGAC
* * * * *
5800878 TGACGTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGCTCAATAGTTTTTTAGGC-AGTGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
5800942 GGTTTTTATATATTGCGTTACTTGTTGTAGCGAGAGTGGTGGCGCG
66 GGTTTTTATATATTGCGTTACTTGTTGTAGCGAGAGTGGTGGCGCG
* *
5800988 TGACCTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGG-TTGCGTGATT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* *
5801052 GGTTTTTATATATTGCATTACCTGTTGTAGCGAGAGTGGTGGCGCG
66 GGTTTTTATATATTGCGTTACTTGTTGTAGCGAGAGTGGTGGCGCG
*
5801098 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGAC
* * * * * *
5801163 TGGTTTTTATATATTGCGTTACCTATTGTAACAATAGTGGTGGTGCG
65 TGGTTTTTATATATTGCGTTACTTGTTGTAGCGAGAGTGGTGGCGCG
*
5801210 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGGGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* *
5801275 GGTTTTTATATATTGCGTTACATATTGTTATGTATTACGAGAGTGGTGGCACG
66 GGTTTTTATATATTGCGTTAC---TTG-T-TGTA--GCGAGAGTGGTGGCGCG
*
5801328 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGATT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
5801393 GGTTTTTATATATTACGTGACCTGTTGTTATGTATTGCGAGAGTGGTGGCACG
66 GGTTTTTATATATTGCGTTA-C--TTG-T-TGTA--GCGAGAGTGGTGGCGCG
*
5801446 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
5801511 -GCTTTTATATATTACGTGACTTGTTGT
66 GGTTTTTATATATTGCGTTACTTGTTGT
5801538 TATATATTGC
Statistics
Matches: 505, Mismatches: 34, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
110 154 0.30
111 29 0.06
112 106 0.21
113 1 0.00
114 4 0.01
115 1 0.00
116 5 0.01
117 18 0.04
118 186 0.37
119 1 0.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (111 bp):
TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
GGTTTTTATATATTGCGTTACTTGTTGTAGCGAGAGTGGTGGCGCG
Found at i:5801609 original size:117 final size:118
Alignment explanation
Indices: 5801198--5801577 Score: 609
Period size: 118 Copynumber: 3.2 Consensus size: 118
5801188 TTGTAACAAT
**
5801198 AGTGGTGGTGCGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
1 AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
* * * * *
5801263 GCTTGGGTGACTGGTTTTTATATATTGCGTTACATATTGTTATGTATTACGAG
66 GCTTGCGTGACTGGTTTTTATATATTACGTGACATGTTGTTATGTATTGCGAG
5801316 AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
1 AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
* *
5801381 GCTTGCGTGATTGGTTTTTATATATTACGTGACCTGTTGTTATGTATTGCGAG
66 GCTTGCGTGACTGGTTTTTATATATTACGTGACATGTTGTTATGTATTGCGAG
*
5801434 AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAG
1 AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
* * *
5801499 GCTTGCGTGACT-GCTTTTATATATTACGTGACTTGTTGTTATATATTGCGAG
66 GCTTGCGTGACTGGTTTTTATATATTACGTGACATGTTGTTATGTATTGCGAG
* * *
5801551 AGCGATGGCTCGTGACTTGTGCAATTC
1 AGTGGTGGCACGTGACTTGTGCAATTC
5801578 GCCTCTTGTT
Statistics
Matches: 245, Mismatches: 17, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
117 61 0.25
118 184 0.75
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (118 bp):
AGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAG
GCTTGCGTGACTGGTTTTTATATATTACGTGACATGTTGTTATGTATTGCGAG
Found at i:5804166 original size:78 final size:78
Alignment explanation
Indices: 5804051--5804195 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 78
5804041 TTGTAGTAGT
* * *
5804051 TGTGACCCGAACAACGAAGCAAAATGACTGCTGTGATTGGGGGACAATCAAATTTAAAACACAAG
1 TGTGACCAGAACAACGAAGCAAAATGACTGCTGTGATTGGGGGACAAGCAAATCTAAAACACAAG
5804116 ATGTTACAACAGC
66 ATGTTACAACAGC
* * * *
5804129 TGTGACCAGTACAACGAAGCAAACTGAGTGC-GATGATTGGGGGACAAGCAAATCTAAAATACAA
1 TGTGACCAGAACAACGAAGCAAAATGACTGCTG-TGATTGGGGGACAAGCAAATCTAAAACACAA
5804193 GAT
65 GAT
5804196 ATCTCTCTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 1 0.02
78 58 0.98
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (78 bp):
TGTGACCAGAACAACGAAGCAAAATGACTGCTGTGATTGGGGGACAAGCAAATCTAAAACACAAG
ATGTTACAACAGC
Found at i:5807730 original size:83 final size:86
Alignment explanation
Indices: 5807591--5807839 Score: 306
Period size: 92 Copynumber: 2.9 Consensus size: 86
5807581 ATGTGGATTA
* * * *
5807591 GTGACGTGATTCCATATTAACTACCGACCTGATTCAAAATTTAGTACTCGCGTGACTCTATAACA
1 GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
*
5807656 AATACTCTCAT-GA-ATC-TG
66 AATACTCTCATCAATATCATG
** * *
5807674 GTGACGCGATTCTGTATTAACTACCGATGTGATTCAACATTTAGTACTCGTGTGACTCCATAACA
1 GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
*
5807739 AATACTCCGGTGAATCAATATCAAATG
66 AATACT-C--T-CATCAATATC--ATG
* *
5807766 ATGACGCGATTCCATATTAACTACCTACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
1 GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
*
5807831 ATTACTCTC
66 AATACTCTC
5807840 GCGAATCAAT
Statistics
Matches: 139, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
83 63 0.45
84 1 0.01
86 1 0.01
87 2 0.01
88 1 0.01
89 4 0.03
91 1 0.01
92 66 0.47
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (86 bp):
GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
AATACTCTCATCAATATCATG
Found at i:5807837 original size:92 final size:92
Alignment explanation
Indices: 5807674--5807868 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
5807664 CATGAATCTG
** * *
5807674 GTGACGCGATTCTGTATTAACTACCGATGTGATTCAACATTTAGTACTCGTGTGACTCCATAACA
1 GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
*
5807739 AATACTC-CGGTGAATCAATATCAAAT-
66 AATACTCTC-GCGAATCAATATCAAATA
*
5807765 GATGACGCGATTCCATATTAACTACCTACGTGATTCAACATTTAGTACTCGCGTGACTCCATAAC
1 G-TGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAAC
* *
5807830 AATTACTCTCGCGAATCAATATCAACTA
65 AAATACTCTCGCGAATCAATATCAAATA
5807858 GTGACGCGATT
1 GTGACGCGATT
5807869 TCATTTCCAC
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
91 1 0.01
92 90 0.97
93 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (92 bp):
GTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
AATACTCTCGCGAATCAATATCAAATA
Found at i:5807893 original size:92 final size:92
Alignment explanation
Indices: 5807675--5807894 Score: 248
Period size: 92 Copynumber: 2.4 Consensus size: 92
5807665 ATGAATCTGG
** * * * * *
5807675 TGACGCGATTCTGTATTAACTACCGATGTGATTCAACATTTAGTACTCGTGTGACTCCATAACAA
1 TGACGCGATTCCATATTAACCACCTACGTAATTCAACATTTAGTACTCGCGTGACTCCATAACAA
*
5807740 ATACTCCGGTGAATCAATATCAAATGA
66 ATACTCCGGCGAATCAATATCAAATGA
* *
5807767 TGACGCGATTCCATATTAACTACCTACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACAA
1 TGACGCGATTCCATATTAACCACCTACGTAATTCAACATTTAGTACTCGCGTGACTCCATAACAA
* *
5807832 TTACTCTC-GCGAATCAATATCAACT-A
66 ATACTC-CGGCGAATCAATATCAAATGA
* * **
5807858 GTGACGCGATTTCAT-TTCCACCATTTACGTAATTCAA
1 -TGACGCGATTCCATATT-AACCACCTACGTAATTCAA
5807895 TAGCAACTGC
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
91 3 0.03
92 107 0.96
93 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (92 bp):
TGACGCGATTCCATATTAACCACCTACGTAATTCAACATTTAGTACTCGCGTGACTCCATAACAA
ATACTCCGGCGAATCAATATCAAATGA
Found at i:5808126 original size:23 final size:23
Alignment explanation
Indices: 5808094--5808159 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
5808084 TTATCACATG
* *
5808094 AATGAATACAAAGAATAATTTGTA
1 AATG-ATACAAAGAATAATATGGA
5808118 AATGATACAATAAAGAATAATATGGA
1 AATGATAC---AAAGAATAATATGGA
5808144 AATGATAC--AGAATAAT
1 AATGATACAAAGAATAAT
5808160 GTTAATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 8 0.22
23 4 0.11
24 4 0.11
26 21 0.57
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (23 bp):
AATGATACAAAGAATAATATGGA
Found at i:5808136 original size:26 final size:26
Alignment explanation
Indices: 5808103--5808152 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5808093 GAATGAATAC
* *
5808103 AAAGAATAATTTGTAAATGATACAAT
1 AAAGAATAATATGGAAATGATACAAT
5808129 AAAGAATAATATGGAAATGATACA
1 AAAGAATAATATGGAAATGATACA
5808153 GAATAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (26 bp):
AAAGAATAATATGGAAATGATACAAT
Found at i:5809809 original size:45 final size:45
Alignment explanation
Indices: 5809755--5809902 Score: 170
Period size: 45 Copynumber: 3.2 Consensus size: 45
5809745 GATATGCTCA
* *
5809755 TGCAGTGACTGCCTCTACATCTGCATCGCCCGCTGGATCTCCAAC
1 TGCATTGACTGCATCTACATCTGCATCGCCCGCTGGATCTCCAAC
* * * * * *
5809800 TGCATTGACTGTTGGATCTCCAACTGCATTGACTGCTGGATCTCCAAC
1 TGCATTGAC---TGCATCTACATCTGCATCGCCCGCTGGATCTCCAAC
* * *
5809848 TGCATTGACTGCATCTGCATCTGCATCACCCGCTAGATCTCCAAC
1 TGCATTGACTGCATCTACATCTGCATCGCCCGCTGGATCTCCAAC
5809893 TGCATTGACT
1 TGCATTGACT
5809903 ACTGGATCTC
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
45 46 0.55
48 38 0.45
ACGTcount: A:0.20, C:0.32, G:0.19, T:0.28
Consensus pattern (45 bp):
TGCATTGACTGCATCTACATCTGCATCGCCCGCTGGATCTCCAAC
Found at i:5809815 original size:24 final size:24
Alignment explanation
Indices: 5809786--5809926 Score: 182
Period size: 24 Copynumber: 6.0 Consensus size: 24
5809776 TGCATCGCCC
5809786 GCTGGATCTCCAACTGCATTGACT
1 GCTGGATCTCCAACTGCATTGACT
*
5809810 GTTGGATCTCCAACTGCATTGACT
1 GCTGGATCTCCAACTGCATTGACT
5809834 GCTGGATCTCCAACTGCATTGACT
1 GCTGGATCTCCAACTGCATTGACT
* * * *
5809858 GC---ATCTGCATCTGCA-TCACCC
1 GCTGGATCTCCAACTGCATTGA-CT
*
5809879 GCTAGATCTCCAACTGCATTGACT
1 GCTGGATCTCCAACTGCATTGACT
*
5809903 ACTGGATCTCCAACTGCATTGACT
1 GCTGGATCTCCAACTGCATTGACT
5809927 ACATCTGCAT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.02
21 14 0.14
24 82 0.82
25 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.29
Consensus pattern (24 bp):
GCTGGATCTCCAACTGCATTGACT
Found at i:5809899 original size:93 final size:93
Alignment explanation
Indices: 5809755--5809926 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
5809745 GATATGCTCA
* * * **
5809755 TGCAGTGACTGCCTCTACATCTGCATCGCCCGCTGGATCTCCAACTGCATTGACTGTTGGATCTC
1 TGCAGTGACTGCATCTACATCTGCATCACCCGCTAGATCTCCAACTGCATTGACTACTGGATCTC
5809820 CAACTGCATTGACTGCTGGATCTCCAAC
66 CAACTGCATTGACTGCTGGATCTCCAAC
* *
5809848 TGCATTGACTGCATCTGCATCTGCATCACCCGCTAGATCTCCAACTGCATTGACTACTGGATCTC
1 TGCAGTGACTGCATCTACATCTGCATCACCCGCTAGATCTCCAACTGCATTGACTACTGGATCTC
5809913 CAACTGCATTGACT
66 CAACTGCATTGACT
5809927 ACATCTGCAT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (93 bp):
TGCAGTGACTGCATCTACATCTGCATCACCCGCTAGATCTCCAACTGCATTGACTACTGGATCTC
CAACTGCATTGACTGCTGGATCTCCAAC
Found at i:5812029 original size:23 final size:23
Alignment explanation
Indices: 5811995--5812067 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
5811985 CAATATTCAT
*
5811995 GCAATAACCTAGAAACCAGTCAC
1 GCAATGACCTAGAAACCAGTCAC
*
5812018 GCAATGATCTAGAAACCAGTCAC
1 GCAATGACCTAGAAACCAGTCAC
** *
5812041 GCAATGACCTATCAATCAGTCAC
1 GCAATGACCTAGAAACCAGTCAC
5812064 GCAA
1 GCAA
5812068 AGTTAAACCC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (23 bp):
GCAATGACCTAGAAACCAGTCAC
Found at i:5814122 original size:15 final size:14
Alignment explanation
Indices: 5814104--5814140 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
5814094 CGTATATATA
5814104 TTATAATTAATAATT
1 TTATAATT-ATAATT
5814119 TTATAAGTTATAATT
1 TTATAA-TTATAATT
5814134 TTATAAT
1 TTATAAT
5814141 GTTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTATAATTATAATT
Found at i:5814192 original size:19 final size:20
Alignment explanation
Indices: 5814155--5814202 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5814145 ACACAAAATA
*
5814155 AAAAGTAAATATACTTATATT
1 AAAAGTATATATAC-TATATT
*
5814176 TAAAGTATATATA-TATATT
1 AAAAGTATATATACTATATT
5814195 AAAAGTAT
1 AAAAGTAT
5814203 TTTAGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
21 11 0.46
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (20 bp):
AAAAGTATATATACTATATT
Found at i:5819471 original size:24 final size:24
Alignment explanation
Indices: 5819437--5819504 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
5819427 TTCAAATAAT
*
5819437 TATGTTAGAAAACAAACAATTATA
1 TATGTTGGAAAACAAACAATTATA
* *
5819461 TTTGTTGGAAAA-AAGACAATTGTA
1 TATGTTGGAAAACAA-ACAATTATA
* *
5819485 TATATTGG-AAACAGACAATT
1 TATGTTGGAAAACAAACAATT
5819505 GTCTCTGTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (24 bp):
TATGTTGGAAAACAAACAATTATA
Found at i:5819504 original size:23 final size:24
Alignment explanation
Indices: 5819444--5819506 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
5819434 AATTATGTTA
* * * *
5819444 GAAAACAAACAATTATATTTGTTG
1 GAAAACAGACAATTGTATATATTG
*
5819468 GAAAAAAGACAATTGTATATATTG
1 GAAAACAGACAATTGTATATATTG
5819492 G-AAACAGACAATTGT
1 GAAAACAGACAATTGT
5819507 CTCTGTCGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.29
Consensus pattern (24 bp):
GAAAACAGACAATTGTATATATTG
Found at i:5823236 original size:2 final size:2
Alignment explanation
Indices: 5823229--5823332 Score: 154
Period size: 2 Copynumber: 52.0 Consensus size: 2
5823219 TCCAATTTTC
* *
5823229 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5823271 AT AT AT AT GT AT AT AT AT AT AT AT GT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5823313 AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5823333 TCAAATTCGA
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5833095 original size:254 final size:250
Alignment explanation
Indices: 5832412--5833236 Score: 906
Period size: 254 Copynumber: 3.3 Consensus size: 250
5832402 GCCATTGAGT
* * * *
5832412 TAAAAGTATTTAATAG-TTTAAAAATTTTAATTCATAAATGAGTAATAATAAGGATAAAAATAAT
1 TAAAAGTATTTAACAGATTTATAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAATAAT
* * ** *
5832476 TATAATGAAAATTAGCAATTGAAAATTTTTAACATAAATCTGTA-AA-AATTAATGTAAAAAATC
66 TATAATGAAAATTAGCAATTGAAAAATCTT-ATGTAAA-CT-TATAAGAATTAATGTAAAAAATT
* * * ** * *
5832539 ATAAATGTGGAATAAGCATTGTTCAAATATTGATGTAAATATGTGAGAGTTAATATAATAAGTTA
128 ATAAATGTGGAATAAGCATTGTTAAAATATTGATGTAAATGTGTGAGATTTAAGGTAACAAGTCA
* * * *
5832604 ATTAAGTCAAAA-AAATTTAA-TTGT-AAAAATTTAA-ATTTATA-TTC--TT-AAGC
193 ATTAAGTCAAAATAAATATAATTTTTGAAAAATTAAACATTTAAATTTCTATTCAAGC
* *
5832654 TAAAAGTATTTAAC-GATTTATAAATTTTAATTTATAAATAAATAATAATAAGTATAAAAATAAT
1 TAAAAGTATTTAACAGATTTATAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAATAAT
* * * * * * *
5832718 TATAGTGAAAATCAGTAATTAAAAAATCTTGATGTAAAGTTGTAAGAATTAATGTAAAAAATTAC
66 TATAATGAAAATTAGCAATTGAAAAATCTT-ATGTAAACTTATAAGAATTAATGTAAAAAATTAT
* * * * * *
5832783 AAAAGTGGAACAAGCACTGTTAAAATATTGATATAAATGTATAAGATTTAAGGTAACAAGTCAAT
130 AAATGTGGAATAAGCATTGTTAAAATATTGATGTAAATGTGTGAGATTTAAGGTAACAAGTCAAT
* *
5832848 TAGGTCAAAATAAATATAATTTTTGACAAAATTAAACATTTAAATTTCTAATGTCGAGC
195 TAAGTCAAAATAAATATAATTTTTGA-AAAATTAAACATTTAAATTTCT-AT-TCAAGC
* * * **
5832907 TAAAAGTATTTAA-AGATTTACAAATTTTAATTTATAAATTAATAATAAAAAAAAATAAAAATAA
1 TAAAAGTATTTAACAGATTTATAAATTTTAATTTATAAATGAATAAT-AATAAGGATAAAAATAA
* * *
5832971 TTATAATGTAAATTAGCAATTGAAAAACCTTATTGTAAACTTATAAGAATTAACGTAAAAAATTA
65 TTATAATGAAAATTAGCAATTGAAAAATCTTA-TGTAAACTTATAAGAATTAATGTAAAAAATTA
* * * *
5833036 TAAATGTAGAATAAGTATTGTTAAAATATTGACGTAAATGTGTGAGATTT-GGAGTAACAAGTCA
129 TAAATGTGGAATAAGCATTGTTAAAATATTGATGTAAATGTGTGAGATTTAAG-GTAACAAGTCA
* * * * *
5833100 ATTAAGTCGAAATAAATATAATTTTTGTGAAAGTTAAACATTTAAATTTATATTATCAAGT
193 ATTAAGTCAAAATAAATATAATTTTTG-AAAAATTAAACATTTAAATTTCTA-T-TCAAGC
* * *
5833161 TAAAAGTGTTTAACA-ATTTATAAATTTTAATTTATAAATGAATAACAACAAGGATAAAAATAAT
1 TAAAAGTATTTAACAGATTTATAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAATAAT
*
5833225 TATAGTGAAAAT
66 TATAATGAAAAT
5833237 GTATGAGGGG
Statistics
Matches: 482, Mismatches: 80, Indels: 31
0.81 0.13 0.05
Matches are distributed among these distances:
240 1 0.00
241 4 0.01
242 163 0.34
243 7 0.01
244 3 0.01
245 1 0.00
246 8 0.02
247 6 0.01
248 3 0.01
251 1 0.00
252 1 0.00
253 74 0.15
254 209 0.43
255 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (250 bp):
TAAAAGTATTTAACAGATTTATAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAATAAT
TATAATGAAAATTAGCAATTGAAAAATCTTATGTAAACTTATAAGAATTAATGTAAAAAATTATA
AATGTGGAATAAGCATTGTTAAAATATTGATGTAAATGTGTGAGATTTAAGGTAACAAGTCAATT
AAGTCAAAATAAATATAATTTTTGAAAAATTAAACATTTAAATTTCTATTCAAGC
Found at i:5834930 original size:11 final size:13
Alignment explanation
Indices: 5834904--5834935 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
5834894 ACTTCATTCA
5834904 TTTATATGTTATT
1 TTTATATGTTATT
5834917 TTTAT-TGTTATT
1 TTTATATGTTATT
5834929 TTTATAT
1 TTTATAT
5834936 TTGTAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTATATGTTATT
Found at i:5837028 original size:43 final size:44
Alignment explanation
Indices: 5836962--5837111 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 44
5836952 AAAAAAAAGG
* *
5836962 AAAAAAAGGAAAAGAAAAATAATTCCAAAATTTGAGCTAAG-GA
1 AAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGCTAAGAAA
* *
5837005 AAAAAAAAGAAAATAAAAGTAATTCCAAAATTTGAGCTAAGCAAAA
1 AAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGCTAAG--AAA
* *
5837051 AAAGGAAAAAAAAAAGAAAAATAATTCCAAAATTTCAGCTAAGCAAA
1 AAA--AAAAAGAAAAGAAAAATAATTCCAAAATTTGAGCTAAG-AAA
*
5837098 AAAGAAAAGTAAAA
1 AAAAAAAAG-AAAA
5837112 TAATTACAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
43 38 0.42
45 4 0.04
46 8 0.09
47 6 0.07
48 34 0.38
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (44 bp):
AAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGCTAAGAAA
Found at i:5837080 original size:48 final size:49
Alignment explanation
Indices: 5836953--5837100 Score: 184
Period size: 48 Copynumber: 3.1 Consensus size: 49
5836943 GCTAAGGAAA
*
5836953 AAAAAAAGGAAAAAAAGGAAAAGAAAAATAATTCCAAAATTTGAGCTAAG-
1 AAAAAAAGG-AAAAAA-GAAAAGAAAAATAATTCCAAAATTTCAGCTAAGC
* * * *
5837003 ---GAAA--AAAAAAGAAAATAAAAGTAATTCCAAAATTTGAGCTAAGC
1 AAAAAAAGGAAAAAAGAAAAGAAAAATAATTCCAAAATTTCAGCTAAGC
5837047 AAAAAAAGGAAAAAA-AAAAGAAAAATAATTCCAAAATTTCAGCTAAGC
1 AAAAAAAGGAAAAAAGAAAAGAAAAATAATTCCAAAATTTCAGCTAAGC
5837095 AAAAAA
1 AAAAAA
5837101 GAAAAGTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
43 31 0.36
44 6 0.07
47 6 0.07
48 36 0.42
49 6 0.07
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (49 bp):
AAAAAAAGGAAAAAAGAAAAGAAAAATAATTCCAAAATTTCAGCTAAGC
Found at i:5837435 original size:21 final size:23
Alignment explanation
Indices: 5837386--5837433 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
5837376 AAAAATAGAA
5837386 TAAAATAAAAATTAAATAACAAT
1 TAAAATAAAAATTAAATAACAAT
*
5837409 TAAAAT-AAAA-TAAATAA-ATT
1 TAAAATAAAAATTAAATAACAAT
5837429 TAAAA
1 TAAAA
5837434 ATGGGTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 4 0.17
23 6 0.25
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAATAAAAATTAAATAACAAT
Found at i:5838060 original size:22 final size:23
Alignment explanation
Indices: 5838001--5838094 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
5837991 TATGTGATTG
* * *
5838001 GTTGATATGTCATTGCTTGACTG
1 GTTGATATGGCATTGCATGACTA
* *
5838024 GTTGATATGGCATTGCCTAACTA
1 GTTGATATGGCATTGCATGACTA
5838047 GTTGATA-GGCATTGCATGACTA
1 GTTGATATGGCATTGCATGACTA
* * * *
5838069 GTTAATAAGGCGTTACATGACTA
1 GTTGATATGGCATTGCATGACTA
5838092 GTT
1 GTT
5838095 TTTAGACATT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 19 0.31
23 42 0.69
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (23 bp):
GTTGATATGGCATTGCATGACTA
Found at i:5838148 original size:22 final size:22
Alignment explanation
Indices: 5838120--5838172 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5838110 ACTTAGGCAT
* * *
5838120 TGCCTAAAAATCAGTCATGCAA
1 TGCCTAAAAACCAGCCACGCAA
5838142 TGCCTAAAAACCAGCCACGCAA
1 TGCCTAAAAACCAGCCACGCAA
5838164 TGCCTAAAA
1 TGCCTAAAA
5838173 TAAGTCACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (22 bp):
TGCCTAAAAACCAGCCACGCAA
Found at i:5838181 original size:21 final size:21
Alignment explanation
Indices: 5838120--5838186 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
5838110 ACTTAGGCAT
* *
5838120 TGCCTAAAAATCAGTCATGCAA
1 TGCCT-AAAATAAGTCACGCAA
*
5838142 TGCCTAAAA-ACCAGCCACGCAA
1 TGCCTAAAATA--AGTCACGCAA
*
5838164 TGCCTAAAATAAGTCACGTAA
1 TGCCTAAAATAAGTCACGCAA
5838185 TG
1 TG
5838187 ATTAAGTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 14 0.38
22 22 0.59
23 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
TGCCTAAAATAAGTCACGCAA
Found at i:5839681 original size:23 final size:24
Alignment explanation
Indices: 5839636--5839684 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
5839626 CTATAAAATC
*
5839636 TCACCTGTATGCTTAAACTTCTTT
1 TCACCTGTATACTTAAACTTCTTT
*
5839660 TCACCTGTATAC-TGAACTTCTTT
1 TCACCTGTATACTTAAACTTCTTT
5839683 TC
1 TC
5839685 CTATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.45
Consensus pattern (24 bp):
TCACCTGTATACTTAAACTTCTTT
Found at i:5841417 original size:18 final size:19
Alignment explanation
Indices: 5841390--5841434 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
5841380 GAGAAGAAAG
5841390 AGAAAAAGACAAGA-AGGA
1 AGAAAAAGACAAGACAGGA
* *
5841408 AGAAAGAGACAAGACTGGA
1 AGAAAAAGACAAGACAGGA
5841427 AGAAAAAG
1 AGAAAAAG
5841435 TAAGAAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.62, C:0.07, G:0.29, T:0.02
Consensus pattern (19 bp):
AGAAAAAGACAAGACAGGA
Found at i:5847250 original size:27 final size:27
Alignment explanation
Indices: 5847216--5847275 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
5847206 CATAAGTTAT
5847216 GTTT-TTAATATGAAAAGGAAATGGTA
1 GTTTCTTAATATGAAAAGGAAATGGTA
5847242 GTTTCTTAATATGAAAAGGAAATGGTA
1 GTTTCTTAATATGAAAAGGAAATGGTA
5847269 GTTTCTT
1 GTTTCTT
5847276 CATTTTAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (27 bp):
GTTTCTTAATATGAAAAGGAAATGGTA
Found at i:5850125 original size:70 final size:70
Alignment explanation
Indices: 5850010--5850185 Score: 187
Period size: 70 Copynumber: 2.5 Consensus size: 70
5850000 CAATTGATTA
* * *** *
5850010 AAATTGTCTAATTAAG---TTATGCCTAATTAATTAAACTATTTAATTAAATCATTTAGCCTAAT
1 AAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAACTAAACAATTAAATCATTGAGCCTAAT
5850072 TAAGT
66 TAAGT
* * *
5850077 AAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAATTAAACAATTAAGTCATTGGGCCTAAT
1 AAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAACTAAACAATTAAATCATTGAGCCTAAT
* *
5850142 TGATT
66 TAAGT
* * * *
5850147 AAATTTGTTTAATTAAATCATTGGGTCTAATTGATTAAA
1 AAA-TTGTTTAATTAAGTCATTAGGCCTAATTAATTAAA
5850186 ATTATTTAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
67 15 0.17
70 44 0.49
71 31 0.34
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (70 bp):
AAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAACTAAACAATTAAATCATTGAGCCTAAT
TAAGT
Found at i:5850159 original size:18 final size:18
Alignment explanation
Indices: 5850138--5850215 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 18
5850128 TCATTGGGCC
*
5850138 TAATTGATTAAATTTGTT
1 TAATTAATTAAATTTGTT
* * * *
5850156 TAATTAAAT-CATTGGGTC
1 TAATTAATTAAATT-TGTT
* * *
5850174 TAATTGATTAAAATTATT
1 TAATTAATTAAATTTGTT
*
5850192 TAATTAATTAAA-TTATT
1 TAATTAATTAAATTTGTT
5850209 TAATTAA
1 TAATTAA
5850216 GTTATTGGGC
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
17 15 0.33
18 28 0.62
19 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
TAATTAATTAAATTTGTT
Found at i:5850168 original size:36 final size:35
Alignment explanation
Indices: 5850030--5850198 Score: 185
Period size: 35 Copynumber: 4.8 Consensus size: 35
5850020 ATTAAGTTAT
* * **
5850030 GCCTAATTAATTAAACTATTTAATTAAATCATTTA
1 GCCTAATTAATTAAATTATTTAATTAAGTCATTGG
* * *
5850065 GCCTAATTAAGTAAATTGTTTAATTAAGTCATTAG
1 GCCTAATTAATTAAATTATTTAATTAAGTCATTGG
***
5850100 GCCTAATTAATTAAATTAAACAATTAAGTCATTGG
1 GCCTAATTAATTAAATTATTTAATTAAGTCATTGG
* * *
5850135 GCCTAATTGATTAAATTTGTTTAATTAAATCATTGG
1 GCCTAATTAATTAAA-TTATTTAATTAAGTCATTGG
* *
5850171 GTCTAATTGATTAAAATTATTTAATTAA
1 GCCTAATTAATT-AAATTATTTAATTAA
5850199 TTAAATTATT
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
35 72 0.64
36 37 0.33
37 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATTTAATTAAGTCATTGG
Found at i:5850206 original size:17 final size:18
Alignment explanation
Indices: 5850174--5850215 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
5850164 TCATTGGGTC
*
5850174 TAATTGATTAAAATTATT
1 TAATTAATTAAAATTATT
5850192 TAATTAATT-AAATTATT
1 TAATTAATTAAAATTATT
5850209 TAATTAA
1 TAATTAA
5850216 GTTATTGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:5853640 original size:55 final size:54
Alignment explanation
Indices: 5853551--5853655 Score: 185
Period size: 54 Copynumber: 1.9 Consensus size: 54
5853541 ATGGGGGCTA
5853551 GCCACGTGGAACAAAGGGAAGAAGGAAAAGAAAAAAAATGGTAAGGGGTCGNTTG
1 GCCACGTGGAACAAAGGGAAGAAGGAAAAGAAAAAAAATGGTAAGGGGTCG-TTG
*
5853606 GCCATGTGGAACAAAGGGAA-AAGGAAAAGAAAAAAAATGGTAAGGGGTCG
1 GCCACGTGGAACAAAGGGAAGAAGGAAAAGAAAAAAAATGGTAAGGGGTCG
5853656 GTTAAAGAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 30 0.61
55 19 0.39
ACGTcount: A:0.46, C:0.09, G:0.34, T:0.10
Consensus pattern (54 bp):
GCCACGTGGAACAAAGGGAAGAAGGAAAAGAAAAAAAATGGTAAGGGGTCGTTG
Found at i:5853840 original size:30 final size:31
Alignment explanation
Indices: 5853772--5853840 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
5853762 AATCGATAAG
5853772 AGAAAGAAAGAAGAAATGAGAAAGGAAAGAA
1 AGAAAGAAAGAAGAAATGAGAAAGGAAAGAA
* *
5853803 AG-GAGAAAGAGGGAAA-GAGAAA-G-AAGAAA
1 AGAAAGAAAGA-AGAAATGAGAAAGGAAAG-AA
5853832 AGAAAGAAA
1 AGAAAGAAA
5853841 AGGAGAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 3 0.09
29 5 0.16
30 18 0.56
31 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (31 bp):
AGAAAGAAAGAAGAAATGAGAAAGGAAAGAA
Found at i:5854104 original size:23 final size:24
Alignment explanation
Indices: 5854058--5854108 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
5854048 GCCGACCAAG
*
5854058 AAAGAGAGAGAGAAGAAAGAAAAA
1 AAAGAGAGAGAAAAGAAAGAAAAA
5854082 AAAGAGA-AGAAAAGAAATGAAAAA
1 AAAGAGAGAGAAAAGAAA-GAAAAA
5854106 AAA
1 AAA
5854109 AGGGCATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (24 bp):
AAAGAGAGAGAAAAGAAAGAAAAA
Found at i:5858369 original size:40 final size:39
Alignment explanation
Indices: 5858324--5858408 Score: 152
Period size: 40 Copynumber: 2.2 Consensus size: 39
5858314 CATAGAGACA
5858324 CAATTGTTAGATGAATTTGAATCCACATACAAGAGGTAG
1 CAATTGTTAGATGAATTTGAATCCACATACAAGAGGTAG
*
5858363 CCAATTGTTAGATGAATTTGAATCCACATACGAGAGGTAG
1 -CAATTGTTAGATGAATTTGAATCCACATACAAGAGGTAG
5858403 CAATTG
1 CAATTG
5858409 GCTTTGTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 6 0.14
40 38 0.86
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (39 bp):
CAATTGTTAGATGAATTTGAATCCACATACAAGAGGTAG
Found at i:5859657 original size:35 final size:35
Alignment explanation
Indices: 5859588--5859837 Score: 227
Period size: 35 Copynumber: 7.2 Consensus size: 35
5859578 CACTTGATTA
*
5859588 AAATTATTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
* * * *
5859620 AAATTACTTAATTAAATGATTGGGCTTAATTAATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
* * * * *
5859655 AAATTGTTTAATTAAGTTATTGAGCCAAATTAATA
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
*** * *
5859690 AAATTAAACAATTAAGTCATTGGACCTAATTGATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
* *
5859725 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTCATTGGGCCTAATTAATT
* ** ** *
5859761 AAAATTATTTAATTAAATTGTTAAGCTTAATTAATT
1 -AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
* * *
5859797 AAATTATTTAATTAAGTTATTTGGCCTAATTGATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
5859832 AAATTA
1 AAATTA
5859838 AACAATTAAG
Statistics
Matches: 172, Mismatches: 41, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
32 14 0.08
35 104 0.60
36 51 0.30
37 3 0.02
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (35 bp):
AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:5859808 original size:142 final size:138
Alignment explanation
Indices: 5859581--5859848 Score: 369
Period size: 142 Copynumber: 1.9 Consensus size: 138
5859571 TCTCAAGCAC
* **
5859581 TTGATTAAAATTATTTAATTAAGTTGTGCCTAATTAATTAAATTACTTAATTAAATGATTGGGCT
1 TTGATTAAAATTATTTAATTAAGTTGGGCCTAATTAATTAAATTACTTAATTAAATGATTAAGCT
*
5859646 TAATTAATTAAATTGTTTAATTAAGTTA-TTGAGCCAAATTAATAAAATTAAACAATTAAGTCAT
66 TAATTAATTAAATTATTTAATTAAGTTATTTG-GCCAAATTAATAAAATTAAACAATTAAGTCAT
5859710 TGGACCTAA
130 TGGACCTAA
* * * *
5859719 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTG-TT
1 TTGATTAAAATTATTTAATTAAG---TTGGGCCTAATTAATT-AAATTACTTAATTAAA-TGATT
* * *
5859783 AAGCTTAATTAATTAAATTATTTAATTAAGTTATTTGGCCTAATTGATTAAATTAAACAATTAAG
61 AAGCTTAATTAATTAAATTATTTAATTAAGTTATTTGGCCAAATTAATAAAATTAAACAATTAAG
5859848 T
126 T
5859849 TAACTAAGCT
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
138 21 0.19
141 14 0.12
142 73 0.65
143 5 0.04
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (138 bp):
TTGATTAAAATTATTTAATTAAGTTGGGCCTAATTAATTAAATTACTTAATTAAATGATTAAGCT
TAATTAATTAAATTATTTAATTAAGTTATTTGGCCAAATTAATAAAATTAAACAATTAAGTCATT
GGACCTAA
Found at i:5859812 original size:71 final size:70
Alignment explanation
Indices: 5859588--5859838 Score: 237
Period size: 71 Copynumber: 3.6 Consensus size: 70
5859578 CACTTGATTA
* * *
5859588 AAATTATTTAATTAAG---TTGTGCCTAATTAATT-AAATTACTTAATTAAA-TGATTGGGCTTA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAAATTAATTAATTAAATTG-TT-GGCTTA
5859648 ATTAATT
64 ATTAATT
* * * * ** * ** *
5859655 AAATTGTTTAATTAAGTTATTGAGCCAAATT-AATAAAATTAAACAATTAAGTCATTGGACCTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAAATTAATTAATTAAATTGTTGG-CTTAA
*
5859719 TTGATT
65 TTAATT
* * * *
5859725 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTGTTAAGCTTA
1 AAA-TTATTTAATTAAGTTATTGGGCCTAATTGATTAAAATTAATTAATTAAATTGTT-GGCTTA
5859790 ATTAATT
64 ATTAATT
*
5859797 AAATTATTTAATTAAGTTATTTGGCCTAATTGATT-AAATTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAAATTAA
5859839 ACAATTAAGT
Statistics
Matches: 146, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
67 15 0.10
69 4 0.03
70 42 0.29
71 54 0.37
72 30 0.21
73 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (70 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAAATTAATTAATTAAATTGTTGGCTTAAT
TAATT
Found at i:5860426 original size:13 final size:13
Alignment explanation
Indices: 5860408--5860456 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
5860398 GGTGAGGCGT
5860408 AATTTAATTTTTA
1 AATTTAATTTTTA
5860421 AATTTAATTTTTA
1 AATTTAATTTTTA
5860434 AATTTAATTTTTA
1 AATTTAATTTTTA
5860447 AATTT-ATTTT
1 AATTTAATTTT
5860457 GCTAGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 5 0.14
13 31 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTAATTTTTA
Found at i:5868013 original size:15 final size:14
Alignment explanation
Indices: 5867991--5868035 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
5867981 TCCTCCTCTA
5867991 CACCCCCCCCCCCC
1 CACCCCCCCCCCCC
*
5868005 NACCCCCCCCCCCC
1 CACCCCCCCCCCCC
*
5868019 CACCCCCCCCCCAC
1 CACCCCCCCCCCCC
5868033 CAC
1 CAC
5868036 ACACACACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.11, C:0.87, G:0.00, T:0.00
Consensus pattern (14 bp):
CACCCCCCCCCCCC
Found at i:5868995 original size:2 final size:2
Alignment explanation
Indices: 5868988--5869041 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
5868978 TATTGCTTAA
*
5868988 CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
5869029 CT GT CT CT TT CT C
1 CT CT CT CT CT CT C
5869042 ACCAATTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (2 bp):
CT
Found at i:5873710 original size:3 final size:3
Alignment explanation
Indices: 5873698--5873730 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5873688 AGTTCACTCA
5873698 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5873731 GAATCTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5878801 original size:2 final size:2
Alignment explanation
Indices: 5878794--5878832 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5878784 TCTAACATTT
5878794 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5878833 ATGGAAAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5885247 original size:22 final size:23
Alignment explanation
Indices: 5885216--5885258 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5885206 AATAAAAGTT
5885216 ATAAACAAAAATAAATGAAAATG
1 ATAAACAAAAATAAATGAAAATG
*
5885239 ATAAA-AAAAATAAATTAAAA
1 ATAAACAAAAATAAATGAAAA
5885259 AAAAGAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (23 bp):
ATAAACAAAAATAAATGAAAATG
Found at i:5885259 original size:23 final size:23
Alignment explanation
Indices: 5885206--5885259 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5885196 TAGAAATTAT
* *
5885206 AATAAAAGTTATAAACAAAAATA
1 AATAAAAATGATAAACAAAAATA
*
5885229 AATGAAAATGATAAA-AAAAATA
1 AATAAAAATGATAAACAAAAATA
5885251 AATTAAAAA
1 AA-TAAAAA
5885260 AAAGAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (23 bp):
AATAAAAATGATAAACAAAAATA
Found at i:5885686 original size:34 final size:34
Alignment explanation
Indices: 5885643--5885722 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
5885633 TTAGGGGGGA
* *
5885643 TAAAGCTTGGGTATTTGCCGCTGGTTAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGATTAGAGTGGG
*
5885677 TAAAGCTTGGGTATTTGTCGCCGATTAGAGTGGG
1 TAAAGCTTGGGTATTTGCCGCCGATTAGAGTGGG
5885711 TAAAGCTTGGGT
1 TAAAGCTTGGGT
5885723 TAGCCGGCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.20, C:0.11, G:0.36, T:0.33
Consensus pattern (34 bp):
TAAAGCTTGGGTATTTGCCGCCGATTAGAGTGGG
Found at i:5886904 original size:15 final size:14
Alignment explanation
Indices: 5886870--5886949 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 14
5886860 AAAAAAATAA
*
5886870 AAAATATATAAAAT
1 AAAATATAGAAAAT
5886884 AAAAAATATAGAAGAAT
1 --AAAATATAGAA-AAT
*
5886901 AAAAAATAGAAAAT
1 AAAATATAGAAAAT
* *
5886915 ATAATAATAAAAAAT
1 AAAAT-ATAGAAAAT
* *
5886930 -ATATAAAGTAAAAT
1 AAAATATAG-AAAAT
5886944 AAAATA
1 AAAATA
5886950 ATAATTAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
13 2 0.04
14 13 0.26
15 22 0.44
16 10 0.20
17 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AAAATATAGAAAAT
Found at i:5886945 original size:10 final size:10
Alignment explanation
Indices: 5886915--5886971 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
5886905 AATAGAAAAT
5886915 ATAATAATAA
1 ATAATAATAA
*
5886925 AAAATATATAA
1 ATAATA-ATAA
5886936 AGTAA-AATAAA
1 A-TAATAAT-AA
5886947 ATAATAATTAA
1 ATAATAA-TAA
5886958 ATAATAATAA
1 ATAATAATAA
5886968 ATAA
1 ATAA
5886972 AAAAATAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 17 0.43
11 20 0.50
12 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAATAATAA
Found at i:5886958 original size:22 final size:21
Alignment explanation
Indices: 5886898--5886968 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
5886888 AATATAGAAG
* *
5886898 AATAAAAAATAGAAAATATAAT
1 AATAAAAAATATATAA-ATAAT
5886920 AATAAAAAATATATAAAGTAA-
1 AATAAAAAATATATAAA-TAAT
5886941 AATAAAATAATA-ATTAAATAAT
1 AATAAAA-AATATA-TAAATAAT
5886963 AATAAA
1 AATAAA
5886969 TAAAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.28
22 31 0.72
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
AATAAAAAATATATAAATAAT
Found at i:5886976 original size:29 final size:28
Alignment explanation
Indices: 5886865--5886978 Score: 83
Period size: 32 Copynumber: 3.9 Consensus size: 28
5886855 TTAGGAAAAA
5886865 AATAAAAAATATATAAA-ATAAAAAAT-AT
1 AATAAAAAATA-ATAAATA-AAAAAATAAT
* * * *
5886893 -A-GAAGAATAAAAAATAGAAAATATAAT
1 AATAAAAAATAATAAATA-AAAAAATAAT
5886920 AATAAAAAATATATAAAGTAAAATAAAATAAT
1 AATAAAAAATA-ATAAA-T-AAA-AAAATAAT
*
5886952 AATTAAATAATAATAAATAAAAAAATA
1 AA-TAAAAAATAATAAATAAAAAAATA
5886979 GACAATTGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
25 4 0.06
26 13 0.19
27 3 0.04
28 1 0.01
29 12 0.18
30 7 0.10
31 4 0.06
32 15 0.22
33 8 0.12
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (28 bp):
AATAAAAAATAATAAATAAAAAAATAAT
Found at i:5898765 original size:13 final size:13
Alignment explanation
Indices: 5898747--5898771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5898737 TTTCAGAAAA
5898747 TTTATAAAATCAT
1 TTTATAAAATCAT
5898760 TTTATAAAATCA
1 TTTATAAAATCA
5898772 CAATTTCCCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5899949 original size:28 final size:27
Alignment explanation
Indices: 5899913--5899965 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5899903 ATATCCTGGT
*
5899913 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
5899940 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
5899966 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:5900033 original size:20 final size:20
Alignment explanation
Indices: 5900010--5900055 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5900000 CTTCTAAACC
5900010 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
5900030 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
5900050 TCAAAT
1 TCAAAT
5900056 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:5902376 original size:38 final size:38
Alignment explanation
Indices: 5902323--5902691 Score: 379
Period size: 38 Copynumber: 9.8 Consensus size: 38
5902313 AGAAAAGGAA
*
5902323 AAAAGGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAA-GTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* *
5902362 AAAAATGTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * * *
5902400 AAAAGTTTCGTT-AC-CAGTTTTGAGGAGTTTATTTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * * *
5902436 AAAAGTCTCATTGCCTTAGTTTTGAGGAGTTTA-TTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * * *
5902473 AGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* *
5902511 AAAAGTCTCATTGCCTCAGTTTTGAGGAGTTCATTTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * *
5902549 AAAAGTCTCATTGCCTCAGTTTTGAGGAGTTTA-TTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * ** * ***
5902586 AGAAGTTTCGTTATCTTAGCTTTGAGGAGTTCATTAAA
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * **
5902624 AAAAGTTTCGTAGCCTCAATTTTGAGGAGTTCATTTTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
* * *
5902662 AAAA-TTTCATCGCCTCAACTTTGAAGAGTT
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTT
5902692 TTCATTTTAC
Statistics
Matches: 275, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
36 30 0.11
37 84 0.31
38 157 0.57
39 4 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (38 bp):
AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
Found at i:5902518 original size:75 final size:76
Alignment explanation
Indices: 5902323--5902782 Score: 419
Period size: 75 Copynumber: 6.0 Consensus size: 76
5902313 AGAAAAGGAA
* * *
5902323 AAAAGGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAATGTCATTGCCTCAGCTTTGAG
1 AAAA-GTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAG
5902388 GAGTTCATTTTT
65 GAGTTCATTTTT
* * * *
5902400 AAAAGTTTCGTT-AC-CAGTTTTGAGGAGTTTATTTTTAAAAGTCTCATTGCCTTAGTTTTGAGG
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
*
5902463 AGTTTA-TTTT
66 AGTTCATTTTT
* * * * *
5902473 AGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGTTTTGAGG
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
5902538 AGTTCATTTTT
66 AGTTCATTTTT
* * * * * * ** *
5902549 AAAAGTCTCATTGCCTCAGTTTTGAGGAGTTTA-TTTTAGAAGTTTCGTTATCTTAGCTTTGAGG
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
***
5902613 AGTTCATTAAA
66 AGTTCATTTTT
* * * * * *
5902624 AAAAGTTTCGTAGCCTCAATTTTGAGGAGTTCATTTTTAAAA-TTTCATCGCCTCAACTTTGAAG
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
*
5902688 AGTTTTCATTTTACAAAAAAA
66 AG--TTCATTTT--------T
* * * * ** *
5902709 AAAAGTTTCGTAGCCTCAATTTTGAAGAGTTCATTTTT-AAAGTTTCATCACCTCAACTTTGAGG
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
5902773 AGTCTCATTT
66 AGT-TCATTT
5902783 AAAAAAAAAC
Statistics
Matches: 317, Mismatches: 50, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
73 15 0.05
74 49 0.15
75 128 0.40
76 45 0.14
77 10 0.03
83 1 0.00
84 9 0.03
85 60 0.19
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (76 bp):
AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAGCTTTGAGG
AGTTCATTTTT
Found at i:5902559 original size:113 final size:113
Alignment explanation
Indices: 5902334--5902692 Score: 472
Period size: 113 Copynumber: 3.2 Consensus size: 113
5902324 AAAGGTTTCG
* * * * * * * *
5902334 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAATGTCATTGCCTCAGCTTTGAGGAGTTCATTTT
1 TTGCCTCAGTTTTGAGGAGTTTA-TTTTAGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTT
* *
5902399 TAAAAGTTTCGTT-AC-CAGTTTTGAGGAGTTTATTTTTAAAAGTCTCA
65 TAAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCA
*
5902446 TTGCCTTAGTTTTGAGGAGTTTATTTTAGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTT
1 TTGCCTCAGTTTTGAGGAGTTTATTTTAGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTT
* *
5902511 AAAAGTCTCATTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCA
66 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCA
* ***
5902559 TTGCCTCAGTTTTGAGGAGTTTATTTTAGAAGTTTCGTTATCTTAGCTTTGAGGAGTTCATTAAA
1 TTGCCTCAGTTTTGAGGAGTTTATTTTAGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTT
* * *
5902624 AAAAGTTTCGTAGCCTCAATTTTGAGGAGTTCATTTTTAAAA-TTTCA
66 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCA
* ** *
5902671 TCGCCTCAACTTTGAAGAGTTT
1 TTGCCTCAGTTTTGAGGAGTTT
5902693 TCATTTTACA
Statistics
Matches: 218, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
111 46 0.21
112 43 0.20
113 129 0.59
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (113 bp):
TTGCCTCAGTTTTGAGGAGTTTATTTTAGAAGTTTCGTTGTCTTAGCTTTGAGGAGTTCATTTTT
AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTCTCA
Found at i:5902764 original size:85 final size:82
Alignment explanation
Indices: 5902621--5902791 Score: 270
Period size: 85 Copynumber: 2.0 Consensus size: 82
5902611 GGAGTTCATT
* *
5902621 AAAAAAAGTTTCGTAGCCTCAATTTTGAGGAGTTCATTTTTAAAATTTCATCGCCTCAACTTTGA
1 AAAAAAAGTTTCGTAGCCTCAATTTTGAAGAGTTCATTTTTAAAATTTCATCACCTCAACTTTGA
*
5902686 AGAGTTTTCATTTTACAAAA
66 AGAG-TCTCA-TTTA-AAAA
*
5902706 AAAAAAAGTTTCGTAGCCTCAATTTTGAAGAGTTCATTTTTAAAGTTTCATCACCTCAACTTTGA
1 AAAAAAAGTTTCGTAGCCTCAATTTTGAAGAGTTCATTTTTAAAATTTCATCACCTCAACTTTGA
*
5902771 GGAGTCTCATTTAAAAA
66 AGAGTCTCATTTAAAAA
5902788 AAAA
1 AAAA
5902792 CAAACAAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
82 8 0.10
83 4 0.05
84 4 0.05
85 65 0.80
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (82 bp):
AAAAAAAGTTTCGTAGCCTCAATTTTGAAGAGTTCATTTTTAAAATTTCATCACCTCAACTTTGA
AGAGTCTCATTTAAAAA
Found at i:5902789 original size:1 final size:1
Alignment explanation
Indices: 5902783--5902849 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
5902773 AGTCTCATTT
* * * * * * * * *
5902783 AAAAAAAAACAAACAAAAAAAAAACACAAAACAAAACAAAACAAAAAAAAATAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5902848 AA
1 AA
5902850 CTTGGTAAGA
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:5902803 original size:15 final size:15
Alignment explanation
Indices: 5902783--5902850 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
5902773 AGTCTCATTT
5902783 AAAAAAAAACAAACA
1 AAAAAAAAACAAACA
5902798 AAAAAAAAAC--AC-
1 AAAAAAAAACAAACA
*
5902810 AAAACAAAACAAAACA
1 AAAAAAAAAC-AAACA
5902826 AAAAAAAATA-AAACA
1 AAAAAAAA-ACAAACA
5902841 AAAAAAAAAC
1 AAAAAAAAAC
5902851 TTGGTAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 9 0.20
13 2 0.04
14 1 0.02
15 25 0.56
16 7 0.16
17 1 0.02
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.01
Consensus pattern (15 bp):
AAAAAAAAACAAACA
Found at i:5902813 original size:10 final size:9
Alignment explanation
Indices: 5902784--5902847 Score: 67
Period size: 10 Copynumber: 6.9 Consensus size: 9
5902774 GTCTCATTTA
5902784 AAAAAAAAC
1 AAAAAAAAC
*
5902793 AAACAAAA-
1 AAAAAAAAC
*
5902801 AAAAAACAC
1 AAAAAAAAC
5902810 AAAACAAAAC
1 AAAA-AAAAC
*
5902820 AAAACAAAAA
1 AAAA-AAAAC
5902830 AAAATAAAAC
1 AAAA-AAAAC
5902840 AAAAAAAA
1 AAAAAAAA
5902848 AACTTGGTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
8 6 0.13
9 15 0.33
10 25 0.54
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:5903017 original size:22 final size:22
Alignment explanation
Indices: 5902981--5903038 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5902971 ATAATTAAAA
5902981 AAAATATAAACAAAAATAAATG
1 AAAATATAAACAAAAATAAATG
*
5903003 AAAATGATAAA-AAAAATAAATT
1 AAAAT-ATAAACAAAAATAAATG
5903025 AAAA-A-AAACAAAAA
1 AAAATATAAACAAAAA
5903039 AAAAGGTACG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
22 19 0.58
23 5 0.15
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (22 bp):
AAAATATAAACAAAAATAAATG
Found at i:5903454 original size:34 final size:34
Alignment explanation
Indices: 5903404--5903483 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
5903394 TTATGGGGGA
* * *
5903404 TAAAGCTTAGGCATTTGCTGCTGGTTAGAGTGGG
1 TAAAGCTTGGGTATTTGCAGCTGGTTAGAGTGGG
5903438 TAAAGCTTGGGTATTTGCAGCTGGTTAGAGTGGG
1 TAAAGCTTGGGTATTTGCAGCTGGTTAGAGTGGG
5903472 TAAAGCTTGGGT
1 TAAAGCTTGGGT
5903484 TAGCCAGCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (34 bp):
TAAAGCTTGGGTATTTGCAGCTGGTTAGAGTGGG
Found at i:5903661 original size:113 final size:113
Alignment explanation
Indices: 5903492--5903730 Score: 329
Period size: 113 Copynumber: 2.1 Consensus size: 113
5903482 GTTAGCCAGC
* * *
5903492 CGGCGGCAAGAAGGGCGAAGCCCGATCCGAGTGGTAAAAGAAGAGCTCGATTTGGGCAAAGAAAT
1 CGGCGGTAAGAAGGGCGAAGCCCGATCCGAGTGGTAAAAGAAGAGCCCGATTTGGGCAAAGAAAG
* ** *
5903557 AGCAGATCTAGGCAGTCGGTAGAGGGAGGTCC-GACTTGGGGTAGTGG-
66 AGCAGATCTAGGCAGCCGACAGAGGGAGGTCCAG-CATGGGGTAGTGGT
* * * * *
5903604 CTGGCGGTAAGGAGGGCGAAGCCCGATCCGGGTGGTAAAGGGAGAGCCCGATTTGGGCAAAGAGA
1 C-GGCGGTAAGAAGGGCGAAGCCCGATCCGAGTGGTAAAAGAAGAGCCCGATTTGGGCAAAGAAA
5903669 GAGCAGATCTAGGCAGCCGACAGAGGGAGGTCCAGCATGGGGTAGTGGT
65 GAGCAGATCTAGGCAGCCGACAGAGGGAGGTCCAGCATGGGGTAGTGGT
*
5903718 CGGCGGTAGGAAG
1 CGGCGGTAAGAAG
5903731 AGAGCTGCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
112 1 0.01
113 107 0.97
114 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.42, T:0.14
Consensus pattern (113 bp):
CGGCGGTAAGAAGGGCGAAGCCCGATCCGAGTGGTAAAAGAAGAGCCCGATTTGGGCAAAGAAAG
AGCAGATCTAGGCAGCCGACAGAGGGAGGTCCAGCATGGGGTAGTGGT
Found at i:5904636 original size:7 final size:7
Alignment explanation
Indices: 5904626--5904728 Score: 73
Period size: 7 Copynumber: 13.9 Consensus size: 7
5904616 ATGAGTTAGG
5904626 AAAAAAT
1 AAAAAAT
5904633 AAAAAAT
1 AAAAAAT
5904640 ATAAAATAT
1 A-AAAA-AT
5904649 AAAAGAAT
1 AAAA-AAT
5904657 AAAAAAT
1 AAAAAAT
*
5904664 AGAAAAT
1 AAAAAAT
*
5904671 ATAATAAT
1 A-AAAAAT
5904679 AAAAAAAT
1 -AAAAAAT
5904687 ATAATAAA-
1 A-AA-AAAT
*
5904695 ATAAAAT
1 AAAAAAT
* *
5904702 AATAATT
1 AAAAAAT
*
5904709 AAATAAT
1 AAAAAAT
*
5904716 AATAAAT
1 AAAAAAT
5904723 AAAAAA
1 AAAAAA
5904729 ATAGACAATT
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
6 3 0.04
7 38 0.51
8 25 0.34
9 8 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (7 bp):
AAAAAAT
Found at i:5904662 original size:17 final size:16
Alignment explanation
Indices: 5904626--5904731 Score: 92
Period size: 15 Copynumber: 6.5 Consensus size: 16
5904616 ATGAGTTAGG
5904626 AAAAAATAAAAAATAT
1 AAAAAATAAAAAATAT
* *
5904642 AAAATATAAAAGA-AT
1 AAAAAATAAAAAATAT
*
5904657 AAAAAATAGAAAATAT
1 AAAAAATAAAAAATAT
*
5904673 -AATAATAAAAAAATAT
1 AAAAAAT-AAAAAATAT
5904689 AATAAAATAAAATAATAATT
1 AA-AAAATAAAA-AAT-A-T
* *
5904709 AAATAATAATAAATA-
1 AAAAAATAAAAAATAT
5904724 AAAAAATA
1 AAAAAATA
5904732 GACAATTGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
15 24 0.33
16 21 0.29
17 6 0.08
18 10 0.14
19 8 0.11
20 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAAATAAAAAATAT
Found at i:5904662 original size:24 final size:24
Alignment explanation
Indices: 5904626--5904706 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 24
5904616 ATGAGTTAGG
5904626 AAAA-AATAAAAAATATAAAATAT
1 AAAATAATAAAAAATATAAAATAT
* *
5904649 AAAAGAATAAAAAATAGAAAATAT
1 AAAATAATAAAAAATATAAAATAT
*
5904673 --AATAATAAAAAAATATAATAAAAT
1 AAAATAAT-AAAAAATATAA-AATAT
5904697 AAAATAATAA
1 AAAATAATAA
5904707 TTAAATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.10
23 14 0.29
24 22 0.45
25 2 0.04
26 6 0.12
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAATAATAAAAAATATAAAATAT
Found at i:5904686 original size:40 final size:43
Alignment explanation
Indices: 5904642--5904731 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 43
5904632 TAAAAAATAT
5904642 AAAATATAA-AAGAATAAAA-AATAGA-AAAT-ATAAT-AATAAA
1 AAAATATAATAA-AATAAAATAATA-ATAAATAATAATAAATAAA
5904682 AAAATATAATAAAATAAAATAATAATTAAATAATAATAAATAAA
1 AAAATATAATAAAATAAAATAATAA-TAAATAATAATAAATAAA
5904726 AAAATA
1 AAAATA
5904732 GACAATTGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
40 17 0.39
41 6 0.14
42 4 0.09
43 5 0.11
44 12 0.27
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (43 bp):
AAAATATAATAAAATAAAATAATAATAAATAATAATAAATAAA
Found at i:5904723 original size:26 final size:26
Alignment explanation
Indices: 5904630--5904717 Score: 53
Period size: 24 Copynumber: 3.5 Consensus size: 26
5904620 GTTAGGAAAA
*
5904630 AATAAAA-AAT-ATAAAATATAA-AA
1 AATAAAATAATAAAAAAATATAATAA
*
5904653 GAATAAAA-AAT-AGAAAATATAATAA
1 -AATAAAATAATAAAAAAATATAATAA
* * *
5904678 TAAAAAAAT-ATAATAAAATAAAATAA
1 -AATAAAATAATAAAAAAATATAATAA
*
5904704 TAATTAAATAATAA
1 -AATAAAATAATAA
5904718 TAAATAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
24 20 0.38
25 10 0.19
26 19 0.36
27 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (26 bp):
AATAAAATAATAAAAAAATATAATAA
Found at i:5904726 original size:26 final size:26
Alignment explanation
Indices: 5904642--5904717 Score: 52
Period size: 26 Copynumber: 3.0 Consensus size: 26
5904632 TAAAAAATAT
*
5904642 AAAATATAA-AAGAATAAAA-AAT-AG
1 AAAATATAATAA-AATAAAATAATAAA
* *
5904666 AAAATATAATAATAAAAAAAT-ATAAT
1 AAAATATAATAA-AATAAAATAATAAA
* *
5904692 AAAATAAAATAATAATTAAATAATAA
1 AAAATATAATAA-AATAAAATAATAA
5904718 TAAATAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
24 9 0.21
25 10 0.24
26 19 0.45
27 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (26 bp):
AAAATATAATAAAATAAAATAATAAA
Found at i:5906073 original size:2 final size:2
Alignment explanation
Indices: 5906066--5906108 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5906056 NNNNNNNNNN
5906066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5906108 T
1 T
5906109 CTTTTAAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5907279 original size:19 final size:19
Alignment explanation
Indices: 5907252--5907297 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
5907242 AGGAGACAAG
*
5907252 ATAAAATTTT-TAGAATAAA
1 ATAATATTTTATA-AATAAA
5907271 ATAATATTTTATAAATAAA
1 ATAATATTTTATAAATAAA
5907290 ATAATATT
1 ATAATATT
5907298 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATTTTATAAATAAA
Done.