Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 174 of 221
Found at i:51976652 original size:19 final size:19
Alignment explanation
Indices: 51976621--51976686 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
51976611 AAAAACATAA
51976621 ATTTTGAAATTTTTATAAAT
1 ATTTTG-AATTTTTATAAAT
*
51976641 ATTTTGAA-TTTTAAAAAT
1 ATTTTGAATTTTTATAAAT
*
51976659 -TATTTAAACTTTTT-TAAAAT
1 AT-TTTGAA-TTTTTAT-AAAT
51976679 ATTTTGAA
1 ATTTTGAA
51976687 ACTTTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 1 0.03
18 14 0.38
19 2 0.05
20 19 0.51
21 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTTATAAAT
Found at i:51976675 original size:21 final size:21
Alignment explanation
Indices: 51976621--51976694 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
51976611 AAAAACATAA
51976621 ATTTTGAAA--TTTTTATAAAT
1 ATTTTGAAACTTTTTTA-AAAT
51976641 ATTTTG-AA---TTTTAAAA-
1 ATTTTGAAACTTTTTTAAAAT
*
51976657 ATTATTTAAACTTTTTTAAAAT
1 ATT-TTGAAACTTTTTTAAAAT
51976679 ATTTTGAAACTTTTTT
1 ATTTTGAAACTTTTTT
51976695 CATTTTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.07
17 5 0.11
18 7 0.15
19 2 0.04
20 6 0.13
21 20 0.43
22 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTTTGAAACTTTTTTAAAAT
Found at i:51978932 original size:49 final size:49
Alignment explanation
Indices: 51978860--51978957 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
51978850 AATTCATTCG
*
51978860 ACACTCTTGTGCTGGGAAAAAGCACAACCTTATCTCAATATATATTTTA
1 ACACTCTTGTGCTGAGAAAAAGCACAACCTTATCTCAATATATATTTTA
51978909 ACACTCTTGTGCTGAGAAAAAGCACAACCTTATCTCAATATATATTTTA
1 ACACTCTTGTGCTGAGAAAAAGCACAACCTTATCTCAATATATATTTTA
51978958 TAATATCATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (49 bp):
ACACTCTTGTGCTGAGAAAAAGCACAACCTTATCTCAATATATATTTTA
Found at i:51982633 original size:16 final size:18
Alignment explanation
Indices: 51982602--51982639 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
51982592 TATTTGTACT
51982602 TTATTATTATTATTTTAA
1 TTATTATTATTATTTTAA
*
51982620 TTATT-TTA-TATTTTCA
1 TTATTATTATTATTTTAA
51982636 TTAT
1 TTAT
51982640 AATTTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTATTATTTTAA
Found at i:51983046 original size:45 final size:44
Alignment explanation
Indices: 51982995--51983087 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
51982985 GATTCGCTGT
*
51982995 AATGGAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
51983040 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
51983084 AATG
1 AATG
51983088 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:51983096 original size:39 final size:41
Alignment explanation
Indices: 51982995--51983099 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
51982985 GATTCGCTGT
51982995 AATGGAATAGA-GCTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
51983035 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
51983079 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
51983100 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 8 0.14
40 9 0.16
41 2 0.04
42 2 0.04
43 3 0.05
44 22 0.39
45 10 0.18
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:51983286 original size:17 final size:17
Alignment explanation
Indices: 51983246--51983279 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
51983236 TTATTATTAA
51983246 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
51983263 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
51983280 TCTTAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:51983330 original size:55 final size:54
Alignment explanation
Indices: 51983227--51983331 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
51983217 TAATCATATT
*
51983227 TTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTC
1 TTAACATAATTATTATT-AATATAATTTAATAAAATATATAATATAATAAAATTC
* * *
51983282 TTAATATAATTATTCTT-ATATGAATTTACTAAAATCATA-ATATATAATAA
1 TTAACATAATTATTATTAATAT-AATTTAATAAAAT-ATATA-ATATAATAA
51983332 TATAAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
53 4 0.09
54 13 0.30
55 26 0.60
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (54 bp):
TTAACATAATTATTATTAATATAATTTAATAAAATATATAATATAATAAAATTC
Found at i:51990704 original size:3 final size:3
Alignment explanation
Indices: 51990698--51990767 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
51990688 ATAATTTTGA
* * *
51990698 TAT TAT TAT TAT TAT TACT T-T CAT TAT TAT TAG TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
**
51990743 TAT TGC TAT TAT TGA- TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT T
51990768 CGCTTATATA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:51991136 original size:29 final size:29
Alignment explanation
Indices: 51991103--51991183 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
51991093 CTCTTTCAAA
* *
51991103 TATTTTAACATTTTTAATTTATTTGAACT
1 TATTTTAATATTTTTAATTTATTTAAACT
* * *
51991132 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTTAATATTTTTAATTTATTTAAACT
*
51991161 TATTTTAATATTTATATATTTAT
1 TATTTTAATATTTTTA-ATTTAT
51991184 ATATTATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 37 0.86
30 6 0.14
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (29 bp):
TATTTTAATATTTTTAATTTATTTAAACT
Found at i:51991216 original size:11 final size:12
Alignment explanation
Indices: 51991151--51991222 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
51991141 ATTGTTAATT
51991151 TATTTAAATTTA
1 TATTTAAATTTA
51991163 T-TTTAATATTTA
1 TATTTAA-ATTTA
51991175 TA--T--ATTTA
1 TATTTAAATTTA
*
51991183 TATATTATATTTA
1 TAT-TTAAATTTA
*
51991196 TTTCTTAAA-TTA
1 TAT-TTAAATTTA
51991208 TATTTAAATTTA
1 TATTTAAATTTA
51991220 TAT
1 TAT
51991223 ACTTCGTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
8 7 0.15
11 12 0.25
12 18 0.38
13 11 0.23
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTAAATTTA
Found at i:51993076 original size:21 final size:21
Alignment explanation
Indices: 51993047--51993093 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
51993037 AGACATCATG
51993047 ATCTTTCTT-TTCT-TCTTT-T
1 ATCTTT-TTCTTCTCTCTTTGT
51993066 ATCTTTTTCTTCTCTCTTTGT
1 ATCTTTTTCTTCTCTCTTTGT
*
51993087 TTCTTTT
1 ATCTTTT
51993094 ATTCCCTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 5 0.21
21 7 0.29
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.72
Consensus pattern (21 bp):
ATCTTTTTCTTCTCTCTTTGT
Found at i:51998526 original size:12 final size:12
Alignment explanation
Indices: 51998511--51998546 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
51998501 AAAAGAGTCA
51998511 ATAAACGAGCTT
1 ATAAACGAGCTT
*
51998523 ATAAATGAGCTT
1 ATAAACGAGCTT
*
51998535 TTAAACGAGCTT
1 ATAAACGAGCTT
51998547 GTTCTTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:51998771 original size:5 final size:5
Alignment explanation
Indices: 51998755--51998805 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
51998745 TGTAAAACTT
** *
51998755 TTAAA TTAAAA TTAAA TTAAA TTATAA AAAAA TTAAA CT-AA TTAAA TTAAA
1 TTAAA TT-AAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA TTAAA
51998806 ACTTTTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 26 0.70
6 8 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (5 bp):
TTAAA
Found at i:51998776 original size:16 final size:16
Alignment explanation
Indices: 51998755--51998805 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
51998745 TGTAAAACTT
51998755 TTAAATTAAAATTAAA
1 TTAAATTAAAATTAAA
*
51998771 TTAAATTATAAA-AAAA
1 TTAAATTA-AAATTAAA
*
51998787 TTAAACT--AATTAAA
1 TTAAATTAAAATTAAA
51998801 TTAAA
1 TTAAA
51998806 ACTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
16 17 0.57
17 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAATTAAAATTAAA
Found at i:52003155 original size:13 final size:13
Alignment explanation
Indices: 52003137--52003161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52003127 TAATTTAATA
52003137 TTATTTTGTGTGT
1 TTATTTTGTGTGT
52003150 TTATTTTGTGTG
1 TTATTTTGTGTG
52003162 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:52004748 original size:41 final size:41
Alignment explanation
Indices: 52004691--52004866 Score: 298
Period size: 41 Copynumber: 4.3 Consensus size: 41
52004681 GTTTGAAATT
52004691 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
52004732 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* *
52004773 GGTGATTTGAATCAGGCTATAAGCCTAGTAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
52004814 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
*
52004855 AGTGATCTGAAT
1 GGTGATCTGAAT
52004867 ATGTTAAATT
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
Found at i:52007375 original size:28 final size:27
Alignment explanation
Indices: 52007336--52007399 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
52007326 GAAGAAACTA
*
52007336 TTTTACTTTTACTTCAAAGTCAAAGAG
1 TTTTACTTTTACTTCAAACTCAAAGAG
52007363 TTTTATCTTTTACTTCAAACTCAAAGAG
1 TTTTA-CTTTTACTTCAAACTCAAAGAG
*
52007391 TTTGACTTT
1 TTTTACTTT
52007400 CAATGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (27 bp):
TTTTACTTTTACTTCAAACTCAAAGAG
Found at i:52009794 original size:18 final size:18
Alignment explanation
Indices: 52009751--52009794 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
52009741 TTCTAAGAAA
*
52009751 CACTTTTAGGACAAAAAG
1 CACTTTTGGGACAAAAAG
52009769 CACTTTTGGGACAAAAAG
1 CACTTTTGGGACAAAAAG
*
52009787 TACTTTTG
1 CACTTTTG
52009795 AGATAAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (18 bp):
CACTTTTGGGACAAAAAG
Found at i:52009802 original size:18 final size:18
Alignment explanation
Indices: 52009751--52009802 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
52009741 TTCTAAGAAA
52009751 CACTTTT-AGGACAAAAAG
1 CACTTTTGA-GACAAAAAG
*
52009769 CACTTTTGGGACAAAAAG
1 CACTTTTGAGACAAAAAG
* *
52009787 TACTTTTGAGATAAAA
1 CACTTTTGAGACAAAA
52009803 GCATTCCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (18 bp):
CACTTTTGAGACAAAAAG
Found at i:52012046 original size:58 final size:60
Alignment explanation
Indices: 52011956--52012079 Score: 216
Period size: 58 Copynumber: 2.1 Consensus size: 60
52011946 CACAACCTTA
52011956 ATTAACTTGTAACCCAGTTTATAATCGACCTAATTAGGTC-ATA-ATGGAAACTATAAAT
1 ATTAACTTGTAACCCAGTTTATAATCGACCTAATTAGGTCAATACATGGAAACTATAAAT
52012014 ATTAACTTGTAACCCAGTTTATAATCGACCTAATTAGGTCATAATACATGGAAACTATAAAT
1 ATTAACTTGTAACCCAGTTTATAATCGACCTAATTAGGTC--AATACATGGAAACTATAAAT
52012076 ATTA
1 ATTA
52012080 GCTCAAAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
58 40 0.65
61 3 0.05
62 19 0.31
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (60 bp):
ATTAACTTGTAACCCAGTTTATAATCGACCTAATTAGGTCAATACATGGAAACTATAAAT
Found at i:52017298 original size:41 final size:42
Alignment explanation
Indices: 52017191--52017300 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 42
52017181 CAAGCTTTAT
* * * * *
52017191 GCCTAGCAGGCGTCATGCCAATGTATT-AATTTAGGCTTTGT
1 GCCTAGCAGGCTTTATGCCGATGTATTGAATTTAGGCCTTGA
* * *
52017232 GCCTAGTAGGCTTTGA-GCTGGTGTATTGAA-TTAGGCCTTGA
1 GCCTAGCAGGCTTT-ATGCCGATGTATTGAATTTAGGCCTTGA
52017273 GCCTAGCAGGCTTTATGCCGATGTATTG
1 GCCTAGCAGGCTTTATGCCGATGTATTG
52017301 TATCAAGTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
40 1 0.02
41 51 0.93
42 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (42 bp):
GCCTAGCAGGCTTTATGCCGATGTATTGAATTTAGGCCTTGA
Found at i:52021442 original size:21 final size:22
Alignment explanation
Indices: 52021409--52021450 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
52021399 AATTTTAAAA
*
52021409 TTTTTGATAGTCATATAATATT
1 TTTTTCATAGTCATATAATATT
52021431 TTTTTCAT-GTCATATAATAT
1 TTTTTCATAGTCATATAATAT
52021451 AAATGTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTTCATAGTCATATAATATT
Found at i:52021508 original size:44 final size:44
Alignment explanation
Indices: 52021454--52021545 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
52021444 ATAATATAAA
* *
52021454 TGTGTGCCGCATATAATATTAGGTGTTCCATTTAATACATAGCT
1 TGTGTGCCGCATATAATACTAAGTGTTCCATTTAATACATAGCT
* *
52021498 TGTGTGCCGCATATAATACTAAGTGTTTCATTTAATGCATAGCT
1 TGTGTGCCGCATATAATACTAAGTGTTCCATTTAATACATAGCT
52021542 TGTG
1 TGTG
52021546 AGGTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (44 bp):
TGTGTGCCGCATATAATACTAAGTGTTCCATTTAATACATAGCT
Found at i:52032810 original size:6 final size:6
Alignment explanation
Indices: 52032801--52032827 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52032791 TTATTTTTAG
52032801 TTTGGT TTTGGT TTTGGT TTTGGT TTT
1 TTTGGT TTTGGT TTTGGT TTTGGT TTT
52032828 TTAGCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (6 bp):
TTTGGT
Found at i:52039221 original size:25 final size:27
Alignment explanation
Indices: 52039166--52039222 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
52039156 CACATTTAAA
* * *
52039166 AAATATATATCAATTTATTTTTATATT
1 AAATAAATATCAATTTATTTGTATATG
*
52039193 AAATAAATAT-AA-TTATTTGTGTATG
1 AAATAAATATCAATTTATTTGTATATG
52039218 AAATA
1 AAATA
52039223 TATAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 15 0.58
26 2 0.08
27 9 0.35
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATAAATATCAATTTATTTGTATATG
Found at i:52041739 original size:28 final size:26
Alignment explanation
Indices: 52041664--52041742 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
52041654 CTGGACATTT
* *
52041664 TTAATTCAAGTATTAATGTG-CTGTAA
1 TTAATACAAATATTAATGTGTCT-TAA
*
52041690 TTAATACATATATTAA-GTTGTCTTAA
1 TTAATACAAATATTAATG-TGTCTTAA
*
52041716 TTTAATACAAATTTTTAATGTGTCTTA
1 -TTAATACAAA-TATTAATGTGTCTTA
52041743 GGCCAGCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.02
26 18 0.42
27 11 0.26
28 12 0.28
29 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (26 bp):
TTAATACAAATATTAATGTGTCTTAA
Found at i:52043375 original size:12 final size:12
Alignment explanation
Indices: 52043358--52043382 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52043348 GGTGTTCATT
52043358 CGGTTAACCGAC
1 CGGTTAACCGAC
52043370 CGGTTAACCGAC
1 CGGTTAACCGAC
52043382 C
1 C
52043383 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:52043557 original size:9 final size:9
Alignment explanation
Indices: 52043543--52043621 Score: 122
Period size: 9 Copynumber: 8.8 Consensus size: 9
52043533 TTTGGTTAGA
52043543 AATTACCCG
1 AATTACCCG
52043552 AATTACCCG
1 AATTACCCG
52043561 AATTACCCG
1 AATTACCCG
52043570 AATTACCCG
1 AATTACCCG
*
52043579 AATTACCTG
1 AATTACCCG
*
52043588 AATTAACCG
1 AATTACCCG
*
52043597 AATTAACCG
1 AATTACCCG
*
52043606 AATTAACCG
1 AATTACCCG
52043615 AATTACC
1 AATTACC
52043622 GAAAAATACC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:52051957 original size:39 final size:39
Alignment explanation
Indices: 52051914--52051990 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
52051904 AATGATATTT
*
52051914 AAATTTATTAATATTATGATATATGAAATATATAAACTC
1 AAATTGATTAATATTATGATATATGAAATATATAAACTC
* *
52051953 AAATTGGTTAATATTATGATATATGGAATATATAAACT
1 AAATTGATTAATATTATGATATATGAAATATATAAACT
52051991 TTGATACTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (39 bp):
AAATTGATTAATATTATGATATATGAAATATATAAACTC
Found at i:52052558 original size:43 final size:43
Alignment explanation
Indices: 52052510--52052693 Score: 172
Period size: 43 Copynumber: 4.3 Consensus size: 43
52052500 TTTTAGAAAT
* *
52052510 AAACGCCGCTATAGATTAGGATCTTTAGCGGCGCTTTTCTAAC
1 AAACGCCGCTATAGATTAAGACCTTTAGCGGCGCTTTTCTAAC
* ** * * *
52052553 AAACGCCGCTATAGCTTGGGATCTTTAGCGGCACTTTTTTAAC
1 AAACGCCGCTATAGATTAAGACCTTTAGCGGCGCTTTTCTAAC
* * * *
52052596 AAACGCCACTATAGCTCAAGACCTTTAGCGGCGCTTTTAC-CAC
1 AAACGCCGCTATAGATTAAGACCTTTAGCGGCGCTTTT-CTAAC
* * * * ** *
52052639 AAATGCCACTATAGATCAAAGACCTTTAGCGACGCTTTGATTAC
1 AAACGCCGCTATAGAT-TAAGACCTTTAGCGGCGCTTTTCTAAC
52052683 AAACGCCGCTA
1 AAACGCCGCTA
52052694 AAAACACCAT
Statistics
Matches: 117, Mismatches: 21, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
43 87 0.74
44 30 0.26
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATTAAGACCTTTAGCGGCGCTTTTCTAAC
Found at i:52052676 original size:44 final size:43
Alignment explanation
Indices: 52052594--52052676 Score: 130
Period size: 44 Copynumber: 1.9 Consensus size: 43
52052584 CACTTTTTTA
* *
52052594 ACAAACGCCACTATAGCTCAAGACCTTTAGCGGCGCTTTTACC
1 ACAAACGCCACTATAGATCAAGACCTTTAGCGACGCTTTTACC
*
52052637 ACAAATGCCACTATAGATCAAAGACCTTTAGCGACGCTTT
1 ACAAACGCCACTATAGATC-AAGACCTTTAGCGACGCTTT
52052677 GATTACAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 17 0.47
44 19 0.53
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
ACAAACGCCACTATAGATCAAGACCTTTAGCGACGCTTTTACC
Found at i:52052685 original size:44 final size:43
Alignment explanation
Indices: 52052594--52052689 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 43
52052584 CACTTTTTTA
* * *
52052594 ACAAACGCCACTATAGCTCAAGACCTTTAGCGGCGCTTTTACC
1 ACAAACGCCACTATAGATCAAGACCTTTAGCGACGCTTTGACC
* **
52052637 ACAAATGCCACTATAGATCAAAGACCTTTAGCGACGCTTTGATT
1 ACAAACGCCACTATAGATC-AAGACCTTTAGCGACGCTTTGACC
52052681 ACAAACGCC
1 ACAAACGCC
52052690 GCTAAAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 17 0.38
44 28 0.62
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
ACAAACGCCACTATAGATCAAGACCTTTAGCGACGCTTTGACC
Found at i:52052786 original size:16 final size:16
Alignment explanation
Indices: 52052765--52052798 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52052755 AAATATTAAA
*
52052765 TATTAAAATAAAACAT
1 TATTAAAATAAAAAAT
*
52052781 TATTAATATAAAAAAT
1 TATTAAAATAAAAAAT
52052797 TA
1 TA
52052799 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATAAAAAAT
Found at i:52054233 original size:14 final size:14
Alignment explanation
Indices: 52054214--52054243 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
52054204 CAGATTAGGT
52054214 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
52054228 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
52054242 GT
1 GT
52054244 TGCTTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (14 bp):
GTGGGAAAAGGTTA
Found at i:52066738 original size:15 final size:15
Alignment explanation
Indices: 52066714--52066743 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52066704 CAATACAGAC
*
52066714 TTCAGTCCAATACCA
1 TTCAGCCCAATACCA
52066729 TTCAGCCCAATACCA
1 TTCAGCCCAATACCA
52066744 CTAGCCCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.23
Consensus pattern (15 bp):
TTCAGCCCAATACCA
Found at i:52067679 original size:15 final size:15
Alignment explanation
Indices: 52067656--52067707 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
52067646 TGTTTTTATT
* *
52067656 TATTTTTATTATTAA
1 TATTATTATTATTAC
*
52067671 TATTATTATTACTAC
1 TATTATTATTATTAC
52067686 T-TTCATTATTATTAC
1 TATT-ATTATTATTAC
52067701 TATTATT
1 TATTATT
52067708 GCTATTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:52069348 original size:22 final size:22
Alignment explanation
Indices: 52069318--52069380 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
52069308 ACACCAAAAC
*
52069318 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
52069340 AGGCCTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
52069362 AGGCCTTTAGCGGCGCTTT
1 AGGCCTTTAGCGGCGCTTT
52069381 GAGAAGTGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.10, C:0.22, G:0.29, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:52069551 original size:43 final size:43
Alignment explanation
Indices: 52069478--52069766 Score: 343
Period size: 43 Copynumber: 6.7 Consensus size: 43
52069468 TTTAGCGACG
* *
52069478 TTAGCGGCGCTTTTTCCATAAACACCGCTAAAGACC-CTGACCT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAC-GACCT
* **
52069521 TTAGCAGCGCTTTTTCCACAAACGTTGCTAAAGACC-CTGACCT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAC-GACCT
*
52069564 TTAGCGACGCTTTTTCCAC-AACGCCGCTAAAGACCACGACCT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGACCT
* * *
52069606 TTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGACCACGATCT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGACCT
* * * * *
52069649 TTAACGGTGCTTTTCCCACAAACGCCACTAAAGACCACGATCT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGACCT
* *
52069692 ATAGCGGCGC-TTTTCTCACAAACGCCCCTAAAGACCACGACCT
1 TTAGCGGCGCTTTTTC-CACAAACGCCGCTAAAGACCACGACCT
* ** *
52069735 TTAGCGGCGCTTCTAGCAAAAACGCCGCTAAA
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
52069767 AACATAATCT
Statistics
Matches: 215, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
42 39 0.18
43 174 0.81
44 2 0.01
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (43 bp):
TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGACCT
Found at i:52069712 original size:128 final size:129
Alignment explanation
Indices: 52069478--52069766 Score: 343
Period size: 128 Copynumber: 2.2 Consensus size: 129
52069468 TTTAGCGACG
* * * * *
52069478 TTAGCGGCGCTTTTTCCATAAACACCGCTAAAGACCCTGACCTTTAGCAGCGCTTTTTCCACAAA
1 TTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGACCCTGACCTTTAACAGCGCTTTTCCCACAAA
*** * *
52069543 CGTTGCTAAAGACCCTGACCTTTAGCGACGCTTTTTCCAC-AACGCCGCTAAAGACCACGACCT
66 CGCCACTAAAGACCCTGACCTATAGCGACGCTTTTTCCACAAACGCCCCTAAAGACCACGACCT
* * * * * *
52069606 TTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGACCAC-GATCTTTAACGGTGCTTTTCCCACAA
1 TTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGACC-CTGACCTTTAACAGCGCTTTTCCCACAA
* *
52069670 ACGCCACTAAAGACCAC-GATCTATAGCGGCGC-TTTTCTCACAAACGCCCCTAAAGACCACGAC
65 ACGCCACTAAAGACC-CTGACCTATAGCGACGCTTTTTC-CACAAACGCCCCTAAAGACCACGAC
52069733 CT
128 CT
* *
52069735 TTAGCGGCGCTTCTAGCAAAAACGCCGCTAAA
1 TTAGCGGCGCTTTTACCAAAAACGCCGCTAAA
52069767 AACATAATCT
Statistics
Matches: 136, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
127 5 0.04
128 80 0.59
129 51 0.38
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (129 bp):
TTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGACCCTGACCTTTAACAGCGCTTTTCCCACAAA
CGCCACTAAAGACCCTGACCTATAGCGACGCTTTTTCCACAAACGCCCCTAAAGACCACGACCT
Found at i:52071412 original size:22 final size:21
Alignment explanation
Indices: 52071350--52071413 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
52071340 CTTAAGTACT
* * *
52071350 AAATTAAAAAAATCAAACACC
1 AAATTAAAAAAATAAAATAAC
**
52071371 AAATTAAAAAAAATTTAATAAC
1 AAATT-AAAAAAATAAAATAAC
52071393 AAATTAGAAAAAATAAAATAA
1 AAATTA-AAAAAATAAAATAA
52071414 TTAAGGGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATTAAAAAAATAAAATAAC
Found at i:52071580 original size:5 final size:5
Alignment explanation
Indices: 52071572--52071624 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
52071562 TAATAAGATA
52071572 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
52071622 ATT
1 ATT
52071625 GATTGGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:52074308 original size:7 final size:7
Alignment explanation
Indices: 52074302--52074334 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
52074292 AAAACATAAA
52074302 CCCTAAAC
1 CCCT-AAC
52074310 CCCTAAC
1 CCCTAAC
52074317 CCCTAAC
1 CCCTAAC
52074324 CCCTAAC
1 CCCTAAC
52074331 CCCT
1 CCCT
52074335 CTTTTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.27, C:0.58, G:0.00, T:0.15
Consensus pattern (7 bp):
CCCTAAC
Found at i:52074449 original size:15 final size:15
Alignment explanation
Indices: 52074413--52074442 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52074403 CCCTAACCCG
*
52074413 ACCTTAAATCTCTAA
1 ACCTTAAATCACTAA
52074428 ACCTTAAATCACTAA
1 ACCTTAAATCACTAA
52074443 CTCTTAACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (15 bp):
ACCTTAAATCACTAA
Found at i:52074463 original size:21 final size:21
Alignment explanation
Indices: 52074447--52074540 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 21
52074437 CACTAACTCT
52074447 TAACCCCTAACCCCTAACCCC
1 TAACCCCTAACCCCTAACCCC
* * * *
52074468 TAACCCCAAATCCCAAACCCT
1 TAACCCCTAACCCCTAACCCC
*
52074489 TAACCCCTAACCCCAAACCCC
1 TAACCCCTAACCCCTAACCCC
* * ***
52074510 TAACCCCAAACCCATAAATAC
1 TAACCCCTAACCCCTAACCCC
52074531 TAACCCCTAA
1 TAACCCCTAA
52074541 ACCTTATTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.37, C:0.49, G:0.00, T:0.14
Consensus pattern (21 bp):
TAACCCCTAACCCCTAACCCC
Found at i:52074540 original size:7 final size:7
Alignment explanation
Indices: 52074447--52074522 Score: 98
Period size: 7 Copynumber: 10.9 Consensus size: 7
52074437 CACTAACTCT
52074447 TAACCCC
1 TAACCCC
52074454 TAACCCC
1 TAACCCC
52074461 TAACCCC
1 TAACCCC
52074468 TAACCCC
1 TAACCCC
* *
52074475 AAATCCC
1 TAACCCC
* *
52074482 AAACCCT
1 TAACCCC
52074489 TAACCCC
1 TAACCCC
52074496 TAACCCC
1 TAACCCC
*
52074503 AAACCCC
1 TAACCCC
52074510 TAACCCC
1 TAACCCC
*
52074517 AAACCC
1 TAACCC
52074523 ATAAATACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.34, C:0.54, G:0.00, T:0.12
Consensus pattern (7 bp):
TAACCCC
Found at i:52075002 original size:33 final size:32
Alignment explanation
Indices: 52074965--52075037 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
52074955 AAATTTAACC
**
52074965 ATTTTAAAAAATATTCTGTTAAAAATAAATTGA
1 ATTTTAAAAAAT-TAATGTTAAAAATAAATTGA
***
52074998 ATTTTTATTTAATTAATGTTAAAAATAAATTGA
1 A-TTTTAAAAAATTAATGTTAAAAATAAATTGA
52075031 ATTTTAA
1 ATTTTAA
52075038 TTAAAAGCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 5 0.15
33 20 0.61
34 8 0.24
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (32 bp):
ATTTTAAAAAATTAATGTTAAAAATAAATTGA
Found at i:52075096 original size:41 final size:41
Alignment explanation
Indices: 52075039--52075168 Score: 217
Period size: 41 Copynumber: 3.2 Consensus size: 41
52075029 GAATTTTAAT
*
52075039 TAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCAC
1 TAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
*
52075080 TAAAAGCCTGAGCATTAGCGGTGC-TTTTCAAAAACGCCGC
1 TAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
* *
52075120 TAGAAGCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
52075161 TAAAAGCC
1 TAAAAGCC
52075169 CAGAAAGGTT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 37 0.45
41 45 0.55
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (41 bp):
TAAAAGCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
Found at i:52078693 original size:10 final size:10
Alignment explanation
Indices: 52078678--52078703 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
52078668 CTTATTGATC
52078678 TGTTAGTATT
1 TGTTAGTATT
52078688 TGTTAGTATT
1 TGTTAGTATT
52078698 TGTTAG
1 TGTTAG
52078704 CACTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTAGTATT
Found at i:52079627 original size:37 final size:35
Alignment explanation
Indices: 52079577--52079658 Score: 137
Period size: 37 Copynumber: 2.3 Consensus size: 35
52079567 TACTAACTCA
*
52079577 TATATATAATCAAATTTCTGTTAATGTATATTTTTT
1 TATAAATAATCAAATTTCTGTTAATGTATA-TTTTT
52079613 CTATAAATAATCAAATTTCTGTTAATGTATATTTTT
1 -TATAAATAATCAAATTTCTGTTAATGTATATTTTT
52079649 TATAAATAAT
1 TATAAATAAT
52079659 ATGTTAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 10 0.23
36 5 0.11
37 29 0.66
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (35 bp):
TATAAATAATCAAATTTCTGTTAATGTATATTTTT
Found at i:52081643 original size:35 final size:36
Alignment explanation
Indices: 52081599--52081667 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
52081589 ATTTGTTAGA
52081599 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
52081635 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
52081668 ATGATTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:52083046 original size:20 final size:20
Alignment explanation
Indices: 52083021--52083061 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52083011 CATCCAAACA
52083021 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
52083041 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
52083061 C
1 C
52083062 CGGAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (20 bp):
CTAGAAAAGTAAATCATTTT
Found at i:52083067 original size:20 final size:20
Alignment explanation
Indices: 52083023--52083068 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
52083013 TCCAAACACT
*
52083023 AGAAAAGTAAATCATTTTCT
1 AGAAAAGTAAATCATTTTCC
52083043 AGAAAAGTAAATCATTTTCC
1 AGAAAAGTAAATCATTTTCC
*
52083063 GGAAAA
1 AGAAAA
52083069 CATTTTACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (20 bp):
AGAAAAGTAAATCATTTTCC
Found at i:52089463 original size:21 final size:22
Alignment explanation
Indices: 52089434--52089480 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
52089424 CAGAAGGAGT
*
52089434 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
52089456 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
52089477 GAGT
1 GAGT
52089481 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:52104475 original size:19 final size:18
Alignment explanation
Indices: 52104451--52104496 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
52104441 CGCTCCTTTT
* *
52104451 TGCATTCATTTCATGCATC
1 TGCATTCATGTCAT-CATA
52104470 TGCATTACATGTCATCATA
1 TGCATT-CATGTCATCATA
52104489 TGCATTCA
1 TGCATTCA
52104497 AGATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (18 bp):
TGCATTCATGTCATCATA
Found at i:52113113 original size:44 final size:44
Alignment explanation
Indices: 52113061--52113571 Score: 302
Period size: 44 Copynumber: 11.3 Consensus size: 44
52113051 TCCCTAAGCA
*
52113061 ACAGTGGAGCAGATTGAAGCCAGAAAGCTTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* * * * *
52113105 ATAGTGGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* ** *
52113149 ACAGTGGAGCGGATT-AAGATA-AAGGATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TT
* * *
52113193 ACAGT--AG-AG-TAG-A-TC-G-CATCTTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
** * * *
52113229 ACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* *** *
52113273 ACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TT
*
52113317 ACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCTTGAGATT
1 ACAGT---G--GA--G---CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* * *
52113371 ACA-TCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGT-GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* *** *
52113415 ACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TT
*
52113459 ACAGTAGAGTAGATCGCACCAGATTGAATCCAGAAATCTTATCTCCCTGAGATT
1 ACAGT---G--GA--G---CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
* * *
52113513 ACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
52113557 ACAGTGGAGCAGATT
1 ACAGTGGAGCAGATT
52113572 AAGATAAAGG
Statistics
Matches: 361, Mismatches: 59, Indels: 94
0.70 0.11 0.18
Matches are distributed among these distances:
36 20 0.06
37 1 0.00
38 2 0.01
39 2 0.01
40 4 0.01
41 2 0.01
42 5 0.01
43 17 0.05
44 229 0.63
45 1 0.00
47 4 0.01
49 8 0.02
51 4 0.01
53 1 0.00
54 49 0.14
55 8 0.02
56 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
Found at i:52113231 original size:36 final size:36
Alignment explanation
Indices: 52113174--52113242 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
52113164 AAGATAAAGG
* * *
52113174 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGC
1 ATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGC
52113210 ATCTTATCTCCCTG-AGATTACAGCAGAGCAGAT
1 ATCTTATCTCCCTGAAG-TTACAGCAGAGCAGAT
52113243 TGAAGCTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (36 bp):
ATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGC
Found at i:52113308 original size:124 final size:124
Alignment explanation
Indices: 52113088--52113336 Score: 453
Period size: 124 Copynumber: 2.0 Consensus size: 124
52113078 AGCCAGAAAG
* **
52113088 CTTATCTCCCTGAGATTATAGTGGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
1 CTTATCTCCCTGAGATTACAGCAGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
*
52113153 TGGAGCGGATTAAGATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
*
52113212 CTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
1 CTTATCTCCCTGAGATTACAGCAGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
52113277 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
52113336 C
1 C
52113337 AGATTGAAGC
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (124 bp):
CTTATCTCCCTGAGATTACAGCAGAGCAGACTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:52113466 original size:142 final size:142
Alignment explanation
Indices: 52113210--52113622 Score: 738
Period size: 142 Copynumber: 2.9 Consensus size: 142
52113200 AGTAGATCGC
* *
52113210 ATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
52113275 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
66 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
52113340 TTGAAGCCAGAA
131 TTGAAGCCAGAA
*
52113352 ATCTTATCTCCTTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
*
52113417 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGA
66 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
*
52113482 TTGAATCCAGAA
131 TTGAAGCCAGAA
52113494 ATCTTATCTCCCTGAGATTACAGT-GGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 ATCTTATCTCCCTGAGATTACA-TCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
* * *
52113558 CAGTGGAGCAGATTAAGATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
65 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
52113623 GTCTTATCTC
Statistics
Matches: 260, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
142 259 1.00
143 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (142 bp):
ATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
TTGAAGCCAGAA
Found at i:52113559 original size:98 final size:97
Alignment explanation
Indices: 52113380--52113570 Score: 224
Period size: 98 Copynumber: 1.9 Consensus size: 97
52113370 TACATCGGAG
* * * * *
52113380 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGAATCCT
* *
52113445 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
65 ATCTCCCTGAAGTTACAGTAGAGCAGATCGCAC
* * **
52113478 CAGATTGAATCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG-AATCC
*
52113542 TATCTCCCTG-AGATTACAGTGGAGCAGAT
64 TATCTCCCTGAAG-TTACAGTAGAGCAGAT
52113571 TAAGATAAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
97 4 0.05
98 71 0.91
99 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (97 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGCAGATCGCAC
Found at i:52113590 original size:44 final size:42
Alignment explanation
Indices: 52113494--52113649 Score: 156
Period size: 44 Copynumber: 3.6 Consensus size: 42
52113484 GAATCCAGAA
* *
52113494 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAGATAG-G
*
52113538 ATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAGATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAGAT--AGG
* * * * *
52113582 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCACATCAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAGAT-AGG
*
52113624 -TCTTATCTCCCTGAAATTACAGTGGA
1 ATCTTATCTCCCTGAGATTACAGTGGA
52113650 ATAGACCGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 22 0.23
42 4 0.04
43 9 0.09
44 59 0.61
45 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (42 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAGATAGG
Found at i:52119374 original size:16 final size:17
Alignment explanation
Indices: 52119341--52119374 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52119331 AGATTCATCC
52119341 TCAAAACTTGTATTTGA
1 TCAAAACTTGTATTTGA
*
52119358 TCAAATCTTGT-TTTGA
1 TCAAAACTTGTATTTGA
52119374 T
1 T
52119375 TTGCTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TCAAAACTTGTATTTGA
Found at i:52125375 original size:4 final size:4
Alignment explanation
Indices: 52125358--52125396 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
52125348 ACTCGCTTCT
* * *
52125358 TTAC TTAC TCAC TTAC TTGC TTAC TTAC TTGC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
52125397 AATAACTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (4 bp):
TTAC
Found at i:52125388 original size:12 final size:12
Alignment explanation
Indices: 52125358--52125396 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
52125348 ACTCGCTTCT
* *
52125358 TTACTTACTCAC
1 TTACTTGCTTAC
52125370 TTACTTGCTTAC
1 TTACTTGCTTAC
52125382 TTACTTGCTTAC
1 TTACTTGCTTAC
52125394 TTA
1 TTA
52125397 AATAACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:52125713 original size:50 final size:50
Alignment explanation
Indices: 52125645--52125887 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
52125635 TTTTTTGTAC
* * * ** *
52125645 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
52125695 TGCCCATGCCATGTCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
52125745 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
52125795 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAC--CTC-TCATCTC---GG
*
52125851 TGCCAATGCCATGTCCCAGGCATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
52125888 TCTTATTCCC
Statistics
Matches: 169, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 124 0.73
52 3 0.02
53 6 0.04
56 36 0.21
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:52132895 original size:50 final size:50
Alignment explanation
Indices: 52132836--52133021 Score: 221
Period size: 50 Copynumber: 3.7 Consensus size: 50
52132826 CTACCAATGT
* ** * * *
52132836 CATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGC
1 CATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAAAGC
*
52132886 CATATCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGGTGCCAAAGC
1 CATATCCCAGACATGGTCTTACATGA-GACCTCTCATCTCGGTGCCAAAGC
* * * *
52132936 CATGTCCCAGACATGGTGTTACATGGGACCTCTCATCTCGGTGCCAACGC
1 CATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAAAGC
* * * *
52132986 CATGTCCTAGACATGGTCTTACATGGGACATCTCAT
1 CATATCCCAGACATGGTCTTACATGAGACCTCTCAT
52133022 AATCTCAATG
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 2 0.02
50 116 0.97
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
CATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAAAGC
Found at i:52133020 original size:100 final size:100
Alignment explanation
Indices: 52132840--52133066 Score: 242
Period size: 100 Copynumber: 2.2 Consensus size: 100
52132830 CAATGTCATA
* ** * *
52132840 TCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATATCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCT
*
52132905 TACGGAGGACCTCTCATCTCGGTGCCAAAGCCATG
66 TACGGAGGACATCTCATCTCGGTGCCAAAGCCATG
* * * * *
52132940 TCCCAGACATGGTGTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCTAGACATGGTCT
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCT
* *
52133005 TACATG-GGACATCTCATAATCTCAATGAG-GCCAATGCCATG
66 TAC-GGAGGACATCTC---ATCTC---G-GTGCCAAAGCCATG
*
52133046 TCCCAAACATGGTCTTACATG
1 TCCCAGACATGGTCTTACATG
52133067 GGATCTTATT
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
100 66 0.63
101 1 0.01
103 5 0.05
106 31 0.30
107 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (100 bp):
TCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCT
TACGGAGGACATCTCATCTCGGTGCCAAAGCCATG
Found at i:52133402 original size:12 final size:12
Alignment explanation
Indices: 52133385--52133411 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52133375 CCTAACTATG
52133385 GCTTCCCCCCTT
1 GCTTCCCCCCTT
52133397 GCTTCCCCCCTT
1 GCTTCCCCCCTT
52133409 GCT
1 GCT
52133412 AATTTCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.56, G:0.11, T:0.33
Consensus pattern (12 bp):
GCTTCCCCCCTT
Found at i:52137390 original size:20 final size:20
Alignment explanation
Indices: 52137365--52137423 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
52137355 ATGCATAACG
*
52137365 GAGGCACCAAAGTGCAGACA
1 GAGGCACCAAAGTGCAAACA
*
52137385 GAGGCACCAAAGTGCAAATA
1 GAGGCACCAAAGTGCAAACA
* *
52137405 GAGGCACCGAAGTGAAAAC
1 GAGGCACCAAAGTGCAAAC
52137424 CTGTACAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.29, T:0.07
Consensus pattern (20 bp):
GAGGCACCAAAGTGCAAACA
Found at i:52141119 original size:17 final size:16
Alignment explanation
Indices: 52141097--52141134 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
52141087 ACAAAATCTG
52141097 AATTTATTTCGCAATTT
1 AATTTATTTC-CAATTT
52141114 AATTTATTTCCAATTT
1 AATTTATTTCCAATTT
52141130 -ATTTA
1 AATTTA
52141135 ATTGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTATTTCCAATTT
Found at i:52142530 original size:16 final size:16
Alignment explanation
Indices: 52142500--52142536 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
52142490 CAAAATCAAA
52142500 ATTTATTTCCCAATTT
1 ATTTATTTCCCAATTT
52142516 CATTTATTT-CCAATTT
1 -ATTTATTTCCCAATTT
52142532 ATTTA
1 ATTTA
52142537 ACTGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTTCCCAATTT
Found at i:52142564 original size:31 final size:31
Alignment explanation
Indices: 52142526--52142598 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
52142516 CATTTATTTC
52142526 CAATTTATTTAACTGTTTATTTATGCTGTTT
1 CAATTTATTTAACTGTTTATTTATGCTGTTT
52142557 CAATTTATTTAACTGTTTATTTATGCTGTTT
1 CAATTTATTTAACTGTTTATTTATGCTGTTT
52142588 CAA-TTATTTAA
1 CAATTTATTTAA
52142599 TTTCTAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 8 0.19
31 34 0.81
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (31 bp):
CAATTTATTTAACTGTTTATTTATGCTGTTT
Found at i:52142596 original size:18 final size:18
Alignment explanation
Indices: 52142542--52142597 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
52142532 ATTTAACTGT
52142542 TTATTTATGCTGTTTCAA
1 TTATTTATGCTGTTTCAA
*
52142560 TTTATTTA-ACTG--T---
1 -TTATTTATGCTGTTTCAA
52142573 TTATTTATGCTGTTTCAA
1 TTATTTATGCTGTTTCAA
52142591 TTATTTA
1 TTATTTA
52142598 ATTTCTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 1 0.03
16 1 0.03
18 10 0.34
19 7 0.24
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (18 bp):
TTATTTATGCTGTTTCAA
Found at i:52145945 original size:18 final size:18
Alignment explanation
Indices: 52145924--52145958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52145914 GATTTTTCAT
*
52145924 AAAAAATTGATTGCTTGG
1 AAAAAAATGATTGCTTGG
*
52145942 AAAAAAATGTTTGCTTG
1 AAAAAAATGATTGCTTG
52145959 TACATGAATA
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:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (18 bp):
AAAAAAATGATTGCTTGG
Found at i:52150709 original size:40 final size:40
Alignment explanation
Indices: 52150625--52150808 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
52150615 TTGAATGCTG
* * * *
52150625 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
52150664 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
52150705 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
52150745 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
52150785 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52150809 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:52150762 original size:80 final size:81
Alignment explanation
Indices: 52150625--52150805 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
52150615 TTGAATGCTG
* *
52150625 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
52150689 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
52150705 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
52150766 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
52150785 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
52150806 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:52155093 original size:56 final size:50
Alignment explanation
Indices: 52154857--52155105 Score: 180
Period size: 50 Copynumber: 4.9 Consensus size: 50
52154847 TGATAATAAC
* * * *** * * *
52154857 ATGCCAAAGCCGTGTCCCAGACATGGTCTTACATGGGGTGTTTC-CTGTA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTTTA
* * * * * ** * *
52154906 CTGCCAATGCCATATCCCAGATATGGTCTTACATGGAAGTTCTCATATTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTTTA
* * * *
52154956 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATTTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTTTA
* * * *
52155006 GTGCCAACGCCATGTCCCGGACATGATCTTACGTGGGACCTCTCATAACCTTAATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT----TT--TA
*
52155062 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGG--CTCTCAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT
52155106 CCCCTAATGT
Statistics
Matches: 158, Mismatches: 35, Indels: 9
0.78 0.17 0.04
Matches are distributed among these distances:
49 34 0.22
50 82 0.52
54 9 0.06
56 33 0.21
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATTTTA
Found at i:52158284 original size:52 final size:51
Alignment explanation
Indices: 52158155--52158286 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 51
52158145 ATGTGTTCTG
* * * *
52158155 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTGCAT
* *
52158206 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAG-TTAAGTCTGCAT
*
52158257 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
52158287 ATTTGTTCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 31 0.44
51 15 0.21
52 24 0.34
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTGCAT
Found at i:52160603 original size:18 final size:19
Alignment explanation
Indices: 52160564--52160619 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
52160554 AAAAAGCATG
52160564 TGAAAAAGAAAAAGA-AAT
1 TGAAAAAGAAAAAGAGAAT
52160582 TGAAAAAGAAAAAGAGAA-
1 TGAAAAAGAAAAAGAGAAT
52160600 TGAAAGAGAGCAAAAAGAGA
1 TGAAA-A-AG-AAAAAGAGA
52160620 TTGTGAGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 20 0.59
19 3 0.09
20 2 0.06
21 9 0.26
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (19 bp):
TGAAAAAGAAAAAGAGAAT
Found at i:52160632 original size:17 final size:16
Alignment explanation
Indices: 52160607--52160653 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
52160597 GAATGAAAGA
*
52160607 GAGCAAAAAGAGATTGT
1 GAGCAAAAA-AGAATGT
*
52160624 GAGCGAAAAAGAATGT
1 GAGCAAAAAAGAATGT
52160640 GAGCAAGAAAAGAA
1 GAGCAA-AAAAGAA
52160654 AGCTGAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.53, C:0.06, G:0.30, T:0.11
Consensus pattern (16 bp):
GAGCAAAAAAGAATGT
Found at i:52160642 original size:16 final size:16
Alignment explanation
Indices: 52160607--52160645 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
52160597 GAATGAAAGA
52160607 GAGCAAAAAGAGATTGT
1 GAGCAAAAAGA-ATTGT
52160624 GAGCGAAAAAGAA-TGT
1 GAGC-AAAAAGAATTGT
52160640 GAGCAA
1 GAGCAA
52160646 GAAAAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 7 0.33
17 5 0.24
18 7 0.33
ACGTcount: A:0.49, C:0.08, G:0.31, T:0.13
Consensus pattern (16 bp):
GAGCAAAAAGAATTGT
Found at i:52165630 original size:21 final size:23
Alignment explanation
Indices: 52165577--52165631 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 23
52165567 TATATAAACT
52165577 TAATATTGTATTTATTAAATTTTA
1 TAATATT-TATTTATTAAATTTTA
52165601 T-A-ATTTATTTATTTTAAATTTTA
1 TAATATTTATTTA--TTAAATTTTA
52165624 TAATATTT
1 TAATATTT
52165632 TTAAATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 12 0.44
24 2 0.07
25 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TAATATTTATTTATTAAATTTTA
Found at i:52166240 original size:27 final size:27
Alignment explanation
Indices: 52166210--52166269 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
52166200 AATTTTTTTG
*
52166210 AAAAAATGTAAATA-TTCATAAAATTCT
1 AAAAAAT-TAAAAATTTCATAAAATTCT
*
52166237 AAAAAATTAAAAATTTCCTAAAATTCT
1 AAAAAATTAAAAATTTCATAAAATTCT
52166264 AAAAAA
1 AAAAAA
52166270 ATACATCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAATTAAAAATTTCATAAAATTCT
Found at i:52166471 original size:18 final size:18
Alignment explanation
Indices: 52166439--52166485 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
52166429 TGCATTTCCC
52166439 TTTTCTATTGT-TTTTAAA
1 TTTTCTATT-TATTTTAAA
*
52166457 TTATT-TATTTATTTTTAA
1 TT-TTCTATTTATTTTAAA
52166475 TTTTCTATTTA
1 TTTTCTATTTA
52166486 ATTTCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 20 0.80
19 2 0.08
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTCTATTTATTTTAAA
Found at i:52167723 original size:20 final size:19
Alignment explanation
Indices: 52167700--52167775 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 19
52167690 ACTTCGATAC
52167700 CCCTATTTGTACATACGTGT
1 CCCTATTTGTAC-TACGTGT
* *
52167720 CCCTGTTTGTACTTCG-GT
1 CCCTATTTGTACTACGTGT
* *
52167738 ACCTCTGA-TTGCACATACGTGC
1 -CC-CT-ATTTGTAC-TACGTGT
52167760 CCCTATTTGTACTACG
1 CCCTATTTGTACTACG
52167776 GTTGTAACAC
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
18 2 0.05
19 10 0.23
20 25 0.58
21 5 0.12
22 1 0.02
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (19 bp):
CCCTATTTGTACTACGTGT
Found at i:52167727 original size:40 final size:40
Alignment explanation
Indices: 52167663--52167772 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 40
52167653 AATTATTGAA
* * *
52167663 TGATGGCACATACATGTCCTTGTTTGTACTTCGATACCCC
1 TGATTGCACATACGTGTCCCTGTTTGTACTTCGATACCCC
* * *
52167703 T-ATTTGTACATACGTGTCCCTGTTTGTACTTCGGTACCTC
1 TGA-TTGCACATACGTGTCCCTGTTTGTACTTCGATACCCC
* *
52167743 TGATTGCACATACGTGCCCCTATTTGTACT
1 TGATTGCACATACGTGTCCCTGTTTGTACT
52167773 ACGGTTGTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 57 0.97
41 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.38
Consensus pattern (40 bp):
TGATTGCACATACGTGTCCCTGTTTGTACTTCGATACCCC
Found at i:52169154 original size:27 final size:27
Alignment explanation
Indices: 52169124--52169303 Score: 184
Period size: 27 Copynumber: 6.6 Consensus size: 27
52169114 GTATATTGAG
* *
52169124 CTCGCACACTCAGTGCTATATAATCAA
1 CTCGCACACTTAGTGCTACATAATCAA
*
52169151 CTCGCACACTTAGTGCTACGTAATCAA
1 CTCGCACACTTAGTGCTACATAATCAA
* *
52169178 ATCGCACACTTAGTGCTACATAGTCAAA
1 CTCGCACACTTAGTGCTACATAATC-AA
** **
52169206 CTCGCACACTTAGTGCCGCATGGTCAA
1 CTCGCACACTTAGTGCTACATAATCAA
* * *
52169233 TTCGCACACTTAGTGC-ATCATATTCAT
1 CTCGCACACTTAGTGCTA-CATAATCAA
* * *
52169260 TTCGCACACTTAGTGCAACATAGTCAAA
1 CTCGCACACTTAGTGCTACATAATC-AA
52169288 C-CGCACACTTAGTGCT
1 CTCGCACACTTAGTGCT
52169304 GTACAATTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CTCGCACACTTAGTGCTACATAATCAA
Found at i:52169265 original size:82 final size:81
Alignment explanation
Indices: 52169147--52169302 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52169137 TGCTATATAA
* *
52169147 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGCA
52169212 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52169229 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
52169293 CACTTAGTGC
65 CACTTAGTGC
52169303 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
ACTTAGTGCCGCATGG
Found at i:52176448 original size:27 final size:27
Alignment explanation
Indices: 52176418--52176595 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
52176408 ATATTGAGCC
* *
52176418 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
52176445 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
52176472 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
52176500 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
52176527 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
52176554 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
52176581 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52176596 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 103 0.80
28 25 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:52176557 original size:82 final size:81
Alignment explanation
Indices: 52176439--52176594 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52176429 TGCTATATAA
* *
52176439 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGCA
52176504 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52176521 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
52176585 CACTTAGTGC
65 CACTTAGTGC
52176595 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
ACTTAGTGCCGCATGG
Found at i:52179552 original size:41 final size:40
Alignment explanation
Indices: 52179498--52179611 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 40
52179488 AATCACATAC
*
52179498 TGATGCCACTGTCCCAGACAAGGTCTTACACAAAACAAAT
1 TGATGCCAATGTCCCAGACAAGGTCTTACACAAAACAAAT
* * * *
52179538 ATGATGCCAATGTCCCAGATATGGTCTTACACGCAACACAAGT
1 -TGATGCCAATGTCCCAGACAAGGTCTTACA--CAAAACAAAT
* * * *
52179581 CGATGCCAACGTCCTAGACGAGGTCTTACAC
1 TGATGCCAATGTCCCAGACAAGGTCTTACAC
52179612 GATAACTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 1 0.02
41 27 0.45
42 24 0.40
43 8 0.13
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (40 bp):
TGATGCCAATGTCCCAGACAAGGTCTTACACAAAACAAAT
Found at i:52184254 original size:19 final size:19
Alignment explanation
Indices: 52184230--52184268 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
52184220 AATAAATTAC
52184230 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTGAGT
*
52184249 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTGAGT
52184268 T
1 T
52184269 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (19 bp):
TCATCTTAGTTAATTGAGT
Found at i:52187764 original size:9 final size:9
Alignment explanation
Indices: 52187750--52187792 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
52187740 TTAGGGGACT
*
52187750 AAATTGCAA
1 AAATTGTAA
52187759 AAATTGTAA
1 AAATTGTAA
52187768 AAATTGTAA
1 AAATTGTAA
52187777 AAATTGTAA
1 AAATTGTAA
52187786 AAATTGT
1 AAATTGT
52187793 TCCCTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (9 bp):
AAATTGTAA
Found at i:52192075 original size:27 final size:26
Alignment explanation
Indices: 52192030--52192108 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
52192020 GAGACCCTAA
52192030 AATAGGTAAAATGACCGAAATACCCC
1 AATAGGTAAAATGACCGAAATACCCC
*
52192056 AATAGGGTAAAATGATCGAAATACCCC
1 AATA-GGTAAAATGACCGAAATACCCC
* * * *
52192083 CATAAGGTAAAGTAACCAAAATACCC
1 AAT-AGGTAAAATGACCGAAATACCC
52192109 TAAGAGATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.09
27 40 0.89
28 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.16
Consensus pattern (26 bp):
AATAGGTAAAATGACCGAAATACCCC
Found at i:52193609 original size:3 final size:3
Alignment explanation
Indices: 52193601--52193631 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52193591 GTGTTATTTG
*
52193601 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
52193632 TCATAACACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52199270 original size:15 final size:16
Alignment explanation
Indices: 52199241--52199271 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52199231 CAATATTTCA
52199241 CTTCCTTTATTCTCTT
1 CTTCCTTTATTCTCTT
52199257 CTTCCTTT-TTCTCTT
1 CTTCCTTTATTCTCTT
52199272 TTTTTTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTCCTTTATTCTCTT
Found at i:52211142 original size:33 final size:31
Alignment explanation
Indices: 52211105--52211183 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
52211095 TTATTTTTCG
52211105 ATTTCAATTTCTTTTTCCTCACACTATCT-TTTT
1 ATTTCAATTTCTTTTT-CTCACA-T-TCTCTTTT
*
52211138 ATTTCAACTTC-TTTTCTCACATTCTCTTTT
1 ATTTCAATTTCTTTTTCTCACATTCTCTTTT
*
52211168 -TCTCACATTTCTTTTT
1 ATTTCA-ATTTCTTTTT
52211184 TTCTTCTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 10 0.25
32 4 0.10
33 10 0.25
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTCAATTTCTTTTTCTCACATTCTCTTTT
Found at i:52211166 original size:31 final size:33
Alignment explanation
Indices: 52211105--52211168 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
52211095 TTATTTTTCG
*
52211105 ATTTCAATTTCTTTTTCCTCACACTATCTTTTT
1 ATTTCAACTTCTTTTTCCTCACACTATCTTTTT
* *
52211138 ATTTCAACTTC-TTTT-CTCACATTCTCTTTTT
1 ATTTCAACTTCTTTTTCCTCACACTATCTTTTT
52211169 CTCACATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.50
32 4 0.14
33 10 0.36
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTTCAACTTCTTTTTCCTCACACTATCTTTTT
Found at i:52211184 original size:16 final size:16
Alignment explanation
Indices: 52211111--52211184 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 16
52211101 TTCGATTTCA
*
52211111 ATTTCTTTTTCCTCAC
1 ATTTCTTTTTTCTCAC
* *
52211127 ACTATCTTTTTATTTCA-
1 A-TTTCTTTTT-TCTCAC
*
52211144 ACTTC--TTTTCTCAC
1 ATTTCTTTTTTCTCAC
52211158 A-TTCTCTTTTTCTCAC
1 ATTTCT-TTTTTCTCAC
52211174 ATTTCTTTTTT
1 ATTTCTTTTTT
52211185 TCTTCTCTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
13 7 0.16
14 4 0.09
16 18 0.40
17 13 0.29
18 3 0.07
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTCTTTTTTCTCAC
Found at i:52211187 original size:17 final size:16
Alignment explanation
Indices: 52211149--52211183 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
52211139 TTTCAACTTC
52211149 TTTTCTCACATTCTCT
1 TTTTCTCACATTCTCT
52211165 TTTTCTCACATT-TCT
1 TTTTCTCACATTCTCT
52211180 TTTT
1 TTTT
52211184 TTCTTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTCTCACATTCTCT
Found at i:52213232 original size:14 final size:14
Alignment explanation
Indices: 52213213--52213246 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
52213203 CACATGTACT
52213213 TGAAGCCGATTCAA
1 TGAAGCCGATTCAA
*
52213227 TGAAGCCGATTCAT
1 TGAAGCCGATTCAA
52213241 TGAAGC
1 TGAAGC
52213247 TCAATCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (14 bp):
TGAAGCCGATTCAA
Found at i:52216566 original size:18 final size:18
Alignment explanation
Indices: 52216543--52216583 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
52216533 AAAGTCGTAT
*
52216543 GAAAAGATAAGAGAAAAA
1 GAAAAGAAAAGAGAAAAA
*
52216561 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGAGAAAAA
52216579 GAAAA
1 GAAAA
52216584 AACAAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (18 bp):
GAAAAGAAAAGAGAAAAA
Found at i:52219140 original size:20 final size:20
Alignment explanation
Indices: 52219111--52219148 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52219101 TAACAGCTGC
*
52219111 TGGCCTTTAATTCAACTTTT
1 TGGCCATTAATTCAACTTTT
52219131 TGGCCATTAATTCAACTT
1 TGGCCATTAATTCAACTT
52219149 CATAACAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (20 bp):
TGGCCATTAATTCAACTTTT
Found at i:52219372 original size:19 final size:19
Alignment explanation
Indices: 52219345--52219437 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 19
52219335 TGATTTAAGC
*
52219345 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
52219364 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* * * * *
52219383 -A-GTAATTTATTCCAG--C
1 AACTTAATTAACT-AAGATG
52219399 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
52219418 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
52219437 A
1 A
52219438 GTAATTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
17 10 0.18
18 10 0.18
19 37 0.65
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:52219408 original size:54 final size:54
Alignment explanation
Indices: 52219342--52219458 Score: 200
Period size: 54 Copynumber: 2.2 Consensus size: 54
52219332 TAATGATTTA
* *
52219342 AGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATGAGTAATTTATTCC
1 AGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAATTTATTCC
*
52219396 AGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAATTTATTCT
1 AGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAATTTATTCC
52219450 AGCAA-TTAA
1 AGCAACTTAA
52219459 ATACTTATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 4 0.07
54 56 0.93
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (54 bp):
AGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAATTTATTCC
Found at i:52221630 original size:27 final size:27
Alignment explanation
Indices: 52221575--52222011 Score: 463
Period size: 27 Copynumber: 16.2 Consensus size: 27
52221565 TAATGGGCCT
52221575 AAATGACCGAAATACCC-CGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
52221601 AAATGATTGAAATACCCGCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221628 AAATGACTGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221655 AAATGACTGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** *
52221682 AAATAACTAAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221709 AAATGATCGAAATACCC-CTGAAGGATA
1 AAATGACCGAAATACCCTC-GAAGGGTA
*
52221736 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** * *
52221763 AAATAACTAAAATAACCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
52221790 AAATAATCGAAATACCCTCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221817 AAATGACCGAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
52221844 AAATGACCAAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
** *
52221871 AAATGACTAAAATACCC-CTGAAAGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* * *
52221898 AAATGATCGAAATACCCTCAAAGAGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221925 AAATGACCGAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
52221952 AAATGATCGAAATACCCTAGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
52221979 AAATGACCAAAATAGCCC-C-ATAGGGTA
1 AAATGACCGAAATA-CCCTCGA-AGGGTA
52222006 AAATGA
1 AAATGA
52222012 TTGTTATGCC
Statistics
Matches: 352, Mismatches: 52, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
26 17 0.05
27 330 0.94
28 5 0.01
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:52222250 original size:52 final size:52
Alignment explanation
Indices: 52222193--52222310 Score: 182
Period size: 52 Copynumber: 2.3 Consensus size: 52
52222183 ACTGTTACCG
52222193 GTAGCTTTGTTGCGTTACTATTACTGGCAGCTTTACTGCGTTACTATTACAA
1 GTAGCTTTGTTGCGTTACTATTACTGGCAGCTTTACTGCGTTACTATTACAA
* * * *
52222245 GTAGCTTTGTTGCGTTACTGTTACTGGCAGCTTTGCTGCGTTATTATTACAG
1 GTAGCTTTGTTGCGTTACTATTACTGGCAGCTTTACTGCGTTACTATTACAA
* *
52222297 GCAGCTTTGCTGCG
1 GTAGCTTTGTTGCG
52222311 ATATTGGTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (52 bp):
GTAGCTTTGTTGCGTTACTATTACTGGCAGCTTTACTGCGTTACTATTACAA
Found at i:52222315 original size:26 final size:26
Alignment explanation
Indices: 52222195--52222310 Score: 151
Period size: 26 Copynumber: 4.5 Consensus size: 26
52222185 TGTTACCGGT
* *
52222195 AGCTTTGTTGCGTTACTATTACTGGC
1 AGCTTTGCTGCGTTACTATTACAGGC
* * *
52222221 AGCTTTACTGCGTTACTATTACAAGT
1 AGCTTTGCTGCGTTACTATTACAGGC
* * *
52222247 AGCTTTGTTGCGTTACTGTTACTGGC
1 AGCTTTGCTGCGTTACTATTACAGGC
*
52222273 AGCTTTGCTGCGTTATTATTACAGGC
1 AGCTTTGCTGCGTTACTATTACAGGC
52222299 AGCTTTGCTGCG
1 AGCTTTGCTGCG
52222311 ATATTGGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (26 bp):
AGCTTTGCTGCGTTACTATTACAGGC
Found at i:52222450 original size:30 final size:30
Alignment explanation
Indices: 52222416--52222475 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52222406 ACTGCATTGT
** *
52222416 ACTGTTACTGTGTTGGGCTAGGGCCCACAC
1 ACTGTTACTGTAATGGGCTAAGGCCCACAC
*
52222446 ACTGTTACTGTAATGGGCTAAGGCTCACAC
1 ACTGTTACTGTAATGGGCTAAGGCCCACAC
52222476 TGTACTGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (30 bp):
ACTGTTACTGTAATGGGCTAAGGCCCACAC
Found at i:52226032 original size:80 final size:79
Alignment explanation
Indices: 52225948--52226119 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
52225938 GGACTAAGAT
*
52225948 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
52226012 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
52226028 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
52226093 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
52226107 CCGAAGGCATTTG
1 CCGAAGGCATTTG
52226120 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:52226099 original size:39 final size:39
Alignment explanation
Indices: 52225895--52226117 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
52225885 TTGAATGCTG
* * * * *
52225895 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
52225935 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
52225974 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
52226015 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
52226055 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
52226094 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52226118 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:52226137 original size:79 final size:80
Alignment explanation
Indices: 52225975--52226152 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
52225965 AGATACAAAT
* * * *
52225975 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
52226040 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
52226055 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
52226119 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
52226134 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
52226153 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:52245528 original size:47 final size:47
Alignment explanation
Indices: 52245474--52245567 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
52245464 AACGCTAGAC
*
52245474 CACCTCCACATGCATTAATCAAATCCTAAATTATCTTTTAGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
* * *
52245521 CACCTCCATATGCATTAATCAAGCCCTAAATTATCTTTTGGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
52245568 AATCGAAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (47 bp):
CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
Found at i:52250772 original size:37 final size:37
Alignment explanation
Indices: 52250722--52250795 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
52250712 CAAAGCCCCT
52250722 TTACTCCTGGTGCATCCATCCCATGGTGTTAAAACCA
1 TTACTCCTGGTGCATCCATCCCATGGTGTTAAAACCA
52250759 TTACTCCTGGTGCATCCATCCCATGGTGTTAAAACCA
1 TTACTCCTGGTGCATCCATCCCATGGTGTTAAAACCA
52250796 CCAAAAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (37 bp):
TTACTCCTGGTGCATCCATCCCATGGTGTTAAAACCA
Found at i:52254024 original size:31 final size:31
Alignment explanation
Indices: 52253989--52254071 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
52253979 ATTAAATTAT
**
52253989 CCCGGGTTGCCCGACAACGATAATTCACCAC
1 CCCGGGTTGCCCGACAACGATAACCCACCAC
* * *
52254020 CCCGGGTTGCTCGACAATGATAACCCTCCAC
1 CCCGGGTTGCCCGACAACGATAACCCACCAC
*
52254051 CCTGGGTTGCCCGACAACGAT
1 CCCGGGTTGCCCGACAACGAT
52254072 GGCTTACTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.23, C:0.37, G:0.22, T:0.18
Consensus pattern (31 bp):
CCCGGGTTGCCCGACAACGATAACCCACCAC
Found at i:52254306 original size:35 final size:35
Alignment explanation
Indices: 52254217--52254386 Score: 178
Period size: 35 Copynumber: 4.8 Consensus size: 35
52254207 TTGATTTAAC
* * *
52254217 ATAATGACATGCTTAACATGCGAATCAAAATTAAAA
1 ATAATAACATGCTTAACATGCGAATCAAAA-TCAGA
** *
52254253 ATAATGGCATGCTTAACATGCGAGTCAAAATCAGA
1 ATAATAACATGCTTAACATGCGAATCAAAATCAGA
* **
52254288 TTAATAACATGCTTAACATGCGAGCCAAAATCAGA
1 ATAATAACATGCTTAACATGCGAATCAAAATCAGA
* * **
52254323 TTAATAGCATGCTTAACACACGAATCAAAATATCAGA
1 ATAATAACATGCTTAACATGCGAATC-AAA-ATCAGA
* *
52254360 ATATTAACATGTTTAACATGCGAATCA
1 ATAATAACATGCTTAACATGCGAATCA
52254387 GAACATCAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
35 55 0.49
36 32 0.28
37 26 0.23
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (35 bp):
ATAATAACATGCTTAACATGCGAATCAAAATCAGA
Found at i:52257594 original size:30 final size:30
Alignment explanation
Indices: 52257568--52257626 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52257558 TAATTATTTT
*
52257568 TTATTTGTTGTTATTATACTA-TATTATTAC
1 TTATTTGTTATTATT-TACTATTATTATTAC
*
52257598 TTGTTTGTTATTATTTACTATTATTATTA
1 TTATTTGTTATTATTTACTATTATTATTA
52257627 ATATTGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (30 bp):
TTATTTGTTATTATTTACTATTATTATTAC
Found at i:52257767 original size:22 final size:22
Alignment explanation
Indices: 52257737--52257779 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52257727 ACACCAAAAC
*
52257737 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
52257759 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
52257780 AGCGCCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:52257880 original size:43 final size:42
Alignment explanation
Indices: 52257827--52257975 Score: 156
Period size: 43 Copynumber: 3.5 Consensus size: 42
52257817 TAAAGGTGTT
* * *
52257827 GGTCTATAGCGGCGTTTTTAATATAACCGCCGCTATAGAT-TG
1 GGTCTTTAGCGGCGTTTTT-ATATAAGCGCCGCTATAGATCAG
* ** *
52257869 GTGTCTTTAGCGGTGTTTTCTGGATAAGTGCCGCTATAGATCAG
1 G-GTCTTTAGCGGCGTTTT-TATATAAGCGCCGCTATAGATCAG
* *
52257913 GGTTTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCAT
1 GGTCTTTAGCGGCG-TTTTTATATAAGCGCCGCTATAGATCAG
* *
52257956 GGCCTTTAGCGGCGCTTTTA
1 GGTCTTTAGCGGCGTTTTTA
52257976 CCAAAAACGC
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
42 6 0.07
43 74 0.85
44 7 0.08
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (42 bp):
GGTCTTTAGCGGCGTTTTTATATAAGCGCCGCTATAGATCAG
Found at i:52257987 original size:43 final size:43
Alignment explanation
Indices: 52257898--52258163 Score: 130
Period size: 43 Copynumber: 6.1 Consensus size: 43
52257888 CTGGATAAGT
* * * * * * *
52257898 GCCGCTATAGATCAGGGTTTTTAGCGGCGTTTTTTA-TATAAGC
1 GCCGCAATAGATCATGGTCTTTAGCGGCG-CTTTTACCAAAAAC
* *
52257941 GCCGCTATAGATCATGGCCTTTAGCGGCGCTTTTACCAAAAAC
1 GCCGCAATAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAAC
* * * * *
52257984 GCCGCAATAGACCCTGATCTATAGCGGCGCTTAT-CCAGAAAAC
1 GCCGCAATAGATCATGGTCTTTAGCGGCGCTTTTACCA-AAAAC
* * * * *
52258027 GCCGCAATAGACCCTGATCTATAGCGGCGCTTAT-CCAGAAAAC
1 GCCGCAATAGATCATGGTCTTTAGCGGCGCTTTTACCA-AAAAC
* ** * * **
52258070 GCTGCTAAATA-CCCTTTGTCTATATAGCGGCGC-TTCGCGCAAAAAC
1 GCCGC--AATAGATCATGGTCT-T-TAGCGGCGCTTTTAC-CAAAAAC
* * ** *
52258116 GCCGCTAA-AGACCCTAATCTATAGCGGCGCTTTTACCAAAAAC
1 GCCGC-AATAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAAC
52258159 GCCGC
1 GCCGC
52258164 TAAATTTGGC
Statistics
Matches: 182, Mismatches: 31, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
42 8 0.04
43 130 0.71
44 10 0.05
45 13 0.07
46 19 0.10
47 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (43 bp):
GCCGCAATAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAAC
Done.