Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold409
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: 3905031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 20 of 25
Found at i:3085521 original size:227 final size:228
Alignment explanation
Indices: 3085122--3085622 Score: 718
Period size: 227 Copynumber: 2.2 Consensus size: 228
3085112 ATACGACCTT
* * * * *
3085122 TTTTCAAAAGCCCACAAGTTAATGGCACCCTCTAAAGCCCACACAAGTCAGTGGTAATCTCTCTC
1 TTTTC-AAAGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGCGATAATCACTCTC
* *
3085187 AAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
65 AAAGCCCATAA--CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTGCAAAGCCCA
* * * * * *
3085252 CAAGTTAGTGGCACCCTTTCAATGCCTAGAAGTCAGTGGCACTCCTCTCAAAAGCCCACAAGTTA
128 CAAGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCA
* *
3085317 GTGGCACCCTTTCAAAGCCCAGAAGTCAGTGGCACC
193 GAGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * * *
3085353 TTTTCAAGAGTCCATAAGTTAGCGGCACCCTTTAAAGCCCACACAAGTTAGCGATGATCACTCTT
1 TTTTCAA-AGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGCGATAATCACTCTC
* *
3085418 AAAGCCCA-CA-AGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTGCAAAGCCCACA
65 AAAGCCCATAACAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTGCAAAGCCCACA
3085481 AGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAGA
130 AGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAGA
3085546 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
195 GGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* *
3085580 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
1 TTTTCAAAGCCCACAAGTTAGTGGCACCCTTT-AAAGCCCACA
3085623 AGTCAGTGGC
Statistics
Matches: 240, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
226 21 0.09
227 157 0.65
230 3 0.01
231 59 0.25
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (228 bp):
TTTTCAAAGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGCGATAATCACTCTCA
AAGCCCATAACAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTGCAAAGCCCACAA
GTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAGAG
GCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:3085675 original size:227 final size:226
Alignment explanation
Indices: 3085123--3085706 Score: 716
Period size: 227 Copynumber: 2.6 Consensus size: 226
3085113 TACGACCTTT
* * * *
3085123 TTTCAAAAGCCCACAAGTTAATGGCACCCTCTAAAGCCCACACAAGTCAGTGGTAATCTCTCTCA
1 TTTC-AAAGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGTGG--ATCACTTTCA
* * *
3085188 AAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
63 AAGCCCACAAAT-AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC-CTTCAAAGCCCAC
* * * * * *
3085253 AAGTTAGTGGCACCCTTTCAATGCCTAGAAGTCAGTGGCACTCCTCTCAAAAGCCCACAAGTTAG
126 AAGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAG
* * *
3085318 TGGCACCCTTTCAAAGCCCAGAAGTCAGTGGCACCT
191 AGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
3085354 TTTCAAGAGTCCATAAGTTAGCGGCACCCTTTAAAGCCCACACAAGTTAGCGATGATCACTCTT-
1 TTTCAA-AGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGTG--GATCACT-TTC
*
3085418 AAAGCCCAC--A-AGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTGCAAAGCCCAC
62 AAAGCCCACAAATAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTT-CAAAGCCCAC
3085480 AAGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAG
126 AAGTCAGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAG
3085545 AGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
191 AGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
3085581 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCA-CCCTTTCGA
1 TTTCAAAGCCCACAAGTTAGTGGCACCCTTT-AAAGCCCACACAAGTCAGTGG-ATCACTTTCAA
* * * * *
3085643 AGCCCACAAATTAGTTGCATCTTTTTAAAGCCCACAAGCCAGTGGCAAC-CCTTCAAAGCCCACA
64 AGCCCACAAA-TAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCCTTCAAAGCCCACA
3085707 CAAGTTAGTG
Statistics
Matches: 304, Mismatches: 36, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
222 2 0.01
223 12 0.04
224 1 0.00
225 11 0.04
226 36 0.12
227 181 0.60
228 2 0.01
230 2 0.01
231 55 0.18
232 1 0.00
233 1 0.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.20
Consensus pattern (226 bp):
TTTCAAAGCCCACAAGTTAGTGGCACCCTTTAAAGCCCACACAAGTCAGTGGATCACTTTCAAAG
CCCACAAATAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTCAAAGCCCACAAGTC
AGTGGCACCCTTTCAAAGCCCAGAAGTCAATGGCACTCCTCTAAAAAGCCCACAAGTCAGAGGCA
CCCTTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:3085735 original size:31 final size:31
Alignment explanation
Indices: 3085683--3085793 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
3085673 CCCACAAGCC
*
3085683 AGTGGCAACCCTTC-AAAGCCCACACAAGTT
1 AGTGGAAACCCTTCTAAAGCCCACACAAGTT
* * *
3085713 AGTGGTAACCCTTCTAAAGCCCATATAAGTT
1 AGTGGAAACCCTTCTAAAGCCCACACAAGTT
* *
3085744 GGTGGAAACCTTCTCTAAAGCCCACACAAGTT
1 AGTGGAAACCCT-TCTAAAGCCCACACAAGTT
*
3085776 GGTGGAAACCCTTCTAAA
1 AGTGGAAACCCTTCTAAA
3085794 CCTAATGTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
30 13 0.19
31 29 0.41
32 28 0.40
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (31 bp):
AGTGGAAACCCTTCTAAAGCCCACACAAGTT
Found at i:3085766 original size:32 final size:32
Alignment explanation
Indices: 3085697--3085790 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
3085687 GCAACCCTTC
* * *
3085697 AAAGCCCACACAAGTTAGTGGTAACCCT-TCT
1 AAAGCCCACACAAGTTGGTGGAAACCTTCTCT
* *
3085728 AAAGCCCATATAAGTTGGTGGAAACCTTCTCT
1 AAAGCCCACACAAGTTGGTGGAAACCTTCTCT
3085760 AAAGCCCACACAAGTTGGTGGAAACCCTTCT
1 AAAGCCCACACAAGTTGGTGGAAA-CCTTCT
3085791 AAACCTAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.43
32 25 0.46
33 6 0.11
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (32 bp):
AAAGCCCACACAAGTTGGTGGAAACCTTCTCT
Found at i:3089666 original size:32 final size:31
Alignment explanation
Indices: 3089630--3089712 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
3089620 AGAGTGGTTT
*
3089630 TGTATCGATACATTGTACCGATGCAAAACTTA
1 TGTATCGATACATT-TACCGATACAAAACTTA
* * ** *
3089662 TGTATTGATACAATATATTGATATAAAACTTA
1 TGTATCGATAC-ATTTACCGATACAAAACTTA
*
3089694 TGTATCTATACATTTACCG
1 TGTATCGATACATTTACCG
3089713 TTTGTATCGA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
31 5 0.13
32 32 0.82
33 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (31 bp):
TGTATCGATACATTTACCGATACAAAACTTA
Found at i:3090476 original size:61 final size:59
Alignment explanation
Indices: 3090349--3090544 Score: 173
Period size: 61 Copynumber: 3.2 Consensus size: 59
3090339 CTAGTGTGCA
* * *
3090349 GATTCAAGGCCTA-CAACACTGGACTTAAAGATGAT-AAGAATGA-GAAGAGTGCCAATGTGTT
1 GATTCAA-GCC-AGCAACATTGGACTT-AAGATG-TGAAGAATGATAAAG-GTGCCAATATGTT
* *
3090410 GATTCAAGGTCAGCAACATTGGACTTAAGGATGTGAAGAATGATAAAGGTGCCAATATGCT
1 GATTCAA-GCCAGCAACATTGGACTTAA-GATGTGAAGAATGATAAAGGTGCCAATATGTT
* * * * * * *
3090471 AATTCACAGCCAGCGATATCGGGCTTGAAGATGAGAAGAATGATAAAGGTGCTAATATGTT
1 GATTCA-AGCCAGCAACATTGGACTT-AAGATGTGAAGAATGATAAAGGTGCCAATATGTT
3090532 GATTCAAAGCCAG
1 GATTC-AAGCCAG
3090545 TGAAAAATGA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
60 4 0.04
61 102 0.90
62 7 0.06
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (59 bp):
GATTCAAGCCAGCAACATTGGACTTAAGATGTGAAGAATGATAAAGGTGCCAATATGTT
Found at i:3090701 original size:52 final size:53
Alignment explanation
Indices: 3090560--3090912 Score: 254
Period size: 52 Copynumber: 6.6 Consensus size: 53
3090550 AATGACAAAG
* * * * *
3090560 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-TAA-AGATGA-CAAA
1 GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
** * * * * * *
3090610 GACACTAATATGTTGATTCAAGGCCAGCGATATTAGACTTAAGA-AAGAGAAAT
1 G-TGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
* * * * *
3090663 GTGCCAATGTACTGATTCAAGGTTAGTAACATTGGACTTAAAGATGAGAGGAATGATAAA
1 GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTT-AAGA-GA-A-G-A-GA-AAA
* * * * *
3090723 GGTGTTAATATGCTGATTCAAGGCTAGTGATATTGGGCTTAA-AGATGACAAAA
1 -GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
* * * * *
3090776 GTGCCAATATACTGATTCAAGGCTAGCGACATTGGACTTAA-AGATGATAAAA
1 GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
* *
3090828 GCGCTAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAGA-AAGA-AAAA
1 GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
* * * *
3090879 TGTGCTAGTGTGCTGATTCAAGGCCAATGACATT
1 -GTGCTAATATGCTGATTCAAGGCTAGTGACATT
3090913 AAACTTAAAG
Statistics
Matches: 237, Mismatches: 51, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
50 1 0.00
51 34 0.14
52 143 0.60
53 12 0.05
54 1 0.00
55 2 0.01
56 2 0.01
57 1 0.00
58 3 0.01
59 3 0.01
60 4 0.02
61 31 0.13
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (53 bp):
GTGCTAATATGCTGATTCAAGGCTAGTGACATTGGACTTAAGAGAAGAGAAAA
Found at i:3090813 original size:113 final size:110
Alignment explanation
Indices: 3090614--3091035 Score: 330
Period size: 113 Copynumber: 3.8 Consensus size: 110
3090604 GACAAAGACA
* * * * *
3090614 CTAATATGTTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAGAAATGTGCCAATGTACTGAT
1 CTAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAGAAAGA-AAAAGTGCCAATATACTGAT
* ***
3090679 TCAAGGTTAGTAACATTGGACTTAAAGATGAGAGGAATGATAAAGGTG
65 TCAAGGCTAACGACATTGGACTTAAAGATGA-A-GAATGATAAAGGTG
* * * *
3090727 TTAATATGCTGATTCAAGGCTAGTGATATTGGGCTTAA-AGATGACAAAAGTGCCAATATACTGA
1 CTAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAGA-AAGA-AAAAGTGCCAATATACTGA
* *
3090791 TTCAAGGCTAGCGACATTGGACTTAAAGAT---G-AT-A-AAA-GCG
64 TTCAAGGCTAACGACATTGGACTTAAAGATGAAGAATGATAAAGGTG
* * * * *
3090831 CTAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAGAAAGAAAAATGTGCTAGTGTGCTGAT
1 CTAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAGAAAGAAAAA-GTGCCAATATACTGAT
* * ** * *
3090896 TCAAGGCCAATGACATTAAACTTAAAGATGATA-AA-GATGCGAAGAATGG
65 TCAAGGCTAACGACATTGGACTTAAAGATGA-AGAATGAT--AAAG-GT-G
* * * * * *
3090945 C-AATGTGTTGATTCAAGGCCAG-GACATTGGGCTTAA-AAATGATAAAGGTGCCAATATGCTGA
1 CTAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAGAAA-GA-AAAAGTGCCAATATACTGA
* *
3091007 TTCAAGGCTAACGATATCGGACTTAAAGA
64 TTCAAGGCTAACGACATTGGACTTAAAGA
3091036 AAAAAGCTTT
Statistics
Matches: 248, Mismatches: 44, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
103 4 0.02
104 77 0.31
105 4 0.02
106 1 0.00
107 2 0.01
108 3 0.01
111 5 0.02
112 50 0.20
113 100 0.40
114 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (110 bp):
CTAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAGAAAGAAAAAGTGCCAATATACTGATT
CAAGGCTAACGACATTGGACTTAAAGATGAAGAATGATAAAGGTG
Found at i:3090845 original size:165 final size:164
Alignment explanation
Indices: 3090550--3090868 Score: 374
Period size: 165 Copynumber: 1.9 Consensus size: 164
3090540 GCCAGTGAAA
3090550 AATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTAAAGATGACAAAGACAC
1 AATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTAAAGATGACAAAGACAC
** * * * *
3090615 TAATATGTTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAGAAATGTGCCAATGTACTGATT
66 TAATATACTGATTCAAGGCCAGCGACATTAGACTTAAGAAAGAGAAAAGCGCCAATATACTGATT
*
3090680 CAAGGTTAGTAACATTGGACTTAAAGATGAGAGG
131 CAAGGCTAGTAACATTGGACTTAAAGATGAGAGG
* ** * * * * *
3090714 AATGATAAAGGTGTTAATATGCTGATTCAAGGCTAGTGATATTGGGCTTAAAGATGACAAAAGTG
1 AATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-TAAAGATGAC-AAAG-A
* * * * * *
3090779 C-C-AATATACTGATTCAAGGCTAGCGACATTGGACTTAA-AGATGATAAAAGCGCTAATATGCT
63 CACTAATATACTGATTCAAGGCCAGCGACATTAGACTTAAGA-AAGAGAAAAGCGCCAATATACT
* *
3090841 GATTCAAGGCTAGTGATATTGGACTTAA
127 GATTCAAGGCTAGTAACATTGGACTTAA
3090869 GAAAGAAAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
164 41 0.32
165 81 0.63
166 5 0.04
167 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (164 bp):
AATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTAAAGATGACAAAGACAC
TAATATACTGATTCAAGGCCAGCGACATTAGACTTAAGAAAGAGAAAAGCGCCAATATACTGATT
CAAGGCTAGTAACATTGGACTTAAAGATGAGAGG
Found at i:3090925 original size:217 final size:215
Alignment explanation
Indices: 3090547--3091035 Score: 599
Period size: 217 Copynumber: 2.3 Consensus size: 215
3090537 AAAGCCAGTG
* *
3090547 AAAAATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-TAAAGATGACAAAG
1 AAAAATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAAAAG
* *
3090611 ACACTAATATGTTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAGAAATGTGCCAATGTACT
66 ACACTAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAAAAATGTGCCAATGTACT
** * ** * **
3090676 GATTCAAGGTTAGTAACATTGGACTTAAAGATGAGAGGAATGAT-AAAG-GTGTTAATATGCTGA
131 GATTCAAGGCCAATAACATTAAACTTAAAGATGAGA--AA-GATCAAAGAATGGCAATATGCTGA
* *
3090739 TTCAAGGCTAGTGATATTGGGCTT
193 TTCAAGGCCAG-GACATTGGGCTT
* * *
3090763 AAAGATGACAAAAGTGCCAATATACTGATTCAAGGCTAGCGACATTGGACTTAAAGATGATAAAA
1 AAAAATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGA-AAAA
* * * * * * *
3090828 G-CGCTAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAGAAAGAAAAATGTGCTAGTGTGC
65 GACACTAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAAAAATGTGCCAATGTAC
* * * * *
3090892 TGATTCAAGGCCAATGACATTAAACTTAAAGATGATAAAGATGCGAAGAATGGCAATGTGTTGAT
130 TGATTCAAGGCCAATAACATTAAACTTAAAGATGAGAAAGAT-CAAAGAATGGCAATATGCTGAT
3090957 TCAAGGCCAGGACATTGGGCTT
194 TCAAGGCCAGGACATTGGGCTT
* * * *
3090979 AAAAATGATAAAGGTGCCAATATGCTGATTCAAGGCTAACGATATCGGACTTAAAGA
1 AAAAATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGA
3091036 AAAAAGCTTT
Statistics
Matches: 232, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
214 3 0.01
215 2 0.01
216 110 0.47
217 113 0.49
218 4 0.02
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (215 bp):
AAAAATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAAAAG
ACACTAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAGAAAGAAAAATGTGCCAATGTACT
GATTCAAGGCCAATAACATTAAACTTAAAGATGAGAAAGATCAAAGAATGGCAATATGCTGATTC
AAGGCCAGGACATTGGGCTT
Found at i:3091142 original size:33 final size:33
Alignment explanation
Indices: 3091090--3091704 Score: 453
Period size: 33 Copynumber: 19.0 Consensus size: 33
3091080 CATTAGGCTT
* ** *
3091090 AGAAAGGTTACCATTGACTTGTATGGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
3091123 AGAAAGGTTGCTACCGACTTATGTGGGCTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
** **
3091156 A-AGGGGTTGCCACCGACTTGAATGGGCTTTA-
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * * *
3091187 A-AACAGGGGTTGTCATCGACTTATGGGGGGTTTA-
1 AGAA-A--GGTTGCCACCGACTTGTGTGGGCTTTAG
** *
3091221 A-AGGGGTTGCCACCGATTTGTGTGGGCTTT-G
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
3091252 AGAAAAGTTGCCACCGACTTGTGTGGGCTTTTG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
3091285 AAGAAAGGTTGCCATCGACTTGTGTAGGCTTTAG
1 -AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * * *
3091319 AG--GGGTTGCCACCAATTTCTATGGGCTTT-G
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3091349 AGAAGGGTTGCCACCTACTTGTGTGGGCTTTTAA
1 AGAAAGGTTGCCACCGACTTGTGTGGGC-TTTAG
* * *
3091383 AGAAGGGTTGCCACTGACTTGTGTGGGCTTTTG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
3091416 A-AAAGGGTTGCCACTGACTTGTGTTGGCTTT-G
1 AGAAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3091448 A-AGAGGTTGCCACCAACTTGTGTGGGGTTTAG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
3091480 AGAAAGGTTGCCACC-AGCTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCGA-CTTGTGTGGGCTTTAG
* * ** *
3091513 AGAAGGGTTGCCATCGACTAATCTGGGCTTT--
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
* * ** * *
3091544 AGAAGGGGTGCCAGTGACTTATGTGGGCTTTTG
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
** **
3091577 A-AGGGGTTTGCCACTAACTTGTGTGGGCTTTAG
1 AGAAAGG-TTGCCACCGACTTGTGTGGGCTTTAG
* *
3091610 A-AAAGGGTTGCCATCAACTTGTGTGGGCTTT-G
1 AGAAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
*
3091642 AG-AAGGTTGCCA-CTATCTTGTGTGGGCTTTAG
1 AGAAAGGTTGCCACCGA-CTTGTGTGGGCTTTAG
* * * *
3091674 A-AGATGTTGCCACCAACTTATGTGGGCTTTA
1 AGAAAGGTTGCCACCGACTTGTGTGGGCTTTA
3091705 AAAGAAAAAA
Statistics
Matches: 470, Mismatches: 87, Indels: 51
0.77 0.14 0.08
Matches are distributed among these distances:
30 5 0.01
31 113 0.24
32 110 0.23
33 162 0.34
34 80 0.17
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (33 bp):
AGAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:3091249 original size:97 final size:97
Alignment explanation
Indices: 3091128--3091671 Score: 435
Period size: 97 Copynumber: 5.6 Consensus size: 97
3091118 TTTAGAGAAA
* * * ** * *
3091128 GGTTGCTACCGACTTATGTGGGCTTT-AGAAGGGGTTGCCACCGACTTGAATGGGCTTTAAAACA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAA-AGGTTGCCACCGACTTGTGTGGGCTTTTAAAGA
* * * *
3091192 GGGGTTGTCATCGACTTATGGGGGGTTTAAAGG
65 AGGGTTGCCATCGACTTGTGGGGGCTTTAAAGG
* * *
3091225 GGTTGCCACCGATTTGTGTGGGCTTTGAGAAAAGTTGCCACCGACTTGTGTGGGCTTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAA
* ** *
3091290 AGGTTGCCATCGACTTGTGTAGGCTTTAGAGG
66 GGGTTGCCATCGACTTGTGGGGGCTTTAAAGG
* * * * * *
3091322 GGTTGCCACCAATTTCTATGGGCTTTGAGAAGGGTTGCCACCTACTTGTGTGGGCTTTTAAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAA
* *
3091387 GGGTTGCCA-CTGACTTGTGTGGGCTTTTGAAAAG
66 GGGTTGCCATC-GACTTGTGGGGGC-TTT-AAAGG
* * * * * *
3091421 GGTTGCCACTGACTTGTGTTGGCTTTGA-AGAGGTTGCCACCAACTTGTGTGGG-GTTTAGAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAA
* * * *
3091484 AGGTTGCCA-CCAGCTTGTGTGGGCTTTAGAGAAG
66 GGGTTGCCATCGA-CTTGTGGGGGCTTTA-A-AGG
* ** * * * ** * *
3091518 GGTTGCCATCGACTAATCTGGGCTTT-AGAAGGGGTGCCAGTGACTTATGTGGGCTTTTGAAG--
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAA
* * *
3091580 GGGTTTGCCA-CTAACTTGTGTGGGCTTTAGAAAAG
66 GGG-TTGCCATC-GACTTGTGGGGGCTTT--AAAGG
* * *
3091615 GGTTGCCATCAACTTGTGTGGGCTTTGAG-AAGGTTGCCA-CTATCTTGTGTGGGCTTT
1 GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGA-CTTGTGTGGGCTTT
3091672 AGAAGATGTT
Statistics
Matches: 363, Mismatches: 69, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
95 1 0.00
96 10 0.03
97 288 0.79
98 38 0.10
99 26 0.07
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (97 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAA
GGGTTGCCATCGACTTGTGGGGGCTTTAAAGG
Found at i:3091456 original size:130 final size:127
Alignment explanation
Indices: 3091224--3091671 Score: 473
Period size: 130 Copynumber: 3.5 Consensus size: 127
3091214 GGGTTTAAAG
* *
3091224 GGGTTGCCACCGATTTGTGTGGGCTTTGAGAA-AA-GTTGCCACCGACTTGTGTGGGCTTTTGAA
1 GGGTTGCCACC-ACTTGTGTGGGCTTT-A-AAGAAGGTTGCCACTGACTTGTGTGGGCTTTTGAA
* * * *
3091287 GAAAGGTTGCCATCGACTTGTGTAGGCTTT-AGAGGGGTTGCCACCAATTTCTATGGGCTTT-GA
63 -AAGGGTTGCCAT-GACTTGTGTAGGCTTTGA-AGGGGTTGCCACCAACTTGTGTGGGCTTTAGA
3091350 GAA
125 GAA
3091353 GGGTTGCCACCTACTTGTGTGGGCTTTTAAAGAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAA
1 GGGTTGCCACC-ACTTGTGTGGGC-TTTAAAGAA-GGTTGCCACTGACTTGTGTGGGCTTTTGAA
* * *
3091418 AAGGGTTGCCACTGACTTGTGTTGGCTTTGAAGAGGTTGCCACCAACTTGTGTGGGGTTTAGAGA
63 AAGGGTTGCCA-TGACTTGTGTAGGCTTTGAAGGGGTTGCCACCAACTTGTGTGGGCTTTAGAGA
3091483 A
127 A
* * ** * *
3091484 AGGTTGCCACCAGCTTGTGTGGGCTTTAGAGAAGGGTTGCCA-TCGACTAATCTGGGC-TTT-AG
1 GGGTTGCCACCA-CTTGTGTGGGCTTTAAAGAA-GGTTGCCACT-GACTTGTGTGGGCTTTTGAA
* * * *
3091546 AAGGGGTGCCAGTGACTTATGTGGGCTTTTGAAGGGGTTTGCCACTAACTTGTGTGGGCTTTAGA
63 AAGGGTTGCCA-TGACTTGTGTAGGC-TTTGAAGGGG-TTGCCACCAACTTGTGTGGGCTTTAGA
*
3091611 AAA
125 GAA
* *
3091614 GGGTTGCCATCAACTTGTGTGGGCTTT-GAGAAGGTTGCCACT-ATCTTGTGTGGGCTTT
1 GGGTTGCCA-CCACTTGTGTGGGCTTTAAAGAAGGTTGCCACTGA-CTTGTGTGGGCTTT
3091672 AGAAGATGTT
Statistics
Matches: 275, Mismatches: 29, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
127 1 0.00
128 41 0.15
129 46 0.17
130 129 0.47
131 58 0.21
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.32
Consensus pattern (127 bp):
GGGTTGCCACCACTTGTGTGGGCTTTAAAGAAGGTTGCCACTGACTTGTGTGGGCTTTTGAAAAG
GGTTGCCATGACTTGTGTAGGCTTTGAAGGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAA
Found at i:3091490 original size:194 final size:193
Alignment explanation
Indices: 3091090--3091704 Score: 620
Period size: 194 Copynumber: 3.2 Consensus size: 193
3091080 CATTAGGCTT
* * * * * *
3091090 AGAAAGGTTACCATTGACTTGTATGGGCTTTAGAGAAAGGTTGCTACCGACTTATGTGGGCTTTA
1 AGAAAGGTTGCCATCGACTTGTGTGGGCTTTAGAG-AGGGTTGCCACCGACTTATATGGGCTTTA
* ** * * * * **
3091155 GAAGGGGTTGCCACCGACTTGAATGGGCTTTAAAACAGGGGTTGTCA-TCGACTTATG-GGGGGT
65 GAA-GGGTTGCCACCTACTTGTGTGGGCTTTTAAAGA-GGGTTGCCACT-GACTTGTGTGGGCTT
* * * * * *
3091218 TT-AAAGGGGTTGCCACCGATTTGTGTGGGCTTTGAGAAAAGTTGCCACCGACTTGTGTGGGCTT
127 TTGAAAAGGGTTGCCACTGACTTGTGTGGGCTTTGA-AGAGGTTGCCACCAACTTGTGTGGGCTT
*
3091282 TTG
191 TAG
* * * *
3091285 AAGAAAGGTTGCCATCGACTTGTGTAGGCTTTAGAG-GGGTTGCCACCAATTTCTATGGGCTTTG
1 -AGAAAGGTTGCCATCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCGACTTATATGGGCTTT-
3091349 AGAAGGGTTGCCACCTACTTGTGTGGGCTTTTAAAGAAGGGTTGCCACTGACTTGTGTGGGCTTT
64 AGAAGGGTTGCCACCTACTTGTGTGGGCTTTTAAAG-AGGGTTGCCACTGACTTGTGTGGGCTTT
* *
3091414 TGAAAAGGGTTGCCACTGACTTGTGTTGGCTTTGAAGAGGTTGCCACCAACTTGTGTGGGGTTTA
128 TGAAAAGGGTTGCCACTGACTTGTGTGGGCTTTGAAGAGGTTGCCACCAACTTGTGTGGGCTTTA
3091479 G
193 G
* * * *
3091480 AGAAAGGTTGCCA-CCAGCTTGTGTGGGCTTTAGAGAAGGGTTGCCATCGACTAATCTGGGCTTT
1 AGAAAGGTTGCCATCGA-CTTGTGTGGGCTTTAGAG-AGGGTTGCCACCGACTTATATGGGCTTT
* * * * *
3091544 AGAAGGGGTGCCA-GTGACTTATGTGGGCTTTTGAAG-GGGTTTGCCACTAACTTGTGTGGGCTT
64 AGAAGGGTTGCCACCT-ACTTGTGTGGGCTTTTAAAGAGGG-TTGCCACTGACTTGTGTGGGCTT
* * * *
3091607 TAGAAAAGGGTTGCCA-TCAACTTGTGTGGGCTTTG-AGAAGGTTGCCACTATCTTGTGTGGGCT
127 TTGAAAAGGGTTGCCACT-GACTTGTGTGGGCTTTGAAG-AGGTTGCCACCAACTTGTGTGGGCT
3091670 TTAG
190 TTAG
* * * * *
3091674 A-AGATGTTGCCACCAACTTATGTGGGCTTTA
1 AGAAAGGTTGCCATCGACTTGTGTGGGCTTTA
3091705 AAAGAAAAAA
Statistics
Matches: 355, Mismatches: 51, Indels: 29
0.82 0.12 0.07
Matches are distributed among these distances:
193 31 0.09
194 175 0.49
195 68 0.19
196 81 0.23
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (193 bp):
AGAAAGGTTGCCATCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCGACTTATATGGGCTTTAG
AAGGGTTGCCACCTACTTGTGTGGGCTTTTAAAGAGGGTTGCCACTGACTTGTGTGGGCTTTTGA
AAAGGGTTGCCACTGACTTGTGTGGGCTTTGAAGAGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:3091804 original size:34 final size:35
Alignment explanation
Indices: 3091702--3091823 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 35
3091692 TATGTGGGCT
3091702 TTAAAA-G-AAAAAA-GTGCCACAAAGTTATGGAC
1 TTAAAAGGAAAAAAAGGTGCCACAAAGTTATGGAC
* *
3091734 TTAAAAGGAAAAAAAGGTGCCACAAAGTTGTAGAC
1 TTAAAAGGAAAAAAAGGTGCCACAAAGTTATGGAC
* * ***
3091769 TTAAAAGG-AGAAAGGGTGCCATGTAGTTATGGAC
1 TTAAAAGGAAAAAAAGGTGCCACAAAGTTATGGAC
*
3091803 TTAAAA-G-AAAAAAGATGCCAC
1 TTAAAAGGAAAAAAAGGTGCCAC
3091824 TAGGTCGTGG
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
32 6 0.08
33 12 0.16
34 31 0.42
35 25 0.34
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (35 bp):
TTAAAAGGAAAAAAAGGTGCCACAAAGTTATGGAC
Found at i:3091913 original size:34 final size:34
Alignment explanation
Indices: 3091873--3091954 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
3091863 GACTTTAAAG
* *
3091873 AGAAAAAGGTGTCACAGAGTCATGGACTTAGAAA
1 AGAAAAAGGTGCCACAGAGTCATAGACTTAGAAA
* * *
3091907 ATAAAAAGGTGCCACGGAGTCATAGACTTTGAAA
1 AGAAAAAGGTGCCACAGAGTCATAGACTTAGAAA
*
3091941 GGAAAAAGGTGCCA
1 AGAAAAAGGTGCCA
3091955 TAGGGTCGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.17
Consensus pattern (34 bp):
AGAAAAAGGTGCCACAGAGTCATAGACTTAGAAA
Found at i:3096572 original size:20 final size:20
Alignment explanation
Indices: 3096547--3096653 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
3096537 TTTTCACAAT
3096547 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
3096567 TTGTATCGATACATTTTGGGTTTTACCCA
1 TTGTATCGATACA--TT--G--TT---CA
* **
3096596 GATGTATCGATACATTGTTTG
1 -TTGTATCGATACATTGTTCA
*
3096617 TTGTTTCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
3096637 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
3096654 ATCGATACAT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
20 45 0.65
22 2 0.03
24 3 0.04
26 3 0.04
28 2 0.03
29 2 0.03
30 12 0.17
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:3096651 original size:13 final size:13
Alignment explanation
Indices: 3096635--3096664 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3096625 ATACATTGTT
3096635 CATTGTATCGATA
1 CATTGTATCGATA
3096648 CATTGTATCGATA
1 CATTGTATCGATA
3096661 CATT
1 CATT
3096665 CCGGCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3098718 original size:20 final size:20
Alignment explanation
Indices: 3098693--3098744 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3098683 TACAAGCCAA
**
3098693 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
3098713 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
3098732 TGTATCGATACAA
1 TGTATCGATACAA
3098745 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:3098820 original size:20 final size:21
Alignment explanation
Indices: 3098795--3098850 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3098785 ACATCTTTTT
*
3098795 CATGTATCGATACATTG-CAA
1 CATGTATCGATACATTGAAAA
3098815 CATGTATCGATAC-TTGAAAAA
1 CATGTATCGATACATTG-AAAA
*
3098836 GATGTATCGATACAT
1 CATGTATCGATACAT
3098851 GTCATTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 14 0.45
22 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
CATGTATCGATACATTGAAAA
Found at i:3098906 original size:19 final size:19
Alignment explanation
Indices: 3098881--3098931 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3098871 GTAGCCAAAC
*
3098881 TTGTATCGATACAC-AAAG
1 TTGTATCGATACACAAAAA
3098899 TATGTATCGATACACAAAAA
1 T-TGTATCGATACACAAAAA
3098919 TTGTATCGATACA
1 TTGTATCGATACA
3098932 TATTTGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 25 0.83
20 4 0.13
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (19 bp):
TTGTATCGATACACAAAAA
Found at i:3101052 original size:21 final size:20
Alignment explanation
Indices: 3101023--3101065 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3101013 GACTAGTGTA
* *
3101023 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
3101044 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
3101064 GG
1 GG
3101066 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:3101520 original size:13 final size:13
Alignment explanation
Indices: 3101502--3101539 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3101492 ATAATCCCCC
3101502 TGTATCGATACAG
1 TGTATCGATACAG
*
3101515 TGTATCGATACAT
1 TGTATCGATACAG
3101528 TGTATCGATACA
1 TGTATCGATACA
3101540 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3103638 original size:15 final size:15
Alignment explanation
Indices: 3103618--3103648 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3103608 ATTTCGTTTG
*
3103618 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3103633 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3103648 G
1 G
3103649 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3107686 original size:19 final size:19
Alignment explanation
Indices: 3107662--3107729 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3107652 AATTCAACAA
3107662 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3107681 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3107696 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3107713 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3107730 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3107701 original size:13 final size:13
Alignment explanation
Indices: 3107683--3107707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3107673 ACATAAGTTT
3107683 TGTATCGATACAA
1 TGTATCGATACAA
3107696 TGTATCGATACA
1 TGTATCGATACA
3107708 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3107705 original size:32 final size:32
Alignment explanation
Indices: 3107664--3107726 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3107654 TTCAACAATT
*
3107664 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3107696 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3107727 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3110217 original size:51 final size:53
Alignment explanation
Indices: 3110153--3110494 Score: 219
Period size: 52 Copynumber: 6.5 Consensus size: 53
3110143 AGTTTATCAA
* * * *
3110153 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3110204 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
3110258 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * *
3110316 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA-TTACTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * * *
3110365 TTTTTCACAATCGGGGATACT-CAAATCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTTCACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
3110418 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
3110470 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
3110495 CTCGTTATTT
Statistics
Matches: 223, Mismatches: 41, Indels: 53
0.70 0.13 0.17
Matches are distributed among these distances:
48 1 0.00
49 5 0.02
50 6 0.03
51 39 0.17
52 71 0.32
53 38 0.17
54 31 0.14
55 21 0.09
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3110337 original size:28 final size:27
Alignment explanation
Indices: 3110270--3110338 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
3110260 CTTCACAATC
**
3110270 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
3110297 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
3110325 GGGGATACTCCAAC
1 GGGGATACTCCAAC
3110339 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:3110379 original size:107 final size:105
Alignment explanation
Indices: 3110216--3110608 Score: 332
Period size: 107 Copynumber: 3.7 Consensus size: 105
3110206 TTCTATAATC
*
3110216 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
3110281 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCG
64 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTCCG
* * * * *
3110324 AGGGGATACTCCAACTCCGGTTTTA-TTACTAAAACACTAATTTTTTCACAATCGGGGATACTCA
1 -GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-TTTTTCACAATCGGGGATACTCC
** * ** * * * ** * *
3110388 AATCCTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAAT-C-
64 AA-CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCCG
* *
3110429 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
3110494 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGG
66 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTCC-G
* ** * * *** * * *
3110537 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
3110601 CCCCGTTA
66 CCCCGTTA
3110609 TTTTCAAAGG
Statistics
Matches: 221, Mismatches: 49, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 51 0.23
105 12 0.05
106 16 0.07
107 70 0.32
108 35 0.16
109 28 0.13
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCCG
Found at i:3110514 original size:28 final size:28
Alignment explanation
Indices: 3110478--3110554 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
3110468 ATTTTTCACA
* * *
3110478 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3110506 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
3110534 CGGGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3110555 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3110525 original size:212 final size:212
Alignment explanation
Indices: 3110158--3110562 Score: 627
Period size: 212 Copynumber: 1.9 Consensus size: 212
3110148 ATCAATTCTC
* * *
3110158 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAAATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
* *
3110223 CTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * *
3110288 TTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTAC
131 TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTAC
3110353 TAAAACACTAATTTTTT
196 TAAAACACTAATTTTTT
* * *
3110370 CACAATCGGGGATACT-CAAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 CACAATCGGGGATACTCCAAATCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGA
* *
3110434 TACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCT
64 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
3110497 CGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGGGGGGATACTCCAACCCCGGCTTTAT
129 CGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTAT
3110562 T
193 T
3110563 CCCAAAATAT
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 34 0.19
212 106 0.61
213 35 0.20
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (212 bp):
CACAATCGGGGATACTCCAAATCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTAC
TAAAACACTAATTTTTT
Found at i:3112013 original size:20 final size:20
Alignment explanation
Indices: 3111988--3112039 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3111978 TACAAGCCAA
**
3111988 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
3112008 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
3112027 TGTATCGATACAA
1 TGTATCGATACAA
3112040 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:3113318 original size:16 final size:16
Alignment explanation
Indices: 3113293--3113325 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3113283 TGTCCCTGTT
*
3113293 TTGGTGTTGAACAAAG
1 TTGGTCTTGAACAAAG
3113309 TTGGTCTTGAACAAAG
1 TTGGTCTTGAACAAAG
3113325 T
1 T
3113326 ATTTTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (16 bp):
TTGGTCTTGAACAAAG
Found at i:3113477 original size:79 final size:78
Alignment explanation
Indices: 3113356--3113655 Score: 324
Period size: 79 Copynumber: 3.8 Consensus size: 78
3113346 TTTTTCATTC
* * * * *
3113356 GGGGATGCTCCAACCCCGGCTTTATTTCTAAA-ATATTGATTTTTCATAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAGCT-TCGATTTTTCATAATCGGGGATACTCCAA
*
3113420 TCCCGTTTTTTTCGA
65 -CCCGTTATTTTCGA
* *
3113435 GGGGATACTCCAACCCCAGCCTTATTTCTAAAGCTTCGATTTTTCATGATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAGCTTCGATTTTTCATAATCGGGGATACTCCAAC
*
3113500 CTCGTTATTTTCAA
66 C-CGTTATTTTCGA
* * * *
3113514 GGGGATACTCCAACCCCTA-TTTTATTTTCAAAATGC--C-AATTTTCTATAATCAGGGATACTC
1 GGGGATACTCCAACCCC-AGCTTTA-TTTCTAAA-GCTTCGATTTTTC-ATAATCGGGGATACTC
3113575 CAACCCTGTTATTTTCGA
62 CAACCC-GTTATTTTCGA
* * * *
3113593 GGGGATACTCCAA-CCCAGATTTTATTTCCAAAACATCGATTTTTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCAG-CTTTATTTCTAAAGCTTCGATTTTTCATAATCGGGGATACTCCA
3113656 GCCCCGTTGT
Statistics
Matches: 189, Mismatches: 20, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
77 2 0.01
78 19 0.10
79 151 0.80
80 15 0.08
81 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCAGCTTTATTTCTAAAGCTTCGATTTTTCATAATCGGGGATACTCCAAC
CCGTTATTTTCGA
Found at i:3113653 original size:51 final size:52
Alignment explanation
Indices: 3113593--3113691 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
3113583 TTATTTTCGA
* *
3113593 GGGGATACTCCAACCCAGATT-TTATTTCCAAAACATC-GATTTTTCATAATC
1 GGGGATACTCCAACCCAG-TTGTCATTTCCAAAACATCAAATTTTTCATAATC
* * *
3113644 GGGGATACTCCAGCCCCGTTGTCATTTCCAAAATATCAAATTTTTCAT
1 GGGGATACTCCAACCCAGTTGTCATTTCCAAAACATCAAATTTTTCAT
3113692 CGGGAGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.05
51 30 0.73
52 9 0.22
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCAGTTGTCATTTCCAAAACATCAAATTTTTCATAATC
Found at i:3115967 original size:27 final size:27
Alignment explanation
Indices: 3115930--3115998 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
3115920 TTTTGTTGAA
3115930 AAATGGGGTTGGAGTATCCCCTCAGAG
1 AAATGGGGTTGGAGTATCCCCTCAGAG
3115957 AAATGGGGTTGGAGTATCCCCTCAGAG
1 AAATGGGGTTGGAGTATCCCCTCAGAG
*
3115984 AAATGAGGTTGGAGT
1 AAATGGGGTTGGAGT
3115999 GTCTCCGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
AAATGGGGTTGGAGTATCCCCTCAGAG
Found at i:3118474 original size:51 final size:51
Alignment explanation
Indices: 3118403--3118521 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
3118393 TGAAAATAAT
*
3118403 GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
* *
3118454 GGGGTTGAAGTATCCTCGATTGTGAGAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
*
3118505 GGGGTTGGAGTATCCCC
1 GGGGTTGAAGTATCCCC
3118522 TCAGAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (51 bp):
GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:3118577 original size:79 final size:76
Alignment explanation
Indices: 3118453--3118913 Score: 418
Period size: 79 Copynumber: 5.9 Consensus size: 76
3118443 GAAATAAGGC
* * ** * * *
3118453 CGGGGTTGAAGTATCCTCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCC-CGA-T-TGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
3118518 CCCCTCAGAAATAA
63 CCCCTCGGAAATAA
* ** * * *
3118532 CGGGGTTGGAGTATCCCTGATTGCGGAGTATTGGTGTTTTAGAAATAAAATCGCGGTTGGAGTAT
1 CGGGGTTGGAGTATCCC-GATT--GAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
* *
3118597 CCCTTTGGAAATAA
63 CCCCTCGGAAATAA
* * * *
3118611 TGGGATTGGAGTATTCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTAT
1 CGGGGTTGGAGTA-TCCCGA-T-TGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
* * *
3118676 CCCCGCGAAAATAG
63 CCCCTCGGAAATAA
* * * * * *
3118690 CGAGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTAT-CCCGA-T-TGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
3118755 CCCCTCGGAAATAA
63 CCCCTCGGAAATAA
* * * * *
3118769 CGGGGCTGGAGTATCCCCAATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTGTCCC
1 CGGGGTTGGAGTATCCCGATTGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
3118834 CTCGGAAATAA
66 CTCGGAAATAA
* * * * * * *
3118845 CGGGGTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTGT
1 CGGGGTTGGAGTAT-CCCGATTG-AAAAATTGA-TGTTTTAGAAATAAAACCGGGGTTGGAGTAT
3118910 CCCC
63 CCCC
3118914 GATTATGGAA
Statistics
Matches: 310, Mismatches: 62, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
76 62 0.20
77 7 0.02
78 13 0.04
79 222 0.72
80 5 0.02
81 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (76 bp):
CGGGGTTGGAGTATCCCGATTGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGGAAATAA
Found at i:3118750 original size:158 final size:154
Alignment explanation
Indices: 3118489--3118913 Score: 487
Period size: 158 Copynumber: 2.7 Consensus size: 154
3118479 GAAATCAATA
* * * *
3118489 TTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCTGAT
1 TTTTAGAAATAAA-ACGAGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGAT
* * * * * * * * *
3118553 TGCG-GAGTATTGGTGTTTTAGAAATAAAATCGCGGTTGGAGTATCCCTTTGGAAATAATGGGAT
64 TGTGAGA-AATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGAC
*
3118617 TGGAGTATTCCCGATTATGAAAAATTGATG
128 TGGAGTA-TCCCCA--ATGAAAAATTGATG
* * *
3118647 TTTTAGAAATAAAATCGAGGTTGGAGTATCCCCGCGAAAATAGCGAGGTTGGAGTATCCCCGATT
1 TTTTAGAAATAAAA-CGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* * * ** *
3118712 ATGAGAAATTAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGCTG
65 GTGAGAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGACTG
3118777 GAGTATCCCCAATGAAAAATTGATG
130 GAGTATCCCCAATGAAAAATTGATG
* * *
3118802 TTTTAGAAATAAAACCAGGGTTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
1 TTTTAGAAATAAAACGA-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* * *
3118867 GTGA-AAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTGTCCCC
65 GTGAGAAA-TTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
3118914 GATTATGGAA
Statistics
Matches: 225, Mismatches: 37, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
154 5 0.02
155 105 0.47
157 5 0.02
158 107 0.48
159 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (154 bp):
TTTTAGAAATAAAACGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTG
TGAGAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGACTGG
AGTATCCCCAATGAAAAATTGATG
Found at i:3118852 original size:155 final size:156
Alignment explanation
Indices: 3118489--3118913 Score: 507
Period size: 155 Copynumber: 2.7 Consensus size: 156
3118479 GAAATCAATA
* * * *
3118489 TTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTGATT
1 TTTTAGAAATAAAACC-GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
* * * * * * * * *
3118554 GCG-GAGTATTGGTGTTTTAGAAATAAAATCGCGGTTGGAGTATCCCTTTGGAAATAATGGGATT
65 GTGAGA-AATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGACT
*
3118618 GGAGTATTCCCGATTATGAAAAATTGATG
129 GGAGTATTCCCCA-TATGAAAAATTGATG
* * * * *
3118647 TTTTAGAAATAAAATCGAGGTTGGAGTATCCCCGCGAAAATAGCGAGGTTGGAGTATCCCCGATT
1 TTTTAGAAATAAAACCG-GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
* * * ** *
3118712 ATGAGAAATTAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGCTG
65 GTGAGAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGACTG
3118777 GAGTA-TCCCCA-ATGAAAAATTGATG
130 GAGTATTCCCCATATGAAAAATTGATG
*
3118802 TTTTAGAAATAAAACCAGGGTTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
1 TTTTAGAAATAAAACC-GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
* * *
3118867 GTGA-AAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTGTCCCC
65 GTGAGAAA-TTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
3118914 GATTATGGAA
Statistics
Matches: 224, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
154 3 0.01
155 106 0.47
156 1 0.00
157 6 0.03
158 106 0.47
159 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (156 bp):
TTTTAGAAATAAAACCGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTG
TGAGAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGACTGG
AGTATTCCCCATATGAAAAATTGATG
Found at i:3118904 original size:51 final size:49
Alignment explanation
Indices: 3118849--3119017 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 49
3118839 AAATAACGGG
*
3118849 GTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-T-AGTGTTTTGGAAATAAAATCGGA
* * * *
3118900 GTTGGAGTGTCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTAT-GAAAAT-AGTGTTTTGGAAATAAAATCGGA
* * * * * * *
3118951 GTTGTAGTATCCTCGATTAAGAAAAATTGATGTCTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATAG-TGTTTTGGAAATAAAATCGGA
3119001 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
3119018 GATAAAAAAT
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
50 3 0.03
51 88 0.92
52 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTATGAAAATAGTGTTTTGGAAATAAAATCGGA
Found at i:3121322 original size:20 final size:21
Alignment explanation
Indices: 3121297--3121339 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3121287 AAAATGCCTG
*
3121297 AATGTATCGATACAT-TGGGT
1 AATGTATCAATACATCTGGGT
3121317 AATGTATCAATACATCTGGGT
1 AATGTATCAATACATCTGGGT
3121338 AA
1 AA
3121340 AATTTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
AATGTATCAATACATCTGGGT
Found at i:3121386 original size:13 final size:13
Alignment explanation
Indices: 3121349--3121395 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
3121339 AAATTTTCAG
3121349 ATGTATCGATACA
1 ATGTATCGATACA
3121362 A-G-A--GAT-CA
1 ATGTATCGATACA
3121370 ATGTATCGATACA
1 ATGTATCGATACA
*
3121383 ATGTATGGATACA
1 ATGTATCGATACA
3121396 TTGAGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
8 3 0.11
9 4 0.14
10 1 0.04
11 1 0.04
12 4 0.14
13 15 0.54
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3121492 original size:21 final size:19
Alignment explanation
Indices: 3121446--3121499 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3121436 CAACGATACA
3121446 TTGTATCGATACAACACTT
1 TTGTATCGATACAACACTT
* *
3121465 ATGTATCGATACAATTACTAT
1 TTGTATCGATACAA-CACT-T
*
3121486 TTGTATCGAGACAA
1 TTGTATCGATACAA
3121500 ATTGTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACAACACTT
Found at i:3122813 original size:19 final size:20
Alignment explanation
Indices: 3122789--3122839 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3122779 GATACATTAC
3122789 ATCAATACAAAACT-TATGT
1 ATCAATACAAAACTGTATGT
** *
3122808 ATCAATACATTTACTGTTTGT
1 ATCAATACA-AAACTGTATGT
3122829 ATCAATACAAA
1 ATCAATACAAA
3122840 TTGTTGAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 9 0.36
20 3 0.12
21 13 0.52
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (20 bp):
ATCAATACAAAACTGTATGT
Found at i:3125489 original size:33 final size:32
Alignment explanation
Indices: 3125447--3125510 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3125437 TACAAGCCAA
*
3125447 TGTATCGATACATTTTGGGATGAATCGATACAT
1 TGTATCGATACATCTTGGG-TGAATCGATACAT
* *
3125480 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGAATCGATACA
3125511 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGAATCGATACAT
Found at i:3125599 original size:13 final size:13
Alignment explanation
Indices: 3125581--3125605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3125571 ACATTTAGTC
3125581 ATGTATCGATACA
1 ATGTATCGATACA
3125594 ATGTATCGATAC
1 ATGTATCGATAC
3125606 TGTGCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3126453 original size:20 final size:20
Alignment explanation
Indices: 3126428--3126467 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3126418 TAATCACATA
3126428 TTTCTTTCTCCCCCTTAAAC
1 TTTCTTTCTCCCCCTTAAAC
3126448 TTTCTTTCTCCCCCTTAAAC
1 TTTCTTTCTCCCCCTTAAAC
3126468 ATAAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.40, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTCTTTCTCCCCCTTAAAC
Found at i:3128315 original size:13 final size:13
Alignment explanation
Indices: 3128297--3128332 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3128287 AAACCCTTTG
*
3128297 TATCGATACACTA
1 TATCGATACAATA
*
3128310 TATCGATACAATG
1 TATCGATACAATA
3128323 TATCGATACA
1 TATCGATACA
3128333 GAGAATGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:3133937 original size:19 final size:20
Alignment explanation
Indices: 3133906--3133956 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3133896 TTACAAGCCA
*
3133906 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
3133926 ATGTAT-GATACATCTTGTG
1 ATGTATCGATACATCTTGGG
*
3133945 -TGTATGGATACA
1 ATGTATCGATACA
3133957 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 17 0.61
20 6 0.21
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:3134045 original size:20 final size:21
Alignment explanation
Indices: 3133998--3134050 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3133988 GCCAATGACC
*
3133998 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
3134019 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
3134039 TGTATCGATACA
1 TGTATCGATACA
3134051 AAGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:3139990 original size:34 final size:34
Alignment explanation
Indices: 3139947--3140016 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
3139937 CACTCGATAG
3139947 GAGCCACTACCCTTTCACAGCTAGGCTAAACTTT
1 GAGCCACTACCCTTTCACAGCTAGGCTAAACTTT
*
3139981 GAGCCACTACCTTTTCACAGCTAGGCTAAACTTT
1 GAGCCACTACCCTTTCACAGCTAGGCTAAACTTT
3140015 GA
1 GA
3140017 TTGCACAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (34 bp):
GAGCCACTACCCTTTCACAGCTAGGCTAAACTTT
Found at i:3141383 original size:12 final size:13
Alignment explanation
Indices: 3141366--3141398 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3141356 TACTATGCCT
3141366 AAAATAAAA-AAC
1 AAAATAAAACAAC
3141378 AAAATAAAACAAC
1 AAAATAAAACAAC
3141391 AAAA-AAAA
1 AAAATAAAA
3141399 GGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAATAAAACAAC
Found at i:3143577 original size:189 final size:190
Alignment explanation
Indices: 3143256--3143684 Score: 623
Period size: 189 Copynumber: 2.3 Consensus size: 190
3143246 AATTTTTGAT
* * * * *
3143256 TTTTCATGCCCTTACGGAAAACCTATAGCAATATAAAAATATGACTCAAGCAAATAAACGATCAC
1 TTTTCATACCCTTACGGAAAACC-ATAGGAATATAAAAACATGACTCGAGAAAATAAACGATCAC
* * *
3143321 ATATTTTTTAAAAAATATTAATTTAAGGAAACTGAATTTTTCTAAAGTTTTATATTTAACTTCTA
65 ATATTTTTTAAAAAATATTAATTTAAGGAAAATGAATTTTTCTAAAGTTTTAAACTTAACTTCTA
* * *
3143386 AATTTCGAACATTATGTTTCGTACCC-ACCGGAATACCAGGGGATACAAAAGGTGTTAAAAA
130 AATTTCGAACATTATGTTTCGTACCCGA-CGAAAAACCAGGGGACACAAAAGGTGTTAAAAA
3143447 TTTTCATACCCTTACGGAAAACCATAGGAATATAAAAACATGACTCGAGAAAATAAACGATCACA
1 TTTTCATACCCTTACGGAAAACCATAGGAATATAAAAACATGACTCGAGAAAATAAACGATCACA
* *
3143512 TATTTTTT-TAAAATATTAATTT-AGGAAAATCGAATTTTTCTAAATTTTTAAACTTAACTTCTA
66 TATTTTTTAAAAAATATTAATTTAAGGAAAAT-GAATTTTTCTAAAGTTTTAAACTTAACTTCTA
* *
3143575 AATTTCGAACATTATGTTTCGTACCCGATGAAAAACTAGGGGACACAAAAGGTGTTAAAAA
130 AATTTCGAACATTATGTTTCGTACCCGACGAAAAACCAGGGGACACAAAAGGTGTTAAAAA
** * *
3143636 TTTTCATATCCC-TACAAAAAACCATAGGAATATGAAAACACGACTCGAG
1 TTTTCATA-CCCTTACGGAAAACCATAGGAATATAAAAACATGACTCGAG
3143685 TGGGCATAAA
Statistics
Matches: 216, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
188 7 0.03
189 137 0.63
190 50 0.23
191 22 0.10
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (190 bp):
TTTTCATACCCTTACGGAAAACCATAGGAATATAAAAACATGACTCGAGAAAATAAACGATCACA
TATTTTTTAAAAAATATTAATTTAAGGAAAATGAATTTTTCTAAAGTTTTAAACTTAACTTCTAA
ATTTCGAACATTATGTTTCGTACCCGACGAAAAACCAGGGGACACAAAAGGTGTTAAAAA
Found at i:3144766 original size:35 final size:36
Alignment explanation
Indices: 3144726--3144839 Score: 144
Period size: 35 Copynumber: 3.2 Consensus size: 36
3144716 TATTTTTCTC
*
3144726 TTTCTTTATTCTTCTCGCTGTTTCGATGGCTA-TTT
1 TTTCTTTATTCTTCTTGCTGTTTCGATGGCTACTTT
3144761 TTTCTTTATTCTTCTTGCTGTTTCGATGGCTACTTT
1 TTTCTTTATTCTTCTTGCTGTTTCGATGGCTACTTT
* * * *
3144797 ATTTCTTTTATT-TTCTTACTGCTTCGAT-TCTATTTT
1 -TTTC-TTTATTCTTCTTGCTGTTTCGATGGCTACTTT
3144833 TTTCTTT
1 TTTCTTT
3144840 TTTCGTTTCT
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.04
35 35 0.49
36 9 0.13
37 18 0.25
38 6 0.08
ACGTcount: A:0.10, C:0.18, G:0.11, T:0.61
Consensus pattern (36 bp):
TTTCTTTATTCTTCTTGCTGTTTCGATGGCTACTTT
Found at i:3144849 original size:37 final size:36
Alignment explanation
Indices: 3144726--3144880 Score: 104
Period size: 35 Copynumber: 4.3 Consensus size: 36
3144716 TATTTTTCTC
* ** *
3144726 TTTCTTTATTC-TTCTCGCTGTTTCGATGGCTA-TTT
1 TTTCTTTTTTCTTTCTTACTGTTTCGAT-TCTATTTT
* * * *
3144761 TTTCTTTATTC-TTCTTGCTGTTTCGATGGCTACTTTA
1 TTTCTTTTTTCTTTCTTACTGTTTCGAT-TCTA-TTTT
* *
3144798 TTTCTTTTAT-TTTCTTACTGCTTCGATTCTATTTT
1 TTTCTTTTTTCTTTCTTACTGTTTCGATTCTATTTT
* * * *
3144833 TTTCTTTTTTCGTTTC-TACTATTTTGATTTTGTTTT
1 TTTCTTTTTTC-TTTCTTACTGTTTCGATTCTATTTT
3144869 CTTTCTTTTTTC
1 -TTTCTTTTTTC
3144881 ATTTTTGCTA
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
35 43 0.43
36 18 0.18
37 39 0.39
ACGTcount: A:0.09, C:0.17, G:0.10, T:0.64
Consensus pattern (36 bp):
TTTCTTTTTTCTTTCTTACTGTTTCGATTCTATTTT
Found at i:3144892 original size:37 final size:36
Alignment explanation
Indices: 3144829--3144898 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
3144819 TTCGATTCTA
*
3144829 TTTTTTTCTTTTTTCGTTTCTACTATTTTGATTTTG
1 TTTTTTTCTTTTTTCATTTCTACTATTTTGATTTTG
* *
3144865 TTTTCTTTCTTTTTTCATTTTTGCTATTTTGATT
1 TTTT-TTTCTTTTTTCATTTCTACTATTTTGATT
3144899 CCTTCTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (36 bp):
TTTTTTTCTTTTTTCATTTCTACTATTTTGATTTTG
Found at i:3145206 original size:31 final size:29
Alignment explanation
Indices: 3145143--3145207 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3145133 GTAGCTGTTT
* *
3145143 TTTTTTGTATTTATTGCTACAACTATTTC
1 TTTTTTGTATTCATTGCTACAACTATTGC
* *
3145172 TTTTTTGTCTTCATTGCTACAGCTTAATTGC
1 TTTTTTGTATTCATTGCTACAAC-T-ATTGC
3145203 TTTTT
1 TTTTT
3145208 CATTGCATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.67
30 1 0.03
31 9 0.30
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTTTGTATTCATTGCTACAACTATTGC
Found at i:3145409 original size:51 final size:51
Alignment explanation
Indices: 3145336--3145469 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 51
3145326 TCATGTTCTC
* *
3145336 GTGTGAAA-ACATGCATAAAAGCATGCATGAAATGTTTCACTGATGTTAAT
1 GTGTGAAATGCATGCATGAAAGCATGCATGAAATGTTTCACTGATGTTAAT
*
3145386 GTGTGAAATGCATGCATGAAAGCATGCTTGAAATGCATGAAATGTTTCGCTGATGTTAAT
1 GTGTGAAATGCATGCATG-AA--A-GC-----ATGCATGAAATGTTTCACTGATGTTAAT
3145446 GTGTGAAATGCATGCATGAAAGCA
1 GTGTGAAATGCATGCATGAAAGCA
3145470 ATGAAATGCA
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
50 8 0.11
51 8 0.11
52 2 0.03
54 1 0.01
55 2 0.03
56 2 0.03
57 1 0.01
59 2 0.03
60 45 0.63
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (51 bp):
GTGTGAAATGCATGCATGAAAGCATGCATGAAATGTTTCACTGATGTTAAT
Found at i:3145412 original size:12 final size:13
Alignment explanation
Indices: 3145389--3145424 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3145379 TGTTAATGTG
3145389 TGAAATGCATGCA
1 TGAAATGCATGCA
*
3145402 TGAAA-GCATGCT
1 TGAAATGCATGCA
3145414 TGAAATGCATG
1 TGAAATGCATG
3145425 AAATGTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
TGAAATGCATGCA
Found at i:3145703 original size:11 final size:11
Alignment explanation
Indices: 3145689--3145720 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3145679 ATTAATCAAC
*
3145689 TATTACTATTT
1 TATTATTATTT
3145700 TATTATTATTT
1 TATTATTATTT
3145711 TATTATTATT
1 TATTATTATT
3145721 ATTTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATTATTT
Found at i:3145716 original size:14 final size:14
Alignment explanation
Indices: 3145699--3145725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3145689 TATTACTATT
3145699 TTATTATTATTTTA
1 TTATTATTATTTTA
3145713 TTATTATTATTTT
1 TTATTATTATTTT
3145726 TTAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:3146458 original size:42 final size:42
Alignment explanation
Indices: 3146317--3146996 Score: 415
Period size: 42 Copynumber: 16.2 Consensus size: 42
3146307 AAAGGTGGAA
* * * * *
3146317 AAGTCTCCAAGGTCAAAGTCGACAAGCAGATTTGAGAGTAAGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG-GTAAGG
* ** * **
3146360 CAA-TCTCTAGGGTCAAAGCCGACAGGTTGACTGAAGGTAAAA
1 -AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * *
3146402 AAATCTCCAAGGTCAAAGCTGACAGGCAGACTTAAGGCAAGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * ** * * *
3146444 CAGTCTCGAGGGTCAAAGCTAACAGGCAGACTTGAGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * *
3146486 TAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAAGGT-AGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
** * * *
3146527 AAAGTCTCC-GTGGTCAAAGTTGACAGGCAGACTTGAGATGAGG
1 -AAGTCTCCAG-GGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * * *
3146570 CAGCCTCTAGGGTCAAAGCCGACAAGCAGACTAAAGGT-CGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * * *
3146611 AAAGTCTCTAAGGTCAAAGCCGATAGGTAGACCTGAGGTAA-G
1 -AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* ** * * *
3146653 CAGTCTCCAGGGTCAAAGCTAATAGGTAGACTGAAGGT-AGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * *
3146694 AAAGTCTCCAAGGTCAAAGTCGATAGGCAGACTTGAGGTAA-G
1 -AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * *
3146736 TAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGGT-AGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * * *
3146777 AAAGTCTCTAAGGTCAAAGCCGACAGGTAGACTTGAGATGAGG
1 -AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * * * **
3146820 TAGTCTCTAGGGTCAAAGCTGATAGGTAGACTAAAGAGTAAAA
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG-GTAAGG
* * * * * *
3146863 AAGTCTCCAAGGTCAAAGCCCACAGGCAAACTTGAGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * **
3146905 CAGTCTCCAGGGTCAAAGCCGACAGGCAAACTGAGGGTAAAA
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
* * * * * * *
3146947 AAGTCT-CTGGGTCAAAACTGACAGACAGACTTGAGATGAGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
*
3146988 TAGTCTCCA
1 AAGTCTCCA
3146997 AAGTCAAAAC
Statistics
Matches: 475, Mismatches: 146, Indels: 32
0.73 0.22 0.05
Matches are distributed among these distances:
40 2 0.00
41 98 0.21
42 313 0.66
43 60 0.13
44 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (42 bp):
AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGG
Found at i:3146696 original size:83 final size:84
Alignment explanation
Indices: 3146405--3147024 Score: 609
Period size: 83 Copynumber: 7.4 Consensus size: 84
3146395 GGTAAAAAAA
* * * * * * * * **
3146405 TCTCCAAGGTCAAAGCTGACAGGCAGACTTAAGGCAAGG-CAGTCTCGAGGGTCAAAGCTAACAG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGG-TAGGAAAGTCTCCAAGGTCAAAGCCGACAG
*
3146469 GCAGACTTGAGATGAGGTAG
65 GCAGACTTGAGATGAGGCAG
* ** **
3146489 TCTCCAAGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCGTGGTCAAAGTTGACAGG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
3146554 CAGACTTGAGATGAGGCAG
66 CAGACTTGAGATGAGGCAG
* * * * * * * *
3146573 CCTCTAGGGTCAAAGCCGACAAGCAGACTAAAGGTCGGAAAGTCTCTAAGGTCAAAGCCGATAGG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
* * * *
3146638 TAGACCTGAGGT-AAGCAG
66 CAGACTTGAGATGAGGCAG
** * * *
3146656 TCTCCAGGGTCAAAGCTAATAGGTAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGTCGATAGG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
* * *
3146721 CAGACTTGAGGT-AAGTAG
66 CAGACTTGAGATGAGGCAG
* * *
3146739 TCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGGTAGGAAAGTCTCTAAGGTCAAAGCCGACAGG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
* *
3146804 TAGACTTGAGATGAGGTAG
66 CAGACTTGAGATGAGGCAG
* * * * ** *
3146823 TCTCTAGGGTCAAAGCTGATAGGTAGACTAAAGAGTAAAAAAGTCTCCAAGGTCAAAGCCCACAG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAG-GTAGGAAAGTCTCCAAGGTCAAAGCCGACAG
*
3146888 GCAAACTTGAGATGAGGCAG
65 GCAGACTTGAGATGAGGCAG
* * * ** ** * * *
3146908 TCTCCAGGGTCAAAGCCGACAGGCAAACTGAGGGTAAAAAAGTCT-CTGGGTCAAAACTGACAGA
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
*
3146972 CAGACTTGAGATGAGGTAG
66 CAGACTTGAGATGAGGCAG
** * * *
3146991 TCTCCAAAGTCAAAACCGATAGGTAGATTGAAGG
1 TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGG
3147025 ATAAAAAAAT
Statistics
Matches: 444, Mismatches: 89, Indels: 7
0.82 0.16 0.01
Matches are distributed among these distances:
83 200 0.45
84 174 0.39
85 70 0.16
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (84 bp):
TCTCCAGGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGCCGACAGG
CAGACTTGAGATGAGGCAG
Found at i:3146769 original size:250 final size:253
Alignment explanation
Indices: 3146467--3147009 Score: 646
Period size: 250 Copynumber: 2.2 Consensus size: 253
3146457 CAAAGCTAAC
* * *
3146467 AGGCAGACTTGAGATGAGGTAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAAGGTAGGAAAGT
1 AGGCAGACTTGAGATGAAGTAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAAGGTAGGAAAGT
** **
3146532 CTCCGTGGTCAAAGTTGACAGGCAGACTTGAGATGAGGCAGCCTCTAGGGTCAAAGCCGACAAGC
66 CTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGCAGCCTCTAGGGTCAAAGCCGACAAGC
*** * * * * * *
3146597 AGACTAAAG-GTCGGAAAGTCTCTAAGGTCAAAGCCGATAGGTAGACCTGAGGT-AAGCAGTCTC
131 AGACTAAAGAGTAAAAAAGTCTCCAAGGTCAAAGCCCACAGGCAAACCTGAGATGAAGCAGTCTC
3146660 CAGGGTCAAAGCTAATAGGTAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGTCGAT
196 CAGGGTCAAAGCTAATAGGTAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGTCGAT
* *
3146718 AGGCAGACTTGAGGT-AAGTAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAAGGTAGGAAAGT
1 AGGCAGACTTGAGATGAAGTAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAAGGTAGGAAAGT
* * * * * * * *
3146782 CTCTAAGGTCAAAGCCGACAGGTAGACTTGAGATGAGGTAGTCTCTAGGGTCAAAGCTGATAGGT
66 CTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGCAGCCTCTAGGGTCAAAGCCGACAAGC
* *
3146847 AGACTAAAGAGTAAAAAAGTCTCCAAGGTCAAAGCCCACAGGCAAACTTGAGATGAGGCAGTCTC
131 AGACTAAAGAGTAAAAAAGTCTCCAAGGTCAAAGCCCACAGGCAAACCTGAGATGAAGCAGTCTC
** * * * * ** ** * *
3146912 CAGGGTCAAAGCCGACAGGCAAACTGAGGGTAAAAAAGTCT-CTGGGTCAAA-ACTGAC
196 CAGGGTCAAAGCTAATAGGTAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGTC-GAT
* * * *
3146969 AGACAGACTTGAGATGAGGTAGTCTCCAAAGTCAAAACCGA
1 AGGCAGACTTGAGATGAAGTAGTCTCCAAGGTCAAAGCCGA
3147010 TAGGTAGATT
Statistics
Matches: 242, Mismatches: 46, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
250 108 0.45
251 71 0.29
252 63 0.26
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.17
Consensus pattern (253 bp):
AGGCAGACTTGAGATGAAGTAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAAGGTAGGAAAGT
CTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGCAGCCTCTAGGGTCAAAGCCGACAAGC
AGACTAAAGAGTAAAAAAGTCTCCAAGGTCAAAGCCCACAGGCAAACCTGAGATGAAGCAGTCTC
CAGGGTCAAAGCTAATAGGTAGACTGAAGGTAGGAAAGTCTCCAAGGTCAAAGTCGAT
Found at i:3148616 original size:16 final size:16
Alignment explanation
Indices: 3148595--3148627 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3148585 TTTCATTCAA
3148595 TTTTTTCT-TTTTCTTT
1 TTTTTTCTCTTTT-TTT
3148611 TTTTTTCTCTTTTTTT
1 TTTTTTCTCTTTTTTT
3148627 T
1 T
3148628 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTT
Found at i:3148635 original size:12 final size:12
Alignment explanation
Indices: 3148620--3148652 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
3148610 TTTTTTTCTC
3148620 TTTTTTTTAATT
1 TTTTTTTTAATT
3148632 TTTTTTTTAATT
1 TTTTTTTTAATT
3148644 TTTCTTTTT
1 TTT-TTTTT
3148653 TTATGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTAATT
Found at i:3152334 original size:107 final size:107
Alignment explanation
Indices: 3152160--3152411 Score: 398
Period size: 107 Copynumber: 2.4 Consensus size: 107
3152150 TATCCCCTCG
* * *
3152160 GAAATAAC-AGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGT
1 GAAATAACGA-GGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGT
3152224 TAGAGTATCCACTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
65 TAGAGTATCCACTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
*
3152267 GAAATAATGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTT
1 GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTT
* * * *
3152332 AGAGTATCCCCTCGGAGGTAACGGGGTTGGGGTATCCTCGAT
66 AGAGTATCCACTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
* *
3152374 GAAATAACGAGGTTGGAGTATCCTCGTTTGTGAAAAAT
1 GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAAT
3152412 TGGCATTTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
107 132 0.99
108 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (107 bp):
GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTT
AGAGTATCCACTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
Found at i:3152420 original size:107 final size:107
Alignment explanation
Indices: 3152160--3152449 Score: 384
Period size: 107 Copynumber: 2.7 Consensus size: 107
3152150 TATCCCCTCG
* * * *
3152160 GAAATAAC-AGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGT
1 GAAATAACGA-GGTTGGAGTATCCTCGATTATGAAAAATCAACATTTTGGAAATAAAGCCGGGGT
*
3152224 TAGAGTATCCACTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
65 TAGAGTATCCCCTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
* *
3152267 GAAATAATGAGGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTT
1 GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAACATTTTGGAAATAAAGCCGGGGTT
* * *
3152332 AGAGTATCCCCTCGGAGGTAACGGGGTTGGGGTATCCTCGAT
66 AGAGTATCCCCTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
* * *** ** *
3152374 GAAATAACGAGGTTGGAGTATCCTCGTTTGTGAAAAATTGGCATTTTTGGAAATAAAATCGGAGT
1 GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAACA-TTTTGGAAATAAAGCCGGGGT
*
3152439 TGGAGTATCCC
65 TAGAGTATCCC
3152450 TGATTAAAGG
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
107 133 0.82
108 29 0.18
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (107 bp):
GAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAACATTTTGGAAATAAAGCCGGGGTT
AGAGTATCCCCTCGGAGGTAACGAGGTTGGAGTATCCCCGAT
Found at i:3152643 original size:28 final size:27
Alignment explanation
Indices: 3152587--3152658 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
3152577 GGAATAAAGC
**
3152587 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTAT-CCCTCGGAAATAA
3152615 CGGGGTTGGAGTATCCCT-GATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
*
3152643 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3152659 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 4 0.10
28 34 0.87
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:3152716 original size:52 final size:50
Alignment explanation
Indices: 3152385--3152763 Score: 196
Period size: 51 Copynumber: 7.2 Consensus size: 50
3152375 AAATAACGAG
* *
3152385 GTTGGAGTATCCTCGTTTGTGAAAAATTGGCAT-TTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGG--TGTTTTGGAAATAAAA-CGGA
* ** * * *
3152437 GTTGGAGTATCCCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACGGA
* * * * *
3152488 GGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACTGGG
1 -GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC-GGA
* * *** * * * *
3152540 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAA-ACGGA
* *** * *
3152591 GTTGGAGTATCCCCTCGGA-GGT-AACGGGGTTGGAGTATCCCTGATGAAAT--AAC-GA
1 GTTGGAGTAT-CCC-C-GATTGTGAA--AAATTGGTGT-T--TTG--GAAATAAAACGGA
*
3152646 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAA-CGGA
** * *
3152699 GTTGGAGTATCCCCGATTAAAAGGAAAATTGGTGTTTT-GAGAATAAAATCGGG
1 GTTGGAGTATCCCCGATT--GTGAAAAATTGGTGTTTTGGA-AATAAAA-CGGA
3152752 GTTGGAGTATCC
1 GTTGGAGTATCC
3152764 TTGATTATGA
Statistics
Matches: 247, Mismatches: 54, Indels: 51
0.70 0.15 0.14
Matches are distributed among these distances:
49 5 0.02
51 81 0.33
52 70 0.28
53 48 0.19
54 19 0.08
55 6 0.02
56 11 0.04
57 3 0.01
59 4 0.02
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACGGA
Found at i:3155208 original size:19 final size:18
Alignment explanation
Indices: 3155180--3155278 Score: 76
Period size: 19 Copynumber: 5.9 Consensus size: 18
3155170 TCGTAGCGAT
3155180 ACAT-TGTATCGATACAAA
1 ACATATGTATCGATAC-AA
3155198 ACATATGTATCGAT----
1 ACATATGTATCGATACAA
3155212 ACA-ATGTATCGATACAA
1 ACATATGTATCGATACAA
*
3155229 CACTTATGTATCGAT----
1 -ACATATGTATCGATACAA
3155244 ACA-ATGTATCGATACAA
1 ACATATGTATCGATACAA
*
3155261 CACTTATGTATCGATACA
1 -ACATATGTATCGATACA
3155279 TTTACAGTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
13 20 0.31
14 5 0.08
18 8 0.12
19 32 0.49
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (18 bp):
ACATATGTATCGATACAA
Found at i:3155220 original size:13 final size:13
Alignment explanation
Indices: 3155202--3155260 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 13
3155192 TACAAAACAT
3155202 ATGTATCGATACA
1 ATGTATCGATACA
3155215 ATGTATCGATACAACA
1 ATGTATCGAT---ACA
3155231 CTTATGTATCGATACA
1 ---ATGTATCGATACA
3155247 ATGTATCGATACA
1 ATGTATCGATACA
3155260 A
1 A
3155261 CACTTATGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 24 0.60
16 6 0.15
19 10 0.25
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3155220 original size:32 final size:32
Alignment explanation
Indices: 3155176--3155278 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
3155166 AGCTTCGTAG
* * *
3155176 CGATACATTGTATCGATACAAAACATATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
3155208 CGATACAATGTATCGATACAACACTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
3155240 CGATACAATGTATCGATACAACACTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
3155272 CGATACA
1 CGATACA
3155279 TTTACAGTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (32 bp):
CGATACAATGTATCGATACAACACTTATGTAT
Found at i:3155407 original size:14 final size:15
Alignment explanation
Indices: 3155380--3155424 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3155370 ATTTGGACAA
3155380 AATTATATATTTTTTT
1 AATTATA-ATTTTTTT
3155396 AATT-TAATTTTTTT
1 AATTATAATTTTTTT
* *
3155410 TATTATTATTTTTTT
1 AATTATAATTTTTTT
3155425 TTTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.42
15 11 0.42
16 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
AATTATAATTTTTTT
Found at i:3155409 original size:15 final size:15
Alignment explanation
Indices: 3155381--3155425 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
3155371 TTTGGACAAA
*
3155381 ATTATATATTTTTTTA
1 ATTATA-ATTTTTTTT
3155397 ATT-TAATTTTTTTT
1 ATTATAATTTTTTTT
*
3155411 ATTATTATTTTTTTT
1 ATTATAATTTTTTTT
3155426 TTCCTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.42
15 12 0.46
16 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTATAATTTTTTTT
Found at i:3156004 original size:42 final size:41
Alignment explanation
Indices: 3155958--3156047 Score: 92
Period size: 42 Copynumber: 2.1 Consensus size: 41
3155948 CCCATTTTTC
* *
3155958 GAGGACAAGGGAAAAAGGGAAACGAAA-TACATCCTGCTCTTT
1 GAGGACAA-AGAAAAA-GGAAAAGAAAGTACATCCTGCTCTTT
* * * *
3156000 GAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTCTTT
1 GAGGA-CAAAGAAAAAGGAAAAGAAAGTACATCCTGCTCTTT
3156042 GAGGAC
1 GAGGAC
3156048 TAAAAAGTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
41 8 0.21
42 29 0.74
43 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (41 bp):
GAGGACAAAGAAAAAGGAAAAGAAAGTACATCCTGCTCTTT
Found at i:3156124 original size:61 final size:60
Alignment explanation
Indices: 3156031--3156874 Score: 1007
Period size: 61 Copynumber: 14.4 Consensus size: 60
3156021 ATAAAGTGCA
* **
3156031 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
* ** *
3156092 TCCTGCTTTTTGAGGACTGGAAGGTGCGACCAACTTGTGTGGGCTTTGCAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
** *
3156153 TCCTGCTCTTTGAGGACTGGAAGGTGCCA-CAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-GAAAGGCG
3156213 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G--A--CG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
*
3156268 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGG--A---G
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* *
3156323 TCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
** *
3156384 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-GAAAGGCG
* *
3156445 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTT-----CAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
3156500 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AA-G---GGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* *
3156555 TCCTGCTCTTTGAGGACTAGAAAATGCCAGCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
* * *
3156616 TCCTGCTCCTTGAGGACTGGAAAATGCCACCAACTCGAGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
** * * *
3156677 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTATGTGGGC-TTGCAAAGGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGA-AAGGCG
* * *
3156737 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAGCTTGTGTGGGCTTT---A--AAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* * ** * *
3156791 TCCTGCTCTTTGAGGAATGGGATGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG-AAAGGCG
3156852 TCCTGCTCTTTGAGGACT-GAAAA
1 TCCTGCTCTTTGAGGACTGGAAAA
3156875 GTGGAAGAAG
Statistics
Matches: 695, Mismatches: 58, Indels: 61
0.85 0.07 0.07
Matches are distributed among these distances:
54 24 0.03
55 222 0.32
56 8 0.01
57 3 0.00
58 4 0.01
59 9 0.01
60 122 0.18
61 297 0.43
62 6 0.01
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
Found at i:3156508 original size:232 final size:232
Alignment explanation
Indices: 3156031--3156870 Score: 1127
Period size: 232 Copynumber: 3.6 Consensus size: 232
3156021 ATAAAGTGCA
* **
3156031 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTG-AAAGG-AA---GTCCT
* ** * *
3156096 GCTTTTTGAGGACTGGAAGGTGCGACCAACTTGTGTGGGCTTTGCAAAGGAAAGGCGTCCTGCTC
60 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTC
3156161 TTTGAGGACTGGAAGGTGCCA-CAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTG
125 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTG
* *
3156225 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACG
190 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTCAAAGGCG
*
3156268 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGG-AGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAGTCCTGCTCT
* *
3156332 TTGAGGACTGGAAAATGTCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGA
65 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGA
3156397 GGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGAC
130 GGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGAC
*
3156462 TGGAAAATGCCACCAACTTGTGTGAGCTTTCAAAGGCG
195 TGGAAAATGCCACCAACTTGTGTGGGCTTTCAAAGGCG
**
3156500 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAGGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAGTCCTGCTCT
* * *
3156564 TTGAGGACTAGAAAATGCCAGCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCCTTGA
65 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGA
** * * * *
3156629 GGACTGGAAAATGCCACCAACTCGAGTGGGCTTTGAAAAG-GAAAGGCGTCCTGCTCTTTGAGGA
130 GGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCATCCTGCTCTTTGAGGA
** * * * *
3156693 CT-GAAGGTGCCACCAGCTTATGTGGGCTTGCAAAGGAGAAGGTG
194 CTGGAAAATGCCACCAACTTGTGTGGGCTTTC-----A-AAGGCG
* * * *
3156737 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCA-TCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAGTCCTGCTCTT
* * ** *
3156801 TGAGGAATGGGATGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCCTGCTCTTTGA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGCGTCCTGCTCTTTGA
3156865 GGACTG
130 GGACTG
3156871 AAAAGTGGAA
Statistics
Matches: 545, Mismatches: 46, Indels: 25
0.88 0.07 0.04
Matches are distributed among these distances:
231 115 0.21
232 255 0.47
234 1 0.00
235 6 0.01
236 97 0.18
237 67 0.12
238 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (232 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAGTCCTGCTCTT
TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTCCTGCTCTTTGAG
GACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACT
GGAAAATGCCACCAACTTGTGTGGGCTTTCAAAGGCG
Found at i:3157850 original size:1 final size:1
Alignment explanation
Indices: 3157844--3157909 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
3157834 CATATTCTTC
* * * * * * * *
3157844 TTTTTTTTTCTTTTTTTCTGTTTTTTTTTGTTTTTTTGTTTTTTTGTTGTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3157909 T
1 T
3157910 GAAAAAAGAA
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:3157856 original size:10 final size:10
Alignment explanation
Indices: 3157844--3157908 Score: 75
Period size: 10 Copynumber: 6.9 Consensus size: 10
3157834 CATATTCTTC
*
3157844 TTTTTTTTTC
1 TTTTTTTTTG
*
3157854 TTTTTTTCTG
1 TTTTTTTTTG
3157864 TTTTTTTTTG
1 TTTTTTTTTG
3157874 --TTTTTTTG
1 TTTTTTTTTG
3157882 --TTTTTTTG
1 TTTTTTTTTG
*
3157890 TTGTTTTTTG
1 TTTTTTTTTG
3157900 TTTTTTTTT
1 TTTTTTTTT
3157909 TGAAAAAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
8 16 0.33
10 32 0.67
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3157867 original size:18 final size:18
Alignment explanation
Indices: 3157841--3157908 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
3157831 AAGCATATTC
*
3157841 TTCT-TTTTTTTTCTTTTT
1 TTCTGTTTTTTTT-TGTTT
3157859 TTCTGTTTTTTTTTGTTT
1 TTCTGTTTTTTTTTGTTT
*
3157877 TTTTGTTTTTTTGTTGTTT
1 TTCTGTTTTTTT-TTGTTT
3157896 TT-TGTTTTTTTTT
1 TTCTGTTTTTTTTT
3157909 TGAAAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.04
18 28 0.61
19 16 0.35
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (18 bp):
TTCTGTTTTTTTTTGTTT
Found at i:3166669 original size:13 final size:13
Alignment explanation
Indices: 3166651--3166676 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3166641 TACACAAAGT
3166651 ATGTATCGATACA
1 ATGTATCGATACA
3166664 ATGTATCGATACA
1 ATGTATCGATACA
3166677 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3166674 original size:32 final size:33
Alignment explanation
Indices: 3166633--3166696 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3166623 TAGCCAAACT
**
3166633 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3166665 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3166697 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3167197 original size:34 final size:35
Alignment explanation
Indices: 3167134--3167200 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3167124 CTAAGTGATT
3167134 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
3167170 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
3167201 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:3168893 original size:84 final size:84
Alignment explanation
Indices: 3168715--3168880 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 84
3168705 TCTAAACTCA
* * * *
3168715 AAAAAGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAG
1 AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
* *
3168780 AAGAGTATGAAAGAGTTAC
66 AAGAGAAAGAAAGAGTTAC
* *
3168799 AAAATGAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--
1 AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAG
3168860 AGAAGAGAAAAGAAATGAGTT
64 AGAAGAG-AAAGAAA-GAGTT
3168881 GCAAGTCGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
82 11 0.16
83 6 0.09
84 53 0.76
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (84 bp):
AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
AAGAGAAAGAAAGAGTTAC
Found at i:3170414 original size:13 final size:13
Alignment explanation
Indices: 3170396--3170420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3170386 TTTTCCAGAT
3170396 TGTATCGATACAA
1 TGTATCGATACAA
3170409 TGTATCGATACA
1 TGTATCGATACA
3170421 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3172354 original size:13 final size:13
Alignment explanation
Indices: 3172336--3172361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3172326 TACACAAAGT
3172336 ATGTATCGATACA
1 ATGTATCGATACA
3172349 ATGTATCGATACA
1 ATGTATCGATACA
3172362 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3172359 original size:32 final size:33
Alignment explanation
Indices: 3172318--3172381 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3172308 TAGCCAAACT
**
3172318 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3172350 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3172382 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3172882 original size:34 final size:35
Alignment explanation
Indices: 3172819--3172885 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3172809 CTAAGTGATT
3172819 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
3172855 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
3172886 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:3174908 original size:4 final size:4
Alignment explanation
Indices: 3174901--3174931 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3174891 CAAAACAAAC
3174901 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3174932 CACCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3176194 original size:33 final size:33
Alignment explanation
Indices: 3176150--3176228 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
3176140 AACTTCCTAG
3176150 ATGTATCGATACAAAGATCGATGTATCGATACA
1 ATGTATCGATACAAAGATCGATGTATCGATACA
* *
3176183 ATGTATTGATACAAAGATCGTTGTATCGATACA
1 ATGTATCGATACAAAGATCGATGTATCGATACA
*
3176216 AGGTATCGATACA
1 ATGTATCGATACA
3176229 TTTCTTTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCGATGTATCGATACA
Found at i:3176213 original size:20 final size:19
Alignment explanation
Indices: 3176151--3176216 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
3176141 ACTTCCTAGA
3176151 TGTATCGATACAAAGATCG
1 TGTATCGATACAAAGATCG
3176170 ATGTATCGATAC--A-A---
1 -TGTATCGATACAAAGATCG
*
3176184 TGTATTGATACAAAGATCG
1 TGTATCGATACAAAGATCG
3176203 TTGTATCGATACAA
1 -TGTATCGATACAA
3176217 GGTATCGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 23 0.62
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAGATCG
Found at i:3176270 original size:13 final size:13
Alignment explanation
Indices: 3176252--3176285 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3176242 AGCTTCATAG
*
3176252 CGATACATTGTAT
1 CGATACAATGTAT
3176265 CGATACAATGTAT
1 CGATACAATGTAT
3176278 CGATACAA
1 CGATACAA
3176286 CACTTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (13 bp):
CGATACAATGTAT
Found at i:3177133 original size:20 final size:20
Alignment explanation
Indices: 3177110--3177182 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3177100 ACAACTCAAA
3177110 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3177130 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3177151 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3177171 GTATCGATACAT
1 GTATCGATACAT
3177183 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3177161 original size:41 final size:42
Alignment explanation
Indices: 3177110--3177204 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
3177100 ACAACTCAAA
*
3177110 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3177151 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3177193 GTATCGATACAT
1 GTATCGATACAT
3177205 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3177261 original size:13 final size:13
Alignment explanation
Indices: 3177243--3177268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3177233 TACAGCAAGT
3177243 ATGTATCGATACA
1 ATGTATCGATACA
3177256 ATGTATCGATACA
1 ATGTATCGATACA
3177269 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3181352 original size:15 final size:15
Alignment explanation
Indices: 3181332--3181370 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3181322 TAAAAATGTC
*
3181332 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3181347 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
3181362 CCAAATGAA
1 CAAAATGAA
3181371 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3183456 original size:20 final size:21
Alignment explanation
Indices: 3183378--3183455 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
3183368 ATGTCCAAAA
*
3183378 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
3183398 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
3183422 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
3183443 TGTATCGATACAT
1 TGTATCGATACAT
3183456 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:3183460 original size:13 final size:13
Alignment explanation
Indices: 3183442--3183480 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3183432 ACATTTTTTG
3183442 TTGTATCGATACA
1 TTGTATCGATACA
3183455 TTGTATCGATACA
1 TTGTATCGATACA
*
3183468 CTGTATCGATACA
1 TTGTATCGATACA
3183481 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3185945 original size:20 final size:20
Alignment explanation
Indices: 3185922--3185994 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3185912 ACAACTCAAA
3185922 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3185942 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3185963 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3185983 GTATCGATACAT
1 GTATCGATACAT
3185995 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3185973 original size:41 final size:42
Alignment explanation
Indices: 3185922--3186016 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
3185912 ACAACTCAAA
*
3185922 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3185963 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3186005 GTATCGATACAT
1 GTATCGATACAT
3186017 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3186073 original size:13 final size:13
Alignment explanation
Indices: 3186055--3186080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3186045 TACAGCAAGT
3186055 ATGTATCGATACA
1 ATGTATCGATACA
3186068 ATGTATCGATACA
1 ATGTATCGATACA
3186081 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3195709 original size:188 final size:189
Alignment explanation
Indices: 3195328--3195753 Score: 590
Period size: 189 Copynumber: 2.2 Consensus size: 189
3195318 GAAATTTTTG
* * * * **
3195328 ATTTTTCAT-ACCCTTACGAAAAACCCATAAGAATATGAAAATATGACTCGAGTGAATAAACGAT
1 ATTTTT-ATAACCC-TACGAAAAA-CAATAGGAATATGAAAACATGACTCAAGCAAATAAACGAT
* *
3195392 CACATATTTTTTTAAAATATTAATTTAGGGAAATCAAATTTTTCTAAATTTTTAAATTTAACTTC
63 CACATATTTTTTTAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTC
* * * *
3195457 TAAATTTCAAACATTATGCTTCGTACTCGATGGAAAACTAGGGGATATGAAAGGAGTTAAAA
128 TAAATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
* * *
3195519 ATTTTTA-AACCCTCCGGAAAACAATGGGAATATGAAAACATGACTCAAGCAAATAAACGA-CTA
1 ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTCAAGCAAATAAACGATC-A
*
3195582 CATATTTTTTTAAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTTT
65 CATATTTTTTT-AAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTCT
* * *
3195647 AAATTTCAAACATTATGTTTCATACCCGATGGAAATC-AGAGGATACGAAAGGTGTTAAAA
129 AAATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
* *
3195707 ATTTTTATACCCCTACGAAAAACCATAGGAATATGAAAACATGACTC
1 ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTC
3195754 GAGTGAGCAT
Statistics
Matches: 207, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
187 1 0.00
188 71 0.34
189 124 0.60
190 5 0.02
191 6 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (189 bp):
ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTCAAGCAAATAAACGATCAC
ATATTTTTTTAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTCTAA
ATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
Found at i:3196527 original size:55 final size:56
Alignment explanation
Indices: 3196478--3196582 Score: 151
Period size: 54 Copynumber: 1.9 Consensus size: 56
3196468 ACAAGTGTAT
*
3196478 GACATAAAGAAAGAAAACATGCAATAAAGGAAAA-CAA-AAATGAAAACAAGCTCAC
1 GACATAAAGAAA-AAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAAGCTCAC
* * *
3196533 GGCATAAAGAAACAAACATGCAGCAAAGGAAAATCAAGAAATGAAAACAA
1 GACATAAAGAAAAAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAA
3196583 TAAAGGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
54 18 0.41
55 14 0.32
56 12 0.27
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.09
Consensus pattern (56 bp):
GACATAAAGAAAAAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAAGCTCAC
Found at i:3197107 original size:33 final size:36
Alignment explanation
Indices: 3197052--3197134 Score: 109
Period size: 35 Copynumber: 2.3 Consensus size: 36
3197042 ACTACTTCGA
*
3197052 TTCTATTTTTTTCGTTTCTGCTATTTCGA-T-TCTGTT
1 TTCT-TTTTTTTC-TTTCTGCTATTTCGATTCTCTCTT
*
3197088 TTCTTTTTTTT-TTTTTGCTATTTCGATTCTCTCTT
1 TTCTTTTTTTTCTTTCTGCTATTTCGATTCTCTCTT
3197123 TTCTTTTTTTTC
1 TTCTTTTTTTTC
3197135 GCTGCAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 14 0.33
34 1 0.02
35 23 0.55
36 4 0.10
ACGTcount: A:0.06, C:0.17, G:0.07, T:0.70
Consensus pattern (36 bp):
TTCTTTTTTTTCTTTCTGCTATTTCGATTCTCTCTT
Found at i:3197352 original size:29 final size:29
Alignment explanation
Indices: 3197314--3197375 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
3197304 TAATTTCATT
**
3197314 TTGCAGCAGTTGTTTTGTTGGTGTCTTCA
1 TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
**
3197343 TTGCAGCAGTTGTTTCCTTTTTGTCTTCA
1 TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
3197372 TTGC
1 TTGC
3197376 GACAGCTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.50
Consensus pattern (29 bp):
TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
Found at i:3197385 original size:29 final size:28
Alignment explanation
Indices: 3197335--3197411 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
3197325 GTTTTGTTGG
*
3197335 TGTCTTCATTGCAGCAGTTGTTTCCTTTT
1 TGTCTTCATTGCA-CAGCTGTTTCCTTTT
*
3197364 TGTCTTCATTGCGACAGCTGTTTCTTTTT
1 TGTCTTCATTGC-ACAGCTGTTTCCTTTT
*
3197393 TTTCTTCATTGCTACAGCT
1 TGTCTTCATTGC-ACAGCT
3197412 TAATTGCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.51
Consensus pattern (28 bp):
TGTCTTCATTGCACAGCTGTTTCCTTTT
Found at i:3197638 original size:5 final size:5
Alignment explanation
Indices: 3197623--3197653 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3197613 ATGCATGAAA
*
3197623 GCAAT GAAAT GCAAT GCAAT GCAAT GCAAT G
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT G
3197654 TTTTTGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (5 bp):
GCAAT
Found at i:3197638 original size:10 final size:10
Alignment explanation
Indices: 3197613--3197653 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3197603 TGTGAAATGC
3197613 ATGC-ATGAA
1 ATGCAATGAA
3197622 A-GCAATGAA
1 ATGCAATGAA
*
3197631 ATGCAATGCA
1 ATGCAATGAA
*
3197641 ATGCAATGCA
1 ATGCAATGAA
3197651 ATG
1 ATG
3197654 TTTTTGACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 2 0.07
9 7 0.24
10 20 0.69
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (10 bp):
ATGCAATGAA
Found at i:3197873 original size:3 final size:3
Alignment explanation
Indices: 3197855--3197892 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3197845 ATTAATTAAC
*
3197855 TAT TAG TAT T-T TAT TAT TA- TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3197893 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3198585 original size:43 final size:42
Alignment explanation
Indices: 3198522--3198720 Score: 152
Period size: 43 Copynumber: 4.6 Consensus size: 42
3198512 GACACAGTTC
* * *
3198522 TTTTCTCTTTATCCTTAAGGAGCAGGACACATTCCTTGTTTCCT
1 TTTTC-CTTTGTCCTCAAGGAGCAGGACACATT-CTTCTTTCCT
* * *
3198566 TTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATCTTCTTCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACA-TTCTTCTT-TCCT
* * * * ** *
3198610 TTTCCCTTTGTCTTTAAGGAGCAAGATGCATTCTTTTTTGCCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACATTCTTCTTT-CCT
* *
3198653 TTTTCCTTTGTCCTCAAGGAGCAAGAC-C-TAT-TTCATTCTCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACAT-TCTTCTTTC-CT
* * *
3198694 TTTCCCTTTGTCCTCAAAGAGTAGGAC
1 TTTTCCTTTGTCCTCAAGGAGCAGGAC
3198721 GTACTCCTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 30 0.24
42 3 0.02
43 57 0.46
44 34 0.27
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGGAGCAGGACACATTCTTCTTTCCT
Found at i:3198665 original size:87 final size:85
Alignment explanation
Indices: 3198519--3198707 Score: 256
Period size: 87 Copynumber: 2.2 Consensus size: 85
3198509 CAGGACACAG
* * *
3198519 TTCTTTTCTCTTTATCCTTAAGGAGCAGGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
1 TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
*
3198584 GAGCAGGACCCATTTCATCTTC
66 GAGCAAGACCCATTTCA--TTC
* ** *
3198606 TTCTTTTCCCTTTGTCTTTAAGGAGCAAGATGCATT-CTTTTTTGCCTTTTTCCTTTGTCCTCAA
1 TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTT-CCTTTTTCCTTTGTCCTCAA
*
3198670 GGAGCAAGACCTATTTCATTC
65 GGAGCAAGACCCATTTCATTC
3198691 -TCTTTTCCCTTTGTCCT
1 TTCTTTTCCCTTTGTCCT
3198708 CAAAGAGTAG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
84 16 0.18
85 3 0.03
86 6 0.07
87 66 0.73
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.44
Consensus pattern (85 bp):
TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
GAGCAAGACCCATTTCATTC
Found at i:3198879 original size:31 final size:31
Alignment explanation
Indices: 3198811--3198891 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
3198801 GCACCCTAGT
* *
3198811 CAAAGCCTGCACAAGCTAGCGACACCTGAGT
1 CAAAGCCCGCACAAGCTAGCGACACCTGAGC
* * * * *
3198842 CTAAGCCCGCATAAGTTGGCGACACCTGGGC
1 CAAAGCCCGCACAAGCTAGCGACACCTGAGC
* *
3198873 CAAAGCCCACACACGCTAG
1 CAAAGCCCGCACAAGCTAG
3198892 TGGCACTTAG
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (31 bp):
CAAAGCCCGCACAAGCTAGCGACACCTGAGC
Found at i:3199093 original size:149 final size:148
Alignment explanation
Indices: 3198809--3199407 Score: 494
Period size: 149 Copynumber: 4.0 Consensus size: 148
3198799 TGGCACCCTA
* * * * * **
3198809 GTCAAAGCCTGCACAAGCTAGC-GACAC-CTGAGTCTAAGCCCGCATAAGTTGGCGACACCTGGG
1 GTCAAAGCCTGCACAAGCTCGCAG-CACTC-GAGTCTAAACCCACACAAGTTGGCGACATCTAAG
* * * * * *
3198872 CCAAAGCCCACACACGC-TAGTGGCACTTAGGTTTGAGTCAAGTCCAAATTAGTTGGCACCTGTC
64 TCAAAGCCCACACAAGCGGA-TGCCACCTAAG-TTGAGTCAAGTCCAAATTAGTTGGCACCTGTC
* *
3198936 TAAAGAGGTCAAGCCTTAAAAT
127 TAAGGAGGTCAAGCCTTAGAAT
* * * * ** * *
3198958 GTCACAG-CTCGCACAAGTTGGCGGCACT-GAGTCTATGCTCACACAAGTTGGTGACATCTAAGT
1 GTCAAAGCCT-GCACAAGCTCGCAGCACTCGAGTCTAAACCCACACAAGTTGGCGACATCTAAGT
* * * * * *
3199021 CAAAGCCCACATAAGCCGGGTGCCACCTAAGTCTGAGTCAAGTCCACATTAGTTGGCGCATATCT
65 CAAAGCCCACACAAG-CGGATGCCACCTAAGT-TGAGTCAAGTCCAAATTAGTTGGCACCTGTCT
3199086 AAGGAGGTCAAGCCTTAGAAT
128 AAGGAGGTCAAGCCTTAGAAT
* *
3199107 GTCAAAGCCTGCACAAGCTCGCAGCACTCGAGTCTAAACCCACACAAGTTGGCGGCATCTGAGTC
1 GTCAAAGCCTGCACAAGCTCGCAGCACTCGAGTCTAAACCCACACAAGTTGGCGACATCTAAGTC
* * *
3199172 AAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCCGTCTAA
66 AAAGCCCACACAAGCGGATGCCACCTAAGTT-GAGTCAAGTCCAAATTAGTTGGCACCTGTCTAA
3199237 GGAGGTCAAGCCTTAGAAT
130 GGAGGTCAAGCCTTAGAAT
* ** * * * * * * * * *
3199256 GTTAAAGCCCACACAAGCTGGTTGCACCAAAGTCTGAGTC-AAA-GCTCACAAGCTGGTGGCACC
1 GTCAAAGCCTGCACAAGC---TCGCAGC--ACTC-GAGTCTAAACCCACACAAGTTGGCGACATC
** * * * * * * *
3199319 CGAGTTAAAGCCCACACAAGCTGG-TGGCACCAAAGTCCGAGTCAAGTCCACATTAGCTAGCACC
60 TAAGTCAAAGCCCACACAAGC-GGATGCCACCTAAGT-TGAGTCAAGTCCAAATTAGTTGGCACC
*
3199383 TATCTAAGGAGGTCAAGCCTTAGAA
123 TGTCTAAGGAGGTCAAGCCTTAGAA
3199408 AACCAAAACC
Statistics
Matches: 368, Mismatches: 65, Indels: 30
0.79 0.14 0.06
Matches are distributed among these distances:
148 43 0.12
149 171 0.46
150 46 0.12
152 5 0.01
153 91 0.25
154 7 0.02
155 5 0.01
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (148 bp):
GTCAAAGCCTGCACAAGCTCGCAGCACTCGAGTCTAAACCCACACAAGTTGGCGACATCTAAGTC
AAAGCCCACACAAGCGGATGCCACCTAAGTTGAGTCAAGTCCAAATTAGTTGGCACCTGTCTAAG
GAGGTCAAGCCTTAGAAT
Found at i:3199154 original size:31 final size:31
Alignment explanation
Indices: 3199107--3199187 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
3199097 GCCTTAGAAT
**
3199107 GTCAAAGCCTGCACAAGCTCGCAGCA-CTCGA
1 GTCAAAGCCCACACAAGCTCGCAGCATCT-GA
* * *
3199138 GTCTAAA-CCCACACAAGTTGGCGGCATCTGA
1 GTC-AAAGCCCACACAAGCTCGCAGCATCTGA
3199169 GTCAAAGCCCACACAAGCT
1 GTCAAAGCCCACACAAGCT
3199188 GATGGCACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 33 0.80
32 5 0.12
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (31 bp):
GTCAAAGCCCACACAAGCTCGCAGCATCTGA
Found at i:3199334 original size:29 final size:31
Alignment explanation
Indices: 3199259--3199349 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 31
3199249 TTAGAATGTT
*
3199259 AAAGCCCACACAAGCTGGTTGCACCAAAGTCTGAGTC
1 AAAGCCCACACAAGCTGGTGGCACC-----C-GAGTC
* *
3199296 AAAG--CTCACAAGCTGGTGGCACCCGAGTT
1 AAAGCCCACACAAGCTGGTGGCACCCGAGTC
3199325 AAAGCCCACACAAGCTGGTGGCACC
1 AAAGCCCACACAAGCTGGTGGCACC
3199350 AAAGTCCGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
29 8 0.17
30 1 0.02
31 18 0.38
35 17 0.35
37 4 0.08
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (31 bp):
AAAGCCCACACAAGCTGGTGGCACCCGAGTC
Found at i:3199382 original size:153 final size:149
Alignment explanation
Indices: 3198873--3199407 Score: 509
Period size: 149 Copynumber: 3.6 Consensus size: 149
3198863 ACACCTGGGC
* * * * ** * *
3198873 CAAAGCCCACACACGCTAGTGGCACTTAGGTTTGAGTCAAGTCCAAATTAGTTGGCACCTGTCTA
1 CAAAGCCCACACAAGCTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCACCTATCTA
* * * * * * * ** ** *
3198938 AAGAGGTCAAGCCTTAAAATGTCACAGCTCGCACAAGTTGGCGGCACT-GAGTCTATGCTCACAC
66 AGGAGGTCAAGCCTTAGAATGTCAAAGCCCACACAAGCTCGCACCACTCGAGTCTAAACCCACAC
* * * * **
3199002 AAGTTGGTGACATCTAAGT
131 AAGCTGGCGGCACCCGAGT
* * * * * *
3199021 CAAAGCCCACATAAGCCGGGTGCCACCTAAGTCTGAGTCAAGTCCACATTAGTTGGCGCATATCT
1 CAAAGCCCACACAAG-CTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCACCTATCT
** *
3199086 AAGGAGGTCAAGCCTTAGAATGTCAAAGCCTGCACAAGCTCGCAGCACTCGAGTCTAAACCCACA
65 AAGGAGGTCAAGCCTTAGAATGTCAAAGCCCACACAAGCTCGCACCACTCGAGTCTAAACCCACA
* * *
3199151 CAAGTTGGCGGCATCTGAGT
130 CAAGCTGGCGGCACCCGAGT
* * * **
3199171 CAAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCCGTCTA
1 CAAAGCCCACACAAGCTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCACCTATCTA
* * *
3199236 AGGAGGTCAAGCCTTAGAATGTTAAAGCCCACACAAGCTGGTTGCACCAAAGTCTGAGTC-AAA-
66 AGGAGGTCAAGCCTTAGAATGTCAAAGCCCACACAAGC---TCGCACC--ACTC-GAGTCTAAAC
* * *
3199299 GCTCACAAGCTGGTGGCACCCGAGT
125 CCACACAAGCTGGCGGCACCCGAGT
* * * *
3199324 TAAAGCCCACACAAGCTGGTGGCACCAAAGTCCGAGTCAAGTCCACATTAGCTAGCACCTATCTA
1 CAAAGCCCACACAAGCTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCACCTATCTA
3199389 AGGAGGTCAAGCCTTAGAA
66 AGGAGGTCAAGCCTTAGAA
3199408 AACCAAAACC
Statistics
Matches: 321, Mismatches: 58, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
148 13 0.04
149 155 0.48
150 43 0.13
152 5 0.02
153 94 0.29
154 6 0.02
155 5 0.02
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (149 bp):
CAAAGCCCACACAAGCTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCACCTATCTA
AGGAGGTCAAGCCTTAGAATGTCAAAGCCCACACAAGCTCGCACCACTCGAGTCTAAACCCACAC
AAGCTGGCGGCACCCGAGT
Found at i:3200033 original size:59 final size:59
Alignment explanation
Indices: 3199960--3200092 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 59
3199950 TACATGCCTA
* * * **
3199960 AAATGTATCAATACAAAACTACCCTACATTTTGGAAAGGAAATGCATCAATACATAAGT
1 AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
* * ** *
3200019 GAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGTATGGATGCATAAGT
1 AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
*
3200078 AAATGCATCGATACA
1 AAATGTATCGATACA
3200093 TTCACTGTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (59 bp):
AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
Done.