Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold53
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1214666
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.30
Warning! 104343 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:19158 original size:10 final size:10
Alignment explanation
Indices: 19143--19176 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
19133 ACTTGGGATT
19143 CATAATATAA
1 CATAATATAA
19153 CATAATATAA
1 CATAATATAA
*
19163 CATTATATAA
1 CATAATATAA
19173 -ATAA
1 CATAA
19177 AAGAAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.14
10 19 0.86
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (10 bp):
CATAATATAA
Found at i:26315 original size:27 final size:27
Alignment explanation
Indices: 26282--26360 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
26272 CTTACATATA
*
26282 GAAAGCTTGTGACATCACCTGCTACAT
1 GAAAGCTTGTGACATCACCTGATACAT
* *
26309 GAGAGCTTGTGACATCACCTTATACAT
1 GAAAGCTTGTGACATCACCTGATACAT
*
26336 GAAAGCTTGTGACATCACCTTATAC
1 GAAAGCTTGTGACATCACCTGATAC
26361 GTGAGGGTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (27 bp):
GAAAGCTTGTGACATCACCTGATACAT
Found at i:28549 original size:22 final size:25
Alignment explanation
Indices: 28497--28549 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
28487 GGGAAAATTT
28497 TCGT-TGTAAACGATATTAGAAACA
1 TCGTGTGTAAACGATATTAGAAACA
28521 -CGTTGTGTAAACG-T-TT-GAAACA
1 TCG-TGTGTAAACGATATTAGAAACA
28543 TCGTGTG
1 TCGTGTG
28550 ATTGGGAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
22 10 0.38
23 6 0.23
24 2 0.08
25 8 0.31
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (25 bp):
TCGTGTGTAAACGATATTAGAAACA
Found at i:45884 original size:89 final size:87
Alignment explanation
Indices: 45734--45899 Score: 287
Period size: 89 Copynumber: 1.9 Consensus size: 87
45724 CTCCACCAAT
45734 TATAACCGCCGGATTTGTACCGTATAGGGTATTTTCCGTACCGGGCGATTACTAGGGAATTAGCT
1 TATAACCGCCGGATTTGTACCGTATAGGGTATTTTCCGTACCGGGCGATTACTAGGGAATTAGCT
45799 CAACACTCGCTGNGTGAAAGTAG
66 CAACACTCGCTG-GTGAAAGTAG
* * *
45822 TATAACCGCCGGGTTTTGTACCGTATAGGGTATTTTCTGTCCCGGGCGATTACTAGGGAATTAGC
1 TATAACCGCC-GGATTTGTACCGTATAGGGTATTTTCCGTACCGGGCGATTACTAGGGAATTAGC
45887 TCAACACTCGCTG
65 TCAACACTCGCTG
45900 TATTTTCCAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 10 0.14
89 64 0.86
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (87 bp):
TATAACCGCCGGATTTGTACCGTATAGGGTATTTTCCGTACCGGGCGATTACTAGGGAATTAGCT
CAACACTCGCTGGTGAAAGTAG
Found at i:53516 original size:2 final size:2
Alignment explanation
Indices: 53509--53543 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53499 ATCGATAGAA
53509 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
53544 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:55555 original size:2 final size:2
Alignment explanation
Indices: 55548--55594 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
55538 GAGCAGCACA
55548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55590 TC TC T
1 TC TC T
55595 AAGGTTTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:67491 original size:21 final size:23
Alignment explanation
Indices: 67467--67514 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
67457 TTTTAAAATC
*
67467 TCAAGGTCA-TTGT-ACAAAAGG
1 TCAAGGTCAGTGGTAACAAAAGG
67488 TCAAGGTCAGTGGTAACAAAAGG
1 TCAAGGTCAGTGGTAACAAAAGG
67511 TCAA
1 TCAA
67515 AATGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (23 bp):
TCAAGGTCAGTGGTAACAAAAGG
Found at i:68481 original size:3 final size:3
Alignment explanation
Indices: 68475--68527 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
68465 AGTAAAATTG
* * * * * *
68475 CAT CAT CAT CAT CTT CTT CTT CAT CAT GAT CAT GAT CAT GAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
68523 CAT CA
1 CAT CA
68528 CATTATCTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:69437 original size:2 final size:2
Alignment explanation
Indices: 69430--69455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69420 GTGAAATAAA
69430 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
69456 CCTCACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:83292 original size:19 final size:19
Alignment explanation
Indices: 83268--83310 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
83258 AATGCATGTG
83268 CAAGGATAATTAT-AAAGTT
1 CAAGGA-AATTATCAAAGTT
* *
83287 CAAGGAAATTTTCAGAGTT
1 CAAGGAAATTATCAAAGTT
83306 CAAGG
1 CAAGG
83311 TCAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (19 bp):
CAAGGAAATTATCAAAGTT
Found at i:84581 original size:2 final size:2
Alignment explanation
Indices: 84576--84640 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
84566 TTACACACAT
84576 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
84618 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
84641 TCCGGCAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:87544 original size:2 final size:2
Alignment explanation
Indices: 87537--87594 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
87527 TAGCAAACAC
87537 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
87579 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
87595 GACCTCTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:89964 original size:2 final size:2
Alignment explanation
Indices: 89959--90014 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
89949 ATAGATCAAA
89959 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
90001 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
90015 CACCTCAGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:91725 original size:12 final size:12
Alignment explanation
Indices: 91703--91734 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
91693 GTAATTGGTT
91703 AGATGAGAGAGAG
1 AGAT-AGAGAGAG
91716 AGATAGAGAGAG
1 AGATAGAGAGAG
91728 AGATAGA
1 AGATAGA
91735 TTAAGCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (12 bp):
AGATAGAGAGAG
Found at i:91911 original size:2 final size:2
Alignment explanation
Indices: 91904--91952 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
91894 TTGGTTAGAT
*
91904 GA GA GA GA TA GA GA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA
91947 GA GA GA
1 GA GA GA
91953 CTATACTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (2 bp):
GA
Found at i:96927 original size:61 final size:61
Alignment explanation
Indices: 96832--97014 Score: 339
Period size: 61 Copynumber: 3.0 Consensus size: 61
96822 GAATGATAGT
* *
96832 GAGCAGATAGCCGGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACTATGCAGTG
1 GAGCAGATAGCCTGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
96893 GAGCAGATAGCCTGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
1 GAGCAGATAGCCTGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
*
96954 GAGCAGATAGCCTGTGCATGGCTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
1 GAGCAGATAGCCTGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
97015 CCCATGACAA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 119 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (61 bp):
GAGCAGATAGCCTGTGCATGGTTATAGGATGTTACAGATGTTACATTGTAACCATGCAGTG
Found at i:105318 original size:471 final size:470
Alignment explanation
Indices: 104436--105377 Score: 1875
Period size: 471 Copynumber: 2.0 Consensus size: 470
104426 ATTCAAGATC
104436 AACGAGGCAGAGGTGATGGAGGAGCAGCTCAAACAGTACAAGGTACTGATCAATCCACAGATTTG
1 AACGAGGCAGAGGTGATGGAGGAGCAGCTCAAACAGTACAAGGTACTGATCAATCCACAGATTTG
104501 AACCAGCAACTTCTGTTGTGAAAGCTCAGTGTCCTAAGTGGTTTCAATCATGATACTGTGATTTG
66 AACCAGCAACTTCTGTTGTGAAAGCTCAGTGTCCTAAGTGGTTTCAATCATGATACTGTGATTTG
104566 TATATCTGTGTAAATCAGCTCAGAAATAAAAAAAATTGCAAAATATTTAGTTTGCTTTTCTTTTA
131 TATATCTGTGTAAATCAGCTCAGAAATAAAAAAAATTGCAAAATATTTAGTTTGCTTTTCTTTTA
104631 AAAATCAAATGATTTATGCATAGCTAAAAAAAGGAATAAACATGATATGTCTTCATCTCTCTGTC
196 AAAATCAAATGATTTATGCATAGCTAAAAAAAGGAATAAACATGATATGTCTTCATCTCTCTGTC
104696 TCCTTATCCAACAGCAGAATGTTCATTCTAAATAATTTCATGTGTGTGGAACCTAAGATTATTGA
261 TCCTTATCCAACAGCAGAATGTTCATTCTAAATAATTTCATGTGTGTGGAACCTAAGATTATTGA
104761 GCATTTTTTATTATTTAAAATCAAATTTTTTTTCAGAGCCTGCAGGAGGACTTACAAGAACACCA
326 GCATTTTTTATTATTTAAAATCAAATTTTTTTTCAGAGCCTGCAGGAGGACTTACAAGAACACCA
104826 AGGAAGTTTGGACTACATCAACAAGACGGGAAAAGAGCTGGTAGTGAAATCAGGGCCCCACGACA
391 AGGAAGTTTGGACTACATCAACAAGACGGGAAAAGAGCTGGTAGTGAAATCAGGGCCCCACGACA
104891 AAGCCCAGGCCATGG
456 AAGCCCAGGCCATGG
104906 NAACGAGGCAGAGGTGATGGAGGAGCAGCTCAAACAGTACAAGGTACTGATCAATCCACAGATTT
1 -AACGAGGCAGAGGTGATGGAGGAGCAGCTCAAACAGTACAAGGTACTGATCAATCCACAGATTT
104971 GAACCAGCAACTTCTGTTGTGAAAGCTCAGTGTCCTAAGTGGTTTCAATCATGATACTGTGATTT
65 GAACCAGCAACTTCTGTTGTGAAAGCTCAGTGTCCTAAGTGGTTTCAATCATGATACTGTGATTT
105036 GTATATCTGTGTAAATCAGCTCAGAAATAAAAAAAATTGCAAAATATTTAGTTTGCTTTTCTTTT
130 GTATATCTGTGTAAATCAGCTCAGAAATAAAAAAAATTGCAAAATATTTAGTTTGCTTTTCTTTT
105101 AAAAATCAAATGATTTATGCATAGCTAAAAAAAGGAATAAACATGATATGTCTTCATCTCTCTGT
195 AAAAATCAAATGATTTATGCATAGCTAAAAAAAGGAATAAACATGATATGTCTTCATCTCTCTGT
105166 CTCCTTATCCAACAGCAGAATGTTCATTCTAAATAATTTCATGTGTGTGGAACCTAAGATTATTG
260 CTCCTTATCCAACAGCAGAATGTTCATTCTAAATAATTTCATGTGTGTGGAACCTAAGATTATTG
105231 AGCATTTTTTATTATTTAAAATCAAATTTTTTTTCAGAGCCTGCAGGAGGACTTACAAGAACACC
325 AGCATTTTTTATTATTTAAAATCAAATTTTTTTTCAGAGCCTGCAGGAGGACTTACAAGAACACC
105296 AAGGAAGTTTGGACTACATCAACAAGACGGGAAAAGAGCTGGTAGTGAAATCAGGGCCCCACGAC
390 AAGGAAGTTTGGACTACATCAACAAGACGGGAAAAGAGCTGGTAGTGAAATCAGGGCCCCACGAC
105361 AAAGCCCAGGCCATGG
455 AAAGCCCAGGCCATGG
105377 A
1 A
105378 GAGGAATCTG
Statistics
Matches: 471, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
470 1 0.00
471 470 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (470 bp):
AACGAGGCAGAGGTGATGGAGGAGCAGCTCAAACAGTACAAGGTACTGATCAATCCACAGATTTG
AACCAGCAACTTCTGTTGTGAAAGCTCAGTGTCCTAAGTGGTTTCAATCATGATACTGTGATTTG
TATATCTGTGTAAATCAGCTCAGAAATAAAAAAAATTGCAAAATATTTAGTTTGCTTTTCTTTTA
AAAATCAAATGATTTATGCATAGCTAAAAAAAGGAATAAACATGATATGTCTTCATCTCTCTGTC
TCCTTATCCAACAGCAGAATGTTCATTCTAAATAATTTCATGTGTGTGGAACCTAAGATTATTGA
GCATTTTTTATTATTTAAAATCAAATTTTTTTTCAGAGCCTGCAGGAGGACTTACAAGAACACCA
AGGAAGTTTGGACTACATCAACAAGACGGGAAAAGAGCTGGTAGTGAAATCAGGGCCCCACGACA
AAGCCCAGGCCATGG
Found at i:106735 original size:2 final size:2
Alignment explanation
Indices: 106728--106803 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
106718 GGTAGTGGGA
106728 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
106770 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
106804 GTTTAGAGGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:111668 original size:29 final size:29
Alignment explanation
Indices: 111618--111907 Score: 102
Period size: 29 Copynumber: 10.9 Consensus size: 29
111608 AGGCAGATAG
*
111618 GGTCAAGGTGTATAT-AGGTACAGGTGTAT
1 GGTCAAGGTGTAT-TCAGTTACAGGTGTAT
111647 GGTCAAGGTGTATTCAGTTACAGGTG--T
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
* * * ** * *
111674 GAT-AATG-GT-TGC--TGGCA-G-ATAG
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
*
111696 GGTCAAGGTGTATAT-AGGTACAGGTGTAT
1 GGTCAAGGTGTAT-TCAGTTACAGGTGTAT
111725 GGTCAAGGTGTATTCAGTTACAGGTG--T
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
* * * ** * *
111752 GAT-AATG-GT-TGC--TGGCA-G-ATAG
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
*
111774 GGTCAAGGTGTATAT-AGGTACAGGTGTAT
1 GGTCAAGGTGTAT-TCAGTTACAGGTGTAT
111803 GGTCAAGGTGTATTCAGTTACAGGTG--T
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
* * * ** * *
111830 GAT-AATG-GT-TGC--TGGCA-G-ATAG
1 GGTCAAGGTGTATTCAGTTACAGGTGTAT
*
111852 GGTCAAGGTGTATAT-AGGTACAGGTGTAT
1 GGTCAAGGTGTAT-TCAGTTACAGGTGTAT
111881 GGTCAAGGTGTATTCAGTTACAGGTGT
1 GGTCAAGGTGTATTCAGTTACAGGTGT
111908 GATAATGGTT
Statistics
Matches: 178, Mismatches: 49, Indels: 68
0.60 0.17 0.23
Matches are distributed among these distances:
21 3 0.02
22 15 0.08
23 9 0.05
24 12 0.07
25 9 0.05
26 9 0.05
27 15 0.08
28 7 0.04
29 99 0.56
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (29 bp):
GGTCAAGGTGTATTCAGTTACAGGTGTAT
Found at i:111698 original size:78 final size:78
Alignment explanation
Indices: 111587--111981 Score: 745
Period size: 78 Copynumber: 5.0 Consensus size: 78
111577 TGTGTGCAAG
* *
111587 TACAGGTGTGATAAAGGTTGCAGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
1 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
111652 AGGTGTATTCAGT
66 AGGTGTATTCAGT
111665 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
1 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
111730 AGGTGTATTCAGT
66 AGGTGTATTCAGT
111743 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
1 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
111808 AGGTGTATTCAGT
66 AGGTGTATTCAGT
111821 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
1 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
111886 AGGTGTATTCAGT
66 AGGTGTATTCAGT
111899 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATATAGGTACAGGTGTATGGT
1 TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTG--TATATAGGTACAGGTGTATGGT
*
111964 CATGGTGTATTCAGT
64 CAAGGTGTATTCAGT
111979 TAC
1 TAC
111982 TGAATTCTGA
Statistics
Matches: 312, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
78 273 0.88
80 39 0.12
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (78 bp):
TACAGGTGTGATAATGGTTGCTGGCAGATAGGGTCAAGGTGTATATAGGTACAGGTGTATGGTCA
AGGTGTATTCAGT
Found at i:116622 original size:2 final size:2
Alignment explanation
Indices: 116615--116647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
116605 TGTATACATG
116615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
116648 TCATATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:119639 original size:16 final size:16
Alignment explanation
Indices: 119603--119645 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
119593 CAAGTGTAGA
*
119603 AGGGCGAAAATTACAG
1 AGGGCGAAAATTACAC
* *
119619 GGGGCAAAAATTACAC
1 AGGGCGAAAATTACAC
119635 AGGGCGAAAAT
1 AGGGCGAAAAT
119646 AACCTTGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.30, T:0.12
Consensus pattern (16 bp):
AGGGCGAAAATTACAC
Found at i:122807 original size:14 final size:14
Alignment explanation
Indices: 122788--122814 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
122778 TTTTGAACGT
122788 ATTGGAATTATATG
1 ATTGGAATTATATG
122802 ATTGGAATTATAT
1 ATTGGAATTATAT
122815 TACATTACAT
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:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
ATTGGAATTATATG
Found at i:131449 original size:22 final size:22
Alignment explanation
Indices: 131421--131465 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
131411 TTATAACCGA
131421 TGCCATGTTGTAGGATTTGAGT
1 TGCCATGTTGTAGGATTTGAGT
131443 TGCCATGTTGTAGGATTTGAGT
1 TGCCATGTTGTAGGATTTGAGT
131465 T
1 T
131466 CTGGGATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.31, T:0.42
Consensus pattern (22 bp):
TGCCATGTTGTAGGATTTGAGT
Found at i:131461 original size:77 final size:81
Alignment explanation
Indices: 131368--131525 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 81
131358 ATTACTAGAA
* *
131368 CCATGTTATAGAATTTGAGTTCTGGGATCAAGTAAATAATCA-T-T-T-ATAACCGATGCCATGT
1 CCATGTTATAGAATTTGAGTTCTGGGATCAAGTAAATAATCATTATATAATAACCAATACCATGT
131429 TGTAGGATTTGAGTTG
66 TGTAGGATTTGAGTTG
* * *
131445 CCATGTTGTAGGATTTGAGTTCTGGGATCAAGTAAATGATCATTTATATAATAACCAATACCATG
1 CCATGTTATAGAATTTGAGTTCTGGGATCAAGTAAATAATCA-TTATATAATAACCAATACCATG
131510 TTGTAGGATTTGAGTT
65 TTGTAGGATTTGAGTT
131526 CTGGGATCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
77 39 0.55
79 1 0.01
80 1 0.01
81 1 0.01
82 29 0.41
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (81 bp):
CCATGTTATAGAATTTGAGTTCTGGGATCAAGTAAATAATCATTATATAATAACCAATACCATGT
TGTAGGATTTGAGTTG
Found at i:132757 original size:41 final size:40
Alignment explanation
Indices: 132696--132822 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 40
132686 AGCGGTTTGA
* * *
132696 CAAGGTCAGTGTAGACTCAGGGTAAAACAGAGGTCAATTGT
1 CAAGGTCACTATAGAATCAGGGT-AAACAGAGGTCAATTGT
* * * *
132737 CAAGGTCCCTATGGAATCAGGGGTCAACAGAGGTTAATTGT
1 CAAGGTCACTATAGAATCA-GGGTAAACAGAGGTCAATTGT
* * *
132778 CAAGGTCAGTGTAGACTCAGGGTCAAACAGAGGTCAAATTGT
1 CAAGGTCACTATAGAATCAGGGT-AAACAGAGGTC-AATTGT
132820 CAA
1 CAA
132823 TTGTCAAGGT
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
40 4 0.06
41 52 0.75
42 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (40 bp):
CAAGGTCACTATAGAATCAGGGTAAACAGAGGTCAATTGT
Found at i:132826 original size:49 final size:48
Alignment explanation
Indices: 132772--132904 Score: 134
Period size: 49 Copynumber: 2.8 Consensus size: 48
132762 AACAGAGGTT
132772 AATTGTCAAGGTCAGTGTAGACTCAGGGTCAAACAGAGGTCAAATTGTC
1 AATTGTCAAGGTCAGTGTAGACTCAGGGTCAAACAGAGGT-AAATTGTC
* * *
132821 AATTGTCAAGGTCACTGTGGA-TCAGGGGTCAAGA-A-AGGTTAATTGTC
1 AATTGTCAAGGTCAGTGTAGACTCA-GGGTCAA-ACAGAGGTAAATTGTC
* *
132868 AA-GGTC-AGTGT-AGATTTAGACTCAGGGTCAAACAGAG
1 AATTGTCAAG-GTCAG-TGTAGACTCAGGGTCAAACAGAG
132905 ATAAGAGGTT
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
45 4 0.06
46 17 0.24
47 14 0.20
48 7 0.10
49 27 0.39
50 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (48 bp):
AATTGTCAAGGTCAGTGTAGACTCAGGGTCAAACAGAGGTAAATTGTC
Found at i:137962 original size:54 final size:55
Alignment explanation
Indices: 137858--137967 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 55
137848 ATTCACTTTA
*
137858 GACCAGCTTCAATTTTAACTTTAATTTGATGTTTTAACTAGATAAATACATCATT
1 GACCAGCTTCAATTTTAACTTTAATTTGATGTTTTAAATAGATAAATACATCATT
* **
137913 GACCAGCTTCAATTTTAAC-TTGATTTGATGTTTTAAATAGATAGCTACATCATT
1 GACCAGCTTCAATTTTAACTTTAATTTGATGTTTTAAATAGATAAATACATCATT
137967 G
1 G
137968 CCCAACAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 32 0.63
55 19 0.37
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (55 bp):
GACCAGCTTCAATTTTAACTTTAATTTGATGTTTTAAATAGATAAATACATCATT
Found at i:138321 original size:28 final size:28
Alignment explanation
Indices: 138239--138324 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 28
138229 ACCAACATAG
138239 ACCAGCAGATAGCTAAACAGAAAGTAAGAGTA
1 ACCAGCAGATAGCTAAACAGAAAGT-A-A--A
*
138271 ATTCA-CAG-T-G-TAAACAGAAAGTAAA
1 A-CCAGCAGATAGCTAAACAGAAAGTAAA
138296 ACCAGCAGATAGCTAAACAGAAAGTAAA
1 ACCAGCAGATAGCTAAACAGAAAGTAAA
138324 A
1 A
138325 TCTATTTACT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 2 0.04
25 5 0.11
26 1 0.02
27 2 0.04
28 17 0.36
29 12 0.26
30 1 0.02
31 1 0.02
32 4 0.09
33 2 0.04
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.14
Consensus pattern (28 bp):
ACCAGCAGATAGCTAAACAGAAAGTAAA
Found at i:138342 original size:57 final size:57
Alignment explanation
Indices: 138239--138381 Score: 180
Period size: 57 Copynumber: 2.5 Consensus size: 57
138229 ACCAACATAG
* **
138239 ACCAGCAGATAGCTAAACAGAAAGTAAGAGTAATTCACAGTGTAAACAGAAAGTAAA
1 ACCAGCAGATAGCTAAACAGAAAGTAAGAATAATTCACAGCATAAACAGAAAGTAAA
* * *
138296 ACCAGCAGATAGCTAAACAGAAAGTAA-AATCTATTTACTGCATAAACAGAAAGTAAA
1 ACCAGCAGATAGCTAAACAGAAAGTAAGAAT-AATTCACAGCATAAACAGAAAGTAAA
* ** *
138353 AGCAATAGATAGCTTAACAGAAAGTAAGA
1 ACCAGCAGATAGCTAAACAGAAAGTAAGA
138382 CATACAAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
56 2 0.03
57 71 0.96
58 1 0.01
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (57 bp):
ACCAGCAGATAGCTAAACAGAAAGTAAGAATAATTCACAGCATAAACAGAAAGTAAA
Found at i:138397 original size:57 final size:55
Alignment explanation
Indices: 138281--138408 Score: 150
Period size: 57 Copynumber: 2.3 Consensus size: 55
138271 ATTCACAGTG
* * *
138281 TAAACAGAAAGTAAAACCAGCAGATAGCTAAACAGAAAGTAAAATCTATTTACTGCA
1 TAAACAGAAAGTAAAACCAACAGATAGCTAAACAGAAAGTAAAATCAAATTAC--CA
* * *
138338 TAAACAGAAAGTAAAAGCAATAGATAGCTTAACAGAAAGTAAGACATACAAATTA-CA
1 TAAACAGAAAGTAAAACCAACAGATAGCTAAACAGAAAGTAA-A-AT-CAAATTACCA
138395 TAAACAGAAAGTAA
1 TAAACAGAAAGTAA
138409 TGCCAACCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 54 0.87
58 1 0.02
59 2 0.03
60 5 0.08
ACGTcount: A:0.55, C:0.13, G:0.14, T:0.18
Consensus pattern (55 bp):
TAAACAGAAAGTAAAACCAACAGATAGCTAAACAGAAAGTAAAATCAAATTACCA
Found at i:139495 original size:30 final size:30
Alignment explanation
Indices: 139456--139559 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 30
139446 CCCTATGTTT
* * *
139456 TCAATTTCTCCCAACCAGCACTCTTTGTAG
1 TCAAATTCTCCCAACCACCACTCTCTGTAG
*
139486 TCAAATTCTCCCAACCACCACTCTGTGTAG
1 TCAAATTCTCCCAACCACCACTCTCTGTAG
* * *
139516 TCAAATTCTCCCAACTATCA-TCCTCTGCAG
1 TCAAATTCTCCCAACCACCACT-CTCTGTAG
139546 TCAAATTCTCCCAA
1 TCAAATTCTCCCAA
139560 TTATCATCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 1 0.02
30 65 0.98
ACGTcount: A:0.27, C:0.36, G:0.08, T:0.30
Consensus pattern (30 bp):
TCAAATTCTCCCAACCACCACTCTCTGTAG
Found at i:140536 original size:2 final size:2
Alignment explanation
Indices: 140529--140586 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
140519 GAAAAGTAAT
140529 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
140571 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
140587 AAGGCACTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:140612 original size:42 final size:41
Alignment explanation
Indices: 140566--140648 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 41
140556 AGAGAGAGAG
*
140566 AGAGAGAGAGAGAGAGAGAGAAAGGCACTCAATAACATGTT
1 AGAGAGAGAGAGAGAGAGAGAAAGGAACTCAATAACATGTT
* * *
140607 NAGAGAGAGAGAGAGAGAGAGAAATGAACTTACTAACATGTT
1 -AGAGAGAGAGAGAGAGAGAGAAAGGAACTCAATAACATGTT
140649 TTGGTCTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.14
Consensus pattern (41 bp):
AGAGAGAGAGAGAGAGAGAGAAAGGAACTCAATAACATGTT
Found at i:145921 original size:46 final size:46
Alignment explanation
Indices: 145838--146088 Score: 394
Period size: 46 Copynumber: 5.5 Consensus size: 46
145828 CTATAGCTGC
* * **
145838 TAGGGACCTCTCATTGTACCACTTAACATCCTTGTCAGATAACCAA
1 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
* * * * *
145884 TAGGAACCTGTCCTTTTACCACTTAACATCTCTGTCAGACAACCTT
1 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
* *
145930 TAGGGACCTCTCGTTGTACCACTTAACATCCCTGTCAGATAACCTT
1 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
145976 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
1 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
146022 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
1 TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
*
146068 TAGGGACCTCTCATTGTACCA
1 TAGGAACCTCTCATTGTACCA
146089 TTTGAGGAAC
Statistics
Matches: 187, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 187 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (46 bp):
TAGGAACCTCTCATTGTACCACTTAACATCCCTGTCAGATAACCTT
Found at i:150802 original size:2 final size:2
Alignment explanation
Indices: 150795--150858 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
150785 GTCTGTGATA
* * *
150795 TC TC TC TC TT TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
150837 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
150859 GCCTGCATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:152996 original size:2 final size:2
Alignment explanation
Indices: 152989--153042 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
152979 TCATTCTCAT
152989 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
153031 TC TC TC TC -C TC T
1 TC TC TC TC TC TC T
153043 TTTCTCCCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:153875 original size:2 final size:2
Alignment explanation
Indices: 153868--153905 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
153858 GAGCATTGAG
*
153868 GA GA GA GA GA GA GA GA G- GA GA GA GA G- GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
153906 TCTTATATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:153890 original size:9 final size:9
Alignment explanation
Indices: 153865--153898 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
153855 AAAGAGCATT
153865 GAGGAGAGA
1 GAGGAGAGA
153874 GA-GAGAGA
1 GAGGAGAGA
153882 GAGGAGAGA
1 GAGGAGAGA
153891 GAGGAGAG
1 GAGGAGAG
153899 GGAGAGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (9 bp):
GAGGAGAGA
Found at i:153890 original size:15 final size:14
Alignment explanation
Indices: 153865--153905 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
153855 AAAGAGCATT
153865 GAGGAGA-GAGAGA
1 GAGGAGAGGAGAGA
153878 GA-GAGAGGAGAGA
1 GAGGAGAGGAGAGA
153891 GAGGAGAGG-GAGA
1 GAGGAGAGGAGAGA
153904 GA
1 GA
153906 TCTTATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (14 bp):
GAGGAGAGGAGAGA
Found at i:163150 original size:2 final size:2
Alignment explanation
Indices: 163143--163181 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
163133 TGATATTGCT
163143 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
163182 TTTTCCTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:163521 original size:2 final size:2
Alignment explanation
Indices: 163514--163543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
163504 AAATGTATTC
163514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
163544 GCCAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:165119 original size:69 final size:73
Alignment explanation
Indices: 165012--165222 Score: 349
Period size: 69 Copynumber: 2.9 Consensus size: 73
165002 ATCAGAAAAA
165012 TCTCTCTCTCTCTCTCTCTCTCTGTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGATT
1 TCTCTCTCTCTCTCTCTCTCTCTGTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGATT
165077 TCTCT-T-
66 TCTCTCTC
165083 TCT-T-TCTCTCTCTCTCTCTCTGTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGACT
1 TCTCTCTCTCTCTCTCTCTCTCTGTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGA-T
165146 TCTCTCTCTC
65 T-TCTCTCTC
* *
165156 TCTCTCTCTCTCTCTCTCTCTCTCGTTTCTGTCTGTCTCTCTTTAGTTGGATATTTGAGGTTGAT
1 TCTCTCTCTCTCTCTCTCTCTCT-GTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGAT
165221 TT
65 TT
165223 GCATAGCTTG
Statistics
Matches: 131, Mismatches: 2, Indels: 11
0.91 0.01 0.08
Matches are distributed among these distances:
69 57 0.44
70 3 0.02
71 8 0.06
72 1 0.01
73 3 0.02
74 2 0.02
75 19 0.15
76 38 0.29
ACGTcount: A:0.07, C:0.27, G:0.15, T:0.51
Consensus pattern (73 bp):
TCTCTCTCTCTCTCTCTCTCTCTGTGTCTGTCTGCCTCTCTTTAGTTGGATATTTGAGGTTGATT
TCTCTCTC
Found at i:165197 original size:2 final size:2
Alignment explanation
Indices: 165146--165179 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
165136 GAGGTTGACT
165146 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
165180 GTTTCTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:166409 original size:11 final size:11
Alignment explanation
Indices: 166393--166454 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
166383 TACATAAGCT
166393 ATTACATTTTG
1 ATTACATTTTG
**
166404 ATTACATAAGTG
1 ATTACAT-TTTG
166416 -TTACATTTTG
1 ATTACATTTTG
**
166426 ATTACATAAGTG
1 ATTACAT-TTTG
166438 -TTACATTTTG
1 ATTACATTTTG
166448 ATTACAT
1 ATTACAT
166455 AAGCTGTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 4 0.10
11 31 0.79
12 4 0.10
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (11 bp):
ATTACATTTTG
Found at i:166422 original size:22 final size:23
Alignment explanation
Indices: 166366--166473 Score: 175
Period size: 22 Copynumber: 4.8 Consensus size: 23
166356 AGTCCAACTC
* *
166366 AGCTGTTAAATTTTAATTACATA
1 AGCTGTTACATTTTGATTACATA
*
166389 AGCTATTACATTTTGATTACATA
1 AGCTGTTACATTTTGATTACATA
166412 AG-TGTTACATTTTGATTACATA
1 AGCTGTTACATTTTGATTACATA
166434 AG-TGTTACATTTTGATTACATA
1 AGCTGTTACATTTTGATTACATA
166456 AGCTGTTACATTTTGATT
1 AGCTGTTACATTTTGATT
166474 CACACAGTCT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
22 43 0.54
23 37 0.46
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (23 bp):
AGCTGTTACATTTTGATTACATA
Found at i:166433 original size:45 final size:45
Alignment explanation
Indices: 166366--166473 Score: 173
Period size: 45 Copynumber: 2.4 Consensus size: 45
166356 AGTCCAACTC
* *
166366 AGCTGTTAAATTTTAATTACATAAGCTATTACATTTTGATTACATA
1 AGCTGTTACATTTTGATTACATAAG-TATTACATTTTGATTACATA
*
166412 AG-TGTTACATTTTGATTACATAAGTGTTACATTTTGATTACATA
1 AGCTGTTACATTTTGATTACATAAGTATTACATTTTGATTACATA
166456 AGCTGTTACATTTTGATT
1 AGCTGTTACATTTTGATT
166474 CACACAGTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
44 21 0.36
45 35 0.60
46 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (45 bp):
AGCTGTTACATTTTGATTACATAAGTATTACATTTTGATTACATA
Found at i:167303 original size:2 final size:2
Alignment explanation
Indices: 167296--167362 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
167286 AAGTTCAACA
167296 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
167338 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
167363 GAGTAACGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:171015 original size:180 final size:180
Alignment explanation
Indices: 170712--171072 Score: 668
Period size: 180 Copynumber: 2.0 Consensus size: 180
170702 GGCTGCCAAA
* *
170712 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGTAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
170777 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
170842 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* *
170892 AGGGTACCCTCATTGTATGGATAACTCCTCCTACAGTTCTCAGGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
170957 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
*
171022 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
171072 A
1 A
171073 CATGTAGGGT
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 175 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:176469 original size:22 final size:22
Alignment explanation
Indices: 176444--176486 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
176434 TTTTTGTTTG
* *
176444 TTTTGTTAATGCAACATGGAAT
1 TTTTGTAAATACAACATGGAAT
176466 TTTTGTAAATACAACATGGAA
1 TTTTGTAAATACAACATGGAA
176487 ATACCTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TTTTGTAAATACAACATGGAAT
Found at i:180794 original size:23 final size:22
Alignment explanation
Indices: 180768--180847 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
180758 CACGCATTTC
*
180768 TGAAAAGCGCTATTACGCCTTAT
1 TGAAAGGCG-TATTACGCCTTAT
180791 TGAAAGGCGTTATCT-CGCCTTAT
1 TGAAAGGCG-TAT-TACGCCTTAT
* *
180814 TGAAAGGCGTGGTCACGCCTTAT
1 TGAAAGGCGT-ATTACGCCTTAT
*
180837 TGAAAGACGTA
1 TGAAAGGCGTA
180848 CGTGATCACG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (22 bp):
TGAAAGGCGTATTACGCCTTAT
Found at i:180859 original size:27 final size:23
Alignment explanation
Indices: 180782--180861 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
180772 AAGCGCTATT
*
180782 ACGCCTTATTGAAAGGCGTTATC
1 ACGCCTTATTGAAAGGCGTGATC
* *
180805 TCGCCTTATTGAAAGGCGTGGTC
1 ACGCCTTATTGAAAGGCGTGATC
180828 ACGCCTTATTGAAAGACGTACGTGATC
1 ACGCCTTATTGAAAG--G--CGTGATC
180855 ACGCCTT
1 ACGCCTT
180862 TTGGAAAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 34 0.71
25 1 0.02
27 13 0.27
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
ACGCCTTATTGAAAGGCGTGATC
Found at i:182113 original size:24 final size:24
Alignment explanation
Indices: 182086--182137 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
182076 CGGCTCGGGA
182086 AGGCAATGAT-GTTGTTAGTTTTCC
1 AGGCAATG-TCGTTGTTAGTTTTCC
**
182110 AGGCTCTGTCGTTGTTAGTTTTCC
1 AGGCAATGTCGTTGTTAGTTTTCC
182134 AGGC
1 AGGC
182138 TCTGTCGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.40
Consensus pattern (24 bp):
AGGCAATGTCGTTGTTAGTTTTCC
Found at i:182138 original size:24 final size:24
Alignment explanation
Indices: 182096--182145 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
182086 AGGCAATGAT
182096 GTTGTTAGTTTTCCAGGCTCTGTC
1 GTTGTTAGTTTTCCAGGCTCTGTC
182120 GTTGTTAGTTTTCCAGGCTCTGTC
1 GTTGTTAGTTTTCCAGGCTCTGTC
182144 GT
1 GT
182146 CACCAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.20, G:0.26, T:0.46
Consensus pattern (24 bp):
GTTGTTAGTTTTCCAGGCTCTGTC
Found at i:186666 original size:10 final size:10
Alignment explanation
Indices: 186626--186694 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
186616 TGTTCATAAG
186626 TATAATATACA
1 TATAA-ATACA
186637 TTATAAATACA
1 -TATAAATACA
**
186648 TATTCATACA
1 TATAAATACA
186658 TATAAATACA
1 TATAAATACA
186668 TGTATAAAT---
1 --TATAAATACA
*
186677 TATATATACA
1 TATAAATACA
186687 TATAAATA
1 TATAAATA
186695 TGTACTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
7 6 0.13
10 23 0.50
11 5 0.11
12 12 0.26
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (10 bp):
TATAAATACA
Found at i:188844 original size:59 final size:59
Alignment explanation
Indices: 188736--188851 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 59
188726 TAACAAACAT
* * * * ** *
188736 TTGCAACAAGTACAGAAATCGTATGCAAATTAGTTTCTTGCAATGTGTTTGCGGCAAAG
1 TTGCAACAAGTACAAAAATCGTATGCAAATCAGTTTCTGGAAAACTGTTTGCAGCAAAG
* *
188795 TTGCCACAAGTTCAAAAATCGTATGCAAATCAGTTTCTGGAAAACTGTTTGCAGCAA
1 TTGCAACAAGTACAAAAATCGTATGCAAATCAGTTTCTGGAAAACTGTTTGCAGCAA
188852 GCTTGCAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (59 bp):
TTGCAACAAGTACAAAAATCGTATGCAAATCAGTTTCTGGAAAACTGTTTGCAGCAAAG
Found at i:191768 original size:21 final size:21
Alignment explanation
Indices: 191744--191837 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
191734 CGTGCGACTT
*
191744 TCGTATCGTATAAGAAGCGTA
1 TCGTATCGTATAAGAAACGTA
***
191765 TCGT-TCCGTGCGAGAAACGTA
1 TCGTAT-CGTATAAGAAACGTA
*
191786 TCGTATCGCATGAA-AAACGTA
1 TCGTATCGTAT-AAGAAACGTA
* *
191807 CCGTATCGTATGAGAAACGTA
1 TCGTATCGTATAAGAAACGTA
*
191828 TCATATCGTA
1 TCGTATCGTA
191838 CAAAGCGTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGTATCGTATAAGAAACGTA
Found at i:194011 original size:2 final size:2
Alignment explanation
Indices: 194004--194041 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
193994 TTAAAAGCAT
194004 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
194042 TTGCCACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:202386 original size:34 final size:35
Alignment explanation
Indices: 202320--202389 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
202310 CTTTCCCCCG
*
202320 TTTCCCCATTGCTTTGTCTTCTTTTTTAATCAATC
1 TTTCCCCATTGCTTTGTCATCTTTTTTAATCAATC
*
202355 TTTCCCCATTTCTTTGTCATCTTTTTT-ATCAATC
1 TTTCCCCATTGCTTTGTCATCTTTTTTAATCAATC
202389 T
1 T
202390 ATTTTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.14, C:0.26, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTCCCCATTGCTTTGTCATCTTTTTTAATCAATC
Found at i:202416 original size:16 final size:15
Alignment explanation
Indices: 202376--202413 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
202366 CTTTGTCATC
*
202376 TTTTTTATCAATCTA
1 TTTTTTTTCAATCTA
202391 TTTTTTTTCAATCTA
1 TTTTTTTTCAATCTA
202406 TTTTTTTT
1 TTTTTTTT
202414 TCATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTTCAATCTA
Found at i:209273 original size:2 final size:2
Alignment explanation
Indices: 209266--209292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
209256 CAGGAACCGG
209266 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
209293 GGTGAGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:212640 original size:19 final size:19
Alignment explanation
Indices: 212607--212643 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
212597 CAGGTGCACC
*
212607 AGAGGTAGAGAAAAGAAAG
1 AGAGGTAGACAAAAGAAAG
*
212626 AGAGGTAGACCAAAGAAA
1 AGAGGTAGACAAAAGAAA
212644 CTAAAACCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.32, T:0.05
Consensus pattern (19 bp):
AGAGGTAGACAAAAGAAAG
Found at i:219617 original size:30 final size:30
Alignment explanation
Indices: 219583--219685 Score: 163
Period size: 30 Copynumber: 3.5 Consensus size: 30
219573 AATACGTTGC
219583 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
*
219613 CGGTCCAATAGATCACAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
* *
219643 CGGTCTAATAGATCGCAGTCTATTGACCGA
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
*
219673 CAGT-CAATAGATC
1 CGGTCCAATAGATC
219686 ACTTACAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 8 0.12
30 59 0.88
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (30 bp):
CGGTCCAATAGATCGCAGTCTATTGACCGG
Found at i:225565 original size:8 final size:8
Alignment explanation
Indices: 225552--225588 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
225542 TGCGTCTACA
225552 GACAGACG
1 GACAGACG
225560 GACAGACG
1 GACAGACG
* *
225568 GACGGACA
1 GACAGACG
225576 GACAGACG
1 GACAGACG
225584 GACAG
1 GACAG
225589 GGTGAAACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.38, C:0.24, G:0.38, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:225566 original size:12 final size:12
Alignment explanation
Indices: 225549--225588 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
225539 AGTTGCGTCT
225549 ACAGACAGACGG
1 ACAGACAGACGG
*
225561 ACAGACGGACGG
1 ACAGACAGACGG
225573 ACAGACAGACGG
1 ACAGACAGACGG
225585 ACAG
1 ACAG
225589 GGTGAAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:226996 original size:9 final size:9
Alignment explanation
Indices: 226982--227009 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
226972 ACATTACATT
226982 ATTAAATAC
1 ATTAAATAC
226991 ATTAAATAC
1 ATTAAATAC
227000 ATTAAATAC
1 ATTAAATAC
227009 A
1 A
227010 ACATTTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAATAC
Found at i:227373 original size:32 final size:32
Alignment explanation
Indices: 227337--227405 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
227327 GAATGTGCAG
227337 TCTATGTATTCACATTTAAATATTGTATTTTT
1 TCTATGTATTCACATTTAAATATTGTATTTTT
* *
227369 TCTATGTTTTCACTTTTAAATATTGTATTTTT
1 TCTATGTATTCACATTTAAATATTGTATTTTT
227401 TCTAT
1 TCTAT
227406 AGATCTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (32 bp):
TCTATGTATTCACATTTAAATATTGTATTTTT
Found at i:227727 original size:18 final size:18
Alignment explanation
Indices: 227704--227738 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
227694 GTCTGGGCGG
227704 ACTCCGAAAAAGGAGTAA
1 ACTCCGAAAAAGGAGTAA
*
227722 ACTCCGAAAACGGAGTA
1 ACTCCGAAAAAGGAGTA
227739 TTTGGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (18 bp):
ACTCCGAAAAAGGAGTAA
Found at i:230201 original size:19 final size:19
Alignment explanation
Indices: 230161--230202 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
230151 ACTAAAGGGC
* *
230161 ACCTGCTCAAAAAACTTTA
1 ACCTGCTCAAAAAACCTAA
230180 ACCTGCTTC-AAAAACCTAA
1 ACCTGC-TCAAAAAACCTAA
230199 ACCT
1 ACCT
230203 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (19 bp):
ACCTGCTCAAAAAACCTAA
Found at i:230942 original size:2 final size:2
Alignment explanation
Indices: 230935--230988 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
230925 GAACACTATC
230935 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
230976 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
230989 CTTGCAGCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:237091 original size:2 final size:2
Alignment explanation
Indices: 237072--237105 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
237062 GTACAGATAC
* *
237072 AT AT AG AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
237106 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:243696 original size:18 final size:18
Alignment explanation
Indices: 243669--243706 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
243659 TAGGGAGTAA
*
243669 AAAACTAAGAATATCTTG
1 AAAACCAAGAATATCTTG
243687 AAAACCAAGAATATCTTG
1 AAAACCAAGAATATCTTG
243705 AA
1 AA
243707 GTATCTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (18 bp):
AAAACCAAGAATATCTTG
Found at i:245513 original size:77 final size:79
Alignment explanation
Indices: 245390--245545 Score: 253
Period size: 77 Copynumber: 2.0 Consensus size: 79
245380 TTACTCCACA
* *
245390 TTTTAAAAACTCAGACCTGCTACCAAAAAAATTTTCATTTTC-AAAAAAA-AAAATAAAATAAAC
1 TTTTAAAAACTCAGACCTGCTACCAAAAAAATATTCATTTTCAAAAAAAATAAAAAAAAATAAAC
245453 AGAAATCAAGGACT
66 AGAAATCAAGGACT
* *
245467 TTTTAAATACTCAGACCTGCTACCAAAAAAATATTCCTTTTCAAAAAAAATAAAAAAAAATAAAC
1 TTTTAAAAACTCAGACCTGCTACCAAAAAAATATTCATTTTCAAAAAAAATAAAAAAAAATAAAC
*
245532 AGAAATCGAGGACT
66 AGAAATCAAGGACT
245546 GAAATAAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
77 39 0.54
78 7 0.10
79 26 0.36
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (79 bp):
TTTTAAAAACTCAGACCTGCTACCAAAAAAATATTCATTTTCAAAAAAAATAAAAAAAAATAAAC
AGAAATCAAGGACT
Found at i:252035 original size:102 final size:103
Alignment explanation
Indices: 251851--252050 Score: 348
Period size: 102 Copynumber: 1.9 Consensus size: 103
251841 TTTATATCTC
* * *
251851 AGAACCAACTTAAGGAGGCCGACTTTAGTTTGCATAGCGCATGTTTTTGCGCATTCTAATATAAT
1 AGAACCAACTTAAGGAGGCCAACTTTAGTTTGCATA-CGCACGTTTTTGCGCAATCTAATATAAT
251916 ACAGTTGATTTCTACTTCTTATGAATTTTTTTCTGAGTG
65 ACAGTTGATTTCTACTTCTTATGAATTTTTTTCTGAGTG
*
251955 AGAACCAACTTAAGGAGGCCAACTTTAGTTTGCAT-TGCACGTTTTTGCGCAATCTAATATAATA
1 AGAACCAACTTAAGGAGGCCAACTTTAGTTTGCATACGCACGTTTTTGCGCAATCTAATATAATA
252019 CAGTTGATTTCTACTTCTTATGAATTTTTTTC
66 CAGTTGATTTCTACTTCTTATGAATTTTTTTC
252051 AATTTCATTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 58 0.63
104 34 0.37
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (103 bp):
AGAACCAACTTAAGGAGGCCAACTTTAGTTTGCATACGCACGTTTTTGCGCAATCTAATATAATA
CAGTTGATTTCTACTTCTTATGAATTTTTTTCTGAGTG
Found at i:253415 original size:21 final size:21
Alignment explanation
Indices: 253386--253436 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
253376 CAAATGCGAG
* *
253386 AGCTTGTGCAACGTAAGCAAG
1 AGCTCGTGCAACGTAAGCAAC
* *
253407 GGCTCGTGCAACGTATGCAAC
1 AGCTCGTGCAACGTAAGCAAC
253428 AGCTCGTGC
1 AGCTCGTGC
253437 GAAGCTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (21 bp):
AGCTCGTGCAACGTAAGCAAC
Found at i:254044 original size:25 final size:25
Alignment explanation
Indices: 253990--254038 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
253980 AATATTGTAT
253990 CATATGATAAAATATTGTATCATAG
1 CATATGATAAAATATTGTATCATAG
* * *
254015 CATATGATACAATTTTGTGTCATA
1 CATATGATAAAATATTGTATCATA
254039 CAATATCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (25 bp):
CATATGATAAAATATTGTATCATAG
Found at i:254054 original size:15 final size:15
Alignment explanation
Indices: 254036--254064 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
254026 ATTTTGTGTC
254036 ATACAATATCATATA
1 ATACAATATCATATA
254051 ATACAATATCATAT
1 ATACAATATCATAT
254065 CAAAAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACAATATCATATA
Found at i:254474 original size:19 final size:20
Alignment explanation
Indices: 254450--254488 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
254440 ATCAAAGACT
254450 ACCTGCTCCAAAAA-CTTTA
1 ACCTGCTCCAAAAACCTTTA
254469 ACCTGCTCCAAAAACCTTTA
1 ACCTGCTCCAAAAACCTTTA
254489 TAAAACTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (20 bp):
ACCTGCTCCAAAAACCTTTA
Found at i:260030 original size:15 final size:15
Alignment explanation
Indices: 260010--260046 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
260000 CCGAAATTCT
260010 AAATTTATATCTCTA
1 AAATTTATATCTCTA
*
260025 AAATTTTGTATCTCTA
1 AAA-TTTATATCTCTA
260041 AAATTT
1 AAATTT
260047 TGTTTACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (15 bp):
AAATTTATATCTCTA
Found at i:260038 original size:16 final size:16
Alignment explanation
Indices: 260017--260049 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
260007 TCTAAATTTA
260017 TATCTCTAAAATTTTG
1 TATCTCTAAAATTTTG
260033 TATCTCTAAAATTTTG
1 TATCTCTAAAATTTTG
260049 T
1 T
260050 TTACACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (16 bp):
TATCTCTAAAATTTTG
Found at i:268798 original size:2 final size:2
Alignment explanation
Indices: 268793--268829 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
268783 AAAGCCCCCC
268793 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
268830 CGTTTCCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:273027 original size:29 final size:27
Alignment explanation
Indices: 272995--273054 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
272985 ACTATTATCA
* *
272995 TAATACCAATGATAAAATTATCTTTTTCT
1 TAATACCAATCAT--AATTATCGTTTTCT
*
273024 TAATACCAATCATCATTATCGTTTTCT
1 TAATACCAATCATAATTATCGTTTTCT
273051 TAAT
1 TAAT
273055 CATCGTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 16 0.57
29 12 0.43
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (27 bp):
TAATACCAATCATAATTATCGTTTTCT
Found at i:273251 original size:1 final size:1
Alignment explanation
Indices: 273247--273272 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
273237 TTTTTTTTTT
273247 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
273273 NAACCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:275629 original size:2 final size:2
Alignment explanation
Indices: 275622--275692 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
275612 TAGGGATTAC
275622 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
275664 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
275693 AATTAGTAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:282618 original size:2 final size:2
Alignment explanation
Indices: 282611--282664 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
282601 TGTTTATTTC
282611 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
282653 GA GA GA GA GA GA
1 GA GA GA GA GA GA
282665 TAGATTGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:286752 original size:1 final size:1
Alignment explanation
Indices: 286746--286771 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
286736 CGTCGGAACC
286746 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
286772 CGTGGTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:289214 original size:50 final size:49
Alignment explanation
Indices: 289079--289221 Score: 144
Period size: 49 Copynumber: 2.9 Consensus size: 49
289069 ATAAAAGTTG
* * * *
289079 TTTTGCCGTGTGTTCGGATTGAGTTAAGGGGTTTACCATCAAACATTTT
1 TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCCTCAAACATTTT
* * ** * * *
289128 TTTTGCCCTTTGCTCGGGTTTG-GTTAAGTAGCTTCCCCTCCAAGATTGTT
1 TTTTGCCCTGTGCTC-GGATTGAGTTAAGGGGTTTCCCCTCAAACATT-TT
*
289178 TTTTGCCCTGTGCTCGGATTGAGTTACGGGGTTTCCCCTTCAAA
1 TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCC-TCAAA
289222 AGTGTTTTGT
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
49 35 0.49
50 33 0.46
51 4 0.06
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (49 bp):
TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCCTCAAACATTTT
Found at i:289228 original size:50 final size:49
Alignment explanation
Indices: 289079--289242 Score: 136
Period size: 50 Copynumber: 3.3 Consensus size: 49
289069 ATAAAAGTTG
* * * * *
289079 TTTTGCCGTGTGTTCGGATTGAGTTAAGGGGTTT-ACCATCAAACATTTT
1 TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCCTTCAAA-ATGTT
* * ** * * *
289128 TTTTGCCCTTTGCTCGGGTTTG-GTTAAGTAGCTTCCCCTCCAAGATTGTT
1 TTTTGCCCTGTGCTC-GGATTGAGTTAAGGGGTTTCCCCTTCAA-AATGTT
* *
289178 TTTTGCCCTGTGCTCGGATTGAGTTACGGGGTTTCCCCTTCAAAA-GTG
1 TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCCTTCAAAATGTT
* *
289226 TTTTGTCCTGTGTTCGG
1 TTTTGCCCTGTGCTCGG
289243 GGATTGGATT
Statistics
Matches: 88, Mismatches: 23, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
48 17 0.19
49 27 0.31
50 43 0.49
51 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.41
Consensus pattern (49 bp):
TTTTGCCCTGTGCTCGGATTGAGTTAAGGGGTTTCCCCTTCAAAATGTT
Found at i:290753 original size:2 final size:2
Alignment explanation
Indices: 290746--290784 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
290736 CATTAGAATT
290746 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
290785 GTTTAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:316906 original size:137 final size:137
Alignment explanation
Indices: 316650--317036 Score: 585
Period size: 137 Copynumber: 2.8 Consensus size: 137
316640 AAATAGATAT
* *
316650 CATATAGCGATATTGCGTATTTCACTGTTGATATGCATCTTTAGTTAATATATGGATACATACAG
1 CATAAAGCGGTATTGCGTATTTCACTGTTGATATGCATCTTTAGTTAATATATGGATACATACAG
* *
316715 TATATAAGAGCTTGAAAAGAAATTTGCCACTTCTAGCCACCAAGATATCATATAGCGATATTGCG
66 TATATAAGAGCTTGAAAAGGAATTTGCCACTTCTGGCCACCAAGATATCATATAGCGATATTGCG
316780 TATTACG
131 TATTACG
*
316787 CATAAAGCGGTATTGCGTATTTCACTGTTGATATGCATCTTTAGTTATTATATGGATACATACAG
1 CATAAAGCGGTATTGCGTATTTCACTGTTGATATGCATCTTTAGTTAATATATGGATACATACAG
*
316852 TATATAAGAGCTTGAAAAGGAATTTGCCACTTCTGGCCACCAAGATATCATATAGCGATATTGTG
66 TATATAAGAGCTTGAAAAGGAATTTGCCACTTCTGGCCACCAAGATATCATATAGCGATATTGCG
316917 TATTACG
131 TATTACG
* ** * * *
316924 CATAAAGCGGTATTGCGTATTTCAGTACTGATATGCATCTTTAGTTACTATATGGATACAAAAAG
1 CATAAAGCGGTATTGCGTATTTCACTGTTGATATGCATCTTTAGTTAATATATGGATACATACAG
* **
316989 TATAATTTATGAGGAACTTTCAAAGGAATTTGCCACTTCTGGCCACCA
66 TAT-A--TA--A-GAGCTTGAAAAGGAATTTGCCACTTCTGGCCACCA
317037 TGATTAAATA
Statistics
Matches: 229, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
137 193 0.84
138 1 0.00
140 2 0.01
142 1 0.00
143 32 0.14
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (137 bp):
CATAAAGCGGTATTGCGTATTTCACTGTTGATATGCATCTTTAGTTAATATATGGATACATACAG
TATATAAGAGCTTGAAAAGGAATTTGCCACTTCTGGCCACCAAGATATCATATAGCGATATTGCG
TATTACG
Found at i:326693 original size:19 final size:19
Alignment explanation
Indices: 326671--326713 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
326661 TTTTTAATCC
326671 ACATTAATAAGAACATGGT
1 ACATTAATAAGAACATGGT
*
326690 ACATTAATAAGAATATGGT
1 ACATTAATAAGAACATGGT
326709 ACATT
1 ACATT
326714 GGTACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (19 bp):
ACATTAATAAGAACATGGT
Found at i:326752 original size:13 final size:13
Alignment explanation
Indices: 326736--326760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326726 AAAATGTTAA
326736 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
326749 AAAAAAAAAAAA
1 AAAAAAAAAAAA
326761 AACAAACTTT
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:326752 original size:15 final size:15
Alignment explanation
Indices: 326734--326766 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
326724 AGAAAATGTT
326734 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
326749 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
326764 AAA
1 AAA
326767 CTTTTGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:328974 original size:436 final size:434
Alignment explanation
Indices: 328154--329014 Score: 1074
Period size: 436 Copynumber: 2.0 Consensus size: 434
328144 GTGTAAGAGC
* * *
328154 TTTGTTCAACAAGTGTTTAGAATTCGTCACCATTCTTGAGTTATCTGTGAAAAATGTTTAAGGGG
1 TTTGTTCAACAAGTGTTTAGAAATCGTCACCATTCTTGAGATATCTGAGAAAAATGTTTAAGGGG
** * * *
328219 CCGGTCCCTTATCTCCTTATTGGGGCCACTGAACCAAATTTTTAAGGTTGCATGTTGTTAAGAAC
66 CCGGTCCCTTATAGCCTTATTGGGGCCACTGAACCAAATTTTGAAGATTGCATGTTATTAAGAAC
* * * * * * *
328284 ATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATATTTTTCTTTTTGAGATATAGG
131 ATCATTTTGAGCATCTTCTCCTCTACACTGCATTTCAAAATATATTATCCTTTCTGAGATATAGG
* * *
328349 TGATCAAATTTTTGGTCTTTTGAGCCCTAAAAACCCCTAATTACGTAACACATTAGAAAATCATT
196 TGATCAAAATTTTGGTCTTTTGACCCCTAAAAACCCCTAATTACGTAACACATCAGAAAATCATT
* * * * * *
328414 ATGTTGTTAGGCTACATAAATGTGAGATAAACATTTTGCTTTTATAATCTATTACAAAATATCCC
261 ATATTGTTAGGATACATAAATGTAAAATAAACATTTTGCTTCTATAACCTATTACAAAATATCCC
* * * *
328479 TCGGTTAAGACCTATAGGAAAAAGACTTTAGAGCCATCTAGGTCCCTACATTTAGGGGCCAGCCC
326 TCAGTAAAGACCTACAGGAAAAAGACTTAAGAGCCA-CTAGGTCCCTACATTTAGGGGCCAGCCC
* * * *
328544 CTTTTTCTTGGTATCAGATGTAAGGTCATTTAATTATAAAGACAT
390 CTTTTTCCTGATATCAAATGAAAGGTCATTTAATTATAAAGACAT
* *
328589 TTTGTTCAACAAGTGTTTAGAAATCTGTTACCATTCTTGAGATATCTGAGAAAGAATGTTTTAGG
1 TTTGTTCAACAAGTGTTTAGAAATC-GTCACCATTCTTGAGATATCTGAGAAA-AATGTTTAAGG
** * * * * *
328654 GGCCGGTCCCTTATAGCCTTATTGGGGCCGTTTAACGAAA-TTTGAAGATTGCATTTTATTCAGT
64 GGCCGGTCCCTTATAGCCTTATTGGGGCCACTGAACCAAATTTTGAAGATTGCATGTTATTAAGA
* * * *
328718 ATATCATTTTGGGCATCTTCTCCTCTACACTGCATTTGAAAATAT-TTATCCTTTCTGAGATATG
129 ACATCATTTTGAGCATCTTCTCCTCTACACTGCATTTCAAAATATATTATCCTTTCTGAGATATA
* *
328782 GGTGATCAAAATTTTGG-GTTTTGACCCCTTAAAAACCCCTAATTACGTAACCCATCATG-AAAT
194 GGTGATCAAAATTTTGGTCTTTTGACCCC-TAAAAACCCCTAATTACGTAACACATCA-GAAAAT
*
328845 CATTATATTGCTT-GGATACATAATTGTAAAATAAACATATTTGCTTCTATAACCT-TTCACAAA
257 CATTATATTG-TTAGGATACATAAATGTAAAATAAACAT-TTTGCTTCTATAACCTATT-ACAAA
** * * *
328908 ATATCCCTCAGTAAAGGGCTACA-GATTAAAGACTTAAGAGTCC-CTTGGTTCCTTA-ATTTGAG
319 ATATCCCTCAGTAAAGACCTACAGGA-AAAAGACTTAAGAG-CCACTAGG-TCCCTACATTT-AG
328970 GGGCCAGCCCCTTTTTCCTGATATCAAATGAAAGGTCATTTAATT
380 GGGCCAGCCCCTTTTTCCTGATATCAAATGAAAGGTCATTTAATT
329015 CTTAACACAT
Statistics
Matches: 362, Mismatches: 53, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
434 9 0.02
435 127 0.35
436 180 0.50
437 46 0.13
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (434 bp):
TTTGTTCAACAAGTGTTTAGAAATCGTCACCATTCTTGAGATATCTGAGAAAAATGTTTAAGGGG
CCGGTCCCTTATAGCCTTATTGGGGCCACTGAACCAAATTTTGAAGATTGCATGTTATTAAGAAC
ATCATTTTGAGCATCTTCTCCTCTACACTGCATTTCAAAATATATTATCCTTTCTGAGATATAGG
TGATCAAAATTTTGGTCTTTTGACCCCTAAAAACCCCTAATTACGTAACACATCAGAAAATCATT
ATATTGTTAGGATACATAAATGTAAAATAAACATTTTGCTTCTATAACCTATTACAAAATATCCC
TCAGTAAAGACCTACAGGAAAAAGACTTAAGAGCCACTAGGTCCCTACATTTAGGGGCCAGCCCC
TTTTTCCTGATATCAAATGAAAGGTCATTTAATTATAAAGACAT
Found at i:334658 original size:138 final size:141
Alignment explanation
Indices: 334478--334758 Score: 408
Period size: 138 Copynumber: 2.0 Consensus size: 141
334468 TTTTTCAAAG
* *
334478 AGATATCATATAACGATATTGCGTATTTCGCATAAAGCGGTATTGCGTATATCACTATTGATATG
1 AGATATCATATAACGATATTGCGTATTTCGCATAAAGCGGTATTGCGTATATCAATACTGATATG
* * * *
334543 CATCTTTAGTTACTATATGGATAC-ATACAG-T-A-TACGAGGAGCTTGAAAAGAAATTTGCCAC
66 CATCTTTAGTTACTATATAGATACTA-AAAGATAATTACGAGGAACTTAAAAAGAAATTTGCCAC
334604 TTCTGGCCACCA
130 TTCTGGCCACCA
* * * *
334616 AGATATCATATAGCGATATTGCGTATTTCGCATTAAGCGGTATTGCGTCTTTCAATACTGATATG
1 AGATATCATATAACGATATTGCGTATTTCGCATAAAGCGGTATTGCGTATATCAATACTGATATG
*
334681 CATCTTTAGTTACTATATAGATACTAAAAGTATAATTTATGAGGAACTTAAAAAGAAATTTGCCA
66 CATCTTTAGTTACTATATAGATACTAAAAG-ATAA-TTACGAGGAACTTAAAAAGAAATTTGCCA
334746 CTTCTGGCCACCA
129 CTTCTGGCCACCA
334759 TGATTAAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
138 85 0.67
139 1 0.01
140 1 0.01
141 1 0.01
143 38 0.30
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (141 bp):
AGATATCATATAACGATATTGCGTATTTCGCATAAAGCGGTATTGCGTATATCAATACTGATATG
CATCTTTAGTTACTATATAGATACTAAAAGATAATTACGAGGAACTTAAAAAGAAATTTGCCACT
TCTGGCCACCA
Found at i:337170 original size:166 final size:166
Alignment explanation
Indices: 336856--337724 Score: 1361
Period size: 166 Copynumber: 5.2 Consensus size: 166
336846 GAATCATCTT
336856 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTA
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TT-
* * * *
336921 AC-ACCCCCCA-TGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCATAACTTTGAATCAACA
64 -CGACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
*
336984 CTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTG
128 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* *
337023 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAATATTTACTCTTTATATTCCTATGTAAAACTTCG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
* * * *
337088 ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGATCATGATTTTTACAACTTTGAATTTACACTG
66 ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTA
337153 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
131 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * *
337189 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATTTTCCTATGGAAAATTTCG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
* * * *
337254 ACCCCCCATTGTGGCCCCACCCTACCCCCCGGGGTCATGATTTTTACAACTTTGAATTTACACTG
66 ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTA
337319 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
131 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* * *
337355 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATTTTCCTATGGAAAATTTCG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
* * *
337420 ACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCAACACTA
66 ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTA
*
337485 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCTTG
131 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
*
337521 GCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
1 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
* *
337586 ACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTACACTA
66 ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTA
* *
337651 CCAGAGAATGCTTCCACACAAGTTTCAGCTTTCCTG
131 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
* *
337687 GCT--TTCTGGTTCTTGAGAAGAAGATTTTTGAAA-ATTTA
1 GCTGATT-AGTTTC-TGAGAAGAAGATTTTT-AAAGATTTA
337725 TCGAAATTTT
Statistics
Matches: 664, Mismatches: 33, Indels: 11
0.94 0.05 0.02
Matches are distributed among these distances:
164 3 0.00
165 12 0.02
166 587 0.88
167 62 0.09
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (166 bp):
GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCG
ACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTA
CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
Found at i:337903 original size:8 final size:8
Alignment explanation
Indices: 337890--337918 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
337880 AGTTTACGGG
337890 CGGACAGA
1 CGGACAGA
337898 CGGACAGA
1 CGGACAGA
337906 CGGACAGA
1 CGGACAGA
337914 CGGAC
1 CGGAC
337919 GACAGACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.38, T:0.00
Consensus pattern (8 bp):
CGGACAGA
Found at i:338483 original size:10 final size:10
Alignment explanation
Indices: 338470--338504 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
338460 TATAGAAAAA
338470 TAAAATAAAG
1 TAAAATAAAG
*
338480 TAAAGTAAAG
1 TAAAATAAAG
338490 TAAAATAAAG
1 TAAAATAAAG
338500 -AAAAT
1 TAAAAT
338505 GTCAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (10 bp):
TAAAATAAAG
Found at i:338917 original size:2 final size:2
Alignment explanation
Indices: 338910--338941 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
338900 NNNNNNNNNN
338910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
338942 AAGTTCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:340930 original size:2 final size:2
Alignment explanation
Indices: 340923--340973 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
340913 TATATTTTGC
340923 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
340965 GA GA GA GA G
1 GA GA GA GA G
340974 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:341009 original size:2 final size:2
Alignment explanation
Indices: 341004--341037 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
340994 NNAGAGAGCG
341004 GA GA GA GA GA -A G- GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
341038 ATGAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:343549 original size:2 final size:2
Alignment explanation
Indices: 343544--343578 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
343534 AAAAAGCTCC
343544 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
343579 AAATTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:344125 original size:120 final size:119
Alignment explanation
Indices: 343912--344151 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 119
343902 AAAAGGATAT
343912 CGTGTATATTCAGTTTTTAAAAATATTATATTCTGTAATTAAGTAACAGAAATAAACATATATAA
1 CGTGTATATTCAGTTTTTAAAAATATTATATTCTGTAATTAAGTAACAGAAATAAACATATATAA
343977 ACGTAACAGGTATGAAACAGTATCATATTAAAATCCAAAGGAGTGTGATATTTA
66 ACGTAACAGGTATGAAACAGTATCATATTAAAATCCAAAGGAGTGTGATATTTA
344031 NCGTGTATATTCAGTTTTTAAAAATATTATATTCTGTAATTAAGTAACAGAAATAAACATATATA
1 -CGTGTATATTCAGTTTTTAAAAATATTATATTCTGTAATTAAGTAACAGAAATAAACATATATA
344096 AACGTAACAGGTATGAAACAGTATCATATTAAAATCCAAAGGAGTGTGATATTTA
65 AACGTAACAGGTATGAAACAGTATCATATTAAAATCCAAAGGAGTGTGATATTTA
344151 C
1 C
344152 CGTTAATATG
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 1 0.01
120 119 0.99
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (119 bp):
CGTGTATATTCAGTTTTTAAAAATATTATATTCTGTAATTAAGTAACAGAAATAAACATATATAA
ACGTAACAGGTATGAAACAGTATCATATTAAAATCCAAAGGAGTGTGATATTTA
Found at i:357042 original size:2 final size:2
Alignment explanation
Indices: 357035--357070 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
357025 TTGTTATTTT
357035 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
357071 CTTTAAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:358927 original size:38 final size:38
Alignment explanation
Indices: 358832--358928 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
358822 CGAAGTCAGG
*
358832 ATCAATCGTAAGGAAGTCTCAAAAAGTCCTAACAAAAT
1 ATCAATCGTAAGGAAGTCTTAAAAAGTCCTAACAAAAT
* *
358870 ATTAATCGTAAGGAAGTCTTAAAAAGTCGTAACAAAAT
1 ATCAATCGTAAGGAAGTCTTAAAAAGTCCTAACAAAAT
358908 ATCAATCGTAAGGAAGTCTTA
1 ATCAATCGTAAGGAAGTCTTA
358929 GCAAAGTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (38 bp):
ATCAATCGTAAGGAAGTCTTAAAAAGTCCTAACAAAAT
Found at i:360115 original size:2 final size:2
Alignment explanation
Indices: 360108--360153 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
360098 CATGAGTAAT
360108 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
360150 TC TC
1 TC TC
360154 ATGGATTCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:360208 original size:12 final size:12
Alignment explanation
Indices: 360191--360228 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
360181 CAATCGTGCT
*
360191 TATATATACATG
1 TATATAGACATG
*
360203 TATATAGACATA
1 TATATAGACATG
360215 TATATAGACATG
1 TATATAGACATG
360227 TA
1 TA
360229 ATGAAATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (12 bp):
TATATAGACATG
Found at i:363409 original size:2 final size:2
Alignment explanation
Indices: 363402--363457 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
363392 TCTTACTTAT
363402 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
363444 TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC T
363458 TGTATATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:364667 original size:2 final size:2
Alignment explanation
Indices: 364660--364693 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
364650 TTCAATTCAA
364660 TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
364694 GTGTATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:365826 original size:20 final size:20
Alignment explanation
Indices: 365801--365845 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
365791 TCAAAAGCTG
*
365801 TACAGGGGATGTCAGGGGCA
1 TACAGGGGATGACAGGGGCA
* *
365821 TACAGGGGGTGACAGGGGCT
1 TACAGGGGATGACAGGGGCA
365841 TACAG
1 TACAG
365846 TGGCACACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (20 bp):
TACAGGGGATGACAGGGGCA
Found at i:365878 original size:24 final size:23
Alignment explanation
Indices: 365841--365885 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
365831 GACAGGGGCT
*
365841 TACAGTGGCACACAGGAGGATGTG
1 TACAGGGGCACACAGG-GGATGTG
*
365865 TACAGGGGCGCACAGGGGATG
1 TACAGGGGCACACAGGGGATG
365886 ACAGGGGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.27, C:0.18, G:0.42, T:0.13
Consensus pattern (23 bp):
TACAGGGGCACACAGGGGATGTG
Found at i:365880 original size:54 final size:53
Alignment explanation
Indices: 365802--365926 Score: 166
Period size: 54 Copynumber: 2.3 Consensus size: 53
365792 CAAAAGCTGT
** *
365802 ACAGGGGATGT-CAGGGGCATACAGGGGGTGACAGGGG-CT-TACAGTGGCAC
1 ACAGGGGATGTACAGGGGCGCACAGGGGATGACAGGGGCCTGTACAGTGGCAC
365852 ACAGGAGGATGTGTACAGGGGCGCACAGGGGATGACAGGGGCTCTGTACAGTGGCAC
1 ACAGG-GGA--TGTACAGGGGCGCACAGGGGATGACAGGGGC-CTGTACAGTGGCAC
365909 ACAGGGGATGTACAGGGG
1 ACAGGGGATGTACAGGGG
365927 ATGACAGTGA
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
50 5 0.08
51 3 0.05
53 3 0.05
54 33 0.51
56 5 0.08
57 16 0.25
ACGTcount: A:0.25, C:0.18, G:0.44, T:0.14
Consensus pattern (53 bp):
ACAGGGGATGTACAGGGGCGCACAGGGGATGACAGGGGCCTGTACAGTGGCAC
Found at i:365912 original size:33 final size:34
Alignment explanation
Indices: 365863--365926 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
365853 CAGGAGGATG
*
365863 TGTACAGGGGCGCACAGGGGATG-ACAGGGGCTC
1 TGTACAGGGGCACACAGGGGATGTACAGGGGCTC
*
365896 TGTACAGTGGCACACAGGGGATGTACAGGGG
1 TGTACAGGGGCACACAGGGGATGTACAGGGG
365927 ATGACAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.23, C:0.19, G:0.44, T:0.14
Consensus pattern (34 bp):
TGTACAGGGGCACACAGGGGATGTACAGGGGCTC
Found at i:365933 original size:21 final size:22
Alignment explanation
Indices: 365876--365933 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
365866 ACAGGGGCGC
*
365876 ACAGGGGATGACAGGGGCTCTGT
1 ACAGGGGATGACAGGGGC-ATGT
* *
365899 ACAGTGGCA-CACAGGGG-ATGT
1 ACAG-GGGATGACAGGGGCATGT
365920 ACAGGGGATGACAG
1 ACAGGGGATGACAG
365934 TGAAAACACT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
23 11 0.39
24 3 0.11
ACGTcount: A:0.28, C:0.17, G:0.41, T:0.14
Consensus pattern (22 bp):
ACAGGGGATGACAGGGGCATGT
Found at i:366101 original size:1 final size:1
Alignment explanation
Indices: 366095--366123 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
366085 ATATTAATGC
366095 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
366124 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:371278 original size:136 final size:135
Alignment explanation
Indices: 371107--371420 Score: 328
Period size: 135 Copynumber: 2.3 Consensus size: 135
371097 GACATGACCC
* ** ** * * * * * * *
371107 TAGGAACAAGAATATATATGACTTGTGGTTAGGGATCTCATCTGTTTTCAGGATATTTGGGCATT
1 TAGGAAAAAGAATATATATGGTTTAAGGGTAGGGATCTCAACCGTTTACAAGATATTTAGGCACT
* *
371172 TCCTGTTCAAAAAAGATTCAGGACCACTCCCAGGG-CCCATGATCTATATACCATTTG-ATACCC
66 TCCTGTT-AAAAAAGAGTCAGAACCAC-CCCAGGGTCCCATGATCTATATACCATTTGAAT-CCC
* *
371235 TTTGACACA
128 CTTAACA-A
* *
371244 -AGGAAAAAGAATATATATGGTTTAAGGGTGGGGATCTAAACCGTTTACAAGATATTTAGGCACT
1 TAGGAAAAAGAATATATATGGTTTAAGGGTAGGGATCTCAACCGTTTACAAGATATTTAGGCACT
** ** * * *
371308 TCCTGTTTGAAGGGGGTCAGAACCACCCCCGGGTCCTATGATCTATATACCATTTGAATCCCCTT
66 TCCTGTTAAAAAAGAGTCAGAACCACCCCAGGGTCCCATGATCTATATACCATTTGAATCCCCTT
371373 AACAA
131 AACAA
* *
371378 TAGGAACAAGTATATATATGGTTTAAGGGTAGGGATCTCAACC
1 TAGGAAAAAGAATATATATGGTTTAAGGGTAGGGATCTCAACC
371421 ATTATGAAGA
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
134 7 0.05
135 79 0.54
136 59 0.41
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (135 bp):
TAGGAAAAAGAATATATATGGTTTAAGGGTAGGGATCTCAACCGTTTACAAGATATTTAGGCACT
TCCTGTTAAAAAAGAGTCAGAACCACCCCAGGGTCCCATGATCTATATACCATTTGAATCCCCTT
AACAA
Found at i:371398 original size:135 final size:133
Alignment explanation
Indices: 371208--371781 Score: 421
Period size: 135 Copynumber: 4.2 Consensus size: 133
371198 CTCCCAGGGC
* * *
371208 CCATGATCTATATACCATTTGATACCCTTTGACACAAGGAAAAAGAATATATATGGTTTAAGGGT
1 CCATGATCTATATACCATTTGATACCCCTTAACAGAAGGAAAAAGAATATATATGGTTTAAGGGT
*
371273 GGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTTGAAGGGGGTCAGAACCACCCCC
66 GGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTCGAAGGGGGTCAGAA-CACCCCC
*
371338 GGGT
130 GGGG
* *
371342 CCTATGATCTATATACCATTTGA-ATCCCCTTAACA-ATAGGAACAAGTATATATATGGTTTAAG
1 CC-ATGATCTATATACCATTTGATA-CCCCTTAACAGA-AGGAAAAAGAATATATATGGTTTAAG
* * * * * * *
371405 GGTAGGGATCTCAACC-ATTATGAAGATAATTGGGCAATTCCTGTTCGAGGGGGGAGGGGGGTCA
63 GGTGGGGATCTAAACCGTTTA-CAAGATATTTAGGCACTTCCTGTTCGA------A-GGGGGTC-
*
371469 AGAGGA-ACCCCTGGGG
119 AGA--ACACCCCCGGGG
** * * *
371485 CCAAAACCTATATGCCATTTGATGCCCCTTAACACAAGGGACAAGGAAAAAGAATATATATGGTT
1 CCATGATCTATATACCATTTGATACCCCTT-A-AC-A--G--AAGGAAAAAGAATATATATGGTT
* *
371550 TAAGGGTGGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTCGAGGGGGGTCAGGAC
59 TAAGGGTGGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTCGAAGGGGGTCAGAAC
*
371615 ACCCCTGGGG
124 ACCCCCGGGG
* * * * * * * * * * *
371625 CCCATAACCTACATA-CTTTTCTATGCCCTTTAATACAA-GAAACAAGAAAATATATGG-TTATG
1 -CCATGATCTATATACCATTT-GATACCCCTTAACAGAAGGAAA-AAGAATATATATGGTTTAAG
* * * * * ** *
371687 GTGTGGGGATCTCAATCATTTA-AATATATTTGGGCACTTCCTGTTCG-AGGGGGTTGGGACGAC
63 G-GTGGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTCGAAGGGGGTCAGAAC-AC
*
371750 CCCTGGGG
126 CCCCGGGG
*
371758 CCTATGA-CTTTTATACCATTTGAT
1 CC-ATGATC-TATATACCATTTGAT
371782 GTCTCTTAAC
Statistics
Matches: 354, Mismatches: 53, Indels: 67
0.75 0.11 0.14
Matches are distributed among these distances:
132 13 0.04
133 51 0.14
134 43 0.12
135 88 0.25
138 1 0.00
139 2 0.01
140 15 0.04
141 22 0.06
142 36 0.10
143 14 0.04
144 2 0.01
145 2 0.01
149 61 0.17
150 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (133 bp):
CCATGATCTATATACCATTTGATACCCCTTAACAGAAGGAAAAAGAATATATATGGTTTAAGGGT
GGGGATCTAAACCGTTTACAAGATATTTAGGCACTTCCTGTTCGAAGGGGGTCAGAACACCCCCG
GGG
Found at i:372240 original size:31 final size:30
Alignment explanation
Indices: 372199--372264 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
372189 TGAAAATCCC
* *
372199 CTGTCTTCCCCTGTTAC-CCCCTGTGTTTTCA
1 CTGTCATCCCCT-TTACACCCCTGTG-TGTCA
372230 CTGTCATCCCCTTTACATCCCCTGTGTGTCA
1 CTGTCATCCCCTTTACA-CCCCTGTGTGTCA
372261 CTGT
1 CTGT
372265 ACAGAGCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.13
31 19 0.61
32 8 0.26
ACGTcount: A:0.09, C:0.38, G:0.14, T:0.39
Consensus pattern (30 bp):
CTGTCATCCCCTTTACACCCCTGTGTGTCA
Found at i:372894 original size:2 final size:2
Alignment explanation
Indices: 372889--372923 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
372879 TTAAAATCAT
*
372889 GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
372924 TTGAGTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:374103 original size:2 final size:2
Alignment explanation
Indices: 374096--374127 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
374086 TTCAATTCAA
374096 TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
374128 GTGTATAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.